OpenHelix just opened our new web site. We will still be offering the tutorials we’ve always offered (80 and growing!), but now we have a new search engine and database of many more resources. And it’s publicly available and free. There are now thousands of databases and analysis tools for the researcher to use when [...]
I recently read an article in Science entitled “Lysine Acetylation Targets Protein Complexes and Co-Regulates Major Cellular Functions” written by Choudhary et al. The research uses “high-resolution mass spectrometry to identify 3600 lysine acetylation sites on 1750 proteins” and “demonstrate[s] that the regulatory scope of lysine acetylation is broad and comparable with that of other [...]
Ok, so we don’t have GWAS (Genome-wide Association Study) mondays, but we might as well have. The field of study seems to be growing hugely fast, especially when you consider one of the first major GWAS was published just a short 2 years ago (or 4 years ago, depending on how you define major, still… [...]
We’ve done two tips of the week on Galaxy so far, one showing you the interface and the other how to convert genome coordinates between assemblies. Galaxy is not a database, but rather a analysis tool that allows you to pull in data from many different sourcs such as UCSC Genome Browser database, Ensembl‘s Biomart [...]
From the GBrowse mailing list the other day came notice of a new way to use GBrowse–without programming! A team from Indiana University has lowered the barrier of entry for anyone with a genome they want to display. They have created an interface and web server for GBrowse that lets you simply upload your data [...]
Genome-wide association studies (GWA/GWAS) generate a lot of data that needs to be viewed and analyzed. There are some software tools out there to do that, including UCSC’s Genome Graphs. I haven’t looked at it in detail yet, but this new downloadable, java viewer was recently developed and reported in Bioinformatics: AssociationViewer (download here). I’m [...]
It is somewhat serenditous in that I just completed the first draft of a tutorial that uses several genomic resources to look at the CYP2C9 gene variations and wafarin dosage, but a recent report in the NEJM looks at wafarin dosage from a combined clinical and pharmacogenetic data standpoint. As Daniel MacArthur at Genetic Future [...]
Recently, we are learning a lot about the cold virus. The genomes of many have now been sequenced (that is a subscription-required Science report, you can read more about the report here). You can find more genomic information at the picornaviridae.com at the NCBI’s Entrez Genomes and some structural information at MMDB. (just a side [...]
OpenHelix today announced the free availability of tutorial suites on model organism databases and resources used extensively in research. The first tutorial suites available are GBrowse, Rat Genome Database (RGD), Mouse Genome Informatics (MGI), and WormBase. To be added in the coming weeks are Zebrafish Information Network (ZFIN), FlyBase and Saccharomyces (Yeast) Genome Database (SGD). [...]
Authors Warren Lathe, Donna Karolchik and other members of OpenHelix give an introduction to online, publicly available genomics resources at www.nature.com/scitable. Seattle, WA (PRWEB) February 11, 2009 — OpenHelix today announced the publishing of an article introducing and exploring the many online genomics resources available to the public. With over 3,000 genomic resources, tools and [...]
Recent Comments