Customer Notification

Customer Notification
Customer Notification
PN 9101002 Rev C.1
KCJr software includes a Calibration Test Plate Program that may be used with all Bio-Tek
Automated Readers. If you are using a Bio-Tek Universal Calibration Test Plate, Bio-Tek (PN
9000547), please read this information carefully.
The Calibration Test Plate Program may incorrectly report a Pass for the Turnaround and
Repeatability test results. Other test features which will alert the user to potential
inconsistencies include the Optics Test, the Run Time Self Test, and the Calibration Test
Plate Program. This error is limited to the following versions of KCJr:
♦ Version 1.12 (1994) and Version 1.14 (1995)
This software error is being corrected. An updated version of KCJr will be supplied to the
Users of Record for this program. To expedite this process, please record the information
below and fax to:
Bio-Tek Instruments: 802-655-7941
Attention : Laboratory Product Manager
Thank you for your cooperation.
If you have any questions or comments, please contact the Laboratory Product Manager at:
Phone:
Fax:
E-mail:
800-451-5172
802-655-7941
[email protected]
Model and Serial Number of Autoreader:
Serial Number of KCJr Software (from KCJr Operator’s Manual):
Universal Calibration Test Plate Serial Number:
Shipping Address:
Contact Person:
________________________________
Name:_________________________________
________________________________
Phone:_________________________________
________________________________
Fax/E-mail:______________________________
________________________________
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ii
Notices ______________________________________________________
Copyright
© Copyright 1995, Bio-Tek Instruments, Incorporated. No part of this
publication may be reproduced, transmitted, transcribed, stored in a retrieval
system, or translated into any language without the written permission of
Bio-Tek Instruments, Incorporated.
Trademarks
Bio-Tek is a registered trademark, and CERES 900C is a trademark of Bio-Tek
Instruments, Inc.
Restrictions and Liabilities
Information in this document is subject to change, and does not represent a
commitment by BIO-TEK INSTRUMENTS, Inc. Changes made to the
information in this document will be incorporated in new editions of the
publication. No responsibility is assumed by BIO-TEK for the use or reliability
of software or equipment that is not supplied by BIO-TEK, or its affiliated
dealers.
Revision Appendix
Revision
Date
A
06/94
B
12/94
Page
First Issue
iv
xiv
x
1-1
4-1
C-1
C
Change
2/95
x
1-1
Printed in the United States of America
Bio-Tek Printed Material Part No. 9101002
iii
Warnings
Changed T.O.C.
Changed Intended
Use Statement
Introduction
Added Warnings
Appendix C
Cover Sheet
Changed Intended
Use Statement
Introduction
Warnings and Precautions
When operated in a safe environment, according to the instructions in this
manual, there are no known hazards associated with the CERES 900C.
However, the operator should be aware of certain situations which could result in
serious injury.
Hazard Warnings
Warning! Power Rating. the CERES 900C must be connected to a power
receptacle that provides voltage and current within the specified rating for the
system. Use of an incompatible power receptacle may produce electrical shock
and fire hazards.
Warning! Electrical Grounding. Never use a two-prong plug adapter to
connect primary power to the CERES 900C. Use of a two-prong adapter
disconnects the utility ground, creating a severe shock hazard. Always connect
the system power cord directly to a three-prong receptacle with a functional
ground.
Warning! Internal Voltage. Always turn off the power switch and unplug the
power cord before cleaning the outer surfaces of the instrument.
Warning! Liquids. Avoid spilling liquids on the instrument; fluid seepage into
internal components creates a potential shock hazard. Wipe up all spills
immediately. Do not operate the instrument if internal components have been
exposed to fluid.
Warning! Software. The user of the CERES 900C, utilizing the KCJr software,
must follow the specific manufacturer’s assay package insert when modifying
KCJr software parameters and establishing result calculation methods.
Warning! Data Reduction Protocol. KCJr. is a basic data reduction software
program that does not flag out of range results nor prevent these results from
being sent to any connected information system. It is the user’s responsibility to
verify that all quality control materials are in their expected ranges prior to
utilizing the assay’s results.
iv
Precautions
The following precautions are provided to help you avoid damaging the system:
Caution: Service. The system should be serviced by Bio-Tek-authorized service
personnel. Only qualified technical personnel should perform troubleshooting
and service procedures on internal components.
Caution: Replacement Fuses. Use replacement fuseswith the required current
rating and specification. Improper fuses or short-circuiting the fuse holders may
causefire or damage to the instrument.
Caution: Environmental Conditions. Do not expose the system to temperature
extremes. System performance may be adversely affected.
Caution: Sodium Hypochlorite. Do not expose any part of the instrument to
Sodium Hypochlorite solution (bleach) for more than 30 minutes. Prolonged
contract may damage the instrument surfaces. Be certain to rinse and thoroughly
wipe all surfaces.
Caution: Power Supply. Only use the specified power supply to ensure proper
operation of the unit.
v
Electromagnetic Interference and Susceptibility
USA FCC CLASS A
Warning: Changes or modifications to this unit not expressly approved by BioTek Instruments could void the user's authority to operate the equipment.
This equipment has been tested and found to comply with the limits for a Class A
digital device, pursuant to Part 15 of the FCC Rules.
These limits are designed to provide reasonable protection against harmful
interference when the equipment is operated in a commercial environment. Like
all similar equipment, this equipment generates, uses, and can radiate radio
frequency energy and, if not installed and used in accordance with the instruction
manual, may cause harmful interference to radio communications. Operation of
this equipment in a residential area is likely to cause harmful interference in
which case the user will be required to correct the interference at his own
expense.
Canadian Department of Communications Class A
This digital apparatus does not exceed Class A limits for radio emissions from
digital apparatus set out in the Radio Interference Regulations of the Canadian
Department of Communications.
Le present appareil numerique n'met pas du bruits radioelectriques depassant les
limites applicables aux appareils numerique de la Class A prescrites dans le
Reglement sur le brouillage radioelectrique edicte par le ministere des
Communications du Canada.
vi
EC EN 55011 GROUP 1, CLASS A - EC DIRECTIVE 89/336/EEC
The system has been type tested by an independent testing laboratory and found
to meet the requirements of EC Directive 89/336/EEC and also VDE
0871/CISPR 11:1990 for Radiated Emissions and Line Conducted Emissions.
Verification was to the limits and methods of EN 55011 and VDE 0876/0877.
The device is classified as EN 55011 Group 1, Class A.
EC EN 50082-1
The system was also tested and found to meet requirements for Electrostatic
Discharge Susceptibility, Radiated Susceptibility, and Conducted Susceptibility.
Verification of compliance was conducted to the limits and methods of EN
50082-1:1992; IEC 801-2:1984; IEC-801-3:1984; and 801-4:1988.
Safety
This device has been type tested by an independent laboratory and found to meet
the requirements of:
■
Underwriters Laboratories Standard (UL) UL 1262 Laboratory
Equipment;
■
Canadian Standards Association C22.2 No. 151-M1986 Laboratory
Equipment; and
■
IEC 1010-1 (1990) "Safety requirement for electrical equipment for
measurement, control and laboratory use. Part 1 General requirements."
■
Japanese Industrial Standard JIS t 1001 “ General Requirements for
Safety of Medical Electrical Equipment”
vii
Safety Symbols
The following warning and informational symbols may be found in various
locations on the CERES 900C. The warnings are given here in English, French,
German, Spanish and Italian. Only qualified personnel who recognize shock
hazards and are familiar with the safety precautions should use this instrument.
read the manual carefully before operating this instrument.
Alternating current
Courant alternatif
Dreiphasen-Wechselstrom
Corriente Atterna
Corrente alternata
Earth ground terminal
Borne de terre
Erde (Bettriebserde)
Borne de Tierra
Terra (di funzionamento)
Protective conductor terminal
Borne de terre de protection
Schutzleiteranscluss
Borne de Tierra de Protección
Terra di protezione
On (Supply)
Marche (alimentation)
Ein (Verbindung mit dem Netz)
Connectado
Chiuso
viii
Off (Supply)
Arrest (alimentation)
Aus (Trennung vom Netz)
Desconectado
Aperto (sconnessione dalla rete di alimentazione)
Caution (refer to accompanying documents)
Attention (voir documents d'accompanement)
Achtung siehe Begleitpapiere
Atención (vease los documentos incluidos
Attenzione, consultare la doc annessa
Caution, risk of electric shock
Attention, risque de choc electrique
Gefährliche elektrische Spannung
Atención, riesgo de sacudida eléctrica
Alta tensione (in questo documento Alta tensione non significa
“tensione pericolosa” come definito in IEC 417)
ix
Intended Use Statement
The CERES 900C is an automated, benchtop, general purpose, Enzyme
Immunoassay Analyzer which performs diagnostic analyses of a variety of
samples. The Performance Characteristics of the data reduction software have not
been established with any laboratory (in vitro)diagnostic assay. The user must
evaluate this software in conjunction with the specific laboratory(in vitro)
diagnostic assay. This re-evaluation must include the establishment of new
performance characteristics for the specific assay.
This system is designed for use with a variety of enzyme immunoassays. Assay
protocol variations are addressed by the developer of the ELISA test kit, in
accordance with the test kit's procedure.
KCJr, Bio-Tek’s PC based curve fitting and statistical software program is
included preloaded on every CERES 900C reader. An unlimited number of assay
protocols and blanking patterns can be defined, stored in memory, and instantly
accessed. Plate templates and formulas are automatically combined with the
protocol assay setup. Data results may be displayed on the monitor, printed out,
sent to a mainframe, or merged with other software packages such as Lotus 1-2-3
. Basic DOS utilities are included for convenience. KCJr provides:
■
An easy-to-use menu-driven interface;
■
Kinetic and endpoint curvilinear regressional and statistical
calculations;
■
Curve Fitting, with 4-parameter, cubic, quadratic, and linear methods;
■
Formula calculations for more complex mathematical operations;
■
Limited calculations for positive or negative cutoffs.
Specimen Preparation
Samples should be obtained, treated and stored following instructions and
recommendations contained in the package kit.
x
Table of Contents ___________________________________
Notices ............................................................................................. iii
Warnings and Precautions ............................................................. iv
Intended Use Statement .................................................................. x
Chapter 1 Introduction..................................................................1-1
Introducing the CERES 900C .............................................................. 1-1
Hardware Features ............................................................................. 1-2
Software Features............................................................................... 1-2
Package Contents............................................................................... 1-3
About This Manual .......................................................................................... 1-4
Registration Card ................................................................................ 1-4
Help .................................................................................................................. 1-5
Technical Assistance BBS .................................................................. 1-5
Writing to Bio-Tek ............................................................................... 1-5
Phone Support .................................................................................... 1-5
Chapter 2: Installation
The Operating Environment ........................................................................... 2-1
Unpacking the Instrument .............................................................................. 2-1
Installing the Filter Wheel............................................................................... 2-3
Replacing and Installing Filters ..................................................................... 2-4
Installing a Printer ........................................................................................... 2-6
Serial Connections ......................................................................................... 2-6
Electrical Connections.................................................................................... 2-8
Fuses................................................................................................................ 2-8
xi
Chapter 3: Introducing KC Jr. Software
An Overview of KC Jr...................................................................................... 3-1
Supported Pointing Devices........................................................................... 3-3
Supported Output Devices ............................................................................. 3-4
KC Jr.'s Main Menu.......................................................................................... 3-5
Menu Overview ................................................................................... 3-6
Using the Main menu .......................................................................... 3-7
KC Jr.'s Function Keys ........................................................................ 3-8
KC Jr.'s AutoRun Feature ................................................................... 3-9
Before you Begin: The CERES 900C Setup ................................................ 3-11
g System Utilities/Setup ........................................................................3-12
Filter Table ........................................................................................ 3-13
Standard Filter Configuration ............................................................ 3-13
Filter Configuration For CERES 900C UV......................................... 3-14
Serial Setup....................................................................................... 3-15
A Look at Optics................................................................................ 3-15
Report Device (Printer) ..................................................................... 3-16
d Protocol - Create/Edit .........................................................................3-17
The Protocol Definition Screen ......................................................... 3-17
Editing the Protocol Parameters ....................................................... 3-19
Saving/Aborting Changes ................................................................. 3-20
Protocol Name .................................................................................. 3-20
Protocol Description .......................................................................... 3-21
Reader Control File ........................................................................... 3-21
Assay Type ....................................................................................... 3-22
Number of Reads .............................................................................. 3-22
Reading Interval ................................................................................ 3-23
Prompt for Plate ID............................................................................ 3-23
xii
Fitting method ................................................................................... 3-23
Data/Axis Type.................................................................................. 3-23
Average Sample Replicates.............................................................. 3-24
Units of Measure............................................................................... 3-24
Wells Slopes/R^2 .............................................................................. 3-25
Kinetic / Scanning Y scale ................................................................ 3-25
Standards Results............................................................................. 3-25
Sample Results................................................................................. 3-26
Protocol Definition............................................................................. 3-27
Template Description ........................................................................ 3-27
Absorbance Data .............................................................................. 3-28
Reports of Means.............................................................................. 3-28
Transform Raw Data By.................................................................... 3-28
Report Transformed Data ................................................................. 3-29
Apply Formula................................................................................... 3-29
Report of Limits................................................................................. 3-30
eTemplate (create/edit)..................................................................3-33
Creating a New Template ................................................................. 3-34
Selecting an Existing Template......................................................... 3-34
Modifying a Template........................................................................ 3-35
Entering Standard Concentrations.................................................... 3-36
Replicating Standards....................................................................... 3-38
Entering Sample Unknowns.............................................................. 3-38
Naming a Sample Unknown.............................................................. 3-40
Erasing a Sample Set or Standard Concentration ............................ 3-41
Replicating a Sample Set.................................................................. 3-41
Entering Dilutions.............................................................................. 3-43
Serial Dilutions .................................................................................. 3-44
xiii
Manual Dilutions................................................................................ 3-46
Entering a Description....................................................................... 3-47
Saving the Template ......................................................................... 3-47
Defining Two Templates for Standards per Assays .......................... 3-47
h Data Defaults............................................................................. 3-49
D- Data Drive/Dir............................................................................... 3-50
L- Lotus Drive/Dir .............................................................................. 3-51
P- Default Protocol ............................................................................ 3-51
T- Default Template .......................................................................... 3-52
R- Report Device............................................................................... 3-52
C- Printer Control Code..................................................................... 3-53
f Formula (create/edit) .................................................................. 3-55
Selecting / Creating a Formula File................................................... 3-57
Entering a New Formula File............................................................. 3-58
Modify an Exisiting Formula .............................................................. 3-60
Using the Formula in Calculations .................................................... 3-61
Create/Modify a Data Transformation ............................................... 3-61
Using Transformations in Calculations.............................................. 3-64
Chapter 4: Running KCJr. ........................................................... 4-1
c Calculating Results ............................................................................... 4-1
Starting the Calculations Process ....................................................... 4-3
Reading a Plate and Saving Data ....................................................... 4-4
Retriving Data from a Disk File ........................................................... 4-7
The Kinetics Assay ....................................................................................... 4-11
The 96-Well Graphics Screen ........................................................... 4-11
Printing the Screen............................................................................ 4-12
Saving the screen to disk file ............................................................ 4-12
Adjusting y-scale axis ....................................................................... 4-13
xiv
Selecting time interval....................................................................... 4-13
Mean slope and R2 value ................................................................. 4-14
Zoom-a-well ...................................................................................... 4-15
Edit Graph Screen ............................................................................ 4-16
Change the data/axis type or curve-fit method ................................. 4-17
Return to 96-well screen ................................................................... 4-17
Display standard results.................................................................... 4-17
Fitted Curve Screen .......................................................................... 4-19
Return to Edit Graph Screen............................................................. 4-20
Printing the fitted curve ..................................................................... 4-20
Save as disk file ................................................................................ 4-20
Sample Evaluation ............................................................................ 4-21
Endpoint Assay ............................................................................................. 4-24
Statistical Assay............................................................................................ 4-25
Scanning Assay............................................................................................. 4-26
i Incubate Plate............................................................................4-28
Chapter 5: KC Jr's Utilities ...........................................................5-1
g System Utilities/Setup ........................................................... 5-1
D- DOS File Operations ...................................................................... 5-2
C- Copy a File (or Plate) ..................................................................... 5-3
D- Directory of Files ............................................................................ 5-5
E- Erase a Data File (or Plate)............................................................ 5-7
N-reName a Data File ......................................................................... 5-9
P- Erase a Protocol........................................................................... 5-11
T- Erase a Template ......................................................................... 5-11
Y-copY a Template ........................................................................... 5-12
F- Erase a Formula File .................................................................... 5-13
xv
L- Lotus & Other Transforms ......................................................... 5-14
Lotus transformation ...................................................................... 5-14
VisiCalc transformation.................................................................. 5-15
Importing the data to Lotus ............................................................ 5-17
S-Scattergram ................................................................................... 5-19
Printing the Scattergram ................................................................... 5-21
O- Optics Test ................................................................................... 5-22
C- Calibration Plate Test ................................................................... 5-22
P- Programming Information ............................................................. 5-22
j Exit to DOS Shell.................................................................................5-23
Chapter 6: Troubleshooting ......................................................... 6-1
Troubleshooting .........................................................................6-1
CMOS Utility Software for the CERES 900C ...................................... 6-4
Running the Utility Program ................................................................ 6-5
Removing Junk Files from the CERES 900C ...................................... 6-6
Deleting Unnecessary Files ................................................................ 6-6
Chapter 7: Maintenance................................................................ 7-1
Before you begin .........................................................................7-1
Safety Precautions .............................................................................. 7-1
Replacing the Light Bulb ..................................................................... 7-2
Replacing the Fuses ........................................................................... 7-3
Configuring the CERES 900C for Different Voltages .......................... 7-4
Changing the Line Voltage for Incubation ........................................... 7-5
Cleaning The Optics............................................................................ 7-5
Cleaning the Exterior........................................................................... 7-7
Storage and Shipping.......................................................................... 7-7
xvi
Chapter 8: Performance Verification ...........................................8-1
Testing the System/ Calibration ......................................................... 8-1
Calibration Plate Test.......................................................................... 8-1
Running the Calibration Plate ............................................................. 8-2
Defining the Calibration Plate ............................................................. 8-3
Calibration Test Results...................................................................... 8-9
Test Failures ....................................................................................... 8-9
The Optics Test................................................................................. 8-10
Quality Control .................................................................................. 8-11
Optical Verification ............................................................................ 8-12
Verification of Alignment ................................................................... 8-14
Linearity ............................................................................................ 8-15
Appendix A: Error Messages ...................................................... A-1
Appendix B: Serial, Parallel Pinouts........................................... B-1
Appendix C: Show Scan Scanning Software .......................... C-1
Appendix D: Specifications ......................................................... D-1
Appendix E: Accessories ............................................................ E-1
Appendix F: Reader Control File..................................................F-1
xvii
xviii
Chapter 1:
Introduction
Instrument Revision G
KCJr Version 1.12
This chapter introduces the CERES 900C, and
describes its hardware and software features.
Also included are instructions on how to contact
Bio-Tek, if needed, and information about this
manual.
Introducing the CERES 900C
The CERES 900C EIA Scanning Autoreader and Microplate Workstation is an
integrated reader-assay management system for in-vitro diagnostic use, designed
to automatically perform complete kinetic, endpoint and scanning analysis (up to
35 scan points across a microwell diameter). The CERES 900C can measure the
optical density of solutions in 96-well microplates, and create files from the
resulting data that can be printed in report form or stored as data files for a
variety of ELISA-based applications. The CERES 900C features superior optical
specifications, with an extended dynamic range of up to 4.300 absorbance units,
and an extended wavelength range of 340nm to 900nm.
Assay definitions (consisting of protocols, templates and formulas ) and the data
they produce, are managed by an onboard processor, with a detachable VGA
display and QWERTY keyboard. The CERES 900C is designed to serve either as
a stand-alone system, or as part of a larger laboratory data network, sending,
receiving and manipulating assay data and/or RCD files as needed. The CERES
900C provides direct interfacing to sample processors, LIS, Robotics or Systems
components. Its Incubation Module is programmable to 50° C.
The CERES 900C is backed by Bio-Tek's superior support staff. If the CERES
900C ever fails to work perfectly, please refer to the phone, fax, and BBS
numbers at the end of this chapter to contact Bio-Tek's Technical Support Staff.
Hardware Features _________________________________________________
The CERES 900C hardware features include:
•
An external 14-inch color VGA display
•
A 120 MB hard disk drive
•
A 3.5" high density (1.4 MB) floppy disk drive
•
QWERTY membrane keyboard with numerical keypad, function and
direction keys
•
96-well microplate carrier
•
Two factory-set serial COM ports (COM1 and COM2)
•
LPT1 port (Centronics female 25-pin parallel port for printer)
•
Four PC expansion slots for optional circuit boards ( full, 3 halfs)
•
External keyboard port (5-pin female)
•
Incubator voltage selector switch (120/240)
Software Features_________________________________________________
KC Jr. , Bio-Tek's PC-based curve fitting and statistical software program is
included preloaded on every CERES 900C reader. An unlimited number of
assay protocols and blanking patterns can be defined, stored in memory, and
instantly accessed. Plate templates and formulas are automatically combined
with the protocol assay setup. Data results may be displayed on the monitor,
printed out, sent to a mainframe, or merged with other software packages such
as Lotus 1-2-3. Basic DOS utilities are included for convenience. KC Jr.
provides:
■
An easy-to-use menu-driven interface;
■
Kinetic and endpoint curvilinear regressional and statistical
calculations;
1-2
■
Curve Fitting, with 4-parameter, cubic, quadric, and linear methods;
■
Formula calculations for more complex mathematical operations;
■
Limited calculations for positive or negative cutoffs.
