SimArray
SimArray
A user-friendly and user-configurable microarray design tool [PubMed | Journal]
Cambridge Systems Biology Centre, Tennis Court Road, Cambridge, CB2 1QR, UK  [map]
Tel: +44 (0)1223 760280.   Fax: +44 (0)1223 760241.

Configuration files

Please report all bugs to Richard Auburn (contact details above).

SimArray uses index files to point to the configurations files. This means that the configuration files can be saved in any location and with any name. One copy of SimArray can also be used to model a range of different production environments.

Download the configuration file that is best suited to your production environment. If none are available, you should download and edit one of the other files. Edited files can be sent to Richard Auburn to be added to this site (contact details above).

We hope to build a library of configuration files to help other SimArray users.

Tool:

A tool file is required to define which pin configurations your robotic spotter is able to use. Required, as no currently available robotic spotter is compatible with all possible pin configurations.

Date Version Config. file Notes
1st Oct. 2005 v1.0 Standard Standard version for editing
1st Oct. 2005 v1.0 OmniGrid Genomic Solutions robotic spotter
1st Oct. 2005 v1.0 MicroGrid Genomic Solutions robotic spotter
1st Oct. 2005 v1.0 Qarray2 Genetix robotic spotter
21st Aug. 2006 v1.0 Nanoprint Telechem robotic spotter

Pins:

A pins file is required to record the spotting pins achievable spot density. Most spotting pins are not compatible with all robotic spotters and all pins varywith regard to achievable spot density. Spot density is also dependent on the robotic spotter, spotter parameters, substrate chemistry, spotting buffer, temperature, relative humidity, etc.

Date Version Config. File Notes
1st Oct. 2005 v1.0 Standard Standard version for editing
1st Oct. 2005 v1.0 MicroSpot Genomic Solutions MicroSpot pins
25th Oct. 2005 v1.0 NanoPin Matrix Technologies Corporation ceramic pins
1st Oct. 2005 v1.0 aQu Genetix aQu pins
1st Oct. 2005 v1.0 946 Telechem 946 pins
1st Oct. 2005 v1.0 Stealth Telechem stealth pins
1st Oct. 2005 v1.0 ChipMaker Telechem chipmaker pins

Time:

A time file is required to record the time that it takes to perform a single print cycle, i.e., the time required to print the probes from a single pin loading and then clean the pins. Required because single print cycle time is determined by a range of user-defined options and the robotic spotter itself. The wash conditions also vary according to the production environment, i.e., spotting pin, spotting buffer, etc.

Date Version Config. File Notes
12th Dec. 2005 v1.0 Standard Standard version for editing

Specific versions of this configuration file are not available.