Thermo Fisher Scientific Array Plate Scanner Site Preparation Owner's manual

Brand: Thermo Fisher Scientific

Model: Array Plate Scanner Site Preparation

Type: Owner's manual

P/N 08-0257 Rev.B

February 2007

Site Preparation Guide—HT Array Plate

Scanner

For Research Use Only. Not for Use in Diagnostic Procedures.

Trademarks

Affymetrix®, , GeneChip®, HuSNP®, GenFlex®, Flying Objective™,

CustomExpress®, CustomSeq®, NetAffx™, Tools To Take You As Far As Your Vision®,

The Way Ahead™, Powered by Affymetrix™, and GeneChip-compatible™, are

trademarks of Affymetrix, Inc.

All other trademarks are the property of their respective owners.

Limited License

Limited License. Subject to the Affymetrix terms and conditions that govern your use of

Affymetrix products, Affymetrix grants you a non-exclusive, non-transferable, non-sublicensable

license to use this Affymetrix product only in accordance with the manual and written

instructions provided by Affymetrix. You understand and agree that except as expressly set forth

in the Affymetrix terms and conditions, that no right or license to any patent or other intellectual

property owned or licensable by Affymetrix is conveyed or implied by this Affymetrix product. In

particular, no right or license is conveyed or implied to use this Affymetrix product in

combination with a product not provided, licensed or specifically recommended by Affymetrix

for such use.

Compliant with directive 2002/96/EC (WEEE)

Contents

HT Array Plate Scanner Site Preparation Guide Overview . . .3

Components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

Preparation Checklist . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4

Site Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

Hazards . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

Space Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

Transportation Details and Requirements . . . . . . . . . . . . . . . . . . . . . . . 6

Space . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

Electrical Outlets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

HT Array Plate Scanner Specifications . . . . . . . . . . . . . . . . . . . . . . . . . 7

Networking Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9

Server Hardware and Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

Pre-Installation Requirements and Fax . . . . . . . . . . . . . . . . .11

HT Array Plate Scanner Confirmation of Site Preparation FAX . . . . . . 11

Facilities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12

Space Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12

Electrical Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14

Networking Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14

SQL Server License . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

GCOS Sever Pre-Installation Checklist . . . . . . . . . . . . . . . . . .17

Location . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17

Information Needed Prior to Configuration . . . . . . . . . . . . . . . . . . . . . 17

SQL Server Configuration (if using SQL Server) . . . . . . . . . . . . . . . . . 19

Oracle® Configuration (if using Oracle) . . . . . . . . . . . . . . . . . . . . . . . . 19

Information Needed from the Oracle® DBA . . . . . . . . . . . . . . . . . . . . . 20

Client Stations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21

Staff Requirement During Installation . . . . . . . . . . . . . . . . . . . . . . . . . 21

Training . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21

Other Comments/Questions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21

Technical Support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .23

ii GeneChip® HT Array Plate Scanner Site Preparation Guide

This page intentionally left blank.

HT Array Plate Scanner Site Preparation Guide Overview

Affymetrix, Inc. developed this document to help you through the process of preparing your

laboratory, to ensure a prompt and successful installation of the GeneChip® HT Array Plate

Scanner.

In preparing your site for the installation of the HT Array Plate Scanner, please note the

following points:

• Suitable preparation of your laboratory is essential to a successful installation.

• You may wish to work with your facilities personnel to ensure that your laboratory

meets the minimum electrical and other environmental requirements as outlined

in this document.

Once your site location meets all of the requirements outlined, your laboratory is suitable

for installation of your new HT Array Plate Scanner. At that time:

1. Complete the site verification checklist in Pre-Installation Requirements

and Fax on page 11 and fax the completed checklist to Affymetrix

Instrument Support at (408) 481-9670.

2. Upon receipt of this written confirmation, Affymetrix will contact you

by telephone to schedule the installation of your HT Array Plate

Scanner.

COMPONENTS

The GeneChip HT Array Plate Scanner is one of several components of the HT System (See

Table 1.1 on page 4). This site prep guide lists only the requirements for the scanner and

does not include the other components. Please refer to the GeneChip® Array Station Site

Prep Guide (P/N 702020) for additional information.

Please do not unpack the HT Array Plate Scanner shipping container

prior to the arrival of an Affymetrix Representative. The following

information is provided for reference purposes only.

4GeneChip® HT Array Plate Scanner Site Preparation Guide

PREPARATION CHECKLIST

Site preparation is essential for a successful installation of your instruments. It is important,

therefore, to ensure that all site requirements are met prior to the installation date. Please

use this check list for preparing your laboratory. Detailed information is provided in Pre-

Installation Requirements and Fax on page 11.

• Appropriate power connections for the HT Array Plate Scanner are available.