Introduction
Package Contents
_______________________________________________________________________________________________________________________________________________________
The contents of the CERES 900C package as shipped includes:
•
CERES 900C Microplate Reader
•
CRT Monitor (optional)
•
Power Cord(s) (2 if monitor is included)
•
Filter wheel with 4 standard filters- 405nm, 450 nm, 490nm, 620nm,
(340 nm is included with CERES 900C UV)
•
CERES 900C User Guide & Registration Card including:
∗ KCJr Diskette
∗ Show Scan Diskette
∗ CMOS Diskette (Directions in Manual)
CERES 900C User's Guide
•
DOS Manual and disks
•
Fuses
•
Light Bulb
•
Dust Cover
1-3
About This Manual
____________________________________________________________________________________________________________________________________________________
The intent of this user's guide is to quickly instruct the new user on how to set up
and operate the CERES 900C EIA Reader. To this end, we've employed certain
conventions to help you read and understand this manual.
;;;
First, any important information will be indicated in this way, with the associated
information icon as appears to the left of this paragraph.
Next, anytime a key is discussed, the key is represented this way:
Major topic headings start a new page (like About
> [email protected]
This Manual, above) to
give you a visual and style clue that a new major subject is being broached. One
or more subheadings will appear below each major heading.
Registration Card
Once you have got the CERES 900C up and running successfully, please take a
moment to fill out the postage-paid Registration card and mail it to
Bio-Tek.
1-4
Introduction
Help
_________________________________________________________________________________________________________________________________________________________________________________________
If your new CERES 900C system fails to start or operate successfully, please
contact Bio-Tek immediately.
Writing To Bio-Tek
If you prefer, you can write a letter with your comments and send it to:
Bio-Tek Instruments, Inc.
Technical Assistance Center
Highland Park, Box 998
Winooski, VT USA 05404-0998
Phone Support
You can also telephone our Technical Assistance Center between 8:30 AM and
6:00 PM Eastern Standard Time, Monday through Friday, except Holidays. The
number is (800) 242-4685 ; Outside of the USA (802) 655-4044; European (32)
3-829 0455. Emergency Assistance is available Monday through Friday, 6:00
PM to 9:00 PM.
Whichever method of contact you choose, please provide the following
information.
•
Product name ("CERES 900C") and serial number
•
Revision level of your software
•
The specific steps which reproduce your problem
•
A daytime phone number.
CERES 900C User's Guide
1-5
1-6
Introduction
Chapter 2:
Installation
This chapter includes instructions for unpacking
and setting up the CERES 900C and instructions
for connecting printers and/or serial devices.
The Operating Environment
The CERES 900C is designed to operate optimally when installed on a level
surface in an area where ambient temperatures remain between 15°C (59°F) and
40°C (104°F). The reader is sensitive to extreme environmental conditions, and
these conditions should be avoided:
„
Excessive humidity.
„
Excessive light (particularly bright sunlight) as it may affect the
instrument's optics and readings.
„
Dust. Optical density readings may be affected by extraneous
particles (such as dust) in the microplate wells. A clean work area
is necessary to ensure accurate readings. Always keep the reader
covered with a dust cover when not in use.
Unpacking the Instrument
Use Figure 2-1 as a guide when unpacking and packing the instrument.
■
If the shipping box is damaged, inspect the instrument for visible
dents and scratches as you unpack it.
■
If the instrument is damaged, notify the carrier and your Bio-Tek
representative. Keep the shipping cartons and the packing material
for the carrier's inspection. Bio-Tek will arrange for the repair or
replacement of your instrument immediately, before the shippingrelated claim is settled.
If the CERES 900C is shipped to Bio-Tek for repair or replacement, the
instrument must be carefully packed (use Figure 2-1 as a guide), using the
original packing materials. If the original packing materials have been damaged,
contact Bio-Tek Instruments for replacement materials. Shipping with improper
packaging materials may void your warranty.
To unpack the instrument:
■
Carefully open the top of the box, and remove the accessories box.
■
Lift the CERES 900C out of the box and remove the foam end
caps. Place the instrument on a level surface.
Figure 2-1: Packing the CERES 900C
Installing the Filter Wheel
The filter wheel is packaged separately during shipment to protect it from
damage. Carefully unwrap the filter wheel and install it inside the reader:
2-2
Installation
■
Loosen the two wingnuts holding the Optical Assembly Compartment cover
in place and open the compartment.
Power Module
On/Off Switch
Serial (COM) port
3-prong power cable connector
Printer (LPT1) connector
Fuse compartment
Keyboard connector
Video display connector
RS232 (COM) port
Optical Assembly
Optical Asembly Access Panel wing nuts
Figure 2-2: Optical Assembly Compartment
■
CERES 900C User's Guide
Slide the Optical Assembly outward until it is fully exposed.
2-3
„
Attach the magnetic Filter Wheel Hub to the Mounting Hub (Figure 2-3) so
that the Registration Key on the Filter Wheel Hub fits into the Registration
Slot on the Mounting Hub.
Registration slot
Lamp Assembly
Registration key
Spring-loaded bracket
for lamp
Figure 2-3: Attaching the Filter Wheel to the Optical Assembly
„
Once the Filter Wheel is in place, slide the Optical Assembly back into
position within the instrument, close the Access Panel and re-tighten the two
Access Panel Wingnuts.
Replacing and Installing Filters
The Filter Wheel comes factory-equipped with four filters. A total of 6 optical
interference filters can be installed.
Additional filters are available for the CERES 900C. For information regarding
price and availability, contact your authorized Bio-Tek Representative, or call
(800) 451-5172 or (802) 655-4040 Monday - Friday, 8 AM to 6 PM, Eastern
2-4
Installation
Standard Time. The standard filters are placed in the following positions on the
filter wheel:
CERES 900C
CERES 900C-UV
Position #1 - 405nm
Position #1 - 405nm
Position #2 - 490nm
Position #2 - 340nm
Position #3 - Plug (Blank / no pass filter)
Position #3 - Plug
Position #4 - 450nm
Position #4 - 490nm
Position #5 - 620nm
Position #5 - 620nm
Position #6 - Plug (Blank / no pass filter)
Position #6 - Plug
To replace or install filters:
Figure 2-4: Attaching a filter to the filter wheel
;;;
Be sure to handle the filter wheel by the rim to avoid placing fingerprints on the filters. Filters may be
cleaned using photographic lens cleaner and lens paper, or Q-tips and isopropyl alcohol.
„
Remove the Filter Wheel by pulling it firmly out of the Mounting Hub,
being careful not to touch the filter surfaces (Figure 2-3).
„
Gently press on the Filter tabs until the Filter is released from its slot.
„
Install new Filters by inserting them carefully into the desired slot until the
tabs click into place.
CERES 900C User's Guide
2-5
■
The filter(s) that will be used for testing are software selectable using the
CERES 900C operating program, KCJr. When the CERES 900C is powered
on, KC Jr. automatically loads. Filters may be selected by choosing the
System Utilities item on KCJr.'s Main Menu. Select S-CERES 900 setup,
from the System Utilities submenu. Then select F-Filter Table. For a
detailed discussion of the filter table, refer to Chapter 5, KCJr.'s Utilities.
Installing a printer
The CERES 900C features a parallel port (LPT1) to allow connection to a variety of printers. The port
is shown in Figure 2-5 on the following page. The connector is a 25-pin D-sub state connector. The
pinout is illustrated in Appendix B.
Most printers come equipped with a parallel cable designed to connect the printer to a computer or
other output device. Should the cable that came with the printer become lost or damaged, Bio-Tek
offers a variety of printer cables for IBM-compatible printers. Contact your authorized Bio-Tek Dealer
for information regarding cable prices and availability, and the correct cable for your particular printer.
To attach a printer to your CERES 900C:
;;;
„
Place the printer in a location within five or six feet of the CERES 900C.
„
Attach one end of the cable to the printer's parallel port.
„
Attach the other end of the cable to the CERES 900C Parallel Port LPT1.
„
Make sure the securing screws on both ends of the cable are tightened.
System instability may result if the printer is not connected to the CERES 900C prior to system powerup.
Serial Connections
The CERES 900 provides two Serial Ports. One has a 9-pin D sub connector, and the other, a 25-pin D
sub connector. The Serial ports may be used to send data to an external PC or serial device. The
pinouts for the connectors are illustrated in Appendix B.
2-6
Installation
If serial communications are required between the CERES 900C and another device, make sure that
the communication parameters (Baud Rate, Data Bit Configuration and Parity Status) are set to match
those of the receiving device.
Serial Port (COM1)
Power module
(power cord connector,
fuses, on/off switch)
Serial Port (COM2)
LPT1 (Parallel) Port
for printer
Figure 2-5: CERES 900C Connectors for Printers (LPT1) Serial (COM) ports and Power Module
The CERES 900C default settings are:
■
COM1 and 2: 9600 Baud, 8/2 Data Bits and Even Parity.
These settings may be changed via the CERES 900C operating software, KCJr., which is automatically
loaded when the CERES 900C is powered on. To change the settings, select System Utilities from
KCJr.'s Main Menu. Changing the default COM port settings is discussed in Chapter 5, KCJr.'s
Utilities.
CERES 900C User's Guide
2-7
Electrical Connections
Ensure that the CERES 900C’s Incubator Voltage Select Switch, located on the back panel of the
instrument, is matched to the line voltage being used (100 - 120VAC, set to "115" position / 220 240VAC, set to "230" position).
Attach the female end of the power cable provided to the 3-prong male socket located on the back
panel as shown in Figure 2-5 on the previous page.
■
Plug the male end of the cable into an earth-grounded 120VAC electrical source. (see Chapter 7,
Maintenance for instructions on how to configure the CERES 900C for 220 or 240 Volt operation).
;;;
WARNING!!
Avoid using extension cords or cheater plugs that do not have a protective (Ground) conductor. The
protective earth terminal (chassis) must be connected to the protective earth connector of the power
source, which normally happens when the main power cable is properly connected to the AC power
source. Failure to properly ground this unit can result in a hazardous condition
Fuses
The CERES 900C may be fused for a variety of operating voltages (AC), including: 120, 220
and 240. Detailed instructions on changing fuses can be found in Chapter 7, Maintenance.
2-8
Installation
Chapter 3:
Introducing KC Jr. Software
This chapter introduces KC Jr. software for the
CERES 900C.
An Overview of KC Jr.
KC Jr. is an IBM PC or PC-compatible software program that controls the operation
of the CERES 900C and is designed to provide data reduction for most ELISA
applications using Bio-Tek's microplate readers.
The "junior" version of Bio-Tek's full-featured KinetiCalc program, which is
preloaded on the CERES 900C, provides data reduction for four basic assay types:
■
End point curvilinear regression
■
Kinetic curvilinear regression
■
Statistical nonregression-based calculations
■
Well scanning
KC Jr. is designed to retrieve microplate data in an 8 x12 matrix from a Bio-Tek
reader, store the data in multiple-plate files for future use, and analyze the data based
on a user-specified set of protocol parameters. In addition to the 96 optical density
values, the reading date and time of the original file is recorded as part of the disk
file.
KC Jr. does not require the user to attend the CERES 900C during each plate reading.
If the program and the reader are configured for CONTINUOUS READ, the program
will continue to accept data from the reader and store each 96-well matrix in a
microplate file until the specified number of plates or readings are made, the disk is
full, or the program is interrupted.
KC Jr. allows the user to:
■
Retrieve data from the reader and store the data on a disk (either the reader's hard
disk, or a floppy) under a user-specified file name.
■
Display absorbance data on screen, or print them in raw, 8 x 12 format or as a
scattergram.
■
View a directory of data already stored on disk.
■
Copy, erase, or rename microplate files.
■
Create data files usable with other commercial spread sheet and statistics
programs, such as Lotus 1-2-3 or VisiCalc.
■
Calculate mean, standard deviation, variance, and coefficient of variation for any
user-specified set of standard or sample wells on a plate.
■
Define formulas to analyze optical density data from any user-specified set of
wells.
3-2
KC Jr. Main Menu
■
Correct any group of wells by a constant value to effectively eliminate
background absorbance and optionally save the corrected data to disk.
■
Display or print a report that shows the relationship of all wells to as many as 4
user-specified limit values.
■
Store, retrieve, and modify microplate templates that map any user-specified
combination of standard and sample wells.
■
Store, retrieve, and modify default protocol files that contain parameters
specifying the assay type, curve calculation, and sample evaluation.
■
Edit the data points used to calculate the kinetic or end-point models.
■
Calculate a linear or curvilinear regression model based on the default protocol
parameters.
■
Use back-calculation or extrapolation to evaluate the concentration values of
samples on a microplate.
■
Save most reports to disk files.
Supported Pointing Device (optional)
■
CERES 900C User's Guide
Microsoft-compatible or IBM PS/2 mouse
3-3
Supported Output Devices
3-4
■
IBM graphics or Proprinter; Star NX1001
■
Epson FX, JX-80, LQ1500, LX, and MX printers
■
Epson-compatible dot-matrix printers
■
Kodak Diconix 180 si
■
Okidata (all models)
■
HP Laserjet, Laserjet + or Laserjet II or compatible
■
Texas Instruments printers (or compatibles)
KC Jr. Main Menu
KC Jr.'s Main Menu
KC Jr.'s Main Menu provides an easy, graphical way to customize the reader's
operating environment, design various protocols, and specify how data will be
calculated and reported.
KCJr. software will automatically load when the CERES 900C is powered on. To
access KC Jr.'s Main Menu from the DOS prompt, change to the drive and directory
containing KC Jr. software, and start the program by typing:
KCJR
A menu much like the one shown below will appear:
Figure 3-1: The KCJr Main Menu
CERES 900C User's Guide
3-5
Menu Overview
Main Menu options can be accessed in four ways:
■
Pressing the function key assigned to the option (e.g.: F7 to set Data Defaults)
■
Using the up-down cursor arrow keys and pressing Enter
■
Using an installed mouse to point and click on an option
■
Typing the first letter of the option and pressing Enter
Select any option on the Main Menu, and a pop-up window prompts for information,
or provides a list of choices. Pressing Esc aborts the current operation, and returns
you to the previous level in the menu hierarchy, and ultimately back to the Main
Menu.
KC Jr.'s Main Menu also contains a number of options that allow file maintenance
without leaving the software program. For example, the System Utilities Menu option
(F6) allows you to perform common DOS file operations such as copying or erasing
data files, Templates or Protocols. You may also perform an optics test, verify
instrument calibration, or transform data for use in Lotus 1-2-3, VisiCalc or
Scattergrams. And the "Exit to DOS shell" option allows you to exit to DOS, and
return to KC Jr. without actually exiting the program. The Main Menu also allows
you to set an incubation interval.
The status line appears as the bottom line of the Main Menu. Here you'll find
information on the protocol and template being used for calculations, and the current
operation. The status line also displays prompts for action.
The area at the far right of the status line indicates whether the keyboard's Num
Lock and Cap Lock features are active. When the cursor control pad is set for
numeric function, "NUM" is displayed. If the Caps Lock key is pressed on the
keyboard, "CAPS" is displayed on KC Jr.'s Main Menu. Otherwise this space is
empty.
3-6
KC Jr. Main Menu
Using the Main Menu
The first time you begin KC Jr., you'll want to execute the program functions in the
following order:
Create an operating Protocol (F3). The Protocol file contains information that
tells KC Jr. how to calculate and report ELISA data.
Create a Reader Control File. The RCF must be created before the CERES 900C
can read a microplate. The Reader Control File is selectable on the (F3) Protocol
definition screen.
Create a Microplate Template (F4). A Template defines multiple sets of
standards and samples, and defines concentrations, dilutions and replicates.
Create a Formula (F5). A formula for the transformation of optical densities or
kinetic slopes can be created, edited and saved for later use in data analysis.
Set Data Defaults (F7). This option allows you to specify the drive/directory for
storing O.D. data; and how the data will be reported (displayed on the screen, printed,
or both).
Calculate Results (F2). The calculation process allows you to retrieve and
manipulate the data, and report the results.
These options are discussed in detail in the sections that follow.
CERES 900C User's Guide
3-7
KC Jr.'s Function Keys
KC Jr. utilizes the keyboard Function Keys (F1-9) making it easy to access
commonly-used program functions. The F10 key is used to "save" Protocol,
Template and Formula definitions. Function key assignments are:
3-8
F1
Help
F2
Calculate results
F3
Protocol (create/edit)
F4
Template (create/edit)
F5
Formula (create/edit)
F6
System Utilities
F7
Data Defaults
F8
Incubate Plate / Home Plate
F9
Exit to DOS shell
F10
Save
KC Jr. Main Menu
KC Jr.'s "AutoRun" Feature (Batch File Operations)
Data analysis may also be run directly from the DOS prompt as long as the protocol
and template names are the same. This feature applies both to existing data files and
new plate data taken directly from the reader. The options are as follows:
■
P Option: Using this option, enter the following command at the DOS prompt:
KCJR /P:ENDPOINT:ELISA.DAT
where both the protocol and template names are "ENDPOINT", and the data file
name is "ELISA.DAT".
;;;
This feature allows the user to quickly calculate a standard curve using existing data
before additional plate(s) of samples are read.
■
B Option: This option allows the user to run an analysis of data being read
directly from a reader. The user has the choice of either assigning a file name to
the data to be read as part of the initial command, or waiting until KC Jr. prompts
the user to enter a name for the data.
For example, entering
KCJR /B:ENDPOINT:ELISA.DAT
or
KCJR / B:ENDPOINT:*
will initiate a new plate read, the results of which will be a new data file that KC
Jr. will entitle "ELISA.DAT." Using an asterick for a datafile name will result in
KCJR making a filename based on the current system date: YYMMDD.###,
where ### can be 001, 002, 003 etc.
CERES 900C User's Guide
3-9
If, however, only
KCJR /B:ENDPOINT
is entered, KC Jr. will prompt the user for a file name during the reading.
After the analysis is completed, KC Jr. will return to the DOS prompt.
■
L Option: This option automatically converts any data that is read
during the batch run to a Lotus ".PRN" file.
■
G Option: This option automatically prints the standard curve
generated during the batch run.
KCJR /B:ENDPOINT:ELISA.DAT /L
;;;
3-10
/G
These options are only available when the "B" option is used.
KC Jr. Main Menu
Before You Begin: The CERES 900C Setup
The CERES 900C is set up at the factory for certain default operating parameters.
You'll want to check that these parameters are right for your operating environment.
These parameters include:
■
The Filter Table: The filter table may be accessed through the KC Jr. Main
Menu by selecting F6 System Utilities, and then CERES 900 Setup.
■
Communications Parameters: Also accessed through F6 System Utilities/
CERES 900 Setup, communications parameters allow the CERES 900C to
communicate with another device, like a computer.
■
Reporting Device Parameters: Specifying a Reporting Device (printer) can be
accomplished by selecting Data Defaults on the KC Jr. Main Menu. Data
Defaults are discussed in detail in this chapter.
CERES 900C User's Guide
3-11
C System Utilities / Setup
CERES 900C Setup is accessed from the KC Jr. Main Menu. To check the
instrument's setup:
■
From KC Jr.'s Main Menu, select F6 System Utilities.
■
From the Options submenu, select S - Ceres 900 setup.
A screen similar to the following will appear on the display:
3-12
KC Jr. Main Menu
The Filter Table
This window allows the user to notify the CERES 900C software program when
changes are made to the selection or position of the filters installed on the Filter
Wheel. The factory standard filter configuration is shown in the table below:
CERES 900C Standard Filter Configuration
FILTER TABLE
CERES 900C User's Guide
Position 1
405nm
Position 2
490nm
Position 3
plug/blank
Position 4
450nm
Position 5
620nm
Position 6
blank
3-13
Filter Configuration for CERES 900C UV:
FILTER TABLE
YYY
Position 1
405nm
Position 2
340nm
Position 3
blank/plug
Position 4
490nm
Position 5
620nm
Position 6
blank/plug
The Part Number for the blank / no pass filter (plug) is 3122037.
To install a 660 nm filter in the empty third position, for example, the user would:
■
Remove the filter wheel from the CERES 900C, and install the new filter into
position 3. Installing new filters is discussed in Chapter 2.
■
Select F6- System Utilities from the KC Jr. Main Menu, and then select
S - CERES 900 setup;
■
Select F- Filter table to access the filter options, and the up/down cursor keys
to highlight the fifth filter position on the Filter Table;
■
Using the number keypad on the CERES 900C keyboard, enter 660 next to POS
5;
■
Press the k key to save the new setting.
Once the filters have been saved, a warning message appears on the display:
WARNING: The filter table has changed. Check your protocols for correct filters.
3-14
KC Jr. Main Menu
;;;
Position #1 must contain a filter. The CERES 900C requires that a 405nm filter reside
in Position #1 for calibration purposes.
Serial Setup
This parameter allows the user to set up communication parameters with another
serial device (example: another computer or a modem).
■
To change parameters: Select Serial on the System Utilities option submenu;
■
Use the cursor up/down arrow keys to highlight the parameter you want to
change. Use the spacebar to scroll through the available options;
■
Press the kkey to save the changes.
A Look at the Options
Baud Rate: The baud rate, or rate of data flow may be changed using the spacebar.
The factory set default is 9600 bits/sec. Options include 300, 1200, 2400, 9600 and
19200 bit/sec.
