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GS Junior
Installation Manual
Version: 1.3 FOR INTERNAL USE ONLY
Preface ............................................................................................................................. 3
Revision History ......................................................................................................................................... 3
1 Unpacking and Physical Setup............................................................................ 3
1.1 Verification of delivered Items ............................................................................................................ 3
1.2 Unpacking, Inspection and Physical Setup ........................................................................................ 4
2 Attendant PC (Control Unit) Setup .................................................................... 11
2.1 Applying BIOS Settings .................................................................................................................... 11
2.2 Installing the Factory Image ............................................................................................................. 15
2.3 Password Validation ......................................................................................................................... 22
2.4 Installing the GS Junior Software ..................................................................................................... 23
Data Processing SW ................................................................................................................................ 26
Data Analysis SW ..................................................................................................................................... 27
2.5 Installing the Documentation Disk .................................................................................................... 27
2.6 Installing the Third Party Software Disk............................................................................................ 31
2.7 Installing SW Patches ....................................................................................................................... 32
3 Instrument Start-Up and Validation ................................................................... 33
3.1 Arranging Desktop Icons .................................................................................................................. 33
3.2 Instrument Start-Up .......................................................................................................................... 34
3.3 Instrument Upgrade ............................................................................Error! Bookmark not defined.
3.4 Instrument Validation ........................................................................................................................ 38
4 Teleservice Installation, Configuration and Setup ........................................... 42
4.1 Teleservice Installation ..................................................................................................................... 42
4.2 Teleservice Configuration ................................................................................................................. 43
4.3 Teleservice Activation ....................................................................................................................... 49
4.4 Teleservice Activation Test ............................................................................................................... 50
5 XLTF Testfragment-Run ..................................................................................... 53
5.1 Material Preparation ......................................................................................................................... 53
5.2 Set up Procedure .............................................................................................................................. 53
5.3 Results Verification ........................................................................................................................... 59
6 Installation Report............................................................................................... 61
Revision History
Version Revision Date Revision Information
1.0 May 2010 First release
1.1 May 2010 - Axeda configuration – password handling revised
- minor additions and corrections
1.2 July 2010 - Monitor & PC setup procedure revised
- Install sequence for Teleservice changed
- minor additions and corrections
1.3 Aug 2010 Accounting for changes for SW patch 2.5p1
Download the GS Junior Installation Report from GRIPS, attached to this manual.
1. 2.
ii. Remove the inner side carton, leaving the instrument accessible for pick up
3. 4.
iii. Remove the plastic from the instrument and place the instrument on a bench top
iv. Remove the camera dampening gasket from the camera door area
Note any visible damage that may have incurred during shipping in section 1.3 of
the Installation Report.
1. 2.
Sipper tubes and filters are part of the Sipper Wear gloves when handling the sipper tubes
Maintenance Kit
Tip:
- when right-
handed, start on
left side installing
sippers (as in
picture);
- when left-
handed, start on
right side
3. 4.
Attach each sipper tube to a filter Install the assembly to the sipper manifold
5. 6.
WRONG! Do not hold on the filter CORRECT: Hold by the sipper when tightening white the connection
Note: Tighten the filter assembly to the sipper manifold as tight as possible.
Grabbing it by the blue filter, install the long sipper tube to the luer adapter.
g. Unpack the Attendant PC and monitor and inspect for any damage.
Note: The instrument has been shipped with US standard power cords. Regional power
cords will have to be purchased separately where required.
Connect the DVI and the power cable to the monitor and guide both cables through
the monitor cable support
Note: DHCP is set per default for the public network port
3. Select Advanced -> Power-On Options and set POST Messages to ENABLE
The process will run for approx. 4 minutes while the installation package is confirming
software checksums.
The process will continue running for approx. 20 minutes while the hard drive imaging
operation executes.
13. At the following screen, type in a new hostname for the instrument
Note: Use JR as the prefix, followed by the serial number as the hostname,
e.g. JR12345678
Open the Time Zone tab and select your time zone from the list, confirm with OK
a. Select the Network Time Protocol tab and uncheck the tickbox
16. Confirm with OK and the system will reboot automatically for the settings to take effect.
Note: If the CD drive does not eject the disk when pressing the Eject button, apply
following workaround:
b. Type: cd / (Enter)
UN: adminrig
PW: enter the pwd that was set before
Î The document is intended for end users and can be downloaded from GRIPS. It
is attached to the Installation Manual.
Note: root access is required to install software. Have the root password handy.
Data Acquisition SW
1. Insert the Data Acquisition disk
5. Click Next
10. Close any other open windows and remove the disk from the disk drive.
Î see workaround on page 21 if Eject button does not eject the disk
Data Processing SW
1. Insert the Data Processing disk
2. Double-click on the setup.sh icon and follow the instructions on the screen
3. When the install has completed, remove the disk from the disk drive.
Î see workaround on page 21 if Eject button does not eject the disk
2. Double-click on the setup.sh icon and follow the instructions on the screen
3. When the install has completed, remove the disk from the disk drive.
Î see workaround on page 21 if Eject button does not eject the disk
Note: Following message will appear if the PC is not connected to the internet::
Click to proceed
6. You will be prompted to enter the root password at this point. Enter the password and click
OK to proceed. You will then see the following screen. Follow the prompts as shown
8. Click OK
9. Click Finish
Note: The installation via setup icon is not supported with SW 2.5. The software needs to
be installed via terminal window.