• Network requirements are met.

• Adequate space for the dimensions of the HT Array Plate Scanner and benchtop

support to sustain the total weight are allocated with available service access.

• Once the HT Array Plate Scanner is on-site, ensure that shipping skid and

associated boxes are close to the laboratory installation location. This equipment

must be unpacked only by an Affymetrix Representative.

• Two people are available with proper access to the loading dock and pallet jacks to

move the HT Array Plate Scanner and associated boxes to a location close to the lab

for unpacking by an Affymetrix Representative.

Table 1.1

HT System components depending on use

Target Prep HT Array Plate

Processing

1 Array Station ✔✔

2 Spectrophotometer (user-supplied) ✔✔

3 HT Array Plate Scanner -✔

4 GCOS server hardware (user supplied) -✔

5 HT Software Suite (includes GCOS Server

software) -✔

| Site Requirements 5

SITE REQUIREMENTS

HAZARDS

Table 1.2 summarizes possible hazards.

A qualified Affymetrix Representative must uncrate and install the

HT Array Plate Scanner. Facilities personnel should be assigned to

assist the Affymetrix Representative.

Table 1.2

Hazards

Hazard Present? Description

Chemical No

Control No Control software

Electrical Yes 100-240V power

Ergonomic Yes User interface

Gas No

Mechanical Yes, scanning stage, scanner weight (heavy instrument)

Laser Yes, if you remove the scanner enclosure.

Noise No

Pneumatic No

Radiation No

Temperature No

Ultrasonic No

Vibration No

Heat No Total power generated is less than 100 watts.

E-Fields No

H-Fields No

6GeneChip® HT Array Plate Scanner Site Preparation Guide

SPACE REQUIREMENTS

At the installation site, verify that there is sufficient space and air circulation to

accommodate the GeneChip HT Array Plate Scanner.

Refer to the following diagram for space dimensions.

TRANSPORTATION DETAILS AND REQUIREMENTS

1. Loading dock or a delivery truck with a lift gate

2. Transportation to final location: elevator with 1200 lb. (545 kg)

capacity.

3. Doorways: >40” (1.016 m) wide

4. Cushioned rolling cart: 400 lb. (181.4 kg) capacity (Uncrated

instrument)

5. Lift truck: to remove instrument from crate and place on cart: 600 lb.

(272.1 kg) capacity

HT Array

Plate

Scanner

Array Plate Access

Clearance

29"

(76 cm)

16"

(41 cm)

12"

(30 cm)

(7.6 cm)

Clearance 2"

(5 cm)

| Space 7

SPACE

1. The instrument footprint is 29” (76 cm) depth x 26” (66 cm) height x

16” (41 cm) width.

2. Additional clearance: 12” (30 cm) on left side, 3” (7.5 cm) right side,

and 2” (5 cm) in the rear.

3. Computer workstation: Bench space for monitors: 36” (0.91 m) wide

by 23” (0.58 m) deep; CPU tower needs to be within 80” (2.03 m) of

the right side of the instrument

ELECTRICAL OUTLETS

1. Two separate, dedicated grounded outlets within 4 ft. (1.22 m) of the

instrument (one for the scanner and one for the workstation).

2. Outlet requirements: 100-120 VAC, 50/60 Hz, 20 Amps or more, or

220-240 VAC, 50/60 Hz, 10 Amps or more.

HT ARRAY PLATE SCANNER SPECIFICATIONS

Table 1.3 lists the important instrument specifications.

Table 1.3

The Specifications of the GeneChip® HT Array Plate Scanner

Item Parameter Value

Weight Shipping approx 216 pounds (98

Kg)

Free-standing approx 145 lbs (66 Kg)

Dimensions Width ~16 in.

Depth ~29in.

Height ~26 in.

Power

Voltage

Current

Line Frequency.

100 - 240 V ~

2.8 - 1.2 A

50 - 60 Hz

Working Environment Temperature 59°F-85°F (15°C-30°C)

Humidity 10-90% Non-condensing

Clearance

2 in. (5 cm) in rear

12 in. (30.5 cm) on left

side

8GeneChip® HT Array Plate Scanner Site Preparation Guide

Pollution Degree 2

Installation Category II

Altitude <2000m

Electrical Supply Provide voltage, frequency or power rating per unit

label. Circuit breaker.

Main Supply Voltage

Fluctuations

Are not to exceed ±10% of the nominal supply

voltage

Table 1.3 (Continued)

The Specifications of the GeneChip® HT Array Plate Scanner

Item Parameter Value

Networking Requirements

The GeneChip HT Array Plate Scanner will be installed and tested in local mode. If you

later want to connect the workstation to your network, you may need to arrange for your

network services department to install anti-virus software and to prepare for attachment in

other ways. If your network policies require that the name of the workstation be changed,

you will need to inform Affymetrix so that the workstation software can be reconfigured

accordingly.