Data Bits: The Data Bits setting defines two parameters: Character string bits (each
character string is composed of either 7 or 8 bits), and Stop Bits (either 1 or 2 bits).
The default setting is 8 and 2.
CERES 900C User's Guide
3-15
Parity: The parity setting is used to prevent serial communications errors between
devices. The options are odd or even parity. The default is Even Parity.
;;;
All three parameters -- Baud Rate, Data Bits and Parity should be matched in the
communications software on the device receiving the data.
Report Device (Printer)
If you've attached a printer to the CERES 900C, you'll need to ensure that the reader
recognizes the print device, and and that any required Printer Control Codes have
been entered. Selecting the Reporting Device and specifying Printer Control Codes is
accomplished by selecting F7 Data Defaults on KC Jr.'s Main Menu. Data Default
options are described elsewhere in this chapter.
@Protocol - Create/Edit
The Protocol Definition Screen
A Protocol file contains information that tells KC Jr. how to calculate and report
ELISA data. Once a protocol is created, the parameters it contains are saved on the
3-16
KC Jr. Main Menu
default program disk. The Protocol can then be recalled and used for calculating
curves and evaluating sample unknowns by entering its name as a Data Defaults
parameter or by selecting its name whenever a Protocol is requested within KC Jr.
The name of the active protocol file always appears on the Main Menu status line.
The first time you create a protocol (F3 from the Main Menu), the screen displays a
blank protocol definition screen with a prompt window requesting the new protocol
filename.
Figure 3-2: Protocol Definition screen with filename prompt
Enter a file name up to 8 characters, and press Enter, (A file extension is
unnecessary, as KC Jr. automatically adds a .PRT extension when it saves the
protocol to disk.) The new filename appears at the top of the display with a default set
of parameters that may be edited.
CERES 900C User's Guide
3-17
Figure 3-3: Protocol Definition Screen with default parameters
If protocol files have already been created and saved, a pop-up window appears,
listing available protocol files. To edit an existing protocol file, select the file name
from the window by using a mouse, or up/down cursor control keys and pressing
Enter, as shown in the illustration that follows:
Figure 3-4: Selecting a Protocol from a list of saved filenames
3-18
KC Jr. Main Menu
Editing the Protocol Parameters
If you want to create a new protocol file at this point, press Esc to clear the screen,
then enter a new protocol filename.
;;;
If you edit an existing Protocol file, when you save the file, KC Jr. will overwrite the
original file with the new parameters.
To edit the Protocol parameters:
■
Keyboard method: Use the up/down cursor control keys to move to a
parameter field. Key in parameter information, or use the space bar to cycle
through setting options.
■
Mouse method: Point at the parameter field, and click to key in information
or view setting choices.
The setting displayed on the screen when you move to the next parameter will be the
setting used in the protocol file when it is saved.
Saving/Aborting Changes
When editing is completed:
■
Press F10 to save parameters in the Protocol file, or
■
Press Esc to return to the Main Menu without saving.
Protocol Name
Any name, up to 8 characters, may be used. KC Jr. automatically adds a .PRT
extension to the file name you specify.
CERES 900C User's Guide
3-19
While the protocol name is highlighted, you can press the space bar to bring up a
window listing the protocol file names stored in the default program directory, in the
event the protocol displayed on the definition screen is not the one you wish to
modify. You may then select another protocol to create or edit.
Figure 3-5 Protocol name highlighted
Protocol Description
This line, initially blank, allows you to enter a protocol file description up to 40
characters long.
Reader Control File
The Reader Control File must be created before the CERES 900C reads any plate
data. This option is selectable as part of the Protocol definition screen.
■
To create/edit a Reader Control File, highlight the Reader Control File field
on the Protocol definition screen, and press the space bar. The Reader Control
File definition screen will appear (Figure 3-6 ). For a more detailed explanation
of the Reader Control File, refer to Appendix F, Reader Control File.
3-20
KC Jr. Main Menu
;;;
The Reader Control File is automatically given the same name as the Protocol, with
an .FIL extension.
Figure 3-6: The Reader Control File Definition Screen
■
Use the up/down cursor keys, or a mouse to highlight parameter fields in the
Reader Control File. If reading Method or Blanking Pattern is highlighted,
pressing F1 will pop up a menu of choices.
■
Use the spacebar (or mouse click) to view options.
■
Move to the next parameter to select any given option.
■
Press F10 to save changes in the Reader Control File
■
Press Esc to abort all changes and return to the Protocol Definition screen.
CERES 900C User's Guide
3-21
Assay Type
The assay type definition can be: kinetic, end point, statistical or scanning. To change
the setting, highlight this field and press the space bar to cycle through the four
choices.
Number of Reads
If the Assay Type is kinetic, this parameter must be specified in the Reader Control
File. If the Assay is end point or statistical, this parameter specifies the number of
plates to read. The value you enter here must be in the range of 1 to 250.
;;;
If the reader control file specifies kinetic as the reading method, the number of
readings per plate is automatically taken from the reader control file.
3-22
KC Jr. Main Menu
Reading Interval
This setting specifies the time interval between repeated reads on the plate, and is
applicable only if the Assay Type is kinetic. If the reader control file specifies kinetic
as the reading method, this reading interval is automatically taken from the reader
control file.
Prompt for Plate ID
■
Highlight this parameter and use the spacebar to toggle between Yes and No.
■
If Yes is selected, the user will be asked to enter a plate-specific ID each time a
plate is read.
Fitting Method
This parameter can only be changed if the Assay Type is kinetic or End Point.
The options are linear, quadratic, cubic, 4-parameter, and logit/log.
■
To change this setting, highlight this parameter, and press the space bar to
cycle through the 5 options.
Data / Axis Type
This setting can only be accessed if the Assay Type is kinetic or end point. The
setting options are linear, linear/log, or log/log.
■
To change the setting, highlight the parameter and press the spacebar to cycle
through the options.
If the Fitting Method parameter is either 4-parameter or logit/log, this parameter only
affects the display of the curve. For the other fitting methods, the data will be
transformed by the selected data type. Linear/Log is linear Y -axis, log X-axis.
CERES 900C User's Guide
3-23
Average Sample Replicates
This setting can only be changed if the Assay Type is kinetic or end point. The
options are before, after, or none.
■
To change this setting, highlight the parameter field and press the spacebar to
cycle through the options.
■
If set to before, the program averages the replicate optical densities
(or slopes) before evaluating for the unknown concentrations.
■
If set to after, the back-calculated concentrations of replicates are
averaged.
■
If set to none, the optical densities are not averaged; each one is
evaluated separately.
;;;
Bio-Tek recommends setting this parameter to before to reduce the amount of error
in calculations.
Units of Measure
This parameter allows you to specify the concentration label, up to a 10-character
maximum, for the X-axis on the fitted curve graph. It can only be changed if the
Assay Type is kinetic or end point.
;;;
Spaces entered in this label will become underscored.
■
The Y-axis label is automatically set to Optical Density for an end-point assay or
to Rate for a kinetic assay.
3-24
KC Jr. Main Menu
Well Slopes/R^2
If the Assay Type parameter is set to kinetic, this parameter allows you the option of
reporting the well slopes and R-squared values for each well on all plates in the run.
The report either will be sent to the printer, displayed on the screen, or both,
depending on what was selected as a Report device during setup of Data Defaults.
■
To change this setting, highlight the parameter field and press the space bar
to cycle through the options.
Kinetic/Scanning Y-Scale
Enter the maximum Y-scale value in the highlighted field. If a default value exists,
press the spacebar to clear the field for input.
Standards Results
If the Assay Type parameter is set to either kinetic or end point, this parameter allows
you to report the results of evaluating and back-calculating the standards (Figure 37).
Figure 3-7: Standards Results
CERES 900C User's Guide
3-25
The report either will be sent to the printer, displayed on the screen, or both,
depending on what was selected as a Report device during setup of Data Defaults.
■
To change this parameter, highlight this item, then press the space bar to
toggle between Yes and No.
Sample Results
If the Assay Type parameter is set either to kinetic or endpoint, you may opt to report
the results of evaluating and back calculating the sample unknowns (see Figure 3-8).
The report either will be sent to the printer, displayed on the screen, or both,
depending on what was selected as a Report device during setup of Data Defaults.
Figure 3-8: Sample Evaluation Report Screen (End Point Assay)
■
To change this parameter, highlight the parameter field and press the space
bar to toggle between Yes and No.
3-26
KC Jr. Main Menu
Protocol Definition
This parameter allows you to list all the parameters and their settings from the
currently active protocol.
■
To change the parameter, highlight the Protocol Definition field and press the
spacebar to toggle between Yes and No.
The report either will be sent to the printer, displayed on the screen, or both,
depending on what was selected as a Report device during setup of Data Defaults.
Template Description
This parameter allows you to map the active template in an 8 x 12 matrix, showing
the location and concentration of standards, and the location and dilutions of sample
unknowns (Figure 3-9). The report either will be sent to the printer, displayed on the
screen, or both, depending on what was selected as a Report device during setup of
Data Defaults.
Figure 3-9: Template Map Screen
CERES 900C User's Guide
3-27
■
To change the parameter, highlight the Template Description field and press the
spacebar to toggle between Yes and No.
Absorbance Data
This parameter allows you the option of reporting the optical density data of each
plate reading. If the parameter is set to Yes, the program will automatically produce
an 8 x 12 matrix report of the optical density values for each reading (if the assay
type is set to kinetic), or each plate (if the assay type is set to endpoint or statistical).
■
To toggle between the Yes/No settings, highlight the parameter and press the
space bar. The report will be sent to the printer, displayed on the screen, or
both, depending on what was selected as a Report device during setup of Data
Defaults.
Report of Means
This parameter allows you the option of producing a statistical report of the optical
density data. If the parameter is set to Yes, the program will automatically produce a
means report of optical density data for all sets defined on the template.
■
Highlight the parameter and press the space bar to toggle between Yes and
No. The report will be printed, displayed on the screen, or both, depending on
what was selected as the Report device during Data Defaults setup.
Transform Raw Data By_____
This parameter allows you to specify the name of the formula file which specifies the
transformation to be performed on optical density data, before any other calculations
or reporting is done.
■
Highlight the parameter field and press the spacebar to select from a list of
existing formulas.
3-28
KC Jr. Main Menu
■
If a formula file has not yet been created, return to the Main Menu and select
F5 Formula (create/edit).
Report Transformed Data
This parameter allows you to produce a matrix report of absorbance or kinetic rate
data after it has been transformed by the formula(s) in the "transform raw data by___"
file.
■
To toggle between Yes and No, highlight the parameter field and press the
space bar.
Apply Formula
This parameter allows you to specify the name of the formula file that contains the
calculation to be performed on the optical density data. To select a formula file name:
■
Highlight the parameter field and press the space bar.
■
A pop-up window will list formula files saved in the default program directory
(Figure 3-10).
■
Use the cursor up/down keys, or the mouse to highlight a formula, and press
Enter or click the mouse button.
CERES 900C User's Guide
3-29
Figure 3-10: Applying a Formula
Report of Limits
This parameter allows you the option of producing a limit report for each plate in the
run (Figures 3-11 and 3-12). The options are no, matrix, column, formula-mat, and
formula-col.
Figure 3-11: Matrix Report of Limits
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KC Jr. Main Menu
Figure 3-12: Column Limit Report Screen
;;;
A formula must be entered in the Protocol's Apply Formula field in order to access
the formula-mat and formula-col options.
■
To change the parameter, highlight the parameter field and press the spacebar
to cycle through the options. After calculation is done, the Limits report will be
sent to the printer, displayed on the screen, or both, depending on what was
selected as a Report device during setup of Data Defaults.
■
If you set this parameter to anything other than No, the program will calculate
and print a minus sign (-) for all plate values below or equal to the first limit, a
+1 for all values between the first and second limit, a +2 for all values between
the second and third limit, a +3 for all values between the third and fourth limit,
and a +4 for all values above the fourth limit.
■
To edit the limit settings, press the down arrow key to move down to the limit
settings line. Then use the left/right cursor control keys to move among the
five limit settings and enter up to 4 limit values for the the report. Make sure you
enter these limit values in increasing order.
CERES 900C User's Guide
3-31
If set to formula-mat or formula-col, the limit values will be automatically calculated
by the formula file specified by the Apply Formula parameter.
;;;
If you want to specify your own limits and you have chosen to apply a formula to the
data, make sure the selected formula does not contain limit calculations. Likewise, if
you set this parameter to formula-mat or formula-col, make sure the selected formula
contains limit definitions. Otherwise the results may be erroneous.
■
When you are finished editing the protocol, press F10 to save the new protocol
and return to the Main Menu.
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KC Jr. Main Menu
ATemplate (create/edit)
The Template defines multiple sets or groups of standards and samples and specifies
their concentrations, dilutions, and replicates. Once a Template is created, the
parameters it contains can be saved on the default program disk.
The Template can then be recalled and used in calculations by entering its name as a
Data Defaults parameter or by selecting its name whenever a Template is required
within KC Jr. The status line at the bottom of KC Jr.'s Main Menu lists the active
template file. (Figure 3-13 shows Main Menu with the Template file window.).
Figure 3-13: Main Menu With Active Template Line
;;;
Throughout this section, a sample template will be used to illustrate how to create a
new template, enter and replicate sample sets, and enter dilutions. If you wish to
create a template that duplicates the one used in this example, follow the steps
marked with the pointer. ☛
CERES 900C User's Guide
3-33
Creating a New Template
☛ Press F4, or highlight Template (create/edit) on the Main Menu and press
Enter.
☛ At the prompt window, enter a file name (up to 8 characters) and press Enter
(or click the mouse button). A blank template appears on the screen with the well
marker in well A1.
Figure 3-14: Blank template map
■
Begin entering data, or press the Esc key to return to the Main Menu.
Selecting an Existing Template
■
Select F4 - Template (create/edit) from the Main Menu. A window appears
listing the template filenames stored in the default directory.
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KC Jr. Main Menu
■
To select a Template to edit, use the up/down cursor keys (or enter the first
letter of the Template name to highlight the next file beginning with that letter)
and press Enter.
KC Jr. will retrieve the template from disk and display it on the screen. Wells with a
number prefixed by an S are standard concentration values. Wells holding only
numbers are sample locations.
Modifying a Template
From the template screen, you can enter or modify standards, samples, dilutions, and
replicates.
■
Use the up/down, left/right cursor arrow keys to move to a well location.
If a previously created template is being edited, changes to the standards,
concentrations, and dilutions may be made in any order you wish.
■
Press Esc to abandon the template and return to the Main Menu. Or, press F10
to save the template in the default program directory and return to the Main
Menu.
If a new template is being created, entries are usually made in the following order:
■
Enter the standard concentrations.
■
Replicate standard concentrations.
■
Enter the sample unknowns.
■
Name the sample unknowns.
■
Replicate the sample unknowns.
■
Enter sample dilutions.
■
Enter a template description.
CERES 900C User's Guide
3-35
■
Save the template to disk.
Entering Standard Concentrations
☛
To enter standard concentration values:
■
Move the marker to the well location designated for the Standard concentration.
■
Press the S key. On the status line you will be prompted to enter the
concentration number.
■
Key in the number and press Enter or an arrow key. The well displays the
value entered, preceded by an S to indicate a standard concentration.
Up to 96 unique standards or replicated standards may be entered. Bio-Tek
recommends no more than 36 unique standards be entered, to insure readability if a
standards report is requested.
;;;
For the regression calculations to work properly, the total number of standards must
be at least one greater than the degree of fit requested in the active protocol. Thus,
for a linear (1st-order) fit, there must be at least 2 standards; for a Quadratic (2nd
order) fit there must be at least 3 standards; for a cubic (3rd-order)fit, there must be at
least 4. For either a 4-parameter fit or a logit/log fit, there must be at least 4. If these
requirements are not met, the error message "Unable to calculate curve with this
data!" will appear when the program begins its calculations.
If you want to correct a standard you've already entered:
■
Move the well marker to the appropriate well, then re-enter the correct value.
Press Enter or an arrow key.
If you enter a standard concentration value that is too wide to fit in the well space
(five or more characters), an S replaces the value in the well. When the highlighted
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KC Jr. Main Menu
marker is moved to this well, its standard concentration appears in the top left of the
screen.
☛ Example: If you enter standard concentrations of 1000, 750, 500, 250, 125,
62.5, 31.25, and 15.75 in wells A1 through H1, your screen should show the
template as in Figure 3-15:
Figure 3-15: New template with standard concentrations
Note on the sample template that wells G1 and H1 contain an S because their
concentration values are too wide to fit in the space. The well marker is on well H1,
and its concentration value of 15.75 is displayed in the upper left corner.
CERES 900C User's Guide
3-37
Replicating Standards
☛ Move the well marker to the standard you want to replicate and press Ctrl-R.
Then move the well marker to the last standard of the set. (As you expand the
area covered by the standard you are replicating, the status line will display the
expanded range of wells.)
☛ When the entire standard area is specified, press Enter. The standard number
will appear in each of the wells that belong to the set.
Entering Sample Unknowns
When the plate data is analyzed, calculations are performed individually and by
sample sets within the plate. Thus, if a plate has four sample sets and the Report of
Means parameter is set to Yes in the active protocol, the program will calculate a
mean, standard deviation, variance, and coefficient of variation for each of the sample
sets. Similarly, if the Sample Results parameter is set to Yes in the active protocol,
the program will report the slope, dilution, and concentration for each individual well.
☛ To specify a sample set on the template, use the arrow keys to move the
highlighted well marker to the well where that sample set begins. Then enter the
set number between 1 and 96 and press Enter, or a cursor arrow key. If the
remaining wells in the set are contiguous to this well, you can either replicate the
first sample (see description below), or move the well marker to the appropriate
wells and manually enter the sample number.
;;;
Sample sets do not have to be located in contiguous wells. For example, set 1 may be
wells A1 through A12 and H1 through H12. Or A1, A12, H1, and H12 may be a
sample set. In this case, move the well marker to the desired wells and enter the
sample set number.
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KC Jr. Main Menu
■
Set designations also can be changed. If a well initially is part of set #1, and you
wish to change it to set #2, move the highlighted well marker to the well, type 2,
and press Enter.
■
To remove a well from a group, move the well marker to the appropriate well
and press the spacebar. Press End to move the highlighted well marker to well
H12 (the last well on the plate), and press Home to move the well marker back
to well A1 (the first well on the plate).
☛ Example: In the sample template we are creating, sample 1 will occupy wells
A5 through D5.
Figure 3-16: New template with sample sets
■
Move the well marker to each of these wells and enter 1. Likewise, create sample
2 in wells E5 through H5, sample 3 in wells A9 through D9, and sample 4 in
wells E9 through H9. The template should look like Figure 3-16.
;;;
Any well not defined as part of a set will not be included in the analysis. Be sure to
define your sets carefully and accurately.
CERES 900C User's Guide
3-39
Naming a Sample Unknown
Once a set is designated on the template, you can give the set a name.
Figure 3-17: Sample Template, Naming a Sample Set
☛ Place the well marker on any well in the sample set, then press Ctrl-N.
☛ When prompted in the window, enter a name up to 12 characters, and press
Enter.
Now when you move the well marker around the template, the name of the set where
the well marker rests is displayed above the template. The set names also appear
when the calculations are displayed or printed.
Figure 3-17 shows the prompt for a set name. Set 2 has been given the name, sample
#2. The well marker rests in cell E5, so the name of set #2 appears at the top left
corner of the template.
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KC Jr. Main Menu
Erasing a Sample Set or Standard Concentration
■
To erase a sample set or standard concentration from the template, move the well
marker to any well within the set or standard and press Ctrl-E.
■
At the status line, KC Jr. will ask for confirmation before the program erases the
set or standard. If the response is N(o), KC Jr. will return to the template screen.
If the response is Y(es), the sample set will be removed from the template in
memory. To make the erasure permanent, save the template (F-10) before
returning to the Main Menu.
Replicating a Sample Set
Replication of wells produces exact copies of sample unknowns into contiguous wells
on the template currently being edited. This procedure is performed from the main
template screen, and is normally done after the sample sets have been entered but
before dilutions are entered.
☛ Move the well marker to one corner of the sample set and press Ctrl-R. Then
move the well marker to the opposite corner of the sample set. (As you expand
the area covered by the sample set you are replicating, the status line will display
the range of wells.) When the entire sample area is specified, press Enter. The
sample set number will appear in each of the wells that belong to the current
sample set.
☛ If you want to use all 96 wells of the plate in a single set, move the well marker
to well A1, and key in 1. Press Ctrl-R to replicate, move the well marker to the
last well, then press Enter. The screen will display 1 in each well, and the
program will perform the analyses using the optical density values in all 96 wells
as a single sample set.
☛ Example: Using the sample template, replicate sample 1 in wells A5 through D7.
CERES 900C User's Guide
3-41
■
To do this, move the well marker to well A5, and press Ctrl-R. Then move tthe
well marker to well D7 an press Enter. The sample number 1 should appear in
each of the 12 wells in the replicated range.
■
Replicate sample 2 in wells E5 through H7; sample 3 in wells A9 through D11,
and sample 4 in wells E9 through H11.
The template should look like Figure 3-18:
Figure 3-18: Template With Replicated Sample Sets
;;;
Don't try to replicate more than one sample set at a time, or the sample number where
the replication procedure was initiated will be replicated over the entire range.
If you replicate after dilutions have been entered, press Ctrl-D to display the dilutions
screen, then check the dilution values. You may have to re-enter them.
