MIM – Motif Independent Metric

MIM

:: DESCRIPTION

MIM calculates a measure of sequence specificity called Motif Independent Metric.

::DEVELOPER

Guo-CHeng Yuan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Python

:: DOWNLOAD

 MIM 

:: MORE INFORMATION

Citation

A motif-independent metric for DNA sequence specificity.
Pinello L, Lo Bosco G, Hanlon B, Yuan GC.
BMC Bioinformatics. 2011 Oct 21;12:408.

PathVisio-Validator – Creation of Pathway Diagrams by ensuring Correct usage of the MIM notation

PathVisio-Validator

:: DESCRIPTION

The PathVisio-Validator plugin is aimed at producing standard biological pathway diagrams in PathVisio. The plugin makes it easier for the users to create pathways adhering to a standard (e.g. MIM and SBGN). This validation tool gives a detailed analysis as to which particular elements in the pathway are not diagrammed according to the standard. It basically helps the users of PathVisio to create pathways, which then could be shared among the biologists without any ambiguity. The standard against which PathVisio-Validator validates a pathway, is basically an MIM/SBGN based ruleset or a more generic GPML ruleset, in the form of “.sch/.xml” files

::DEVELOPER

PathVisio-Validator Team

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 PathVisio-Validator

:: MORE INFORMATION

Citation

Kumar Chandan, Martijn P. van Iersel, Mirit I. Aladjem, Kurt W. Kohn and Augustin Luna
PathVisio-Validator: A Rule-based Validation Plugin for Graphical Pathway Notations
Bioinformatics (2011)doi: 10.1093/bioinformatics/btr694

PathVisio-MIM 2.0.11 – Pathvisio Plugin which Adds the Ability to Draw MIM Glyph

PathVisio-MIM 2.0.11

:: DESCRIPTION

PathVisio-MIM is a software of MIM (Molecular Interaction Map) plugin for PathVisio allows users to produce diagrams of bioregulatory systems according to an implementation of notation first developed by Kurt Kohn in 1999. The plugin has two main features: 1) it provides users with the glyphs necessary to draw MIM diagrams and 2) it allows users to import and export to the MIM Markup Language (MIMML) format, a format developed to exchange MIM diagrams between MIM compatible tools and used to validate MIM diagrams. Diagrams produced using the MIM PathVisio plugin can be exported into several image formats including PDF, PNG, SVG, and TIFF.

::DEVELOPER

PathVisio-MIM Team

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 PathVisio-MIM

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Aug 1;27(15):2165-6. Epub 2011 Jun 2.
PathVisio-MIM: PathVisio plugin for creating and editing Molecular Interaction Maps (MIMs).
Luna A, Sunshine ML, van Iersel MP, Aladjem MI, Kohn KW.