SERVER HARDWARE AND SOFTWARE

The GCOS Server software is provided with the HT Array Plate Scanner while the server

hardware component is user-supplied. Due to the large amount of data generated, a GCOS

server (or a server that meets the minimum specifications) is recommended. The

configuration of the server is dependent on the amount of data generated by the HT System.

As such, additional memory, processor speed, and disk drive capacity should be considered

depending on the number of plates processed.

GCOS Server Hardware minimum configuration:

• Dell PowerEdge 6800

• Tower Configuration

• Quad 3.0 GHz Xeon Processors

•8MB Cache

•4GB RAM

• 4x300 GB Hard Drives

• RAID Configuration

• Microsoft® Windows® 2000

•3.5" Floppy Drive

• 24X IDE CD-RW/DVDROM

• 17" Monitor

10 GeneChip® HT Array Plate Scanner Site Preparation Guide

For a more detailed recommendation of hardware specifications tailored to your institution,

please refer to on page 16.

Affymetrix does NOT supply licenses for Microsoft® Windows® 2000

Server, Microsoft® Windows® 2000 Professional or your chosen

RDBMS software (SQL/ORACLE®).

If you plan to purchase a server, additional requirements and site

information are required prior to installation. Please refer to on

page 16 for detailed information.

The USB and Firewire (IEEE 1394 High Speed Serial Bus) cables are

not locking connectors. Insure that the USB and Firewire cables are

plugged securely and in the correct orientation in both the scanner

and the workstation. Avoid snagging or pulling these cables during

the scanner operation.

Pre-Installation Requirements and Fax

To ensure that the GeneChip® HT Array Plate Scanner is installed successfully, please fill

out the information requested for shipping and receiving, space requirements and the site

preparation checklist and fax this information (on page 11 through page 15) to Affymetrix

Instrument Support (408) 481-9670.

HT ARRAY PLATE SCANNER CONFIRMATION OF SITE PREPARATION FAX

Order Reference Number ____________

Contact ___________________(printed)

_________________________(signed)

Institution/Company Name ______________________________________________

Shipping Address

_____________________________________________________

State ___________ZIP code ___________ Country_______

Phone _______________________Fax ____________________

Contact Email_________________________________________

If you plan to purchase a server, please provide a list of contacts for the server installation.

Refer to on page 16 for additional server requirements.

Fax page 1 of 5

12 GeneChip® HT Array Plate Scanner Site Preparation Guide

FACILITIES

Receiving Facilities

Check with your Receiving Department about the shipping requirements we need to

consider when shipping your unit. Please provide Affymetrix with detailed shipping and

receiving requirements deemed necessary by your Receiving Department.

Do you have a loading dock?

Do you require a delivery truck with a lift gate?

I, ____________________________________, have verified the statement checked

above.

Transporting the Instrument

Determine the path that the GeneChip HT Array Plate Scanner system will follow from the

loading dock to your installation site. Note that the scanner is shipped as two units: a large

crate containing the main instrument and a pallet with several boxes. If the instrument will

be transported in the crate, all doorways and passages along that path must be at least 40”

(1.016 m) inches wide. Please verify passageway dimensions with a measuring device.

Should it be necessary to transport the crated scanner on an elevator, make sure that the

elevator can carry at least 1200 lb. (545 kg), the combined weight of the crated instrument

(about 360 lb., or 164 kg) and the transport mechanism and personnel. Consult with on-site

personnel.

I, ____________________________________, have verified our facility meets the

transport requirements above.

Uncrating the GeneChip® HT Array Plate Scanner

Should it not be possible to move the crated instrument through the facility, the instrument

may be transferred to a cushioned rolling cart. This cart should be able to accommodate the

full weight of the instrument (145 lbs., 66 kg, when uncrated), and it should be sufficiently

stable to prevent tipping.

Due to the nature of the instrument, a manual, winch-operated lift truck is recommended

for removing the instrument from the crate and transporting it to the transfer cart or to its

place of installation. The lift truck must be rated in excess of 600 lbs. (272.15 kg). A lift

truck is not recommended for transport of the instrument for significant distances. The lack

of cushioning poses a risk to the instrument, and the high center of gravity of the lift truck

and instrument poses a risk of tipping.

SPACE REQUIREMENTS

At the installation site, verify that there is sufficient space and air circulation to

accommodate the GeneChip HT Array Plate Scanner. The instrument footprint is 29” (76

Fax page 2 of 5

| Space Requirements 13

cm) depth x 26” (66 cm) height x 16” (41 cm) width. In addition to the footprint, when

looking at the instrument from the front, allow for 2” (5 cm) in the back and on the right

side for proper airflow. During installation, access to the front, back, and right-hand side of

the instrument will be required.