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KC Jr. Main Menu
Entering Dilutions
You cannot enter dilutions unless you have first entered standard concentrations or
sample locations.
☛ Press Ctrl-D to enter dilutions. The program will redraw the screen to show the
underlying dilution values on the template. On the newly created template, all the
standard and sample wells will show a value of 1, indicating a 1:1 dilution ratio
(Figure 3-19).
Figure 3-19: Template Showing 1:1 Dilution
The dilution factor shown is a ratio of 1 to the value shown (i.e., if a well on an
existing template shows 2.5, KC Jr. will accept that as a 2.5 dilution).
■
From the dilutions screen, in addition to entering dilutions, you can press F10 to
save the template and return to the Main menu or Esc to return to the main
template screen.
Once the dilution template is displayed, you can let the program calculate serial
dilutions automatically, or you can enter the dilutions manually.
CERES 900C User's Guide
3-43
Serial Dilutions:
☛ Press Ctrl-X to begin serial dilutions. The program will prompt for the dilution
ratio. Enter the dilution ratio 2.000
The dilution ratio shown is either the program default value (2) or the last dilution
ratio entered during this session. The ratio value you enter here will be the dilution
ratio between successive wells within the sample. That is, it is the multiplying factor
to be used in creating successive dilutions.
Example: If the first dilution is 1:10 and the dilution ratio is 2, the dilutions would be
1:10, 1:20, 1:40, 1:80, etc., each dilution being multiplied by the dilution ratio to
create the next dilution. Next, the program will prompt you for the starting dilution:
■
Enter the starting dilution 1. The starting dilution shown is either the program
default value (1) or the last starting dilution ratio you entered during this session.
■
To accept the displayed value, press Enter. Or, enter a new value and press
Enter. Before calculating the dilutions, the program needs to know the direction
to dilute the samples:
■
Dilute DOWN or dilute RIGHT
Your response tells KC Jr. whether to calculate the serial dilutions down the
column or right across the row from the starting point you specify.
■
Enter D if your dilutions go down, or R if your dilutions go right from the
starting well.
■
Finally, before KC Jr. can calculate and display the dilutions, you must specify
the starting well for the first dilution. The windows are removed from the screen
3-44
KC Jr. Main Menu
to redisplay the current template, and you are prompted for the starting well for
the serial dilution.
■
Move the well marker to the beginning well for the sample dilution and press
Enter to lock in the first well for the dilution set. Then move to the opposite
corner of the diluted sample set and press Enter again. The screen will be
redrawn with the dilution values calculated and displayed.
☛ Example: On the sample template we will dilute sample #1 with a dilution
ratio of 2.00 and a starting dilution of 2.00.
■
Press Ctrl-X and enter these values.
■
Specify Dilute Down when prompted.
■
Next, move the cursor to well A5 and press Enter.
■
Then, move the cursor to well D7 and press Enter.
Using the same procedure (Ctrl X, 2, 2, Dilute Down) for diluting samples 2, 3, and
4, the dilution screen should appear as in Figure 3-20:
Figure 3-20: Dilution screen with Serial Dilutions
CERES 900C User's Guide
3-45
Manual Dilutions
☛
To enter dilutions manually,
■
Press Ctrl-D from the main template screen to display the dilutions screen.
■
Move the marker to the wells where you want to add dilution values, and enter
the dilutions manually.
☛ Example: To enter the same dilutions manually that you previously entered in
the sample template, move the well marker to A5 and enter dilutions of 2, 4, 8,
and 16 in wells A5 through D7. As you enter the dilution values, they are
immediately displayed. Continue until all dilutions are entered.
If you try to enter dilutions in wells where samples have not been entered from
the main template screen, you will hear a beep, and KC Jr. will wait for valid
key input.
Entering a Description
☛ To enter a description for the template, press Ctrl-I.
■
At the prompt, type a description of the current template (up to 40 characters).
This description will be printed/displayed with the template.
Saving the Template
☛ When finished editing the template, press F10 from either the main template
screen or the dilutions screen to save the template on the default program disk
and return to the Main Menu.
To use this template for calculations, enter the template's name during Data
defaults setup, or select it during the "Calculate Results" process.
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KC Jr. Main Menu
Using a Previous Standards Curve (Defining two templates for standards)
To run standards-per-assay (as opposed to standards-per-plate), 2 templates must be
defined. Using standards per assay allows you to have standards (with or without
samples) on the first microplate. Subsequent microplates would have samples only.
For example, Template #1 would have standards (and samples if desired) defined on
it. Only samples would be defined on Template #2. To run a standards-per-assay
using the two templates:
■
Make template #1 the default template. (Data Defaults)
■
"Calculate" the standard curve and any samples using the appropriate data file.
■
Return to the Main Menu.
■
Change the default template to template #2 (samples only).
■
"Calculate" just the samples this time, using the appropriate data file(s). A
message appears confirming that there are no standards on template #2:
No standards! Use the previous standard curve? Yes.
If the user defines template #2 as the first template, the following warning message
will appear:
No standards! Use a template w/standards to calculate
a curve!
■
CERES 900C User's Guide
Press Enter to continue.
3-47
The user must then return to the Main Menu and change the default template to
template #1 (the template with standards defined on it).
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KC Jr. Main Menu
D Data Defaults
The Data defaults option allows you to specify how and where data is saved and
reported within KC Jr.
Figure 3-21: Selecting Data Defaults from the Main Menu
■
Select Data Defaults from the Main Menu by pressing F7 or D. You may also
use the curser up/down arrow keys to highlight Data Defaults and press
Enter.
If another KC Jr. menu is on the screen, press Esc to clear the screen, then
select Data Defaults.
The changes you make here will be saved in the KIN.SYS file on your default
program disk and used by KC Jr. as a reference whenever the program is
executed.
CERES 900C User's Guide
3-49
■
To change a Data defaults parameter, enter the initial letter (i.e. D for Data
drive\dir) or highlight the parameter using the up/down cursor keys and press
Enter, or point and click with the mouse.
■
Enter the appropriate data at the pop-up window prompt, or select from the
choices provided.
D - Data Drive/Dir
■
When D is selected from the Data Defaults menu, a window prompts you to enter
the destination drive and directory for absorbance data files:
Enter drive & directory for the O.D. data
Data will be stored in an \EIA subdirectory (created by KC Jr.) of whatever
drive and directory you enter here.
■
For example, if you want to store your data on drive B, then enter B:, and the
platefiles will be stored in an EIA subdirectory on drive B. Or, if your KC Jr.
program is in the KCJ subdirectory on your hard disk drive C:, then you should
enter C:\KCJ for this parameter. KC Jr. will create the EIA subdirectory for
you if the subdirectory doesn't already exist.
;;;
Caution: Unless absolutely necessary, do not store data on the working program
disk. Use an alternative drive and data disk.
■
After you enter the destination drive and directory and press Enter, KC Jr. writes
the new parameter to the Default file in the program directory and returns the
Data defaults menu to the screen.
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KC Jr. Main Menu
L - Lotus Drive/Dir
■
When L is selected from the Data Defaults menu, a window prompts you to enter
the destination drive and directory for data files transformed into a .PRN format
for use by Lotus or VisiCalc applications.
Enter drive & directory for the Lotus data
■
For example, if your KC Jr. program is in a subdirectory on your hard disk
named KCJ, then you should enter C:\KCJ\LOTUS for this parameter. If the
subdirectory doesn't already exist, KC Jr. will create it for you.
■
After you press Enter, KC Jr. writes the new parameter to the Default file in the
program directory and returns the Data defaults menu to the screen.
P - Default Protocol
■
When P is selected from the Data Defaults Menu, a window listing the protocol
file names stored in the default directory appears (Figure 3-42).
■
Highlight the protocol name that will become the default and press Enter or
click the mouse button. Or, enter the first letter of the protocol file name to
highlight the next file beginning with that letter. Press Enter to select the file.
■
If you don't want to make a change, continue to the next data defaults parameter,
or press Esc to return to the Main Menu.
When you change the default protocol, KinetiCalc saves the new parameters to the
Default file in the program directory and displays the new protocol name on the left
corner of the status line.
CERES 900C User's Guide
3-51
T - Default Template
■
When T is selected from the Data Defaults menu, a window listing the template
file names stored in the default program directory appears (Figure 3-43).
■
Highlight the template name that will become the default and press Enter or
click the mouse button. Or, enter the first letter of the template file name to
highlight the next file beginning with that letter. Press Enter to select the file.
■
If you don't wish to make a change, continue to the next parameter, or press Esc
to return to the Main Menu.
When a template is selected, KC Jr saves the new parameter in the program's Default
file and displays the template name on the status line.
R - Report Device
■
When R is selected from the Data Defaults menu, the program prompts for an
output device for calculations and reports:
P - Printer only
D - Display only
B - Printer & Display
■
If you press Esc while this window is displayed, the program returns to the Main
Menu and no change is made. If this parameter is set to D, reports are displayed
on your screen. If set to P, reports are printed. If set to B, the reports are both
displayed and printed, with a pause after each report so you can examine the
results.
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KC Jr. Main Menu
■
After you enter P, D, or B, KC Jr. writes the new parameter to the Default file in
the program directory and returns to the Data Defaults menu.
C - Printer Control Code
■
When C is selected from the Data Defalts menu, a window prompts for a special
escape code sequence to send to the printer before any reports are printed.
Entering an escape code sequence is optional. The escape code sequence is used
by some printers to specify print instructions (condensed print, bold, letterquality print etc.). Refer to the operator's manual that accompanied your printer
for more information on printer control codes
Enter the printer control escape sequence
(27)(15)
■
The program displays the current sequence and waits for input. If you don't want
to change the displayed sequence, press Enter and the program will return to the
Data Defaults menu.
■
To change the control code, enter the decimal value for each code in parentheses.
You can enter a maximum of 15 control code characters, including the
parentheses. For example, if your printer requires an ESC G sequence to select
double-strike printing, you would enter that sequence here as (27)(71). Or if
you want to set condensed print, you might enter the escape sequence here as
(27)(15).
■
After entering a new code and pressing Enter, KC Jr. writes the new parameters
to the Default file in the program directory and returns to the data defaults menu.
CERES 900C User's Guide
3-53
When you have finished editing Data default parameters, press Esc to return to the
Main Menu.
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KC Jr. Main Menu
BFormula (create/edit)
■
Option F5 Formula (create/edit) from the Operations menu allows you to
define plate and transformation formula(s) for the transformation of optical
densities or kinetic slopes.
;;;
Important! Transformations take place before other reports; formulas take place
after other reports.
The formula, which can be named and stored on disk for later recall and modification,
may consist of one equation or Multiple Individually Calculated Equations (MICE).
Once created, the formula may be used in data analysis by entering its name in a
Protocol's Apply Formula parameter. Keep in mind that the formula or
transformations must conform to the following rules in order for the calculations to
be performed properly:
Form.
Trans.
Chars.
Description
✔
✔
+
Represents addition
✔
✔
-
Represents subtraction
✔
✔
*
Represents multiplication
✔
✔
/
Represents division
@
Represents averaging
()
Represents an inclusive unit
✔
✔
✔
for calculation
✔
&
Separates MICE (used only in
the plate formula section)
✔
CERES 900C User's Guide
S
Represents set definition
3-55
Form.
Trans.
Chars.
Description
✔
L
Represents limit definition
✔
'
Separates elements for
averaging
✔
✔
N
Represents all sets
[]
Represents wells to be
referenced by absolute
location(s), no change when
replicated (used only in the
transformation section)
✔
✔
!!
Represents a comment in the
transformation section, and a
label that will be printed in the
plate formula report.
Table 3-1: Allowed letters and symbols in a formula
Aside from well designators A through H, the only other letters and symbols that may
be used to describe arithmetic or mathematical relationships in formulas and
transformations are listed in Table 3-1.
The plate formula may be composed of up to 140 text characters, including single
equations or MICE, separated by ampersands.
■
The transformation formula(s) can each contain up to 15 characters.
■
The only arithmetic operations allowed are addition, subtraction, multiplication,
and division.
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KC Jr. Main Menu
;;;
All formulas are calculated from left to right, and not by mathematical order of
precedence (i.e. multiplication and division functions first, followed by addition and
subtraction functions). If a different order of precedence is required, use parentheses.
Selecting/Creating a Formula File
■
Select Formula (create/edit) from KC Jr.'s Main Menu. If formulas have
previously been created and stored in program's default directory, a window
appears listing the file names.
Figure 3-22: Saved formula files available for selection
■
Select a formula from the list, or press Esc to clear the window and enter a name
for a new formula at the prompt.
■
If no formulas have been created, a prompt windows asks for the name of the
new formula to be created. Enter a name up to 8 characters, and press Enter. An
extension is unnecessary. KC Jr. automatically adds a .FRM extension to the
CERES 900C User's Guide
3-57
filename. If you press the Enter key in response to the file name prompt, KC Jr.
will return to the Main Menu.
Figure 3-23: System prompts for a new formula name
Entering a New Formula
When a new file name is entered, the program displays an empty
formula/transformation entry screen.
■
Use the down arrow key to position the cursor after Plate formula(s). Use the
numeric keypad, the left and right cursor control keys, the delete key, the
backspace key, and the appropriate symbols to enter your formula. You can
enter up to 41 characters for a single formula or single MICE, or up to 140
characters comprising several individual equations (MICE). The maximum
(MICE) length is 41 characters.
;;;
Make sure you separate the MICE with ampersands (&) so the program will
recognize and calculate them properly. Note that there is no space between characters
in a formula line.
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KC Jr. Main Menu
☛ Example: If the template contains one sample set in each row, you may wish to
define a formula that:
■
subtracts the average of set 2 (wells B1 through B12) from the average of
set 1 (wells A1 through A12) and
■
subtracts the average of set 4 (wells D1 through D12) from the average of
set 3 (wells C1 through C12), etc.
Using S to represent the set number, the formula to accomplish this would be
entered as follows:
@[email protected]&@[email protected]&@[email protected]&@[email protected]
Alternatively, you may wish to have paired wells, such as negative and positive
controls, and may wish to compensate each positive based on the associated
negative. The formula might look like this:
A1-B1&A2-B2&A3-B3&A4-B4& ...
or, more succinctly:
S1-S2&S3-S4&S5-S6&S7-S8
A more complex example might be demonstrated by the use of both paired variates
and blanking. Suppose you have paired positive and negative values in rows A and B,
C and D, E and F, and G and H. You want to blank the plate based on the average of
the corrected pairs A1-B1 and A12-B12. The formula might look like this:
@(A1-B1,A12-B12)- S1-S2&@(A1-B1,A12-B12)-S3-S4&
@(A1-B1,A12-B12)-S5-S6& ...
CERES 900C User's Guide
3-59
If you precede individual equations, up to four MICE, with L, the program will
calculate the equation(s) and set the results as the values for the limits parameter
when this formula is entered for a Protocol's Apply Formula parameter.
■
When you have finished entering a formula, press Enter, and the program will
display the formula editing screen:
Figure 3-24: The Formula Editing Screen with example formula
Modify an Existing Formula
When you retrieve a formula file from the default data disk, KC Jr. displays the
formula- editing screen, with the cursor located at the beginning of the formula.
■
Use the cursor arrow keys to position the cursor after Plate formula(s), and the
cursor directional keys to move through the formula and make any necessary
changes. Any characters you type will be inserted to the left of the cursor
position. Use the Del and Backspace keys to delete any unwanted characters.
3-60
KC Jr. Main Menu
■
Pressing Esc while you are entering or editing a formula returns you to the Main
Menu without saving the formula. Pressing F10 saves the formula on your
default program disk and returns you to the Main Menu. You must save the new
or modified formula before it can be used for calculations.
Using the Formula in Calculations
■
To use this formula in calculations, select Protocol (create/edit) from the Main
Menu.
■
At the Protocol description screen, move to Apply Formula parameter field and
press the spacebar.
■
Select the formula name from the window listing saved formulas.
Create/Modify a Data Transformation
When Formula (create/edit) is selected from the Main Menu, the program displays
a window listing the file names of formulas stored in the default directory. On the
status line, the program prompts you to select the formula file to be edited.
■
Select one of the formula listed, or press Esc to bring up a prompt for the name
of a new formula. When a new file name is entered, the program displays an
empty formula entry screen and waits for you to begin a new formula.
The blank Formula Input Screen features an 8 X 12 matrix of 40-character spaces for
defining transformation formulas.
CERES 900C User's Guide
3-61
Figure 3-25: Delta OD formula applied to readings
☛ Example: A Delta O.D. formula of A1-A2 (Figure 3-25) is applied to a set of
microplate well readings. The calculations are carried out and the results shown in
Figure 3-26.
Figure 3-26: Results of well transformations
3-62
KC Jr. Main Menu
;;;
Because only 5 character spaces are available in each well location , the formulas
shown in column 9 of Figure 3-26 display "A9-A1", rather than "A9-A10" which
requires an additional character space to show the zero. As each individual well is
referenced, however, lines one and two at the top of the screen will display the
current well referenced and the complete formula for that well.
Options for simplifying transformation entry include:
Ctrl -D
■
eDit an existing transformation formula: Move the cursor to the well to be edited.
Press Ctrl - D. The cursor moves to line #2 on the screen, allowing editing
(insertion, deletion, etc.) of the formula.
Ctrl - R
■
Replicate transformation formula to other well(s): Press Ctrl - R. Move the
cursor to the well to be replicated. Notice the Prompt on the status line.
■
Press Enter
■
Move the cursor to the first well in which the formula is to be replicated. Press
Enter.
■
Move the cursor to the last well in which the formula is to be replicated. Press
Enter. The formula will then be replicated to the selected wells.
;;;
Any well intended as a formula constant (i.e. any or all well(s) - A2 should be in
brackets so that the formula reads: "A1 - [A2]". If no bracket is used, the formula will
reference the wells in relative increments (i.e. A1 - A2, B1 - B2, rather than A1 - A2,
B1 - A2).
CERES 900C User's Guide
3-63
Ctrl - E
■
Ctrl- E will erase a well, a column of wells, a row of wells, or an entire plate of
transformation formulas. Alternately, pressing the spacebar on an individual
well will erase that well only.
■
Press Esc while you are entering or editing a formula, to return to the Main
Menu without saving the formula / transformation(s). Press F-10 to save the
formula(s) and return you to the Main Menu.
;;;
You must save the new or modified formula before it can be used for calculations.
Using Transformations in Calculations
To use these transformations in the calculations:
■
Select Protocol (create/edit) from the Main Menu.
■
At the Protocol definition screen, move to the parameter field Transform Raw
Data by_____, and press the spacebar.
■
Select the transformation formula from the list of saved formulas in the pop-up
window.
■
Move to the next parameter field, Report Transformed Data. Use the
spacebar to toggle the setting to Yes.
3-64
KC Jr. Main Menu
Chapter 4:
Running KC Jr.
This chapter explains how to calculate results, read a
plate and save data, retrieve data from a disk file, the
Kinetics Assay, the 96-well graphics screen,
endpoint, statistical and scanning assays and
incubating a plate using KC Jr. software for the
CERES 900C.
?Calculating Results
;;;
Warning! Software. The user of the CERES 900C utilizing KCJr Software must
follow the specific manufacturer’s assay package insert when modifying KCJr
software parameters and establishing result calculation methods.
;;;
Warning! Data Reduction Protocol. KCJr is a basic data reduction software
program that does not flag out of range results nor prevent these results from being
sent to any connected information system. It is the user’s responsibility to verify that
all quality control materials are in their expected ranges prior to utilizing the assay’s
results.
Use the checklist that follows to ensure you've completed some preliminary tasks
before you begin your calculations:
■
Define the protocol for the current plate run, and make sure its name appears on
the KC Jr. status line. See Chapter 3, Protocol (create/edit) for instructions on
creating a protocol file, and Data Defaults for information on installing the
protocol as the default.
■
Create a Reader Control File from within the Protocol. Information on creating a
Reader Control File as part of a Protocol is included in Protocol (create/edit)
in Chapter 3.
■
Design the template for the current plate run, and make sure its name appears on
the status line. For instructions on creating a template see Chapter 3, Template
(create/edit), and Data Defaults for information on installing the template as
the default.
■
Set Data Defaults parameters. Otherwise, the data may not be saved where you
want it. Refer to Chapter 3, Data Defaults for details.
4-2
Using KC Jr.
Starting the Calculations Process
Selecting F2 Calculate results from KC Jr.'s Main Menu begins the calculation
process that retrieves data either from disk or directly from the reader, performs all
necessary calculations, and reports the results based on the predefined protocol
currently in use.
Figure 4-1: Selecting Calculate from the Main Menu
Since KC Jr.'s data files can contain multiple plates, the program uses the Assay Type
parameter in the active Protocol file to determine the data configuration.
If the Assay Type is either end point or statistical, KC Jr. assumes that any multipleplate data file contains independent plates of data and performs all calculations
separately on each plate of the file. But if the Assay Type is kinetic, then the program
assumes the multiple plates in the file are consecutive readings of the same plate and
should be treated as kinetic data.
CERES 900C User's Guide
4-3
■
When Calculate results is selected from the Main Menu, the program prompts for
the source of the data:
R - get plate(s) from Reader
D - get plate(s) from Disk
■
Select R (Reader) to retrieve, display, report, and save the optical density values
from one or more plates read by the CERES 900C to a computer through the
RS232 port.
■
Select D (Disk) to retrieve platefiles of data previously read and stored or
entered manually and saved in the EIA subdirectory on the default data disk.
