Bruker BioSpin BEST User manual
Version
BEST
Barcode Reader
Installation Manual
003
The information in this manual may be altered without notice.
BRUKER BIOSPIN accepts no responsibility for actions taken
as a result of use of this manual. BRUKER BIOSPIN accepts
no liability for any mistakes contained in the manual, leading to
coincidental damage, whether during installation or operation of
the instrument. Unauthorised reproduction of manual contents,
without written permission from the publishers, or translation
into another language, either in full or in part, is forbidden.
This manual was written by
Volker Reiß
© June 16, 2003: Bruker Biospin GmbH
Rheinstetten, Germany
P/N: Z31545
DWG-Nr: 1252003
Installation Manual Version 003 iii
Contents
Contents .............................................................. iii
1 Introduction ............................................................ 5
1.1 General ............................................................................... 5
2 Adjusting the Z-Tower Height ................................ 7
2.1 General ............................................................................... 7
2.2 Hardware ............................................................................ 7
2.3 Software .............................................................................. 8
3 Mounting the Barcode Reader................................ 9
3.1 Mounting the Barcode Reader on the Gilson Liquid Handler . 9
3.2 Connecting the Power Supply ............................................ 12
3.3 Connecting the Serial Cable .............................................. 12
4 Software ................................................................ 13
4.1 General ............................................................................. 13
4.2 Defining the Barcode Reader ............................................. 13
4.3 Programming the Barcode Reader ..................................... 14
4.4 Calibration ......................................................................... 15
5 Barcodes............................................................... 17
5.1 General ............................................................................. 17
5.2 Label Size ......................................................................... 17
5.3 General Barcode Information ............................................. 17
5.4 Matrix ID ........................................................................... 18
5.5 Matrix Type ....................................................................... 18
5.6 Barcode Positioning ........................................................... 20
5.7 Examples .......................................................................... 22
Figures ................................................................ 25
Tables .................................................................. 27
iv Installation Manual Version 003
Contents
Installation Manual Version 003 5 (29)
1
Introduction 1
General 1.1
This manual will guide you through the installation of the barcode reader for the
Gilson Liquid Handler.
The installation process consists of three steps:
1. Changing the height of the Gilson Z-tower
2. Mounting the barcode reader on the Gilson Liquid Handler
3. Defining the barcode reader in the software
These steps will be explained in the upcoming chapters.
Installation Manual Version 003 7 (29)
2
Adjusting the Z-
Tower Height 2
General 2.1
Before the barcode reader can be used with the Gilson Liquid Handler´s robot
arm, the working height of the Z-tower must be changed.
Hardware 2.2
The barcode reader set contains two black anodized (e.g. has a black eloxation
layer) adjustment cylinders (one with a height of 127 mm, one with a height of 175
mm), which aid you in mounting the Z-tower at the correct height. The 175 mm ad-
justment cylinder is used for the adjustment when cooling racks are used. In either
case the appropriate value must be set up in the Gilson Control Software.
Be sure that you have the correct adjustment cylinder (black anodized). The
original gray cylinder has a height of only 124 mm and this may cause prob-
lems when reading barcodes!
The first step in modifying the working height of the Z-tower is to turn the power off
and to remove all the racks from the Gilson Liquid Handler´s bed. Move the robot
arms to the center of the bed as shown in "The Gilson Liquid Handler" on page
8.
To achieve the 127 mm (or 175 mm when using a cooling rack) height, loosen the
screw on the backside of the Z-tower and pull the Z-tower upwards slightly. Place
the black anodized adjustment cylinder between the bottom of the Z-tower and
the floor of the Liquid Handler´s bed. Lower the Z-tower until it sits on top of the
adjustment cylinder. The scale should then show the value 127 mm (or 175 mm
when using a cooling rack). Tighten the screw and remove the black anodized
adjustment cylinder.