The table or bench supporting the instrument must be rated for 500 pounds (227 kg) and

support must be sufficient to prevent tipping.

In addition to space for the instrument, there must be room for the workstation. The

workstation includes a CPU tower and two LCD monitors as well as a keyboard and mouse.

Bench space at least 36” (0.91 m) wide by 23” (0.58 m) deep is recommended. The CPU

tower will need to be within 80” (2.03 m) of the right side of the instrument.

I, ____________________________________, have verified our facility meets the space

requirements above.

HT Array

Plate

Scanner

Array Plate Access

Clearance

29"

(76 cm)

16"

(41 cm)

12"

(30 cm)

(7.6 cm)

Clearance 2"

(5 cm)

Fax page 3 of 5

14 GeneChip® HT Array Plate Scanner Site Preparation Guide

ELECTRICAL REQUIREMENTS

Verify that there are at least two separate, dedicated, properly grounded electrical outlets

that are within about 4 feet (1.22 m) of the GeneChip HT Array Plate Scanner location. The

scanner outlets should be 100-120 VAC, 50/60 Hz, 20 Amps or more, or 220-240 VAC,

50/60 Hz, 10 Amps or more. One outlet will be used for the scanner, and the other for the

workstation and its peripherals.

I, ____________________________________, have verified our facility meets the

electrical requirements above.

NETWORKING REQUIREMENTS

The GeneChip HT Array Plate Scanner will be installed and tested in local mode. If you

later want to connect the workstation to your network, you may need to arrange for your

network services department to install anti-virus software and to prepare for attachment in

other ways. If your network policies require that the name of the workstation be changed,

you will need to inform Affymetrix so that the workstation software can be reconfigured

accordingly.

The workstation will ultimately be attached to a network.

The workstation will not be attached to a network.

The workstation name will need to be changed during attachment.

The workstation name will not need to be changed during attachment.

I, ____________________________________, have verified the statement(s) checked

above.

Fax page 4 of 5

| SQL Server License 15

SQL SERVER LICENSE

The GeneChip HT Array Plate Scanner workstation comes with a license to Microsoft® SQL

Server 2000 Standard Edition that can be transferred to an end user in the United States. All

other end users will need to purchase a license on their own.

I, ____________________________________, certify that I am an end user in the

United States, or

I, ____________________________________, certify that I will purchase a license to

Microsoft SQL Server.

Special Installation Requirements

If there are any special requirements on your part that we need to know, please list them

here:

________________________________________________________

Fax page 5 of 5

16 GeneChip® HT Array Plate Scanner Site Preparation Guide

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GCOS Sever Pre-Installation Checklist

Please provide the following information.

LOCATION

Please provide your

• Site Name:

• City/ State:

• Date:

INFORMATION NEEDED PRIOR TO CONFIGURATION

Contacts

Name of contacts who will be involved with the GCOS System:

1. IT personnel:

a. Name

b. Phone number:

c. Email address:

2. DBA personnel:

a. Name

b. Phone number:

c. Email address:

3. Bioinfomatics Specialist personnel:

a. Name:

b. Phone number:

c. Email address:

4. Scientist or Primary End user personnel:

18 GeneChip® HT Array Plate Scanner Site Preparation Guide

a. Name:

b. Phone number:

c. Email Address:

Installation Details

1. Are you purchasing a pre-configured server from Affymetrix?

Yes/No

2. If Yes, are you purchasing the Dell or Compaq? Dell/Compaq

3. Is this a one server or two server configuration? One/Two

4. Which of the following databases will be used:

■MS SQL Server 2000? Yes /No

■Oracle® 8.1.7 for Microsoft® Windows® 2000? Yes/No

5. The site license information: License Key #__________

Non-Configured Server Information

1. Configured for the network/domain

2. Microsoft® Windows® Network Domain name that server resides on:

___________________________

3. Operating System running on the Primary Domain Controller:

______________________

4. Name of local server: ______________________

5. Name of remote AADM server (if applicable): _______________

If purchasing a pre-configured server, please skip to Information

Needed from the Oracle® DBA on page 20.

It is important to make sure that an underscore is not used in the

computer name of the GCOS Server. Otherwise, the GCOS Server

1.0 software will not function properly.

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Thermo Fisher Scientific Array Plate Scanner Site Preparation Owner's manual

Brand: Thermo Fisher Scientific

Model: Array Plate Scanner Site Preparation

Type: Owner's manual

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Thermo Fisher Scientific Array Plate Scanner Site Preparation Owner's manual

Thermo Fisher Scientific Array Plate Scanner Site Preparation Owner's manual

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