2. Open a Terminal window and become root user Î refer to steps 2. -5. in section 2.3
cd /media/454_3rd_Apps_JR_1.0 (Enter)
sh setup.sh (Enter)
Note: The Teleservice software will need to be installed at a later point in time. Proceed
according to the manual.
Note the SW version (and patches) installed on the front page of the in the
Installation Report.
UN: techuser
PW: M@5+3rch13F
adminrig-terminal
GS De Novo Assembler
GS Junior System
GS Reference Mapper
GS Run Browser
root-terminal
open-file-browser
Techuser group
Computer
Trash
techuser’s Home
2. Sign In as Administrator
4. Wait until the instrument becomes “Available” and the status LED turns solid yellow.
Double-check that the status LED on the instrument also turned solid yellow.
Note:
If the software in the electronics module needs to be upgraded, the GUI will not turn amber,
instead it will turn red. If it turns red perform the steps in the Upgrading Electronic Module
Section.
3. When the file transfer is complete, the firmware upgrade will launch automatically
and the instrument GUI will change to the following screen:
Once the self test completes, the status indicator will become yellow, the “Start”
button will be active again and all sensor outputs will be respond normally.
7. Change directory to
cd /opt/454/apps/gsSequencer/firmware (Enter)
8.
type following command into the adminrig-terminal
./setInstrumentTimezone (Enter)
In the GS Sequencer software, click on with the mouse pointer on the instrument
hostname and then click on Recheck to run a self-test
1.
2.
a) All 12 valves are cycled in at a 1 second interval. Listen for the click of the actuation
and release of each valve and the illumination of the corresponding valve status
LED.
Valve
Status
LEDs
b) The Primary Pump turns slightly forward and then backward, watch for the
movement.
Primary
Pump
Purge
Pump
d) The status LED displays the pattern Green, Yellow, Red, Yellow, Green, Yellow,
Red, Yellow… The pattern repeats for 30 seconds. Make sure all colors are
displayed.
Status
LED
The Self Test function also checks Chiller and Heater thermistors and operation,
Bubble sensor operation and E-Box temperature. These tests don’t require user
attention.
Warnings or errors will be displayed on the GUI if any of the test results are not positive.
Note any warnings or error messages in section 2.2 of the Installation Report.
3. Reset the sipper tube counter Î refer to iSDoc ‘Clear Sipper Tube Counter’,
chapter Procedures / Service Software
Note the results in section 2.3 of the Installation Report
4. Reset the pump tubing counter Î refer to iSDoc ‘Clear Pump Tubing Counter’,
chapter Procedures / Service Software
Note the results in section 2.4 of the Installation Report
5. Check the fans for proper operation Î refer to iSDoc ‘Checking Fans’
Note the results in section 2.5 of the Installation Report
While the pump calibration script is running, verify that chiller, heater and camera
are reaching target temperatures.
Note the results in section 2.7 of the Installation Report
8. Run a prime volume verification test Î refer to iSDoc ‘Prime Volume Verification’
Note the results in section 2.9 of the Installation Report
Note: The installation via setup icon is not supported with SW 2.5. The software
needs to be installed via terminal window.
cd /media/454_Axeda_JR_1.0 (Enter)
sh setup.sh (Enter)
5. Once the Axeda Service installation is complete, the following icon will appear on
the desktop:
/opt/axeda/agent/AxedaAgentConfiguration (Enter)
2. Using the TAB key, select ‘Run an Action’ and hit Enter
5. Under Customer Code, enter the name of the institution, and go to the next line
Note: Customer Code and Lab code are mandatory fields. An error message will be
shown if no text is entered.
Note: Country Name and Country Code are preset and cannot be changed.
10. To confirm that the Axeda service is running, type the command below and check
for the output highlighted below
12. Manually add following two lines at the end of the file. Be careful to avoid any typing
mistakes.
Note: The Axeda Agent service needs to be restarted after every computer reboot.
c. When prompted for the password, enter adminrig as the password, hit Enter
e. Then type y (for yes) when prompted as shown below, and hit Enter
2. Ensure that the Junior Attendant PC is running and that the Axeda service
has been restarted since the last reboot Î details see section above
3. The Attendant PC will then automatically register itself on the Axeda server.
Note: This process takes approx. 10 minutes when the network connection
is established.
Note: there is no noticeable action after double-clicking the icon, but services start
running in the background
3. Using your COE computer, login the Roche network and access the Axeda portal
https://sergate.dia.roche.com
Alternatively, enter your S/N in the ‘Device’ field and click on Search
If your S/N is not showing up within 10 minutes, check whether your internet
connection is ok, reboot the PC and go through chapter 4.1 and 4.2 again, making
sure every step is completed.