Installation Manual Version 003 9 (29)
3
Mounting the
Barcode Reader 3
Mounting the Barcode Reader on the Gilson Liquid Handler 3.1
1. Mount the barcode reader on the barcode reader bracket using the 2 M3x10
hexagon screws, as shown below:
Figure 3.1. Mounting the Barcode Reader to the Bracket
2x M3x10
Hexagon
Screws
Barcode Reader Bracket
10 (29) Installation Manual Version 003
Mounting the Barcode Reader
2. Mount the barcode reader bracket on the Z-tower of the Gilson Liquid Handler
using the two M3x10 cylinder screws. Ensure that you mount the bracket just
under the top plate of the Z-tower cover. There should not be a gap between
the Z-tower cover and the bracket. (as shown in Figure 3.2.)
Figure 3.2. Mounting the Barcode Reader Bracket
Cylinder
Screws
No gap!
Side View
Mounting the Barcode Reader on the Gilson Liquid Handler
Installation Manual Version 003 11 (29)
3. Affix the two adhesive fasteners to the Z-tower arm as shown in Figure 3.3.
and fasten the barcode reader cable to them using the two plastic strips.
The lower cable socket should be placed about 20 mm above the motor and
the upper socket about 20 mm below the upper end of the Z-tower.
Figure 3.3. Securing the Barcode Cable
Cable fasteners
with fastening
strips
20 mm
20 mm
12 (29) Installation Manual Version 003
Mounting the Barcode Reader
4. Fix the barcode reader cable to the Gilson Control Unit cable using the spiral
hose (see figure 3.4).
Figure 3.4. Securing the Barcode Reader Cable to the Control Unit Cable
Connecting the Power Supply 3.2
Connect the power supply unit to the barcode reader plug (5 mm stereo connec-
tor) and the power supply unit to a free mains outlet.
Connecting the Serial Cable 3.3
To send the reader information to the control unit, connect one end of the 10
meter serial cable to the barcode reader plug and the other end to a free serial
port (e.g. TTY05) on the CCU of the spectrometer.
Spiral Hose
Barcode Reader Cable
Gilson Control Unit Cable
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4
Software 4
General 4.1
The barcode reader must be setup in the XWIN-NMR software. This procedure is
described in this chapter.
Defining the Barcode Reader 4.2
Using the toolbox BESTADM (type in bestadm in the command line and press en-
ter) select main menu item Hardware (see below).
Figure 4.1. BEST-NMR Administration Toolbox
The window shown in Figure 4.2. will open. Select Associated Hardware from the
left panel and set the barcode readers parameters in the right panel as follows:
„Installed?“ Yes
„Connected to“ means the serial port on the CCU of the spectrometer,
where you connected to barcode reader, e.g. TTY05. Select the appropri-
ate serial port.
Press Apply and then OK. The barcode reader should now be recognized by the
software.
Calibration
Installation Manual Version 003 15 (29)
Normally you only need to click the menu item Tests in the BESTADM toolbox
(see Figure 4.3.). In some cases this will not work, whereas you will need to man-
ually select all the other menu items from the main menu (reading left to right:
Holders, Solvents, Methods) and then close the opening windows once again. Af-
ter this procedure it will be possible to correctly select the menu item Tests. The
following window will then open:
Figure 4.3. BEST-NMR Test Tool
Select the button Configure on the bottom left panel to program the barcode read-
er. If the barcode reader has been correctly programmed, it sends a beep and the
red light on the scanner top will blink once.
Calibration 4.4
The next step is to calibrate the scanner´s position. It is possible that the barcode
reader delays in finding the barcodes due to mechanical tolerance. To ensure a
fast barcode reading with your system a reading profile can be defined. A rack
with a correct barcode label (refer to the chapter "Barcodes" on page 17) is nec-
essary for this test. Place this rack in the second rack position (directly to the right
of the position where the rack type 211 with the solvents is normally placed) and
press the Calibrate button. The system will search different positions to find the
best position for barcode reading. This position is saved in the file SCAN-
NER.SRC. This test takes approximately 10 minutes.
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5
Barcodes 5
General 5.1
This chapter provides information about the barcodes and the barcode labels
used in the Gilson BEST System.
Label Size 5.2
The BEST System is designed to work with barcode labels with a size of 70 mm x
35 mm, e.g. No 3422 from Zweckform.
General Barcode Information 5.3
Each label which is adhered on a rack or wellplate must have two barcodes:
The upper barcode contains the Matrix ID and the lower barcode contains the Ma-
trix Type.
