Archive for July, 2008

NCIBI Tools and Technology Seminar

Thursday’s (7/31) TTS will be nice and long (noon to 2pm). Justin Wilson will present on “Low level deep sequencing data analysis: from preprocessing to alignment” and Jim Calvacoli will lead the “Meeting Report from ISMB 2008”.

If you’re in town, come by for pizza, soda and some great presentations in Room 2036 of the Palmer Commons Building.
You can also watch the live Tools & Technology Seminar via Adobe Connect.

July 25, 2008 at 5:37 pm Leave a comment


In case you are looking for images to use for your presentations and worry about copyright implications, flickr is a great resource for finding images that have a Creative Commons license so that you may use the image according to the CC licensing terms.

July 23, 2008 at 5:38 pm Leave a comment

Mouse miRNA Library

Nature news (Published online16 July 2008 | Nature 454, 264: 2008 | doi:10.1038/454264c) recently described an effort by the Sanger Institute to create a library of all known mouse miRNAs.  Read the entire news item here.

July 22, 2008 at 7:07 pm Leave a comment

PubMed Central

This is a gentle reminder that if you are NIH funded that you must comply with the NIH Public Access policy when publishing and citing your NIH funded work and deposit your peer-reviewed manuscripts into PubMed Central.

Nature Publishing Group will be archiving for authors for free into PubMed Central.  Read their press release here.

Related to this topic is my personal opinion on full-text data mining for natural language processing or other purposes. I’m personally shocked that only a small fraction of the PubMed Central corpus is available under an open access policy which allows for distribution of the papers.  It seems to me that if the entire world is freely able to read the works, then we should be able to mine the words to see if the articles are worth reading.  Aren’t the words, in essence, the data from which we run our NLP processes?  And if we are struggling to cope with understanding millions of articles in the biomedical literature, shouldn’t there be a better way of discovering which articles are, in fact, truly meaningful to us?  Something to think about…

July 22, 2008 at 6:17 pm 1 comment

The Diseaseome

The most recent NCIBI Jamboree discussed “The Diseaseome” based on the paper, The Human Disease Network, by Goh in Proc Natl Acad Sci U S A. 2007 May 22; 104(21): 8685–8690.  This jamboree was a fascinating discussion on the human disease network and gene relationships. 

Also mentioned at the discussion was the recent paper in Nature called Psychiatric Genetics: The Brains of the Family by Abbott in the 2008 Jul 10 issue, pages 154-7.

July 17, 2008 at 3:00 pm Leave a comment

Highlight PubMed Search Terms

Do you want your search terms highlighted for your PubMed searches?  You can use the My NCBI feature and select User Preferences and pick the color you want to highlight your terms.

July 16, 2008 at 7:52 pm 1 comment

Data, data, data

AAAS has a new journal called Science Signaling.  They also have a database available to use, the Database of Cell Signaling.  Enjoy…

July 15, 2008 at 2:49 pm Leave a comment

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Bioinformatics Conferences

A list of upcoming bioinformatics conferences from Conference Alerts.

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