■
To select the source of the data, highlight the option and press Enter or click the
mouse button. Or, key in either R or D to choose the corresponding option.
■
Press Esc to return to the Main Menu without retrieving any data.
Reading a Plate and Saving Data
When you indicate you wish to read a plate, (Select R) KC Jr.:
4-4
■
Asks you to confirm Protocol and Template defaults
■
Requests the Number of Readings
■
Prompts for Plate ID (option selected in Protocol)
Using KC Jr.
Figure 4-3: KC Jr.'s plate read prompts
■
Prompts for a file name to be used for saving data
■
Enter a name that will uniquely identify this file on the disk. The name can be
alphanumeric as long as it does not exceed 8 characters, with a three-character
extension.
After you enter the file name, the program checks the EIA sub-directory on the
default data disk for a file with that name. (The EIA subdirectory is created when you
specify where you want to save the absorbance data files, during Data Defaults
setup).
If a file of plates already has the name, KC Jr. gives you the option of overwriting, or
appending data to, or entering a new name for the specified file.
CERES 900C User's Guide
4-5
Figure 4-4: Selecting Plate File Options: Overwrite, Append or New
KC Jr. uses the setting from the Number of Readings parameter in the active Protocol
file to determine the number of readings to make.
■
If the Assay Type is either End Point or Statistical, KC Jr. uses the Number of
Readings setting as the number of plates to read. When a correct file name has
been entered, the program displays the message:
Waiting for plate #1
Plate reading and data transmission begins automatically.
■
If you press Esc to interrupt the reading process, the program will close the file,
close the RS232 port, and begin the specified calculations and reports based on
the data already read. When the appropriate key is pressed, the CERES 900C will
read the plate and send the data to the computer. As each plate is received by the
computer, it will be saved in the EIA subdirectory on the default data drive
4-6
Using KC Jr.
specified during Data Defaults setup. The transmission speed depends on the
reading options selected in the active protocol, as well as the baud rate selected
on the CERES 900C and specified during KC Jr. Setup.
■
If you want to read another plate, press the appropriate key on the reader, and it
will perform another plate read.
■
If you don't want to read more plates for this file, press Esc, and the program
begins calculations.
Retrieving Data from a Disk File
■
Selecting D - "get plate(s) from disk," allows you to retrieve and make
calculations based on any plate or plates of optical density data stored on disk. If
you've previously retrieved one or more platefiles, either from disk or from the
reader when D is selected from the submenu, KC Jr. gives you the option of
making more calculations on the same plates:
Figure 4-5: KC Jr. prompts for data source
CERES 900C User's Guide
4-7
■
If you select N, KC Jr. reads a microplate and calculates using that data; if you
select P, the program bases its calculations on previously retrieved plates. The
program displays a window listing the platefile names in the EIA subdirectory,
then prompts you to accept the existing Protocol, Template and Formula defaults
or enter new ones. When the defaults have been changed and/or accepted, a
second window will prompt you for the platefile:
Figure 4-6: KC Jr. prompts for the platefile
■
Highlight the name of the file you wish to retrieve, and press Enter, or enter the
first letter of the platefile name to move to the next file beginning with that letter.
■
For information about any stored platefile, highlight the name of that file, and
press Shift-F1. Another window will appear, showing platefile name, the
number of plates it contains, the date the file was created, and the descriptive text
for the first plate in the file. To proceed, press Esc to remove the help window
from the screen.
4-8
Using KC Jr.
■
You can also use DOS wildcard characters to retrieve multiple platefiles. For
example, to retrieve all platefiles with an extension of .TST, press Esc until the
file window disappears from the screen. Then enter *.TST in response to the
prompt as follows:
Figure 4-7: Retrieving multiple plate files using DOS wildcard
■
The program will then retrieve the selected file names under the prompt. If the
selected file contains more than one plate, you will be asked which plates you
want to retrieve:
A - get All plates in file
S - get Specific plates
■
If you want to retrieve only some of the plates in the file, select S. The program
then prompts for the plates to use:
Which of the X plates to use?
where X is the total number of plates in the file.
CERES 900C User's Guide
4-9
■
Enter the range of plate numbers or the individual plate numbers, separated by
commas, that you want to retrieve; then press Enter.
Example: If a platefile contains 9 plates of data and you want to retrieve plate
numbers 4 through 7, and 9, enter 4-7, 9 in response to the prompt. Or if you want to
retrieve plate numbers 3, 6, and 8, enter 3, 6, 8 when prompted.
■
Enter E for all even-numbered or O for all odd- numbered plates in the file.
■
If you enter 0 (zero) or press Enter in response to this prompt, no data will be
retrieved and you will be asked if you wish to retrieve more files or to proceed
with calculations. After you have entered the plate numbers you wish to retrieve,
a cumulative total of plates to be read is displayed in the upper right corner of the
screen.
■
If you want to retrieve all the plates in the selected file, select A and press Enter
or click the mouse button.
■
After you specify which plates to retrieve, the program will give you the
opportunity to retrieve more files:
R - Retrieve more files/plates
P - Proceed with calculations
■
You can choose to retrieve up to 100 plates by selecting the desired file, then
specifying which plates from the file you wish to analyze. If you select P to
proceed, the program reads the plates into memory, and begins the calculations.
4-10
Using KC Jr.
Kinetics Assay
The 96-Well Graphics Screen
Once you choose to proceed with the calculations for a kinetic assay, KC Jr. plots the
absorbance data points for all 96 wells on a graphics screen as each reading is made.
Figure 4-8: 96-Well Graphics Screen
As the plates are read, a counter in the upper right corner of the screen displays the
number of the current reading. Each well is represented as a box, which contains one
mark for each reading. The optical density scale range at the top of the screen is based
on input data, and changes as the readings are made.
When the run is completed, KC Jr. calculates the slopes for each well, then displays a
scaled time axis at the bottom of the screen with one tic mark for each reading. A
pointer (+) in the center of the screen can be used to select a well to zoom in on, or to
specify the time interval to include in the curve calculations.
CERES 900C User's Guide
4-11
Depending on how you want to treat the data, you have several options while the 96well graphics screen is displayed:
■
Print the 96-well graphics screen
■
Save the 96-well graphics screen to disk file.
■
Adjust the y-axis scale
■
Select the time interval for the calculation
■
Display the mean slope and R-squared value table
■
Zoom in on a specific well
■
Edit the standard concentrations
Printing the screen
■
To print the 96-well graphics screen, press Ctrl-P.
Saving the screen to a disk file
■
To save the 96-well graphics screen to disk file, press Ctrl-D. The file
"KINETIC.PCX" will be created.
4-12
Using KC Jr.
Adjusting y-scale axis
■
To adjust the maximum O.D. for the y-scale: Type in the new maximum O.D.
value and press Enter.
Selecting time interval
■
To select time interval: By selecting the readings to use for the calculation of rate
(slope), this option allows you to select only the linear portion of the kinetic
reaction for the ELISA. Selecting the interval is a 4-step procedure:
1)
Move the pointer to the time axis at the bottom of the screen and press
Enter. A small box or arrow appears at the right end of the time axis.
2)
Use the cursor control keys or the mouse pointer to move the small
box or arrow to the tic mark that represents the last reading you wish
included in the calculations and press Enter. The screen will be
redrawn to include only the data points within the selected time
interval.
3)
Move the pointer to the left end of the time axis and press Enter.
4)
Again, use the cursor control keys to move the box or arrow to the
the tic mark that represents the first reading you wish to include in the
calculations, and press Enter. The 96-well graphics screen is then
redrawn so that each well shows only those data points within the time
interval just selected.
■
To restore a reading to the calculation: move the pointer to the appropriate end of
the time axis and press Enter. Then use the cursor control keys to move the
box or arrow to the tic mark you wish to restore and again press Enter.
CERES 900C User's Guide
4-13
You can continue to change the time interval until it includes the readings you want.
Each time you change the interval, the screen will be redrawn and the slopes will be
recalculated.
Mean slope and R2 value
To display slope/R-squared table: From the 96-well graphics screen, press CtrlPgDn to display the mean slopes and R-squared values for each well.
Figure 4-9: Sample slope / R2 Table
The top value in each well in the matrix is the mean slope, and the bottom is the R
squared value for all the readings. From this screen, you can press Ctrl-PgUp to
return to the 96-well graphics screen or PgDn to continue to the edit graph screen.
4-14
Using KC Jr.
Figure 4-10: Edit Graph Screen
Figure 4-11: Sample Zoomed Well Screen
Zoom-a-well
■
To zoom in on a specific well: move the screen pointer to the desired well and
press Enter or click the mouse button.
CERES 900C User's Guide
4-15
When the zoomed well Screen appears, it will show the selected data points, the slope
line, the standard deviation, and the R-squared value for the selected well (Figure 411) . The scaled time-axis becomes the X-axis for the zoomed well, and the optical
density scale is the Y-axis along the left edge of the screen.
■
To print the zoomed well, press Ctrl-P. To save the zoomed well to a disk file
"ZOOM_ _ _.PCX", press Ctrl-D. The "_ _ _" will be the location of the
particular zoomed well. Press Esc to return to the 96-well graphics screen.
Edit Graph Screen
;;;
If the assay type is kinetic, the Edit Graph screen plots slope (rate) values on the Yaxis against the standard concentration values on the X-axis. If the assay type is end
point, the screen shows optical density values on the Y-axis and standard
concentration values on the X-axis.
The edit graph screen deletion of standard values from the equation calculation. An
asterisk represents each standard slope/optical density value on the retrieved plate. If
only one asterisk appears for a standard concentration with replicates, the optical
densities for the replicates of that concentration are too close to plot separately.
On this editing screen, you can now mark for deletion any values you want excluded
from the curve calculation.
■
Use the right, left, up, and down cursor keys to move the blinking cursor to
the value you wish to exclude, and press D to delete that value. A lower-case o
will replace the * asterisk, indicating a deleted value. If you change your mind
and want to restore a standard concentration value, move the cursor to the deleted
value and press R. This action will replace the o with the original * asterisk and
the value will be included in the calculations.
4-16
Using KC Jr.
■
If you decide you want to abort the calculation procedure, press Esc to return to
KC Jr.'s Main Menu.
From the edit graph screen, you have the following options:
1)
Press Shift-PrtSc to get a printed copy
2)
Change the data type or curve-fit method for the plate run.
3)
Return to the 96-well graphics screen (kinetic analysis only)
4)
Display standards results report
5)
Calculate and display the fitted curve and equation
Change the data/axis type or curve-fit method
■
Press F9 to change the curve fit method. Press F10 to change the data/axis type.
Return to 96-well screen
■
Press PgUp from the edit graph screen to review the 96-well graphics screen
(kinetic analysis only - see Figure 4-8). For details, refer to the section entitled
96-Well Graphics Screen.
Display standards results
To display the standards results report, press Ctrl-PgDn.
CERES 900C User's Guide
4-17
Figure 4-12: Sample Standards Results Report
Figure 4-12 shows the standards results for a kinetic analysis. If the assay type were
end point, the second column of data entitled Mean Slope would be replaced by a
column entitled Average Absorbance. Estimated concentrations whose values are
outside the range of the standard concentrations are shown in parentheses.
Figure 4-13: Fitted Curve (Kinetic)
4-18
Using KC Jr.
If the report contains more data then can be displayed on the screen at one time, the
program pauses at the end of the first screen of data and waits for you to press PgDn
to continue. When all the data has been displayed, press PgDn to display the fitted
curve (Figure 4-13), or cubic curve (Figure 4-14); or Ctrl-PgUp to return to the
previous page of the report or to the Edit Graph screen (as shown in Figure 4-8).
Fitted Curve Screen
■
To calculate the curve model and display the fitted curve, press PgDn from
either the Edit Graph screen (Figure 4-10) or the standards results table (Figure
4-13).
Figure 4-14: Fitted Cubic Curve (End Point)
The fitted curve screen plots standard concentration values on the X-axis against rate
(slope) on the Y-axis if the Assay Type is kinetic (Figure 4-14), or against optical
density values on the Y-axis if the Assay Type is end point. The line represents the
least-squares best fit for the data, given the calculating parameters set on the active
protocol and in Data Defaults Setup. Each point is a plot of an individual value. The
CERES 900C User's Guide
4-19
range of values on the X- and Y-axes is automatically scaled from the data on the
plate and the plate map.
From the fitted curve, you have the following options:
1)
Return to the Edit Graph screen
2)
Print the Fitted Curve screen.
3)
Evaluate the sample unknowns
Return to the Edit Graph Screen
■
From the Fitted Curve screen (Figure 4-13 or Figure 4-14), press PgUp to
return to the Edit Graph screen (Figure 4-10). You can then delete or restore
standard concentration values from the equation and change the curve fit or data
type, if desired.
;;;
If you press PgUp to return to the edit graph screen, any previously deleted points
will be restored to the screen and therefore to any further calculations unless you
delete them again.
Printing the fitted curve
■
To print the fitted curve, press Ctrl-P to send a copy of the fitted curve to the
installed printer.
Save as disk file
■
To save the fitted curve to a disk file, press Ctrl-D. The file, STDCRV.PCX will
be created.
4-20
Using KC Jr.
Sample Evaluation
■
From the fitted curve, press PgDn to evaluate the sample unknowns. KC Jr.
feeds the sample optical density values through the formula calculated from the
curve and produces the calculated concentrations of unknowns for linear (Figure
4-15) and cubic (Figure 4-16).
Figure 4-15: Calculated concentrations of unknowns (Linear)
CERES 900C User's Guide
4-21
Figure 4-16: Calculated concentrations of unknowns (Cubic)
KC Jr. then produces the reports called for in the active protocol. If the Report device
parameter in Data Defaults is set to printer only, the results will be sent to the printer.
Otherwise, they will be displayed on the screen, one screenful at a time.
■
When the screen display pauses, press PgDn to continue to the next screen or
report.
KC Jr. prints the series of reports specified by the active protocol for each reading.
For example, if the active protocol specifies 7 readings, 7 sets of absorbance data
reports would be printed or displayed.
The following is a list of available report screens that may be printed:
4-22
■
Kinetic Slopes/^R2
■
Kinetic/Endpoint Standard Report
■
Kinetic Sample Evaluation Results
■
End Point Sample Evaluation
Using KC Jr.
■
Protocol Definition
■
Template Description
■
Absorbance Data
■
Report of Transformed Data
■
Formula Translation
■
Report of Means
■
Report of Limits
When all the reports have been displayed or printed, the program returns to the Main
Menu.
CERES 900C User's Guide
4-23
End Point Assay
If the currently active protocol specifies an End Point Assay, the program displays the
absorbance values on the screen as each plate is read. If the plate was logged from the
reader, all values have already been corrected by the blanking pattern selected on the
reader. Blank wells have either not been read or have no value.
Figure 4-17: End Point Assay Screen
A minus sign (-) precedes any value that was measured or entered as a negative
optical density; otherwise all values are positive. Any well showing asterisks (*****)
has a value outside the range of readability. As each plate is received from the reader,
it is also saved in the EIA subdirectory on the default data drive as specified in Data
Defaults Setup.
After the last plate is read or the reading is interrupted, the program proceeds to the
Edit Graph screen (Figure 4-10). From there the program follows the same sequence
as it would with a kinetic assay. Except for the fitted curve and the sample evaluation
results, the screens and reports are the same as for a kinetic assay.
4-24
Using KC Jr.
With an end point assay, the sample results report shows average absorbance instead
of average slope. Additionally, the fitted curve for an end point assay plots optical
density, (not rate) against standard concentration values.
Statistical Assay
If the currently active protocol specifies a statistical assay type, the plates are read
and the absorbance data values displayed. If the data is being retrieved from the
reader, it is saved to disk. KC Jr. bypasses all the slope calculations and immediately
prints the reports specified in the active protocol, then returns to the Main Menu.
CERES 900C User's Guide
4-25
Scanning Assay
If the currently active protocol specifies a scanning assay type, the reader performs a
user-defined number of multiple reads of each microplate well, based on dividing
each well into a pre-selected number of discrete scan areas.
To perform a scanning assay:
■
Set the operating Protocol's Assay Type parameter to Scanning
■
In the Reader Control File, set the Read Method parameter to Scanning
■
In the Reader Control File enter the appropriate number of scans to the
corresponding well width in the Number of Scans and Well Diameter parameter
fields, using the table below.
Number of Scans
Well Width
1-17
4.0 - 4.4
1-19
4.5 - 4.9
1-22
5.5 - 5.9
1-28
6.0 - 6.4
1-30
7.0 - 7.4
Table 4-1: Valid scans for specific well diameters
When the microplate is read, the absorbance data points are plotted on the 8 x 12
kinetic matrix graph.
■
To zoom-a-well, position the pointer on the well in the matrix graph, and press
Enter.
■
To print the graph, press Ctrl-P while the matrix graph or any of the zoomed
well graphs are displayed.
4-26
Using KC Jr.
■
To save the graph to a disk file, press Ctrl-D while the matrix graph or any of the
zoomed well graphs are displayed.
;;;
Curve fit line, and associated statistics reports are not available.
Figure 4-18 A Twelve- Scan Read
CERES 900C User's Guide
4-27
EIncubate Plate
Selecting F8 / Incubate plate from KC Jr.'s Main Menu allows you to set an
incubation time interval for the microplate. When you press F8, a prompt appears
requesting a time interval (Figure 4-18).
Figure 4-18: Incubate plate time prompt
■
Enter the time interval (hh:mm:ss) and press Enter. The microplate carrier is
retracted and incubation begins. If no time is entered, the incubation interval is
set for an indefinite time (user determined).
■
Press Enter at the time prompt to initiate an indefinite incubation period. The
Incubate Plate line on KC Jr.'s Main Menu, changes to Home Plate.
■
Press F8 again to retrieve the microplate and halt the incubation process. A
window will appear confirming that incubation was interrupted, and post the
incubation time.
4-28
Using KC Jr.
Chapter 5:
KCJr's Utilities
This chapter discusses the system utilities
available with KC Jr. software on the CERES
900C. These utilities include DOS file
operations, Lotus and other Transformations,
and exiting through a DOS shell.
gSystem Utilities
Selecting F6 from KC Jr.'s Main menu allows you to perform a number of
"housekeeping" tasks without leaving the KC Jr. environment. These tasks
include copying, deleting and renaming data files, protocols, templates and
formulas; transforming data into a format readable by Lotus 1-2-3 or VisiCalc,
and receiving information on the version of KC Jr. you are running.
Systems Utilities also includes the Calibration and Optics Test options. We'll
discuss using the Calibration Plate with KC Jr.'s Calibration Verification program
and the Optics Test in Chapter 8, Performance Verification.
Figure 5-1: System Utilities option on Main Menu
D - DOS File Operations
Selecting D - DOS File Operations pops up a menu of options that allows you
to display a directory of files in any user-specified subdirectory on the default
data disk, and to copy, erase, and rename microplate data files stored in the EIA
subdirectory.
■
Move the cursor to highlight the desired function and press Enter or click
the mouse button. Or, type the letters to select the corresponding option.
■
Press Esc while this window is displayed to abandon the DOS operations
and return to the Main Menu.
■
If you wish to perform DOS file operations in a directory other than EIA,
press Esc to return to the Main Menu, and select F9-Exit to DOS shell.
When you are ready to return to KC Jr., type Exit at the DOS prompt.
5-2
KCJr Utilities
Figure 5-2: File Utilities Menu
C - Copy a File (or Plate)
The first item on the File Utilities Menu allows you to copy a file or plate within
the EIA subdirectory, and give that copy a different name. When you select C Copy a data file (or plate), the program lists the files in the EIA subdirectory.
(If there are more than 40 files, press Esc to view additional files.)
■
Highlight the file you wish to copy and press Enter or click the mouse
button. You can also type the first letter of the file name to highlight the next
file beginning with that letter, and press Enter.
■
If you want information about a stored file, highlight the name of the file
and press Shift-F1. Another window will pop up, showing you the file
name, the number of plates it contains, the date and time of the first plate,
and any other descriptive information for the first plate in the file. Press Esc
to remove the help window from the screen.
When you select a file to copy, KC Jr. prompts for a new name for that file.
CERES 900C User's Guide
5-3
Figure 5-3: Copy a data file (or plate)
Copy FILENAME.EXT To:
where FILENAME.EXT is the file you chose to copy.
■
;;;
Type the new name for the file copy, and press Enter.
If you enter the name of a file that already exists, KC Jr. will allow you to cancel
the copy command before the original file is overwritten. If you press Enter
without entering a file name in response to this prompt, the program returns to
the File Utilities Menu without copying the file.
You will be asked which plates from that file you want to copy:
A - copy All plates in FILENAME.EXT
S - copy Specific plates
where FILENAME.EXT is the file you chose to copy.
■
5-4
To copy all the plates in the file, enter A. Otherwise, enter S.
KCJr Utilities
■
You will be asked which plates you want to copy. Key in the range of plate
numbers or the individual plate numbers (separated by commas) that you
want to copy, and press Enter.
;;;
For example, if a platefile contains 9 plates of data and you want to copy plate
numbers 4 through 7 and 9, enter 4-7, 9 in response to the prompt. Or if you want
to copy plate numbers 3, 6, and 8, enter 3,6, 8 in response to the prompt:
Which of the 9 plates to copy?
3, 6, 8
After copying the plates to the new file, KC Jr. will return you to the File Utilities
Menu.
■
If you change your mind, or don't want to copy any plates from the specified
file, press Enter in response to the prompt. The program returns the File
Utilities Menu to the screen.
