GeneChip Command Console Software is the instrument control software for GeneChip systems. Command Console Software provides an intuitive set of tools for instrument control and data management used in the processing of Axiom and GeneChip arrays.

Key features:

  • Provides summary of probe cell intensity data (CEL file generation); enables sample and array registration, data management, instrument control, and automatic and manual image gridding 
  • Enables flexiblility to customize, automate, and integrate workflows with a variety of laboratory information management systems. 
  • Supports the full range of assays by enabling seamless integration with downstream primary analysis applications such as Axiom Analysis Suite and Transcriptome Analysis Console (TAC) Software.
  • Compatible with all the commercially available GeneChip analysis applications through direct import of sample attribute and array data

We enable an open informatics platform that uses industry-standard file formats for sample annotations and open file formats to access Axiom and GeneChip array data. Inside Axiom and GeneChip-compatible analysis applications, sample attributes and array data are merged with automated downloads of library files and NetAffx annotations, providing streamlined data analysis workflows.

GeneChip Command Console 6.0+ provides flexible and powerful tools for:

  • Entering and organizing information about the sample, Axiom, and GeneChip probe arrays
  • Controlling the instruments used to process probe arrays and collect the intensity data
  • Tracking the progress of an array through the array processing workflow
  • Working seamlessly with other tools for downstream analysis
New features
  • Monitor a GeneTitan Multi-Channel (GTMC) instrument remotely using the Connect cloud platform
  • Faster scan time on GTMC instrument

Basic features

  • Instruments serial numbers
  • Hybridization completion
  • Fluidics completion
  • Scanner completion
  • Supports full range of assays through seamless integration with primary downstream analysis application such as Axiom Analysis SuiteAxiom MiDAS, and Transcriptome Analysis Console
  • Sample attribute and array data can be directly imported into any of the commercially available Axiom and GeneChip-compatible applications, allowing researchers to select from a variety of analysis methodologies

Unique functions

  • Monitor instrument in real-time from anywhere
  • Visualize from desktop and mobile device
  • Transfer array data to Connect cloud platform
  • Upload error log files to Connect cloud platform

Supported instruments

  • GeneTitan Multi Channel Instrument
  • GeneChip 3000 Instrument

Applications

  • High throughput genotyping and gene expression
  • Axiom 24-, 96-, 384- and Mini 96- format arrays
  • GeneChip cartridge arrays 

Price/Delivery/Support

  • Included with GeneTitan Multi-Channel Instrument
  • Support: visit thermofisher.com/support
  • Documentation available upon download

 

Benefits

  • File-based software for easy data sharing
  • Flexible GeneChip processing workflow
  • Integrated instrument control
  • Simplified data management
  • Integration and customization for end users and third-party software tools

Instrument support

This release of Command Console Software supports the following instruments:

  • GeneTitan Instrument
  • Fluidics Station 450
  • GeneChip Scanner 3000
  • All research-use-only models are supported. The GeneChip Scanner 3000 Dx is not supported.

Array support

This release of Command Console Software supports all cartridge-based arrays and array plates.

GeneChip Command Console 6.0+ provides flexible and powerful tools for:

  • Entering and organizing information about the sample, Axiom, and GeneChip probe arrays
  • Controlling the instruments used to process probe arrays and collect the intensity data
  • Tracking the progress of an array through the array processing workflow
  • Working seamlessly with other tools for downstream analysis
New features
  • Monitor a GeneTitan Multi-Channel (GTMC) instrument remotely using the Connect cloud platform
  • Faster scan time on GTMC instrument

Basic features

  • Instruments serial numbers
  • Hybridization completion
  • Fluidics completion
  • Scanner completion
  • Supports full range of assays through seamless integration with primary downstream analysis application such as Axiom Analysis SuiteAxiom MiDAS, and Transcriptome Analysis Console
  • Sample attribute and array data can be directly imported into any of the commercially available Axiom and GeneChip-compatible applications, allowing researchers to select from a variety of analysis methodologies

Unique functions

  • Monitor instrument in real-time from anywhere
  • Visualize from desktop and mobile device
  • Transfer array data to Connect cloud platform
  • Upload error log files to Connect cloud platform

Supported instruments

  • GeneTitan Multi Channel Instrument
  • GeneChip 3000 Instrument

Applications

  • High throughput genotyping and gene expression
  • Axiom 24-, 96-, 384- and Mini 96- format arrays
  • GeneChip cartridge arrays 

Price/Delivery/Support

  • Included with GeneTitan Multi-Channel Instrument
  • Support: visit thermofisher.com/support
  • Documentation available upon download

 

Benefits

  • File-based software for easy data sharing
  • Flexible GeneChip processing workflow
  • Integrated instrument control
  • Simplified data management
  • Integration and customization for end users and third-party software tools

Instrument support

This release of Command Console Software supports the following instruments:

  • GeneTitan Instrument
  • Fluidics Station 450
  • GeneChip Scanner 3000
  • All research-use-only models are supported. The GeneChip Scanner 3000 Dx is not supported.

Array support

This release of Command Console Software supports all cartridge-based arrays and array plates.

NOTE:

  • Software downloaded from this site is ONLY for data analysis with offline computers.   Do not attempt to install software on computer connected to instrument without Thermo Fisher Field Service Engineer
  • For more information, please contact your local Field Service Engineer or Technical Support.

 GeneChip Command Console Software 6.1 (zip, 546 MB)

GCC 6.1.1 has been validated on Windows 10 operating system.   Before installation of GCC 6.1.1, please remove prior installation of Microsoft SQL Server 2005 and any previous GCC/AGCC software versions.   Reboot computer, then run GCC 6.1 installation.   After GCC 6.1 is installed, apply GCC 6.1.1 update (zip, 6 MB). For additional information, refer to GCC 6.1 release notes and GCC 6.1.1 release notes.

  GeneChip Command Console Software 4.3.4 Patch Only (zip, 98 MB)

AGCC 4.3.4 is a software patch to improve grid alignment and address the issue of batch registration errors once Microsoft Security Update KB4041681 is applied. The patch requires installation of AGCC 4.1.2 first.  This patch is recommended for all Windows 7 users running AGCC 4.1.2 or higher. Refer to the AGCC 4.3.4 release notes for more information prior to installation of this patch.

 GeneChip Command Console Software 4.1.2 (zip, 383 MB)

AGCC 4.1.2 has been validated on Windows XP 32Bit and Windows 7 64Bit. Customers who currently have a 32-bit instrument workstation may need to either purchase a new 64-bit workstation or upgrade their workstation to 64-bit via an Affymetrix-recommended upgrade path.

Additional information

  • Affymetrix Developers' Network web pages contain archived web talks on the Command Console technology, as well as information on the Fusion SDK (compatible with both GCOS and Command Console Software), including source code. Software developers: learn more about integrating with Command Console Software.