If the Roche network is not accessible at customer site for an immediate check, Level 1
Support (Indy, Penzberg, Shanghai, Tokyo) might be able to assist and check on the
Axeda server whether the instrument has become active.
5.1.2 Tools
• Box with ice for temporary reagent storage
• Magnet Particle Separator
• Centrifuge for 2 ml tubes
• Centrifuge for Bead Deposition Device
• Vortex
• Rotator
• Pipettes (20µl - 1000µl) with according Tips
• Serological pipette
• 10 ml and 25 ml Serological Pipette tubes
• 50 ml conical tube
• Siliconized 1.7 ml tubes
• GS Junior Bead Deposition Device (BDD)
Material # 05996597001
Remove from carton and place on ice.
Material # 05996589001
Remove Common Buffer from carton and leave at ambient.
Set aside carton at ambient for use later in the prewash steps.
Material # 05996643001
Remove from carton and place on ice.
Pre-Wash Prep
Material # 05996589001
Obtain the carton and with the remaining items and perform the following:
1. Remove CB Sipper tube from plastic and mount on the Sipper Manifold using clean gloves.
2. Remove pre-wash cassette from plastic.
3. Rinse the 10 tubes mounted in the pre-wash cassette with nanopure water 2 times.
4. Fill the 10 tubes mounted in the prewash cassette with pre-wash buffer. Fill until ~ 1 cm below
each tube top.
5. Mount the prewash cassette.
6. Place the Pre-Wash bottle into the open position on the left side.
7. Lower the manifold and close the instrument door.
Attention:
BB2
1. Obtain a 50 ml conical tube and Label it BB2.
2. Using 10 ml serological pipette, add 6.6 ml of Supplement CB to the 1100 ml bottle of the
Common Buffer.
Invert the bottle 10 times to mix.
3. Using a 50 ml serological pipette transfer 40 ml of the Common Buffer mixture to the 50 ml
conical tube.
4. Place on ice.
5. Spin the Apyrase in a microcentrifuge for 5 seconds at 10,000 rpm.
6. Using the 20 ul pipette, add 6.5 ul of Apyrase to the 50 ml conical tube.
Invert 10 times to mix and place on ice.
PicoTiterPlate
Material # 05233682001
1. Remove the PTP kit from the carton.
2. Grasp the PTP by the edges and gently lift to remove the PTP from the packaging.
3. Rest it on the tray.
4. Record the PTP serial number for later use.
5. Assemble the BDD as follows:
• Grasp the PTP by the edges and place the PTP on the BDD base so that the notches
on each are aligned.
• Obtain that BDD gasket and secure the gasket to the BDD using the alignment holes to
orient the gasket.
• Align the top cover of the BDD with the alignment dowels and gently rest the cover over
the assembly.
• Gently apply pressure to the BDD assembly and rotate the latches on either side of the
BDD until the latch clicks into the side groove of the BDD.
• Repeat the process for the other latch.
Buffer Layer:
1. Using a 1000 ul pipette, pipette 350 ul of BB2 into the larger hole at the top of the PTP.
2. Place the BDD in a centrifuge and spin for 5 minutes at 1620 rcf (4013 rpm for the Eppendorf
5430).
3. Remove the BDD from the centrifuge and leave resting at room temperature.
1. Obtain the Enzyme (Brown Cap) and PPiase (Green Cap) Packing beads.
2. Repeat the following steps 3 times to wash the beads:
• Add 1 ml of BB2 to each tube.
• Vortex each tube gently and then mount on a magnetic particle concentrator.
• Wait 30 second and then gently invert the magnetic particle concentrator a few times.
• Wait 30 seconds (or until supernatant is clear) then remove the fluid from the tubes.
• Remove the tubes from the magnetic particle concentrator.
3. Add 400 ul of BB2 to the Enzyme Beads ( Brown cap) tube and vortex. Return to the ice.
4. Add 410 ul of BB2 to the PPiase Beads (Green Cap) and vortex. Return to the ice.
1. Obtain two 1.7 ml tubes. Label one Pre and the other Post,
2. To construct the Pre Layer perform the following:
• Add 300 ul of BB2 to the tube labeled Pre.
• Add 110 ul of Enzyme beads to the tube marked Pre.
• Vortex then place on ice.
3. To construct the post layer perform the following:
• Add 180 ul of BB2 to the tube labeled Post.
• Add 230 ul of Enzyme Beads to the tube marked post.
• Vortex then place on ice.
Load L1
1. Retrieve the BDD and pipette out as much BB2 as possible from the port hole of the BDD.
1.
2.
3.
1.
3.
2.
3.
6 Installation Report
Complete the GS Junior Installation Report and send it via email to:
branford.454_sequencing_support@roche.com
Tip: On your COE machine, open the Address Book in MS Outlook and type in 454 s and
select the address shown below: