So, there is ton of information out there on the newly designed PubMed.  It looks different but all of the same information is in there – somewhere.  These are the things I love:

• No need to change views to see MeSH for each citation; simply click on the + sign next to Publication Types, MeSH, etc. at the bottom of the abstract to expand that section
• Database ads – click directly to Homologene, GEO, etc right from the citation view.  Awesome.
• Customizeability – is that a word?  It’s great that you can customize your search results without logging in.  I love having the login option (My NCBI is great folks!), but let’s face it – most of you don’t.

Just my two cents.  There’s a lot of info running around out there on the redesign.  Here’s a link to the NLM Technical Bulletin article on it.

Ah, I understand that people think that books are blase but…    Here’s a new one at the Health Sciences Libraries:

Statistics and informatics in molecular cancer research.  Edited by Carsten Wiuf, Claus L. Andersen

The call number is: RC267 .S83 2009

Our own Dr. Rhodes is the author of Chapter 7: Two methods for comparing genomic data across independent studies in cancer research: Meta-analysis and oncomine concepts map.

Have fun!

Hey, it’s been awhile.  I’m sorry.  The rush of the school year always seems to catch me a little off guard.  The Health Sciences Libraries is co-sponsoring some workshops you may be interested in.

• Bioinformatics Basics: Databases and Tools from the National Center for Biotechnology Information (NCBI)
• BLAST Overview
• Michigan Molecular Interactions (MiMI)
• Cytoscape

In addition, the National Center for Integrative Biomedical Informatics is also holding an overview of its resources.

• Overview of NCIBI Tools and Resources

(I know; it’s bad form to have a single bullet, but hey…)  Registration is available from the Health Sciences Libraries workshops registration page.  Have fun and thanks for being patient about my blogs!

NCBI will be hosting a webinar at the University of Michigan to give an overview on their latest tools and updates to existing ones.  The webinar will take place at 2pm on Tuesday, September 29th.  Those people on campus who are interested in attending should register using the Teaching and Technology Collaborative website (https://www-a1.lsa.umich.edu/es_conf/app/DisplaySession.asp?sessionid=3367).  Login is required.  Contact the Health Sciences Libraries if you have any questions.

NIH is accepting requests for human embryonic stem cell (hESC) lines to be approved for use in NIH-funded research. Information may be submitted at http://stemcells.nih.gov/.

Read the full NIH News release at:
http://www.nih.gov/news/health/sep2009/od-21.htm

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

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!

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.

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.

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!