D - Directory of Files
Option D from the file utilities window allows you to display a list of the files
stored on a given drive and directory, and checks for the amount of free space on
the disk.
■
When D is selected, you are prompted for the drive/ directory name you wish to
display:
Directory of:
CERES 900C User's Guide
5-5
■
Enter the directory or subdirectory name and press Enter. You can also use
wildcard characters (? and *) to display selected files.
For example: If you wish to see all the platefiles with the extension of
.TST stored in the EIA subdirectory, the prompt and your response would
appear as follows:
Directory of:
EIA\*.TST
The names of the files with the extension of .TST currently stored in the
specified subdirectory on the disk will be displayed.
5-6
■
Press Shift-Prt Sc keys to obtain a printout of the displayed directory.
■
Press any key to return to the File Utilities Menu.
KCJr Utilities
E - Erase a Data File (or Plate)
Option E from the file utilities menu allows you to erase a plate within a file or to
erase a complete file within the EIA subdirectory. When you select E from the
file utilities window, a pop-up windows lists the files in the EIA subdirectory.
■
Highlight the file you wish to erase and press Enter or click the mouse
button. You can also enter the first letter of the file name to highlight the
next file beginning with that letter, and press Enter.
CERES 900C User's Guide
5-7
■
If you want information on a stored platefile, highlight the name of the file
and press Shift-F1. A pop-up window will list the file name, the number of
plates it contains, the date and time of the first plate, and any descriptive
information for the first plate in the file. Press Esc to remove the help
window from the screen.
■
KC Jr. will prompt for information on the plates to be erased:
A - erase All plates from FILENAME.EXT
S - erase Specific plates
where FILENAME.EXT is the name of the file you chose to erase.
;;;
If there is only one plate in the file, the file is erased immediately upon selection.
■
If you want to erase all the plates in the file, enter A. Otherwise, enter S to
indicate specific plates to erase.
5-8
KCJr Utilities
■
If you plan to erase specific plates (S) you will be asked to enter the range of
plate numbers or the individual plate numbers, separated by commas, that
are to be deleted.
Example: If a platefile contains 9 plates of data and you want to erase plate
numbers 4 through 7 and 9, enter 4-7, 9 in response to the prompt. Or if you
want to erase plate numbers 3, 6, and 8, enter 3,6, 8 in response to the
prompt:
Which of the 9 files to erase?
3,6,8
Only the plates you specify will be erased from the file. After performing this
function, KC Jr. returns to the File Utilities Menu.
■
If you decide not to erase any plates from the file, press Enter in response to
the prompt. The program returns the File Utilities Menu.
N - reName a Data File
Option N from the File Utilities Menu allows you to change the name of a plate
or file in the EIA subdirectory. When you select N from the file utilities window,
the program lists the files in the EIA subdirectory.
CERES 900C User's Guide
5-9
Figure 5-4: Renaming a data file
■
Highlight the name of the file you wish to rename, and press Enter, or click
the mouse button. You can also enter the first letter of the file name to
highlight the next file beginning with that letter, and press Enter.
■
For information on any stored platefile, highlight the name of the file and
press Shift- F1.
After you select a file, you will be prompted for the file's new name.
Rename to:
■
Key in the new file name (up to 8 characters), and press Enter. The program
will rename the file and return you to the File Utilities Menu.
;;;
If you specify the name of a file that already exists, or if you press Enter without
entering a file name in response to this prompt, KC Jr. immediately returns to the
File Utilities Menu without renaming the file.
5-10
KCJr Utilities
P - erase a Protocol
Option P from the File Utilities Menu allows you to erase one or more protocol
files within the KC Jr. directory. When P is selected, a window listing protocol
files appears.
■
Highlight the protocol file you wish to erase and press Enter or click the
mouse button. You can also enter the first letter of the file name to
highlight the next file beginning with that letter, and press Enter.
T - erase a Template
Option T from the File Utilities Menu allows you to erase one or more template
files in the KC Jr. directory. When T is selected, a list of the template files
appears.
CERES 900C User's Guide
5-11
■
Highlight the template file you wish to erase and press Enter or click the
mouse button. You can also enter the first letter of the file name to
highlight the next file beginning with that letter, and press Enter.
Y - copY a Template
Option Y from the file utilities window allows you to copy template files in the
KC Jr. directory. When Y is selected, a list of the template files appears.
5-12
KCJr Utilities
■
Highlight the template file you wish to copy and press Enter, or click the
mouse button.
■
You will be prompted to enter a new name for the copied file. Key in the
new name and press Enter.
After the file is copied, you will be returned to the File Utilities Menu.
F - erase a Formula file
Option F from the file utilities window allows you to erase one or more formula
files in the KC Jr. directory. When F is selected, a list of the formula files
appears.
■
Highlight the formula file you wish to erase and press Enter, or click the
mouse button. You can also enter the first letter of the file name to
highlight the next file beginning with that letter, then press Enter.
CERES 900C User's Guide
5-13
L- Lotus & Other Transforms
Selecting option L from the System Utilities Menu allows you to transform
microplate file data into a format readable by software applications such as Lotus
1-2-3 or VisiCalc, or create a scattergram. The original file data remains on
disk in its logged form, and a new file or display is created.
When Lotus & other transforms is selected, a pop-up menu appears.
Figure 5-4: Selecting Lotus Transformation
■
Highlight the desired option, and press Enter or click the mouse button.
You can also key in either L, V, or S to select the corresponding option.
Lotus transformation
Option L arranges the plate data in a 8 x 12 matrix and saves the matrix in an
ASCII text file that is readable by Lotus. Each well on the plate will be 9
characters wide to conform to the Lotus default cell width. The new file will have
the same 8-character file name as the logged data but is given a .PRN extension.
5-14
KCJr Utilities
VisiCalc transformation
Option V creates the 8 x 12 matrix in a new disk file that contains the standard
DIF (Data Interchange Format) tuple and vector markers recognized by all
programs that work with DIF files.
Selecting the File
When either L or V is selected, the screen will display a window containing the
microplate files in the EIA subdirectory.
■
Move the highlighted cursor to the name of the file that contains the plate(s)
you wish to transform and press Enter or click the mouse button. You can
also enter the first letter of the plate filename to highlight the next file
beginning with that letter. Press Enter to select the file. As files are selected
for transformation, their names are copied on the screen below the window.
■
If you want information about any stored file, highlight the name of that file,
and press Shift- F1. Press Esc to remove the help window from the screen.
You can also use DOS wildcard characters to retrieve multiple platefiles in a set.
For example:
■
To retrieve all platefiles with an extension of .TST, press Esc until the file
window disappears from the screen. Then enter *.TST in response to the
prompt as follows:
Enter file(s) to retrieve:
*.TST <Enter>
KC Jr. will copy the selected file names to the screen beneath the file window. A
cumulative total of the number of plates to be transformed is displayed in the
upper right corner of the screen.
CERES 900C User's Guide
5-15
■
If any selected file contains more than one plate, you will be asked which
plates from that file you want to transform:
A - get All plates in the file
S - get Specific plates
■
If you want to transform all the plates in the file, enter A. Otherwise, enter S
to indicate specific plates.
■
If you select S, you will be asked to indicate which of the plates you want to
analyze. Enter the range of plate numbers or the individual plate numbers,
separated by commas, that you want to transform, then press Enter.
For example, if a platefile contains 9 plates of data and you want to
transform plate numbers 4 through 7 and 9, enter 4-7, 9 in response to
the prompt. If you want to transform plate numbers 3, 6, and 8, enter 3,
6, 8 in response to the prompt:
Which of the 9 plates to use
3, 6, 8
■
If you change your mind, or don't want to transform any plates from the
specified file, press Enter.
Once you've specified the plates to retrieve, the program displays another
window:
R - Retrieve more files/plates
P - Proceed with calculations
5-16
KCJr Utilities
■
The program will retrieve more platefile names if you enter R in response to
this prompt. When you've finished selecting platefiles, press P(roceed) to
continue. The program then transforms the data and saves it to disk in the
Lotus drive/dir subdirectory you specified during Data Defaults setup.
If you try to save a transformed file with a name that already exists in the
spreadsheet directory, the message center will display the following message:
FILENAME exists. Do you want to
overwrite it? (y/n)
If you answer Yes, the transformed data will overwrite the existing file. If you
answer No, the program will return to the Main Menu without creating any
transformed data or overwriting the existing file.
Importing the data to Lotus
To import a PRN file of transformed data into a Lotus spreadsheet:
■
Place the cell cursor in the upper left corner of the 8-row by 12-column area
where you wish the data to be. Then choose the /FIN (File Import Numbers)
option from the menu.
■
When prompted for the file name to copy, enter the name of the plate
transformed by KC Jr.
( See your Lotus manual for details on importing an ASCII file into the
spreadsheet.) You may also wish to explore the /FCAE and /FCSE options to add
or subtract values in one plate from those in another.
CERES 900C User's Guide
5-17
5-18
KCJr Utilities
S - Scattergram
Option S from the transformation submenu allows you to display/print a
scattergram of plate data. KC Jr. scales the Y-axis to the range of optical
densities for the selected plate.
When S - Scattergram is selected, if a platefile is still held in memory after
having been retrieved by some other option, the program will give you the
opportunity to use the plates already retrieved:
■
N
- get New plate(s)
P
- use Previous plates
If you want to work with previously retrieved files, answer P to this prompt,
and the program will display a scattergram of the current file(s).
Figure 5-5: Scattergram
CERES 900C User's Guide
5-19
■
If there are no files currently in memory, or if you answer N, the screen will
display a window containing the files in the EIA subdirectory and prompt
you for the name of the file to be displayed as a scattergram.
■
Highlight the name of the file that contains the plate(s) you wish to retrieve.
Press Enter or click the mouse button. You can also key in the first letter
of the platefile name to highlight the next file beginning with that letter, and
press Enter. As files are selected, their names are copied on the screen
below the window.
■
If you wish information about any stored platefile, highlight the name of the
file, and press Shift- F1. Press Esc to remove the help window from the
screen.
You can also use DOS wildcard characters to retrieve multiple platefiles in
a set. For example, to retrieve all platefiles with an extension of .TST, press
Esc until the file window disappears from the screen. Then enter *.TST in
response to the prompt.
If a selected file contains more than one plate, you will be asked which plate(s)
from that file you want to retrieve:
A - get All plates in the file
S - get Specific plates
■
If you want all the plates in the file, enter A. Otherwise, enter S to indicate
specific plates.
■
If you select S, you will be asked which of the plates you want to analyze.
Key in the range of plate numbers or the individual plate numbers, separated
by commas, that you want to use, and press Enter.
5-20
KCJr Utilities
■
If you change your mind, or don't want to retrieve any plates from the
specified file, press Enter in response to the above prompt.
Once you've specified the plates to retrieve, the program again prompts:
R - Retrieve more files/plates
P - Proceed with calculations
■
The program will retrieve more plate filenames if you enter R in response to
this prompt. When you've finished selecting platefiles, press P to continue.
After a brief pause while the program is working, the scattergram will appear on
the screen if the Report device parameter in Data Defaults is set to either Display
only or Printer & Display.
Printing the Scattergram
If the Data Defaults parameter is set to either Printer only or Printer & Display
the scattergram will be printed.
The program automatically scales the range of optical density values on the Yaxis to the low-high values for the plate being drawn.
The X-axis represents columns 1 through 12 on the plate. For each column, row
letters mark the relative measure of the optical density of a well compared to the
Y-axis scale. Up to five (5) well row labels can appear at one scale location for a
given column. If more than five wells in a column cluster at a scaling level, then
an asterisk (*) will be displayed. Over-range and blank (nonread) wells appear at
the top of the scale.
CERES 900C User's Guide
5-21
If the platefile contains more than one plate, or you specified additional files,
press any key to display the scattergram of the next plate. You can also press
Esc to return to the Main Menu.
O - Optics Test
Selecting O causes an optics test to be run on the microplate reader. The Optics
Test is discussed in detail in Chapter 8, Performance Verification.
C- Calibration Plate Test
Selecting C allows you to run a Calibration plate with the CERES 900C to verify
the instrument's calibration. Running the calibration plate with KC Jr.'s
Calibration Plate Test is discussed in Chapter 8, Performance Verification.
P - Program Information
Selecting P from the System Utilities submenu brings up a window that displays
the version of KC Jr. being run.
You'll need to have this information if you call Bio-Tek's Technical Service
representative with a question.
5-22
KCJr Utilities
jExit to DOS Shell
Selecting F9 from KC Jr.'s Main Menu allows you to temporarily return to the
DOS prompt to issue a command such as formatting a disk or erasing a file you
no longer need.
■
When you are finished with DOS and want to return to KC Jr., type exit at
the DOS prompt, and the program will return you to KC Jr.'s Main Menu
screen.
CERES 900C User's Guide
5-23
5-24
KCJr Utilities
Chapter 6:
Troubleshooting
This section is designed to provide solutions
to common problems that may occur when
operating the CERES 900C EIA Workstation.
Troubleshooting
If a problem occurs that cannot be solved using this guide or the DOS Manual,
contact Bio-Tek's Technical Assistance Center.
Problem
Cause
Solution
No display
Instrument not plugged in
Check power cable
connection
Faulty outlet
Move instrument to working
outlet
Monitor not plugged in, or
turned on, or VGA cable not
attached
Check power , VGA cable
connections. monitor on/off
switch
Faulty display connection
Replace monitor cable
Fuse blown
Inspect the fuses
Replace if necessary
Faulty bulb connection
Remove and reinstall bulb
Bulb burned out
Remove and replace bulb
Reader bulb does not light
Reported optical density
values are near zero, but
solution in well is obviously
colored
Incorrect interference filter
installed or filter table not
correct
Check the wavelength on
the side of filter and replace
if necessary. Check filter
table and correct if
necessary.
Repeated optical density
readings of same well do not
agree to within +0.005
absorbance units
Defective lamp
Visually inspect microplate
and replace if necessary.
Replace bulb
Using U-bottom PVC
microplates with single
wavelength setting
Use dual wavelength setting
Contaminated sample solids
in well
Replace samples
Optical Density above 2.500
abs
Repeatability specified to
2.500 abs
Pipetting error, or nonuniform washing procedure
Check against former
method of reading
microplate
Optical density readings of
replicate wells do not agree
to within +1% plus 0.010 OD
Non uniform binding
Reported phenomena that
peripheral wells differ in
binding capacity (edge
effect) or temperature from
other wells on the microplate
Optical density readings
vary considerably from
earlier readings of the same
microplate
6-2
Scratches or fingerprints on
well bottom or foreign
particles in well
Use new plate or dual
wavelength feature
Carrier out of alignment
Run CAL Plate Test
Direct sunlight or extreme
ambient light reaching
photo detectors
Relocate reader
Not enough stop solution in
wells
Add more stop solution after
reviewing assay kit
instructions
Defective lamp
Replace bulb
Troubleshooting
Read error occurs while a
microplate is being read
Printer not activated when
printout is requested
Printer head moves but does
not print
Paper jams in printer
Ceres 900C User's Guide
Bulb burned out
Replace bulb
No filter wheel
Install filter wheel
No filter in position #1 or in
test wavelength position
Re-install filters and check
filter table setup
Instrument or printer not
plugged in properly
Turn on printer first, check
when connection, then turn
on the Ceres 900C
CERES 900C System print
defaults not properly set
Review the print setup
section in this manual
No power at wall outlet
Plug another device, or a
lamp into the outlet to
ensure the outlet has power
Printer not online
Depress ONLINE button on
the printer
Printer cable damaged or
improperly installed
Refer to printer manual for
installation instructions.
Replace cable if necessary
Ribbon jammed or worn out
Replace ribbon
Paper jammed
Try advancing paper by
hand, using thumb wheel on
printer. If paper is jammed,
refer to printer manual for
instructions on paper feeder
release. Refeed paper
Improper paper feed
Remove jammed paper and
reinsert paper according to
printer manual instructions
6-3
CMOS Utility Software for the Ceres 900C
The CERES 900C contains a battery which powers the CMOS RAM (Random
Access Memory) on the CERES 900C’s PC motherboard. This CMOS RAM
holds the system’s configuration information. When the battery loses power, the
configuration, or system setup, data is lost from the system’s memory (CMOS
RAM). This data must be restored before the computer can communicate with its
hard disk, and thus operate the CERES 900C.
;;;
The normal battery life is two years. Battery power can be lost if the CERES
900C is left powered off for an extended period of time.
The CERES 900C distribution disks contain a utility program, CMOS.EXE,
which provides a means to read, restore, compare and view the contents of the
CERES 900C CMOS memory. You’ll find the CMOS Utility disk packaged with
the CERES 900C program disks.
The utility is first run at the factory to read the system’s CMOS RAM data when
the system is initially assembled. This instrument-specific information is then
save in a file called cmosdata.sav, and stored on the CMOS Utility disk that is
shipped with the instrument. Should the CERES 900C system lose its
configuration information, this floppy disk can be used to restore the
configuration to original factory settings, after the cause of the problem has been
determined or a new battery inserted. After restoring the data, the user would
then set the system’s date and time, using the DOS date, and time commands.
Remember: The CMOS data file, cmosdata.sav is specific to your CERES 900C
instrument. This file cannot be used to restore CMOS information on other
CERES 900C instruments.
6-4
Troubleshooting
Running the Utility Program
If the CERES 900C has lost its CMOS data, it is probable that the system will not
boot successfully, or be able to read a floppy disk. The CMOS disk provided
with the CERES 900C can be used as a “boot” disk, that is, the system will start
successfully if the disk is inserted into the disk drive before the instrument is
powered on. Use the procedure that follows to view and/or restore the system’s
CMOS configuration data:
•
Place the CERES 900C CMOS Utility disk in disk drive A: and power up the
CERES 900C.
•
When the A: prompt appears on the display, type:
CMOS
followed by the appropriate “switch” which determines the action you wish
to invoke.
For example: To restore the contents of the CERES 900C’s cmosdata.sav
file to system CMOS memory, type:
CMOS /R
Either all upper or upper and lower case letters may be used.
The available switches are:
/R
Restores the CMOS memory (overwrites it) with the contents of
the cmosdata.sav file in the current directory.
/C
Displays the contents of CMOS memory and compare CMOS
memory contents to the backup file in the current directory.
Mismatches are highlighted in reverse video. Mismatches that are
problems will blink. The time, date and some status registers will
not blink, as the system updates these.
Ceres 900C User's Guide
6-5
/F
Displays the file contents of the cmosdata.sav file in the current
directory.
/M
Displays the CMOS memory contents on the CRT
/S
Saves the CMOS data to the file, cmosdata.sav in the current
directory.
•
When you have restored the CMOS data to the CERES 900C, remove the
floppy disk, and reboot the CERES 900C.
Removing Junk Files from the CERES 900C
When using software installed on the CERES 900C, it is possible to inadvertently
create “junk” files on the instrument’s hard disk drive. These junk files are
created when the user exits a software program improperly, or shuts off the
system without first “quitting” the software program.
Junk files can also be created when a user exits incorrectly from a DOS shell, i.e.
forgets that a DOS shell is in operation, and restarts the software that is already
running in the background.
To avoid creating junk files:
•
Type EXIT to return to the reader’s software program from a DOS shell.
(This reminder appears on the screen when the DOS shell function is chosen
by the user.)
•
After using software on the reader, select QUIT to back out of the software
until the DOS prompt is displayed. Then turn off power to the reader.
Deleting Unnecessary Files
If you suspect you are accumulating these unnecessary files on the CERES 900C:
6-6
Troubleshooting
•
Check all directories of the software program for 8-character file names that
are alphanumeric and do not have an extension. Ensure these file names
were not intentionally created by the user.
•
Delete these files using a simple DOS delete command. If you are unfamiliar
with DOS commands, and need assistance with this procedure, please call
Bio-Tek Instruments at 1-800-242-4685.
Ceres 900C User's Guide
6-7
Chapter 7:
Maintenance
This chapter describes the Maintenance
Procedures that can easily be performed by the
user to keep the CERES 900C
operating properly.
Before you begin...
Service procedures other than cleaning or replacing minor components such as fuses, bulbs and filters,
should be left to qualified service personnel. If the instrument malfunctions, refer to Chapter 6,
Troubleshooting, or Appendix A, Error Messages. If the problem cannot be resolved by following
these procedures, contact Bio-Tek's Technical Assistance Center at 1-(800) 242-4685, or (802) 6554040, or your local Bio-Tek Representative. Calls made to our European office can be made to (32) 3829 0455.
Safety Precautions
For safety purposes (and to avoid damage to the instrument) the CERES 900C
must be turned OFF, and its power cord disconnected during the maintenance
procedures described in this chapter.
If you begin maintenance after operation of the instrument, remember that the
bulb and bulb holder are hot, and must be handled with caution. Allow at least 15
minutes before beginning maintenance to allow the instrument to cool off.
During general operation, ensure that the main power cord is plugged into a
power outlet that has a protective earth contact to connect the chassis of the
CERES 900C to ground. Do not disable this feature by using extension cords or
cheater plugs without earth ground, or a hazardous condition may result.
Replacing the Light Bulb
While the tungsten-halogen bulb supplied with the CERES 900C will provide many hours of use,
eventually it will need to be replaced. In addition, a failed self-test may indicate the need for a new
bulb, even if the bulb appears to be functioning. To check a suspect bulb, lower the hinged access
cover on the rear of the reader. If the bulb needs to be replaced:
■
Turn the CERES 900C off, and allow the instrument to cool for 15 minutes.
■
Loosen the two wing nuts and open the hinged Optics Access Cover on the
rear of the reader.
