Archive for November, 2008

MiMI Web 3.0

mimi_iconToday the National Center for Integrative Biomedical Informatics (NCIBI) released a new version of its Michigan Molecular Interactions (MiMI) tool.  This tool is much revised in both look and underlying database merging processes.  A recent publication in Nucleic Acids Research discusses the revised tool. 

The abstract:
Molecular interaction data exists in a number of repositories, each with its own data format, molecule identifier and information coverage. Michigan molecular interactions (MiMI) assists scientists searching through this profusion of molecular interaction data. The original release of MiMI gathered data from well-known protein interaction databases, and deep merged this information while keeping track of provenance. Based on the feedback received from users, MiMI has been completely redesigned. This article describes the resulting MiMI Release 2 (MiMIr2). New functionality includes extension from proteins to genes and to pathways; identification of highlighted sentences in source publications; seamless two-way linkage with Cytoscape; query facilities based on MeSH/GO terms and other concepts; approximate graph matching to find relevant pathways; support for querying in bulk; and a user focus-group driven interface design. MiMI is part of the NIH’s; National Center for Integrative Biomedical Informatics (NCIBI) and is publicly available at:


November 26, 2008 at 7:22 pm Leave a comment

Librarian with a Laptop

Our own Marci Brandenburg is giving the Tools and Technology seminar today.  Just goes to show that good student mentoring and lots of free food produces fine, professional librarians who go to important institutions to do good work and come back to share their talents.  Ah.  I so love being in academia.  Go to to connect live to the seminar today or come over to Palmer Commons and enjoy free bagels and listen to her talk in person.

November 20, 2008 at 2:26 pm Leave a comment

Science Funding

So, now that we’ve elected Obama to be our next president, can we expect any more research funding in the sciences?  I’m going to doubt that there’ll be much money for anything other than fixing the economy which I’m guessing is not going to leave much of anything for us to use.  I think I’m pretty much a fiscal conservative so trying to balance our over 10 trillion dollars of debt seems like a priority to me, but letting science sputter out doesn’t seem like a good investment strategy to me either, so I’m hoping there’s some happy medium somewhere.  Glad I’m not president (or going to be one).  Here‘s a snippet on what Science news has to say on the subject.  Get the full article here (after you login, of course).

November 18, 2008 at 7:54 pm Leave a comment

Genomes, browsers, and databases

newbookOne of the latest new books at Taubman Medical Library can be found here. Genomes, browsers, and databases: data-mining tools for integrated genomic databases by Peter Schattner.  The call number is: QH 442.2 .S33 2008

Read the Product Description and Book Description from Amazon here.

Here is the Table of Contents: The molecular biology data explosion — Introduction to genome browsing with the UCSC genome browser — Browsing with Ensembl, MapViewer, and other genome browsers — Interactive genome-database batch querying — Interactive batch post-processing with galaxy — Introduction to programmed querying — Using the Ensembl API — Programmed querying with Ensembl, continued — Introduction to the UCSC API — More advanced applications using the UCSC API — Customized genome databases — Genomes, browsers, databases : the future.

November 11, 2008 at 3:06 am 1 comment


Well, it’s over and the results are in.  What more can be said?  Congratulations, President Elect Barack Obama!

November 5, 2008 at 2:11 pm 1 comment

Bioinformatics Conferences

A list of upcoming bioinformatics conferences from Conference Alerts.

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