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Developers' Network (ADN)

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


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


To learn more about the ADN Newsletter archives, message boards, archived webcasts and whitepapers, please visit the ADN Archives.

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.

Commercial Applications

Development copies of 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.

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.

External SDK Support Policy

Please learn how SDK modifications to commercial Affymetrix software can affect support limitations.

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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. View a summary table of the differences between the various Affymetrix file SDKs.

Data Resource Center (Sample Data & Data Sets)

A comprehensive collection of Affymetrix sample data and data sets that will aid in your software development efforts.

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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.

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 - Exon Expression Analysis

View a table of all available resources hosted through the NetAffx SDK for the analysis of exon expression arrays.

Deep Linking to Probe Set Information

Review the NetAffx Deep Link 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 Affymetrix® GeneChip® 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.

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.