■
Slide the Optics Assembly out of the compartment until it is fully exposed.
■
Remove the Bulb and Socket Assembly from the support bracket and
remove the bulb from the socket. While the bulb is out of the assembly, you
might wish to clean the optics inside the instrument. Refer to the section,
Cleaning the Optics, in this chapter.
;;;
■
Plug the new bulb into the socket and gently reattach it to the bracket.
■
Slide optics assembly back into the compartment.
Caution: Use caution when working inside of the instrument when power is on, and when working
around the Lamp Assembly and Optics. Avoid touching the lenses and bulb reflector.
7-2
Chapter 7
;;;
Warning: Use of bulbs other than those recommended by Bio-Tek Instruments may cause a fire
hazard. (PN 3400508)
•
Gently close the Access Cover, tighten the screws, and reattach the power
cord and printer cable.
■
Test the CERES 900C by following the instructions in the section, Testing
the System.
Replacing the Fuses
The CERES 900C fuse bay is located on one end of the Power Supply Module at the rear of the
instrument.
;;;
Warning: Using fuse(s) other than those recommended can cause fire and/or shock.
(US/
PN-46063 European/ PN-46056)
To replace the fuses:
■
Power down the CERES 900C, and unplug the main power cord.
■
Using a small-blade screwdriver or similar tool, carefully pry open the
access cover to the fuse compartment access cover. The fuse block assembly
is in the back of this cover (Figure 7-1).
Chapter 7: Maintenance
■
Carefully lift the old fuse(s) from the fuse slot.
■
Replace the fuse(s) with a new one.
7-3
U.S Single Fuse (Hot)
European Dual Fuse
(Both Hot & Neutral)
Figure 7-1: Fuse Assembly
Configuring the CERES 900C for Different Voltages
If you purchased your CERES 900C within the continental United States, it has been factory-set for US
Voltage (either 110 or 120 Volts). Should you decide to use the CERES 900C at a location with 220 or
240 line voltage, you will need to reconfigure the fusing and change the Incubation Voltage Switch
setting (if the Incubation Option is present).
Configured for US current, the fuse block will be mounted on the backside of the Access Cover with
the jumper bar exposed, providing 1 slot for a single fuse (Figure 7-1, upper insert ). To reconfigure
the fusing for European voltages:
■
7-4
Turn off the power and disconnect the line cord.
Chapter 7
■
Remove the fuse block holder by prying it out of the housing.
■
Loosen the Phillips screw that attaches the Fuse Block to the Access Cover (2 turns).
■
Slide the Fuse Block away from the Cover. Turn the Fuse Block over so that the jumper bar
lies flat against the cover and the 2 fuse slots face up (Figure 7-1, lower insert).
■
;;;
Slide the fuse block back onto the Phillips screw and pedestal, and tighten the screw.
Caution: Overtightening the screw may cause stripping of the threads on the fuse holder.
■
Replace the cover to the fuse assembly, and plug in the CERES 900C.
Changing the Line Voltage for Incubation
If the CERES 900C is shipped from Bio-Tek with the Incubation option, a voltage selection switch is
provided that allows the Incubator to accommodate either 110/120 or 220/240 line voltage. The
voltage switch is clearly marked, and is located on the rear panel of the instrument. If the instrument is
moved to a location with one of these voltages, the switch must be reset for the new voltage.
Additionally, the fuses will require reconfiguring as explained in the section titled Configuring the
CERES 900C for Different Voltages in this chapter.
Cleaning the Optics
The optical elements of the CERES 900C should be cleaned periodically to insure proper operation.
The optics may be conveniently cleaned when changing filters or replacing a bulb.
Chapter 7: Maintenance
7-5
To clean the optics:
■
;;;
Turn the CERES 900C OFF and unplug the main power cord.
Warning: To avoid injury, always allow the unit to cool down at least 15 minutes prior to performing
this procedure.
■
Loosen the 2 Wing nuts on the hinged Optics Access Cover and open the cover.
■
Slide the Optical Assembly out until fully exposed.
■
To remove the filter wheel, firmly grab the wheel hub (center) and pull away from the mounting
hub. The wheel is held onto the motor shaft magnetically and will require a certain amount of
force to separate them. Be careful not to bump the lamp assembly while removing the Filter
Wheel.
■
Use photographic lens-cleaning fluid (isopropyl alcohol may be substituted) and lens-cleaning
tissue to clean both sides of the filters.
;;;
Caution: When the filter wheel is removed, the large end of the fiber optics bundle is visible. Do not
attempt to clean this except to blow away dust. Any direct cleaning of the surface of the fiber optics
could scratch the assembly and ruin it.
■
Blow away any dust on the large focusing lens on the lamp assembly with pressurized
photographic air. Pressurized air, designed for cleaning optical equipment, can be purchased at a
photographic supply store.
7-6
Chapter 7
■
To clean the surface of the large lens, use photographic lens-cleaning fluid and lens-cleaning
paper. If you need to clean the lamp side of the lens, remove the bulb from the spring-loaded
bracket by sliding it up and out, and clean the lens with lens-cleaning fluid and lens-cleaning
paper, then reinstall the bulb.
■
Slide the optics assembly back into its compartment.
■
Close the hinged cover; replace and tighten the 2 Wing nuts.
Cleaning the Exterior
Clean all CERES 900C surfaces with a soft towel or sponge moistened with a mild soap and
water solution. Do not use solvents or abrasive cleaners.
Storage and Shipping
The unit may be safely stored or shipped in environments with the following limits:
■
Temperature
-20° to +60° C
Humidity
up to 96%
Altitude
7,620 meters maximum (26,000 feet)
The CERES 900C should be protected from temperature extremes that can cause
condensation within the instrument, and from corrosive fumes and vapors.
■
When the CERES 900C is shipped to Bio-Tek for service or repair, the unit must be shipped
in the original packing; other forms of commercially available packing are not recommended
and may void the warranty. If the original packing has been damaged or lost, contact Bio-Tek
for replacement packing. Repack the CERES 900C for shipping as follows:
Chapter 7: Maintenance
7-7
⇒ Remove microplate from the carrier bed.
⇒ Remove the filter wheel, and pack it in its original padded container.
⇒ Replace the foam end caps above and beneath the instrument and place the
reader in the original shipping carton.
■
Obtain a Return Authorization Number from Bio-Tek Service representatives by calling tollfree in the US 1-(800)242-4685, or (802)655-4044; telex: 94-0136 BIO TEK SHVT; or
Service FAX: 802-655-3399. Outside the US contact your BIO-TEK Sales Representative.
■
Include in the packing box the following information:
⇒ What repairs or adjustments are required (i.e., calibration, cleaning, repair, etc.)
⇒ A tag specifying the return authorization number, the full model and serial
number.
⇒ Name and telephone number of someone Bio-Tek can contact if additional
information is necessary.
7-8
■
Securely fasten the packing carton flaps with packing tape.
■
Insure the CERES 900C for its full value and return it to Bio-Tek for service.
Chapter 7
Chapter 8:
Performance Verification
The CERES 900C has been tested at the factory to
insure that its performance is within the specifications
listed in this manual. In addition to the calibration plate
and optical tests, this chapter details a "wet test" procedure
that can be used to verify CERES 900C performance.
Testing the System / Calibration _________________________________
It is considered good laboratory practice to periodically validate the calibration
of the CERES 900C. KCJr. software provides tests of several system parameters
to ensure the system is installed and functioning properly. Calibration validation
should occur on a weekly basis by performing the tests in this section. The tests
detailed in this section include:
■
Calibration Plate Test
or
■
Linearity Test (wet test)
■
Optics Test
Calibration Plate Test
This test is used to determine the alignment, repeatability, accuracy and linearity
of microplates, and the CERES 900C plate carrier, with the CERES 900C optics
system, and is crucial for ensuring read accuracy. An alternative method used to
determine accuracy, repeatability and linearity is the Linearity or Wet Test
described later in this chapter.
Requirements:
■
Bio-Tek Calibration Plate (PN 9000547) Rev. B or later.
■
Bio-Tek Calibration Plate (PN 9000543) Rev. B or later.
■
Bio-Tek Calibration Plate (PN 9000517) Rev. B or later (Alignment test
invalid for CERES 900C)
Running the Calibration Plate
■
From the KC Jr. Main Menu, select F6- System Utilities.
■
From the Systems Utilities submenu, select option C- Calibration plate
test. An option screen will appear, providing a choice between D - Define
a calibration plate, and R - Run a calibration plate.
8-2
Performance Verification
■
Select D - Define calibration plate.
Defining the Calibration Plate
■
From the option submenu, select:
3 - Test filter Cal Plate (P/N 3110517)
4 - Test filter Cal Plate (P/N 9000543), or
6 - Test filter Cal Plate (P/N 90000547)
CERES 900C User's Guide
8 -3
depending on the number of filters in the version of calibration plate that you are
using. A screen similar to the one pictured below appears when 6 is selected. The
CERES 900C is shipped with a calibration plate with filters in all six positions
(number 6).
■
Using the Specifications sheet provided with the Calibration Plate, enter the
calibration values, using the up/down arrow, and backspace keys. Press
the kkey to save the values. You will be returned to KC Jr.'s Main Menu.
Running the Calibration Plate
8-4
■
From KCJr.'s Main Menu, select F6- System Utilities.
■
Select C- Calibration Plate.
■
From the Options submenu, select R - Run calibration plate test.
Performance Verification
■
Enter the Calibration plate serial number when prompted.
■
From the displayed list of filters, select the filter to be tested, using the
up/down arrow keys, and pressing the y key.
CERES 900C User's Guide
8 -5
;;;
■
An options submenu will prompt you to select a R- get plate(s) from
Reader, or D - get plate(s) from disk.
■
Select R - get plate(s) from reader, unless you wish to use data from a
previously run calibration plate, which has been saved to disk.
If the desired filter is not displayed, refer to Chapter 3, Introducing KC Jr. for
information on setting up the filter table to match filters installed on the CERES
900C filter wheel.
■
You will be prompted to enter a file name for the data. Enter the file name,
and place the Calibration plate in the microplate carrier.
;;;
If the file name duplicates another already saved to disk, you will be asked if you
wish to overwrite the old file with the new data, or select a new filename.
■
8-6
Press
y
to start the calibration test.
Performance Verification
■
After the first calibration plate read, the carrier will exit the reading
chamber, and a screen prompt will direct you to turn the plate 180° and
again press y.
■
At the conclusion of the second read, a Calibration Test Report will be
displayed and/or sent to the printer. The report will be displayed on two
screens -- press any key to get the second half of the report.
CERES 900C User's Guide
8 -7
8-8
Performance Verification
Calibration Test Results
The Calibration Report has four report parameters:
■
Alignment: This portion of the test measures the alignment of the
microplate carrier with the optical path. A reading of > .015 represents and
out-of-alignment condition. Wells A2, A11, H2, H11 are valid for the
CERES 900C when using Cal plates that are part numbered 9000543 and
9000547.
■
Accuracy: Accuracy is a measure of the absorbance (optical density) of
Calibration Plate wells C1, D4, E2, F5, G3 and H6 with known standard
values contained in the Specification Sheet that accompanies each
Calibration plate.
■
Repeatibility: This parameter is a measure of the instrument's ability to read
the same well with minimum variation between two reads with the well in
the same location.
■
Turnaround: The Calibration Plate's six filtered wells (C1, D4, E2 , F5, G3,
and H6) are each read from two positions - once with the Calibration Plate in
the normal position, and once with the plate turned 180°. This portion of the
test meaures the diference between the optics at opposite sides of the read
chamber.
Test Failures
If any of the test parameters report as "FAIL", contact your Bio-Tek
representative, or call Bio-Tek's Technical Assistance center at 1-(800)-2424685.
CERES 900C User's Guide
8 -9
The Optics Test
The Optics Test is designed to compare the integrity of each of the 12 reading
channels to a 13th reference channel. The test checks the light level and system
gain, notifying the user if the measured valves don’t adhere to program limits.
The Optics Test should be performed weekly to ensure consistent assay/plateread accuracy. The optics test is performed every time a plate is read (transparent
to the user). If the valves don’t fit programmed limits, an error message will be
displayed (“Run Optics Test”). When run, the optics test will then report specific
errors.
Running the Optics Test
■
From KC Jr.'s Main Menu, select F6- System Utilities.
■
From the Options submenu, select O- Optics Test, and press y. The
carrier will be retracted and the Optics Test will begin.
.
8-10
Performance Verification
■
At the conclusion of the test, the Optics Test Report will be displayed on the
screen. To send the test results to a printer, it would be necessary to press
Shift/ Print screen.
The Optics Test Report
The displayed results include a PASS/FAIL determination for each of the optics
channels, the reference channel, and signal (gain) level. Should any of the test
results show a FAIL, contact Bio-Tek's Technical Assistance Center, at
1-(800)-242-4685.
Quality Control
It is considered to be good laboratory practice to run laboratory samples
according to instructions and specific recommendations included in the package
insert for the test to be conducted.
Failure to conduct Quality Control checks could result in erroneous test data.
CERES 900C User's Guide
8 -11
Optical Verification
Achieving Maximum Performance
Experience with this and similar instruments indicates that inaccuracies
introduced by the environment, or by laboratory technique are far greater than
any inaccuracies inherent in the basic instrument. What follows is a list of
recommendations for achieving maximum performance from the CERES 900C.
•
The microplate should be perfectly clean and free of dust. Use new
microplates from sealed packages. Do not allow dust to settle on the surface
of the solution; use microplate covers if necessary to protect the solution
(when not reading the plate).
•
Although the CERES 900C works with all flat, U-, and V-bottom
microplates, it performs best with optically clear, flat bottomed wells.
•
Non-uniformity in the optical density of the well bottoms can cause loss of
accuracy, especially with U- and V-bottom polyvinyl microplates. Check for
this by reading an empty microplate. Dual wavelength readings can
eliminate this problem, or bring the variation in density readings to within
acceptable limits for most measurements.
•
The best repeatability from channel to channel is obtained when the
wavelength used corresponds to the peak absorbance for the particular
solution being used. This is most true when the shape of the absorbance
curve is rather narrow.
•
Inaccuracy in pipetting has a large effect on measurements if smaller
volumes of liquid are used. For best results, use at least 100 microliters.
With half-area wells, smaller volumes are acceptable.
8-12
Performance Verification
•
To achieve the highest possible accuracy at optical densities approaching 2.0
OD and higher, eliminate illumination of the shutter by sunlight or strong
ambient light. If interference from ambient light is suspected, read a
microplate of high-density solutions under the suspect conditions, and again
with all the light to the shutter area blocked (with a black cloth, for
example); then compare results. The blocked shutter results will appear as an
increase in optical density readings.
•
The inclination of the meniscus can cause loss of accuracy in some
solutions, especially with small volumes. Agitate the microplate before
reading to help bring this problem within acceptable limits. Use Tween 20
if possible (or some other wetting agent) to normalize the meniscus.
•
Some solutions develop menisci over a period of several minutes. This effect
varies with the brand of microplate. As the center of the meniscus drops and
shortens the light path, the density readings change. The shape of the
meniscus eventually stabilizes.
•
A 10-minute warm-up of the instrument is suggested prior to reading to
achieve the best repeatability from microplate-to-microplate measurements.
•
Always use the reader with a filter in the light path, as continuous operation
without a filter in place may damage the optics.
•
To prevent damage to the carrier mechanism, never move the carrier by
hand.
CERES 900C User's Guide
8 -13
Verification of Alignment ___________________________________________
Use a new microplate, free from dust and scratches which could affect the
readings. Fill the microplate with the time-stable solution you want to measure,
such as the solution suggested for the Linearity Test described below. Use a filter
wavelength corresponding to the maximum absorbance of your solution.
Use different solution volumes (not less than 100 microliters) and densities. For
example, put 100 microliters in rows A through D, and 150 microliters in rows E
through H.
The factory repeatability and accuracy tests that follow are performed with
Costar™ flat (#3590) and round bottom (#3797) microplates with Durkee™
yellow food coloring, using a 405 nm filter. Different solutions and microplates,
may vary repeatability and accuracy.
Repeatability
1.
Read the microplate using a single wavelength, no blanking (or blank on
air), and an 8 x 12 matrix format.
2.
When the readings have printed out, read the microplate a second time.
3.
Compare the readings.
Each well in the first printout should be within 0.5% of the OD, and 0.005 counts
of the same reading in the second printout. For example, A1 in the first printout
should be within +.5% OD, +0.005 OD of A1 in the second printout. If A1 was
initially 1.000 OD, then subsequent readings should be between .990 OD and
1.010 OD
Accuracy
1.
Turn the microplate described in the Repeatability section around and read it
again.
8-14
Performance Verification
2.
Compare the printout with the last printout from the repeatability test. Be
sure to compare the readings from the same wells. Remember that well A1 is
now in the H12 position. The readings should be within 1% of the OD., and
0.010 counts of each other. For example, if A1 was initially 1.000, then the
"turn-around" test should show results between .980 OD and 1.020 OD.
Linearity Test_____________________________________________________
The linearity of the reader can be tested by preparing a series of solutions of
varying absorbances. The absorbance of a solution is a function of how much
light is absorbed by that solution when it contains a colored compound;
therefore, a solution that has twice as much color as another solution will have
twice the optical density. (Any solution that gives a stable color will suffice. This
includes substrates incubated with an enzyme preparation and then stopped with
an acidic or basic solution.) Some enzyme/substrate combinations are given in
Table 8-1.
A more basic method is to use food coloring available at supermarkets.
(Durkee™ food coloring is one such brand.)
Equipment Required:
•
Distilled water
•
Pipet
•
Yellow food coloring (Example: Durkee™ yellow food coloring, .3 oz.
bottle)
•
Flat-bottom microplates (Example: Costar™ #3590)
•
Tween™ 20 (polyoxyethylenesorbitan Monolaurate)
•
Beakers
•
Rack of 10 test tubes (10 ml minimum volume)
CERES 900C User's Guide
8 -15
1.
Create a 0.5% solution of Tween 20 and distilled water. As an example, add
1 ml of Tween 20 to 200 ml of distilled water. Shake well for several
minutes.
2.
Add 6 drops of yellow food coloring to the 200 ml of the 0.5% Tween
solution. This should give an absorbance of 1.4 to 2.0 absorbance units
when using 200 ml in the well. If you wish to attain an absorbance up to
3.0 OD, add 3 additional drops of food coloring (a total of 9 drops).
Table 8-1
Typical Enzyme-Substrate Combinations and Stopping Solutions
Enzyme
Substrate
Alkaline Phosphate
o-nitrophenyl phosphate
3N sodium hydroxide
beta-Galactosidase
o-nitrophenyl -beta-D
galactopyranoside
1M sodium carbonate
Peroxidase
ABTS 2, 2 Amino-di-(3 ethyl[benzthazolin sulfonate]
citrate-phosphate buffer,
pH 2.8
Peroxidase
o-phenylenediamine
0.03N sulfuric acid
3.
Stopping Solution
Stir well to insure all the color is spread throughout the solution. This is
entirely a trial-and-error process. If it does not give enough absorbance, add
another drop of food coloring. The reader will read absorbance units up to
4.300 absorbance units; it is specified to be linear to 3.000 absorbance units.
4.
Set up a rack containing 10 tubes, numbered consecutively.
Table 8-2
Test Tube Dilutions
Tube Number
Volume of
Original
Solution (ml)
Volume of 0.5%
Tween Solution
(ml)
8-16
1
20
2
18
3
16
4
14
5
12
6
10
7
8
8
6
9
4
10
2
0
2
4
6
8
10
12
14
16
18
Performance Verification
Absorbance
(Expected if
original solution
is 2.0 at 200 ul)
2.0
5.
1.8
1.6
1.4
1.2
1.0
0.8
0.6
0.4
0.2
Perform a percentage dilution, beginning with 100% of the original dense
solution in the first tube, 90% of the original solution in the second tube;
80% in the third tube, all the way to 10% in the last tube.
Dilute using amounts of the remaining 0.5% solution of distilled water and
Tween 20, as shown in Table 8-2.
6.
Remove a 200 ml aliquot from each tube, and dispense it into the
appropriate microplate well. There should be enough solution to have
several replicates, if desired.
7.
Read the microplate at 405 nm to determine the absorbance, and then graph
the results, plotting absorbance versus percentage. You should get a straight
line passing through zero, if your pipetting is accurate. You may also use
Kineti-Calc™ or KC-Jr.™ (CERES 900C software) to plot your curve.
8.
The choice of dilutions is strictly arbitrary, as is the absorbance of the
original solution. Use Table 8-2 as a model for calculating the expected
absorbances of a series of dilutions, given a different absorbance of the
original solution.
CERES 900C User's Guide
8 -17
Appendix A
Error Messages
This appendix contains an alphabetical listing
of error messages that may be encountered when
using the CERES 900C EIA Workstation
or KC Junior Software.
Other Error Messages
If you encounter an error message not listed in this section, check the DOS
manual that accompanied the CERES 900C, or contact Bio-Tek's Technical
Assistance Center.
Problem
Cause
Solution
Blank pattern changed,
please edit blank map!
User has attempted to save
a new RCD Blank Map
option without
viewing/editing the new
map before saving it
View and/or edit the new
Blank Map by hitting the
spacebar
Calibration Error. Read
aborted. Run Optics test
Read values outside proper
parameters
Filter defined is not present.
