We are in Singapore (GGID)
OpenHelix (and by “OpenHelix” I mean “I” 
is in Singapore this week for the Genetics and Genomics of Infectious Disease conference sponsored by Nature Publishing Group, American Society of Human Genetics and the Human Genome Organization.
I will be giving an educational workshop on an introduction to genomic resources for infectious disease research. It’s part of a larger session. Bob Kuhn of UCSC and Anton Nekrutenko of the University of Pennsylvania will each be giving sections after mine and will be discussing the UCSC Genome Browser and Galaxy respectively.
Since most of our readers won’t be able to attend, below the fold (click the continue reading) I’ve listed just some of the resources I’ll be introducing.
Unfortunately, I can’t introduce most of you to all the amazing fruits (and other foods) I’ve been sampling like mangosteens, jack fruit, dragon fruit and yes, even durian (which I actually like the taste, not so much the smell) You’ll just have to come to S.E. Asia (if you aren’t already) for yourself.
This list is by no means comprehensive. I’ve only got 75 minutes or so. So I plan on just giving the attendees a taste of some of the huge number of resources available to them.
Genome Browsers
Ensembl http://www.ensembl.org/
UCSC Genome Browser http://genome.ucsc.edu
GBrowse http://gmod.org/wiki/GBrowse
Viral Resources
VBRC http://athena.bioc.uvic.ca
NCBI Viral resources http://www.ncbi.nlm.nih.gov/genomes/GenomesHome.cgi?taxid=10239
Viral Zone http://www.expasy.ch/viralzone
GSID HIV resource http://www.gsid.org
Bacteria Resources
EcoGene http://ecogene.org/
UCSC Archaea Browser http://archaea.ucsc.edu/
IMG http://img.jgi.doe.gov
Ensembl Bacteria http://beta.bacteria.ensembl.org
MBGD http://mbgd.genome.ad.jp/
Multiple, Protozoan and Vector Resources
BioHealthBase http://www.biohealthbase.org
UCSC Malaria Browser http://areslab.ucsc.edu
EUPathdb http://eupathdb.org/eupathdb/
VectorBase http://vectorbase.org
Human Resources
HapMap http://www.hapmap.org/
dbSNP http://www.ncbi.nlm.nih.gov/snp
GVS http://gvs-p.gs.washington.edu/GVS/
UCSC Genome Graphs http://genome.ucsc.edu/cgi-bin/hgGenome
AssociationView http://sourceforge.net/projects/associationview/
dbGap http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gap
HGVBase http://www.hgvbaseg2p.org/
Have any others you’d add to this list?
Here are a few of my own:
RNA Viruses – http://tree.bio.ed.ac.uk/rnavirusdb/
Virus Taxonomy – http://www.virustaxonomyonline.com
Phage Site – http://phage.sdsu.edu/~rob/phage_tree/
Picornaviradae – http://www.picornaviridae.com/
Virus Picture Book – http://www.virology.net/Big_Virology/BVHomePage.html
All Virology – http://www.virology.net/
Oh, there’s another one I was looking at recently, too–that reminds me:
http://poxvirus.org/ Poxvirus Bioinformatics Resource Center
And something related that I was looking at recently is the ROAR Reservoirs of Antibiotic Resistance site–”a comprehensive resource for researchers studying antibiotic resistance in commensal bacteria.”
http://www.roarproject.org/ROAR/html/initiatives.htm
excellent sites Theodore, Virus Picture book is new to me.
And Roar looks interesting.
BacMap is one I saw recently that I thought was a nice way to look at bacterial genomes: http://wishart.biology.ualberta.ca/BacMap/
Let me posit a question to you.
I’m a software architect by trade, and I don’t work in the molecular biology world. All of this is more or less a hobby for me (I’m fascinated by the algorithmic properties of life). So I don’t have a good sense for what’s valuable to professional in the field.
But it seems to me that there is a vast pool of resources out there relating to this subject, but no central way to navigate through it all. Mostly I find these things because I stumble into them and bookmark them. I don’t even have the time to read through a third of them.
My question is: would some sort of central directory of resources, regularly maintained, (including some sort of specialized search engine) be useful to professionals in the field?
-Ted
Well, we do have some thoughts on this, actually
There are a few places you can search for resources. One nice one is at Univ. of Pittsburgh and you can search it here:
http://www.hsls.pitt.edu/guides/genetics/
Another place to look is every January NAR has a database issue:
http://www3.oup.co.uk/nar/database/c/ and a web server issue midyear: http://nar.oxfordjournals.org/content/vol36/suppl_2/index.dtl
And we are working on another type of searchable functionality and we’ll be talking more about that soon. Keep an eye on our blog for updates around that.
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