Notice:
1. The term „Matrix“ is the generic term used for racks and wellplates. So Rack
Type and Wellplate Type are both Matrix Types, and likewise Rack ID and
Wellplate ID are both Matrix ID´s.
2. If a TECAN preparation robot is also used to read the Wellplate ID, the bar-
code for this robot must also be placed in the free space located in the lower
part of the wellplate labels as shown in Figure 5.1.).
It is recommended that you also place the barcode information as human-
readable text on the labels.
Barcode type Code 128 is used for all barcodes. Other barcode types are ignored
by the barcode reader due to its initialization sequence.
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Barcodes
Figure 5.1. Matrix ID and Matrix Type on a Wellplate Label Example
Matrix ID 5.4
The Matrix ID is a user specific, unique ID which may contain a three-character
company name, followed by a serial number, and optionally by the analytical
method divided by a hash - character ( # ).
The Matrix ID is the first part of the spectrometer search string for order
files for this matrix.
Example: When the label with the Matrix ID „XYZ000001#NMR“ (which repre-
sents company XYZ´s first NMR experiment) is placed on a wellplate, all order
files which start with the string „XYZ000001#NMR“ (e.g. XYZ000001#NMR A1,
XYZ000001#NMR A2 etc.) are associated with this wellplate.
Matrix Type 5.5
The Matrix Type is a string in a specific format which contains information about
the geometry of the rack, the position of samples in the rack, the numbering of the
sample in the rack (Arrangement), the Working Order and the Submersion Offset.
The first 5 characters of the string are a code representing the rack type used, fol-
lowed by a hash character ( # ), e.g. 209 # for a rack code 209 or WH12# for a
Wellplate having positions from A to H and from 1 to 12.
Matrix Type
Installation Manual Version 003 19 (29)
Following the Matrix Type code are characters representing the Arrangement and
Working Order. These are encoded as follows:
If the rack contains wellplates (e.g. Rack Type 205), the Matrix Type string ends
after the Working Order. In this case the Wellplate Matrix Type contains the miss-
ing information about the Submersion Offset. Otherwise, the Submersion Offset is
added to that string following a hash - character ( # ). The Submersion Offset is al-
ways a number from -99.9 to 999.9 or the string Rcovr for recover-racks and has
always 5 characters!
Table 5.1. Encoding of Arrangement and Working Order
Upper Left
(ul)
Upper Right
(ur)
Lower Left
(ll)
Lower Right
(lr)
Horizontal
Stacked
(hs)
ulhs =Code 0 urhs =Code 1 llhs =Code 2 lrhs =Code 3
Horizontal
Folded
(hf)
ulhf =Code 4 urhf =Code 5 llhf =Code 6 lrhf =Code 7
Vertical
Stacked
(vs)
ulvs =Code 8 urvs =Code 9 llvs =Code A lrvs =Code B
Vertical
Folded
(vf)
ulvf =Code C urvf =Code D llvf =Code E lrvf =Code F
20 (29) Installation Manual Version 003
Barcodes
Example 1:
You are using Rack Type 209 and you want to count through the rack using the
„llvs“ method. The probes should be measured and/or prepared using the „urvf“-
method. The Submersion Offset for the whole rack is 2.7 mm. You would encode
the string as follows:
Matrix Type = 209 #AD#002.7
Example 2:
You are using Rack Type 205. In this case the Arrangement on the rack label and
on the Wellplate label have to be identical and can only be Code 9 or Code A.
Likewise, the Working Order on the Rack label can only be code 9 or code A,
whereas the Working Order on the Wellplate label can be any code from 0 to F.
The Submersion Offset (here recover-rack) is visible and encoded only on the
Wellplate label:
Matrix Type on the rack = 205 #AA
Matrix Type on the Wellplate = e.g. WH12#A3#Rcovr
It is recommended that you use the Label Designer tool which provides an easy
way to create Matrix Types.
Barcode Positioning 5.6
It is necessary to always place the barcodes in the correct position on the label to
ensure correct barcode reading:
Figure 5.2. Barcode positions on the barcode label
The following specifications should be met by the barcodes:
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