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The Affymetrix® Developers' Network (ADN) is one of the largest collection of life-science related forums for software developers. The ADN includes a broad collection of Affymetrix customers, users, and partners who build informatics tools in and around the Affymetrix platform. The goal of the ADN is to provide a forum for the exchange of ideas and technical information to speed the flow of genomics data.

To join or leave the ADN mailing list, please edit your Affymetrix profile and select the check box to receive "Affymetrix Developer News" at the bottom left of the registration form.

Software developers interested in promoting their applications are welcome to learn more about the GeneChip-compatible™ Applications Program.

Programmatic integration around the Affymetrix Platform is centered around three key components; ARRAY DATA, ANNOTATION DATA and ATTRIBUTE DATA. Additionally the ADN provides resources for ANALYSIS, ADN ARCHIVES, AFFYMETRIX APPLICATIONS, and GCOS.
ARRAY DATA
  At the heart of Affymetrix Informatics is the data generated from a microarray. Affymetrix provides a variety of open solutions to gain access to these data from file format documentation to open source code.
File Formats
 
  Fusion SDK
  The Fusion SDK is a combination of the existing ANSI C++ GCOS 1.x File SDK and Command Console File SDK. Fusion will provide backwards and forward flexibility by providing the ability to parse GCOS 1.x and Command Console files. Click here to view a summary table of the differences between the various Affymetrix file SDKs.
  File Parsing message board
  This forum is intended to be a conduit through which the Affymetrix Developer's Network supports itself on issues regarding the use of the Fusion and GDAC File SDKs.
    GDAC File SDK (deprecated)
  The GeneChip® Data Access Components (GDAC) Files SDK is a set of Application Programming Interfaces (APIs) used to access Affymetrix data files. These APIs include support for accessing information stored within experiment files (*.EXP), image files (*.DAT), cell intensity files (*.CEL), analysis result chip files (*.CHP), and array layout description files (*.CDF). The GDAC File SDK is provided for historical purposes only. Please use the Fusion SDK for compatibility with the most current file formats.
    Affymetrix Data Resource Center
  A collection of Affymetrix data to aid in your software development efforts.
    MAGE Exporter SDK
  The GeneChip Data Access Components (GDAC) Exporter SDK is a set of application programming interfaces used to export gene expression data generated from the GeneChip system to MAGE-ML compliant files. Also included in this SDK is a Windows graphical user interface application that provides export capabilities from the Affymetrix software systems to create MAGE-ML compliant files. Support for the MAGE Exporter SDK can be obtained through the MAGE-ML Exporter Message Board.

A Beta version of the Exporter SDK for creating MAGE-ML documents for files generated by GCOS, Affymetrix GeneChip® Command Console and Expression Console™ software is also available.

    CHP File Verification Tool
  This tool will verify the analysis results and probe set names stored in a GCOS or Affymetrix GeneChip Command Console format CHP file.
 
ANNOTATIONS
  Data from Affymetrix is only as powerful as one's ability to intersect them with the genomic information represented on the array. Affymetrix NetAffx site offers a web-based user-interface to retrieve these annotation information. These same annotation information can be incorporated within a software application through the use of the NetAffx SDK.
  Exon Resources
  View a table of all available resources hosted through the NetAffx SDK for the analysis of exon expression array.
    NetAffx SDK
  The NetAffx SDK is a set of Application Programming Interfaces (APIs) used to download the annotations available on the Affymetrix NetAffx web site. The NetAffx SDK can also be used to automate the download of library files within an application.
    NetAffx SDK Webcast
  This WebTalk presents an overview of the NetAffx Software Developers Kit and how it can be used to automate the retrieval of NetAffx annotation files.
    NetAffx SDK message board
  This forum is intended to be a conduit through which the Affymetrix Developer's Network supports itself on issues regarding the use of the NetAffx SDK.
    Deep linking to probe set information
  Review this manual to learn how to link directly to NetAffx™ probe set summaries from within your own applications or web sites using a convenient deep link URL.
 
ATTRIBUTES
  Analysis of Affymetrix microarrays often is focused on comparing samples that have different attributes. Affymetrix core software like GCOS and Command Console allow users to input sample attributes into the system and associate these attributes with the array data through simple XML files. The associated DTD files will aid software developers in gaining access to this information and maintaining it with its associated microarray data.
  "Command Console" array sample attribute file DTD (April, 2006)
  Sample attributes in Command Console are stored in *.ARR files. This is the DTD for the ARR files.
    DTT version 1.1 DTD (MAGE-ML.DTD version 1.1)
  Sample attributes entered into the GCOS Process Database can be easily extracted using Data Transfer Tool into XML files. This is the DTD for the XML files created.
    Sample Attribute Message Board
  This forum is dedicated to the purpose of discussing reading and writing sample attribute data.
 
