Tag Archives: Entrez

Tip of the Week: WAVe, Web Analysis of the Variome

Today’s Tip of the Week is a short introduction to WAVe, or the Web Analysis of the Variome. The tool was recently introduced to us, and I’ve found it a welcome introduction to the tools available to the researcher to analyze human variation. This is apropos considering the recent paper we’ve been discussing on the clinical assessment of a personal genome (here, here and here) and that papers implications for personalized medicine and the use of online variation resources. WAVe also has introduced me to some additional tools I’ve either not been aware of, or haven’t used, which might be of use such as: LOVD (Leiden Open Variation Database), QuExT (Query Expansion Tool, also from the same developers as WAVe), and others. Of course there are also database information pulled in from Ensembl, Reactome, KEGG, InterPro, PDB, UniProt, NCBI and many others. Take some time to check it out.

BioGene: iPhone app for NCBI searches from MSKCC team

iphoneI can’t remember how I got on this email list–but I like it :)  Today I was notified that there was a handy iPhone app to quickly get gene info out of the NCBI resources.  I wish I had this last week at the ASHG meeting.  You know what happens: you catch a gene name or see a symbol in a talk, it’s just one of several on a slide…but you must know what that is right now!!  This handy-dandy quick interface will let you search for the symbol and links you to Entrez Gene info, which also links to references in PubMed.

I like it.  I expect to use it.  The first reviewer over in the iTunes store says it has already expanded their conversation.  I wish it also covered OMIM, but I haven’t used it too hard yet, maybe I’ll get there.  That also would have been a help last week.  I was hearing about a disease and I wanted some information.

Check out the MSKCC team page here for more details, and download it from the iTunes store (for free) if you like the sound of it.

BioGene: http://cbio.mskcc.org/tools/iphone_ipodtouch.html

For other iPhone apps we’ve come across, check out our earlier post on the iPhone and research.

Demise of the NCBI Field Guide

For funding reasons, NCBI (home of PubMed, BLAST, dbSNP, OMIM and more) has cut their outreach staff, canceled all onsite training seminars and this has to mean decreased support for online help, documentation and tutorials.

When we wrote our NIH grant, one of the models of success in the bioinformatics training area that we highlighted was the NCBI Field Guide program. For those who may be unfamiliar with it, it is a set of training modules delivered by the outreach team at NCBI. They would come to your site, cover many NCBI tools and do hands-on workshops. Another course (Enhanced Field Guide) drew science librarians and other trainers together to train them, and those folks could go back to their institutions and offer more-and-better searches and training for their constituents. We thought the Guides are a terrific group of people who were interested in people getting their hands on the myriad tools at NCBI and using them effectively. It wasn’t really a competitive situation—their remit was only for NCBI tools, and there were plenty of others out there for us to do. In fact, many people who contacted us for training did so because their local users enjoyed the NCBI training and they wanted similar engagements for other tools.

Recently, though, the calls changed. We found we were getting calls from people who said they weren’t going to be able to get any more Field Guide trainings. NCBI is discontinuing the outreach program. Quite frankly, we were surprised. A sample of the notifications people were getting: http://www.library.uiuc.edu/blog/bicnews/archives/2008/02/ncbi_field_cour.html

Unfortunately, that tremendous training opportunity will NOT occur. Yesterday NCBI Field Guide coordinator, Peter Cooper, sent the following email:

Because of budgetary constraints, NCBI has made reductions in some of its programs, and the education programs are affected. In fact, all outreach education programs (Field Guide, Mini-courses, Structures, PubChem) are terminated effective immediately. At this point we cannot reschedule this course or accept requests for future courses of any kind. This was as much a surprise to me as it is to you. Feel free to contact me if you have questions.

The Field Course, as well as the Mini-Courses and the Structure course, has been tremendously popular and useful (see list of sites where the Field Course has been offered recently), but the NCBI budget situation will not allow NCBI to continue to travel and offer these courses for the foreseeable future.

(emphasis mine)

Here’s a link to a similar letter at another location: http://www.twu.edu/as/bio/NCBI/FieldGuide/

We’ve confirmed this with a number of people directly involved; they have laid off nearly all of the outreach team. Some got reassigned. There can hardly be anyone there to even answer emails to the helpdesk anymore—and they get lots of emails every day.

I’ve been through layoffs before, a few times. It actually feels like a punch to the gut when I hear about it anywhere else—especially among people I know. I expect layoffs at companies, though. But if there was any group that was solidly in place, going to be around for a long time, I would have thought it was the NCBI outreach team. I’m quite sorry to hear that it has been dissolved.

In this time of so many resources & so much need for increased understanding, outreach has become an intregal part of a resource’s success – fewer instructional resources is an unfortunate consequence of decreased funding for science.