CCMB/NCIBI MiMI plugin 3.0 release

[Jing Gao]

The CCMB/NCIBI MiMI plugin 3.0 was released on June 16 2008 to
Cytoscape using the latest
version of mimiR2/geneR2 and pubmed_08n databases.

You can download MiMI plugin 3.0 from here:
http://chianti.ucsd.edu/cyto_web/plugins/index.php

MiMI plugin 3.0 has the following improvements:

1. Faster performance due to the use of pre-computed tables for gene
interaction and
gene/interaction attributes
2. Module code with stored prcedures API to minimize depending on
database chages
3. User ability to expand or collapse one or more network nodes
through double clicking
4. User-defined annotations of nodes and links that can now be shared
with others.
5. User access seamlessly to integrated NCIBI tools, including:
-SAGA for sub-network matching to KEGG pathways
-BioNLP, which conceptually mines the Medline database to
displays relevant
sentences from the literature to a selected gene or
interaction.
-MiMI web for rapidly accessing data about gene-gene
interactions that have been
integrated and reliability tested from over 9 established
databases
-Gene2Mesh, which lets users identify genes associated with
specified MeSH terms
and MeSH terms associated with specified genes - beyond
chance occurrences
-GIN and MEAD for getting and displaying summaries of Medline
abstracts through
natural language processing and grouping them by semantic
similarity.
6. A pop up message that prompts users to look for a new version
release
7. Easy to specify parameters for queries on individually entered gene
symbols or lists of
gene, including levels of interactions to display in a network
8. Numerous bugs fixes

MiMI Plugin 3.0 required Cytoscape v2.6.0.

Any suggestions and questions, please send email to ccmb-
he...@umich.edu

Best regards,
The MiMI plugin team