ANALYSIS
  Following the scanning of an array, a DAT file is created. Then a grid is applied onto this file creating a CEL file. The following collection of tools focuses on the data summarization process to generate the downstream CHP file that is created after the CEL file is generated.
  Affymetrix Power Tools
  The Affymetrix Power Tools (APT) contains C++ source code for analyzing Affymetrix data and a set of command line tools.  APT contains several key algorithms of interest around the Affymetrix platform including:  BRLMM, PLIER, RMA, MASv5, DABG, and IterPLIER.  APT also provides key guidance on workflows with pre- and post-processing steps included as well as code to output the data into Affymetrix binary CHP files.
    MAS5 Stat SDK
  The MAS5 Stat SDK provides source code for the implementation of the MAS5 Expression Statistical Algorithm.
    Tiling SDK
  The Tiling SDK is a set of Application Programming Interfaces (APIs) used for the analysis of GeneChip tiling arrays.
    PLIER SDK (deprecated)
  The PLIER (Probe Logarithmic Intensity ERror) SDK provides historical source code to the PLIER algorithm for an improved signal estimator for expression arrays. Affymetrix Power Tools (APT) contains the active PLIER code base. This version of PLIER is provided for historical versioning purposes only.
    ExACT SDK (deprecated)
  The Affymetrix GeneChip® Exon Array Computational Tool (ExACT) software package enables probe level analysis of Affymetrix exon arrays such as the Affymetrix GeneChip® Human Exon 1.0 ST Array. Affymetrix Power Tools (APT) contains the active ExACT code base. This version of ExACT is provided for historical versioning purposes only.
 
ADN ARCHIVES
  Browse a collection of information from the Affymetrix Developers' Network.
  White Paper Documentation for Software Developers
  View whitepapers on probe set structure, masking probes and a variety of other topics.
    Newsletter archive
  ADN offers a collection of historical ADN newsletters.
    WebTalk archive
  Offers an archive collection of webcasts related to software development.
    Message Board
  The message board is a conduit through which the Affymetrix Developer's Network supports itself on issues regarding the use of its SDKs.
 
AFFYMETRIX APPLICATIONS
  The Affymetrix Developers' Network offers a collection of Affymetrix built software applications enabling a software developer to replicate the same environment that Affymetrix customers have for the purposes of software development, testing, and validation.
  GeneChip® Command Console® Software
  Affymetrix GeneChip Command Console® Software (AGCC), the next generation instrument control software, has been released.
    Commercial Applications
  Development copies of the GCOS and other Affymetrix applications are available for software development and integration testing.
    Affymetrix Tools
  A collection of rapidly developed applications allowing Affymetrix to bring the latest in algorithm development to the life science researcher's analysis workstation.
    DevNet Tools
  The tools listed here are all unsupported tools that have been developed internally at Affymetrix. They are not validated products and are provided as is and without warranty.
 
GCOS AND DATA TRANSFER TOOL
  Affymetrix GeneChip Operating Software (GCOS) is the core instrument control and primary data generating software for the Affymetrix platform. The Affymetrix Developers' Network provides a collection of tools and utilities to ease programmatic integration into GCOS.
  AADM
  The Affymetrix® Analysis Data Model (AADM) is the relational database schema the Affymetrix GCOS, LIMS and MicroDB™ systems use to store GeneChip® expression results. The prefered mechanism for extracting Affymetrix results is via direct access to the native Affymetrix data files (CEL, CHP, CDF). Support for AADM can be obtained through the AADM message board.
    GCOS SDK
  The GCOS Software Developer Kit (GCOS SDK) is a suite of online material for Affymetrix GCOS client or server customers and third-party vendors who are looking to develop, customize, and integrate software applications and systems with the Affymetrix GCOS system. Support for the GCOS SDK can be obtained through the GCOS SDK Message Board.
    Data Transfer Tool (DTT) SDK
  Data Transfer Tool allows programmatic transfers of data between separate GCOS instances. A copy of DTT is automatically installed with any installation of GCOS.
 
LICENSING INFORMATION
  Affymetrix grants its partners and customers complimentary access to its full collection of SDK components, documentation, and NetAffx data for evaluation purposes, internal use, or for redistribution in freeware software applications through either a variety of OSI-approved opens source licenses or the GeneChip Non-Commercial SDK license. Please consult the click-through licenses associated with each utility for specific licensing information. A Commercial SDK Use license is also available (part number 690050). Please contact devnet@affymetrix.com for more information on obtaining a commercial license, as well as an override to the open source licenses.
 
SUPPORT POLICY
  Please learn to how SDK modifications to commercial Affymetrix software can affect support limitations. Details here.
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