Bulb is failing
Constant blank value out of
range: valid range is -4.00 4.00
An invalid value has been
entered within the RCD "User
Blank" option
Choose a value from -4.00 to
4.00
Disk full! Unable to proceed
Floppy or hard disk is too full
to accept additional data
Download or delete nonessential data ( “junk files”)
Appendix A
A-1
Problem
Cause
Solution
Factor value out of range:
0.010 -> 1000
A factor value outside of
acceptable parameters has
been entered
Enter a value no less than
0.010 and no greater than
1000
Incubation Set Point out of
range: valid range is 20.0 50.0
An incubation set point
value outside allowable
parameters has been
entered
Enter a value between 20.00
C and 50.00 C
Invalid Calibration Plate
values entered
A non-real number value (0
or a non-numeric value, for
example) has been entered
as a Calibration Plate
standard value during a
calibration test
Enter the standard value
provided by the
specification sheet included
with the calibration plate
Invalid characters in
filename G\*y! Use '_' or '_'
for separators. Press enter to
continue
Invalid characters used as
separators
Use underscores or minus
signs as separators
Invalid drive specified in
default path
Drive/path default
parameter within Setup
System is incorrect
Enter C: for hard drive, or A:
for floppy drive
Invalid Number of scans:
Valid range is 1 to 35
An invalid value has been
entered within an RCD Read
Method parameter
Enter a value => than 1 and
=< 35
Invalid path specified or disk
not ready
An improper drive and/or
directory entered within
System Setup, or no floppy
disk has been inserted into
the disk bay of the CERES
900C
Correct drive/directory
value within System Setup
Drive/Path default box, or
insert a floppy disk in the disk
bay of the CERES 900C
Limit value out of range:
-4.0 -> 4.0
A value outside the
allowable parameters has
been entered within the
RCD screen Limit option
Enter a value => -4.00 or =<
4.00
A-2
Error Codes
Problem
Cause
Solution
Monitor OD value out of
range: valid range is;
-4.0 ->4.0
A value outside the
allowable parameters has
been entered within the
RCD screen Read Method
option
Enter a value => -4.00 or =<
4.00
NO MCB communications.
File AS_MCB.BIN not present
in the AS directory
Copy AS_MCB.BIN file from
the master disk top the AS
directory on the hard drive
Bad monitor controller board
Call The Technical
Assistance Center
Number of readings out of
range: valid range is 1->250
A invalid value has been
entered within an RCD
Kinetic Read method
Enter a whole number
between 1 and 250
Range value out of range:
-4.0->4.0
An invalid number has been
entered within an RCD
Range Report parameter
Enter a value >= -4.0 or <=4.0
The Bottom value must be
< or = to the top value!
An RCD Range Report
bottom range value has
been entered that is greater
than the top value
Enter a bottom number that
is < or = to the top value
The file selected cannot be
opened, or no file selected.
Either no file has been
selected or a file other than
a data file has been
selected
Select a valid data file
The file selected is not a
compatible file. Format not
understood
Either a non-data file, or no
data file has been selected
Select a valid data file.
Convert non standard data
files (spreadsheet format) to
standard format.
The range for hours is 0 to
336
An invalid value has been
entered for the Total Read
Time parameter of an RCD
Kinetic or Monitored Kinetic
read method
Bad or nonexistent board
Appendix A
A non-standard data file has
been selected
Enter a time value between
0 and 336
A-3
Problem
Cause
Solution
The range for hours is 0 to 12
An invalid value has been
entered for the Read Interval
parameter on an RCD
Kinetic or Monitored Kinetic
read method
Enter a time value between
0 and 12 hours
The range for minutes is 0 to
60
An invalid value has been
entered for the RCD shaking
parameter
Enter a time value between
0 and 60 minutes
The range for minutes is 0 to
59
An invalid value has been
entered for the Delay in
Read or Kinetic/Monitored
Kinetic Read Interval
parameters
Enter a time value between
0 and 59 minutes
The range for seconds is 0 to
59
An invalid seconds value has
been entered for any time
parameter
Enter a time value between
0 and 50 seconds
There are too many files
present in one directory to
handle
Combined application and
data files exceed 640
kilobyte DOS capacity
Move some data files into a
separate data file directory
Unable to run batch file
CURV_FIT.BAT
File CURV_FIT.BAT missing
from AS directory
Copy CURV_FIT.BAT from
CERES 900C master disk to
AS directory
Unable to exit to DOS Shell
Insufficient floppy or hard
disk space to access DOS
shell function
Move some data files from
the floppy or hard disk to a
separate location
Warning! Incubator has not
reached setpoint
Plate read has been
attempted before Incubator
has had time to reach preset
temperature
Allow 10 minutes for the
incubator to reach the
setpoint temperature
Well width out of range:
valid range is 4.0 -> 8.0 mm
An invalid value has been
entered within an RCD
Scanning read Well Width
parameter
Enter a well width value
=>4.0 mm or =< 8.0 mm
A-4
Error Codes
Appendix B:
Serial, Parallel Pinouts
This Appendix illustrates the pinout configurations
for the CERES 900C’s parallel (printer)
and Serial (data communication) connectors..
Parallel Port (LPT1)
The CERES 900C’s parallel port (LPT1) is 100 % PC-AT compatible, It
provides the necessary control signals for use as a Centronics-type parallel
interface, allowing the instrument to be connected to a variety of printers. The
connection is done through a DB-25 connector, J7, located at the end of the
board, and visible at the rear of the reader. The pinout is illustrated below.
Signal
Signal Flow
Pin #
Pin #
Signal Flow
Signal
STB*
0
1
2
I/O
P0
P1
I/O
3
4
I/O
P2
P3
I/O
5
6
I/O
P4
P5
I/O
7
8
I/O
P6
P7
I/O
9
10
I
ACK*
BUSY
I
11
12
I
PE
SLCT
I
13
14
0
AFD*
ERR*
I
15
16
0
INIT*
SLIN*
0
17
18
-
GND
GND
-
19
20
-
GND
GND
-
21
22
-
GND
GND
-
23
GND
-
25
24
-
GND
Serial Port Connections
The CERES 900 provides two Serial Ports. One has a 9-pin D sub connection,
and the other, a 25-pin D sub connection. The Serial ports may be used to send
data to an external PC or serial device. The pinouts for the connectors are
illustrated below.
COM1 (9-pin Male D Sub connector)
Signal
Signal Flow
Pin #
Pin #
Signal Flow
Signal
DCD
I
1
2
I
RX
TX
0
3
4
0
DTR
GND
-
5
6
I
DSR
RTS
0
7
8
I
CTS
RI
I
9
COM2 (25-pin Male D Sub connector)
Signal
Signal Flow
Pin #
Pin #
Signal Flow
Signal
DCD
I
8
3
I
DSR
RX
I
2
7
0
RTS
TX
0
7
6
I
CTS
DTR
0
4
5
I
RI
GND
N.C.
B-2
21
1,9,10,11,12,13,14,15,16,17,18,19,22,23,24,25
Serial, Parallel Connector Pinouts
Appendix C:
ShowScan™ Scanning Software
This appendix explains how to use
ShowScan™ Software for pattern
recognition assays.
About ShowScan™ Software
ShowScan is a software package for demonstration of pattern scanning
capabilities of the CERES 900C. It has not been cleared for any in-vitro
diagnostic use.
ShowScan allows the user to visually evaluate the reading of the percentage
transmission patterns on 96-well microplates. It does not, however, support
mathematical interpretation of the scanned patterns (such as formula
determination of positive and negative calls), nor does it allow editing or entry of
reagent files.
ShowScan automatically reads 30 points across each microplate well and
graphically displays the transmittance profile of each well in single or dual
wavelength. Individual wells, rows, columns or the total microplate may be
viewed simultaneously.
Here is how to access and use ShowScan, the on-board scanning software for the
CERES 900C.
Starting ShowScan
ShowScan software is preinstalled on the CERES 900C hard disk drive at the
factory.
To start ShowScan:
•
Key in at the DOS prompt:
CD \SC
ShowScan
•
Press the <Enter> key.
If the optional Power Menu has been loaded onto your system, your DOS prompt
will resemble the following:
C:\Menu>
•
Access the Power Menu by keying in at the DOS prompt:
MENU
•
Select the ShowScan item from the Power Menu list of options. Press
<Enter> to start the program.
ShowScan's Main Menu
Before using ShowScan for the first time, select the SETUP option from the
Main Menu to configure the software for the microplate reader that you are
using. After the first configuration you should not have to perform this procedure
again.
•
Use the left/right cursor keys scroll across the Main Menu bar. As you
highlight a Main Menu item, a pop-down submenu simultaneously displays
available options. Use the up/down cursor keys to select an option, and press
<Enter>.
C-2
ShowScan Scanning Software
The SETUP Option
Highlight SETUP on ShowScan's Main Menu bar to configure ShowScan
software for the CERES 900C. From the pop-down options menu, select:
•
Reader Type. At the device submenu, use the cursor keys to highlight
CERES 900Cand press <Enter>.
•
RS232. At the device submenu, use the cursor keys to select preferences for:
•
Baud Rate:
1200, 2400, 4800, 9600, 19200
•
COM port:
1 or 2
•
Data bits:
7 or 8
•
Stop bits:
1 or 2
•
Parity:
ODD, EVEN, or NO
•
Filters. At the device submenu, enter the filter list for the reader.
Upon completion of Setup, the actual locations are downloaded from the reader.
Other Main Menu Options
READ
Highlight READ on the Main Menu bar. From the pop-down options menu,
highlight, and press <Enter> to choose:
•
Read Plate. Select the filter at which you wish to read the plate. Place the
microplate on the plate carrier, and press <Enter>. To return to the Main
Menu bar, press <Esc>.
Appendix C
C-3
•
Read Reference: Select the measurement and reference reading
wavelengths, and proceed as for Read Plate.
The program will calculate and display the difference between the two readings.
The left part of the display shows the individual well readings (up to 8), and the
right part of the display shows the calculated reference readings (up to 4).
•
Read Scanfile: Select the data file to be read.
The data file can be a scanfile stored with the SHOWSCAN module, or a scanfile
stored by the ScanMaster package. The scanfile must be located in the actual
working directory of the ShowScan program, and must have an extension of
.SCN.
FILES
Highlight FILES on the Main Menu bar. From the pop-down options menu,
highlight, and press <Enter> to choose:
•
Save Scandata: Select the measurement wavelength to be stored from all
available in memory.
A maximum of 8 scans (entire microplate assays) can be stored on the diskette.
Enter the filename (8 characters, without extension) for the raw scanfile.The file
will be stored in the ShowScan working directory.
DISPLAY
Highlight DISPLAY on the Main Menu bar. From the pop-down options menu,
highlight, and press <Enter> to choose:
•
C-4
Display Well: Enter the well number (A1 to H12) to display.
ShowScan Scanning Software
All available scan patterns of the selected well will be shown, including
calculated reference patterns.
•
Display Row: Enter the row number (A to H) to be displayed, and select the
measurement available in memory.
•
Display Column: Enter the column number (1 to 12) to be displayed, and
select the measurement available in memory.
•
Display Total MTP: Select the measurement to be shown from memory.
The screen will show all 96 scan patterns. Each well can be individually
highlighted by moving the cursor right or left, up or down.
•
To ZOOM-A-WELL, highlight the selected well, and press <Enter>.
•
Press <Esc > to return to the total 96-scan view.
Press the <F1> key to reveal the following keys:
•
<Shift><p>
Print Screen
•
<Esc>
Return to menu
•
<F2>
Select another scan from memory
•
<F3>
Select measurement from memory and show color-coded
interpretation of left and right AVERAGED transmission
values.
Appendix C
C-5
•
<F4>
Select measurement from memory and show color-coded
interpretation of transmission values.
•
<F5>
Toggle color-coding for <F3> and <F4> options.
RESET
Up to 8 raw measurement wavelengths and 4 calculated (dual) reference
wavelength readings can be retained in memory. Use these options to delete
either one type or all data:
•
Reset Measurement. Clear raw wavelength measurement data from
memory, retaining reference readings.
•
Reset Reference. Clear calculated reference readings from memory,
retaining raw measurements.
•
Reset All. Clear all calculated reference and raw measurement readings from
memory.
PRINT
•
Select Print and press <Enter> to print the graphic scan patterns shown on
the screen.
EXIT
•
Select Exit and press <Enter> to return to DOS or the Power Menu's
opening screen.
C-6
ShowScan Scanning Software
Appendix D:
Specifications
This chapter provides the specifications for the
CERES 900C EIA Reader. All specifications are
subject to change without notice.
Specifications
Size
The CERES 900C measures 25.5" wide x 8.00" high x 15.5" deep.
Weight
The instrument weighs 35 pounds without monitor (will vary depending on
options); the monitor weighs a maximum of 30 pounds.
Speed
The CERES 900C automatically reads 96-well microplates using a single wave
length in 5 seconds, dual wavelengths in 10 seconds, and prints an 8 x 12 array
of optical density values in approximately 20 seconds, depending on the printer.
Measurement Range
0.000 to 4.300. Absorbance Units over the range of wavelengths specified.
Negative optical densities will occur when the well being read absorbs less light
than an accompanying blank well. While negative readings as low as -4.300 are
possible, minimum possible optical density (OD) is 0.000.
Wavelength Range and Selection
CERES 900C-
380 to 900 nanometers (nm) using narrow band
interference filters.
CERES UV900C-
Filters from 340 to 900 nm are available.
Filter Wheel Configuration
The CERES 900C has a 6-position filter wheel. The user selects the filter(s)
desired for a particular assay from those resident within the filter wheel using the
CERES 900C software. Four standard filters are supplied with the instrument in
the following positions:
Position
Filter
1
405
2
450*
3
none
4
490
5
630
6
none
*340 nm with the UV option
Additional filters are available from Bio-Tek Instruments, Inc. For more
information, contact Bio-Tek Customer service at (800) 451-5172 or (802) 6554040.
Light Source
User-replaceable Tungsten-halogen bulb with an average life of 500 hours or
50000 reads. Replace with Bio-Tek part number 3400508.
D-2
Appendix D
Display
15" VGA color CRT (optional)
Linearity
+/- 1% from 0 to 2.500 OD at 405 nm, 400-750 nm
+/- 1% from 0 to 2.000 OD at 405 nm, 340-399 nm
Reading Accuracy and Repeatability- Factory Acceptance Criteria
+/- 1% +/- 0.010 OD from 0-2.500 OD, 400-750 nm
+/- 1% +/- 0.010 OD from 0-2.000 OD, 340-399 nm
Reading Repeatability
Successive reading of any well will produce readings that are repeatable within
+/- .5% +/- 0.005 OD from 0-2.500 OD, 400-750 nm
+/- 1% +/- 0.005 OD from 0-2.000 OD, 340-399 nm
assuming measurements are made at a single wavelength and blanked on air.
Resolution
0.001 OD
Microplates Accommodated
Uses 96-well (8x12) microplates; flat, U-and V-bottom; polystyrene and
polyvinyl, and removable and strip wells. (Polyvinyl microplates require an
adapter, and strip wells require frames.)
Photometry Method
Single or dual wavelength
Appendix D: Specifications
D-3
Photo detectors
12 measuring photo diodes, 1 Reference photo diode
Printout
External printer, dot matrix or thermal type
Power Requirements
150 VA at 100, 120, 220 or 240 V AC 50/60 Hz
Fuses
2.5A SloBlo for 100-120 VAC operation / 2.5A SloBlo for 220-240VAC
operation
D-4
Appendix D
Appendix E:
Accessories
This chapter lists CERES 900C accessories and
their part numbers, and provides
ordering information.
Accessories
The following accessories are available for the CERES 900C. For more
information, contact your Bio-Tek representative or call (800) 451-5172.
Item
Part Number
Calibration Plate
9000547
Fuses
2.5A Slo-Blo (U.S. application)
46063
2.5A Slo-Blo (European application)
46056
(2) are required
Tungsten Halogen Bulb
3400508
Barcode Wand
97113
Mouse
48210
External Keyboard
48204
Dust cover
9102004
Filters
Many wavelengths
are available. Contact
Bio-Tek.
VGA 120V
48258
VGA Universal Power
48315
E-2
Appendix E
Appendix F:
Reader Control File
This Appendix descibes the parameters and
their options used in a Reader Control File for
the CERES 900C microplate reader.
CERES 900C Reader Control File
Editing a Reader Control File
When the Reader Control file name is opened, the definition screen is displayed,
waiting for your input.
Reader Control File Name
This is the file name you specified to create or edit. Note that KC Jr. has added a
.FIL extension to the file name.
Reading Method
You can choose from five reading options: EndPoint, Monitored EndPoint,
Kinetic, Monitored Kinetic, and Scanning. To change the setting, move the
cursor to highlight this parameter, then press the spacebar to cycle through the
five options.
❑
EndPoint
If you select EndPoint, the reader carries the microplate into the reading
chamber, reads the 96 optical density values, makes the specified calculations
and reports, and returns the microplate to its full-out position.
❑
Monitored EndPoint
If you select Monitored EndPoint, the reader monitors one or more specified
wells until the average optical density of the monitored wells reaches a certain
value. You must select the Well locations to monitor,( i.e., A1 and H10 ), and the
Value to monitor for. If the Wavelength parameter is set to single, the reader
reads the microplate every 5 seconds.
❑
Kinetic
If you select Kinetic to do kinetic reading of the microplate wells, you must also
specify the time Interval between reads and the total number of Reads.
You can set the Interval parameter to 5 seconds or greater if the Wavelength
parameter is set to single, or to 10 seconds or greater if the Wavelength is set to
dual. The Reads parameter can be set to a value between 1-250.
❑
Monitored Kinetic
During a Monitored Kinetic read, the CERES 900C monitors from 1 through 96
preselected wells, until a blanked, unfactored average of those wells reaches a
specified optical density threshold (from -4.300 to 4.300). After the threshold is
reached, the kinetic portion of the read is performed.
❑
Scanning
If you select Scanning, you must also specify the number of scans and the well
diameter. Valid numbers are 4.0 to 7.5 mm. Based on this input, the reader will
perform multiple reads of each microplate well, using a preselected number of
discrete scan areas ( i.e., a 12-scan read ).
F-2
Reader Control File
Figure F-1 A Twelve-Scan Read
Wavelength
The options are Single, Dual and Multi wavelengths. To change the setting,
move the cursor to highlight this parameter, then press the spacebar to toggle
between the two options.
❐
If you select Single, the reader measures the optical density of each
well with a single filter. Set the W1 parameter to the wavelength value
for that reading.
❐
If you select Dual, the reader reads each well twice, each time with a
different filter. Set the W1 and W2 parameters to the appropriate
wavelength values. The microplate is not removed from the reading
chamber between the two readings. The reported optical density is the
difference between the two readings.
Dual wavelength readings significantly reduce optical interference
caused by scratched or fingerprinted microplates (scratches or
fingerprints reduce the amount of light on both wavelengths). Since the
substrate is sensitive to only one wavelength, the difference between the
two readings is attributed to the substrate.
Appendix F
F-3
❐ If you select Multi, the reader measures the optical density of each well
with multiple single filters. Selection can be all the wavelengths
installed in your reader.
Shaking
Available shaking options are determined by the selected read method. The
options are 1st Read, Every Read, and No.
In each case, the user determines the rate of shake speed, and the duration of the
shake. The duration is limited by the read method selected. The speed options are
Very Low, Low, Medium, High and Variable.
The shaking options are:
❐
EndPoint and Scanning Options: 1st Read/No.
The user specifies a shake duration from 1 second to 1 hour, and one of
the shake speed options.
❐
Kinetic Options: 1st Read/Every Read/No.
Shake times between 1 second and 1 hour may be selected. If Every
Read is selected, Continuous shake time may be specified.
❐
Monitored EndPoint Options: 1st Read/Every Read/
No, until a predetermined threshold is reached.
❐
Monitored Kinetic Options: 1st Read/Every Read/
No, until a predetermined threshold is reached. The shake duration must
be specified for the 'monitor' as well as the 'kinetic' portion of the read.
Continuous shake may be selected via the space bar.
F-4
Reader Control File
Blanking Pattern
The options are: Full, Half, Quarter, Row, Column, Constant, Rep.
Down 1st, Rep. Down 2nd, Rep Across 1st, Rep Across 2nd, and
Blank on Air.
❐
If you select Full, Half, Quarter, Row or Column, you can move
the cursor to the Edit Blank Map prompt, and press the spacebar.
The program then displays the corresponding plate map so you can
select the blanking wells for each sector. For example, if the
Blanking Pattern parameter is set to Full, the screen would appear
as in (Figure F-2).
Figure F-2 Blank Map
❐
Use the cursor keys to move the highlighted cursor to the
appropriate well(s).
✔ As wells are selected by hitting the “B” key, their positions are
highlighted.
Appendix F
F-5
✔ If you deselect a well, the highlighting is removed.
The values from the selected blanking wells in each sector will be
subtracted from all wells in that sector before the optical density values
are reported.
❐
When you've finished setting up the blanking map, press F10 to
save the map and return to the Reader Control File definition
screen.
Delay Initial Reading Time
This parameter allows you to specify a delay time after the plate enters
the reading chamber before the reading begins.
❐
Enter any value from 00:00:00 to 12:00:00 seconds for this
parameter.
Incubation Setpoint
This option is available if an incubator is installed.
❐
Use the spacebar to toggle between Off and a Setpoint. The
setpoint can be between 22.0° C and 50.0° C, but must be at least
1.5° C above ambient temperature.
Saving the Reader Control File
When you are finished entering or editing the Reader Control File
parameters, press F10 to save them to disk and return to the Protocol
Definition Menu.
F-6
Reader Control File
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