MAGE-TAB - Tools

Key

Web based tool icon
Web based tool
Installable tool icon
Installable tool
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Compatible OSs
(for installable tools)
Web based tool

MAGE-TAB Template Generation

[Publication]

MAGE-TAB Template Generation is a web based tool to generate a template MAGE-TAB document which you can download and complete on your computer afterwards. Provided by Microarray Informatics team at EBI.

Installable tool
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MAGE-TAB to MAGE-ML converter

[Publication]

MAGE-TAB to MAGE-ML converter is a perl script to generate MAGE-ML from a MAGE-TAB document. Provided by Microarray Informatics team at EBI.

Installable tool
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Tab2MAGE to MAGE-TAB converter

[Publication]

Tab2MAGE to MAGE-TAB converter is a perl script to convert Tab2MAGE spreadsheets to IDF and SDRF components of MAGE-TAB. Provided by Microarray Informatics team at EBI.

Installable tool
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mage2tab

[No publication]

mage2tab provides a simple means to convert MAGE-ML documents to MAGE-TAB format. Also, it contains mage2graph (a visualization tool to convert MAGE-ML and MAGE-TAB files to GraphViz DOT format files). Provided by CBIL team at the University of Pennsylvania.

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caArray

[No publication]

caArray is an open-source, web and programmatically accessible array data management system. caArray guides the annotation and exchange of array data using a federated model of local installations whose results are shareable across the cancer Biomedical Informatics Grid (caBIG). The NCI Center for Bioinformatics and Information technology maintains a publicly-accessible instance of this web-based tool. In addition, installation packages for Windows and Linux are available to allow institutions to maintain their own instances.

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MAGE-TAB v1.1 Object model and supporting applications

[No publication]

Molgenis is being used by EBI and the University of Groningen to build a UML-like model, instantiate a database, GIU and programmatic interfaces for MAGE-TAB 1.1. Mapping is underway between the MAGE-TAB 1.1 and mouse models. The resulting resources will be used to integrate CASIMIR mouse Gen2Phen human functional genomics data sets. The UML model updates previous publicly available models for 1.0 and has html documentation.

Installable tool
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Canonical Java Parser

[No publication]

MAGE-TAB syntactic validator is a MAGE-TAB parser generated from the ANTLR formal grammars: IDF,SDRF,ADF. It incorporates the MAGE-TAB community's latest thinking on the MAGE-TAB 1.1 specification from our January meeting in Rockville.

We invite you to test your IDF, ADF, and SDRF files for validity using the parser. You may run the jar from a command line such as: java -jar MAGE-TAB.jar Invoked with that command, the jar will emit a brief description of its syntax and semantics. One caution: It may not yet work on very large ADF files. The buffer management for that is yet to be done.

Provided by Stanford University School of Medicine.

MAGE-TAB object model, expressed in UML

[No publication]

A UML description of MAGE-TAB can be opened and viewed with MagicDraw. We have used MagicDraw 12.1 and it's likely that more recent versions of MagicDraw work equally well. We have no experience with other UML visualizers.

This object model (we believe) reflects a precise and isomorphic representation of the contents of MAGE-TAB. We are generating very clean Java classes from it using a hand-crafted Velocity template. (There is also a Java class mapping file that maps Collections to a typed Vector subclass that knows its type and deals intelligently with Dates and some other basic data types.)

We believe that the UML satisfies these properties:

  1. It is complete. That is, it is capable of representing any information that can be expressed in MAGE-TAB. Please try to verify this. See if you can find all the MAGE-TAB constructs in the UML. If you think that something is missing, look more closely; if you still can't find it, let us know.
  2. It is concise. That is, it does not represent any information other than what is required for MAGE-TAB. Please try to verify this, too. If you notice something in the UML and can't understand how it relates to MAGE-TAB, then once again, let us know.
  3. MAGE-TAB keywords are almost always used for the names of classes, attributes, and associations. The principal exceptions are the MAGE-TAB Comment[] construct, which conveys a UserDefinedAttritbute; and the MAGE-TAB ProtocolREF construct which is ambiguous between an externally defined protocol and the application of a protocol. In the UML, protocolREF is a possibly defining attribute of a Protocol object, and there is a separate, ProtocolApplication object. Also, some names for classes that are super classes (particularly the abstract ones) don't correspond to MAGE-TAB keywords, but are drawn directly from the descriptive text of the specification.
  4. The diagram is visually clear. That is, no lines cross, no lines have more than one "break", and whenever possible, related elements (for example, subclasses of a common super class) are grouped together and aligned as space permits.
  5. It is well-commented and our code generation template (above) transfers the comments as Javadoc comments to the generated Java classes.

Because the object model is (we claim) isomorphic with the information conveyed by MAGE-TAB, it offers a kind of feedback tool for the specification. We would suggest that, if you don't like something in the object model - for example, it seems to you overly complex - then this may well be a dissatisfaction with MAGE-TAB itself - perhaps meriting a reexamination of it.

Provided by Stanford University School of Medicine.

Installable tool
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ArrayExpress Bioconductor Package

[No publication]

Use the ArrayExpress Bioconductor Package to access ArrayExpress data and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet. The function magetab2bioc can convert your own MAGE-TAB file into an R object in Bioconductor. This package was developed with Emerald funding.

Provided by Huber group at EBI.

Installable tool
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Perl MAGE-TAB module

[No publication]

The MAGE-TAB Utilities project has been created with the aim of providing an easy-to-use API for the parsing, manipulation, visualization and output of data in MAGE-TAB format. Early versions of the API are initially being developed in Perl, although contributions in other languages are welcomed.

Submit your MAGE-TAB supportive tool

If you would like your MAGE-TAB tool to be displayed on this web page, please supply the following information:

  • Tool name
  • URL for the tool
  • Brief description of tool
  • Is the tool web-based or installable?
  • If the tool is installable, which platforms can use it? (Windows / Mac / Unix / Linux / other)? For web-based tools, it is assumed that all platforms can use the tool unless otherwise stated.
  • Is the tool commercial, free to academics, or open source?
  • Any associated publications (please give PubMed ID if available)

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