NCBI Mailing Lists

The National Center for Biotechnology Information has announced that they have three mailing lists for announcing changes to specific resources:

• Molecular Modeling Database (MMDB)
  http://www.ncbi.nlm.nih.gov/mailman/listinfo/structure-announce
• Conserved Domain Database (CDD)
  http://www.ncbi.nlm.nih.gov/mailman/listinfo/cdd-announce
• BioSystems
  http://www.ncbi.nlm.nih.gov/mailman/listinfo/biosystems-announce

Epigenomics Funding

NIH will fund 22 grants on genome-wide studies on epigenomics for a total of $69 million over the next five years. Since many of you are studying epigenomics as part of your bioinformatics work, it may be worth checking out the projects that are getting funded.  The full NIH news release is available here.  Congratulations to the awardees!

NIHMS ID to PMCID ASAP

So the folks at NIH are putting investigators’ feet to the fire with the NIH Public Access Policy.  As of 2009 August 21, the NIHMSID can only be used for up to three months after a paper is published in order to indicate compliance with the NIH Public Access Policy.  An FAQ is available here.

Remember, the NIHMSID is assigned as soon as you submit your final, peer-reviewed, accepted manuscript to NIHMS (the National Institutes of Health Manuscript Submission system).  You may use this identifier only temporarily until the PMCID is assigned.

How do you ensure a timely PMCID assignment?

1. Submit your manuscript as soon as possible
2. Approve your PDF receipt as soon as possible
3. Review and approve the web version as soon as possible

In other words, ASAP.  Hey, we’re around to help so email nihms-library-support (@umich.edu), if you questions.

NCBI Short Read Archive of NexGen Sequencing Data

So the guys at NCBI have been busy, busy, busy.  They are now maintaining the Short Read Archive (SRA) for parallel sequencing technologies.  SRA allows you to:

• Search and display SRA project data through their homepage
• Search and display SRA project data through Entrez
• Download data through Aspera Connect
• BLAST service for sequence similarity searching of 454 sequencing reads for transcriptome studies

There is a nice summary of SRA in the August version of NCBI News.

NCBI 3D Structure Help

So the folks at NCBI have posted a whole bunch of useful help files on the web for their 3D structure resources, 3D Macromolecular Structure and Conserved Domains.  There are also other helpful how-to files which the fabulous Kristi Holmes over at Becker Library at Wash U has already blogged about here.  Oh, there’s a link to that blog, Bioinformatics@Becker, in my blogroll in case you haven’t already checked it out.

Rock on!