Just got an announcement from the Cytoscape mailing list. One of my favorite tutorials* that we’ve developed was Cytoscape–It was an interesting challenge for us because most of our focus has been tools with web interfaces and we had to address installation with this one. But it was such a nice tool with great features [...]
Reactome has long been one of our favorite resources for looking at pathways and interactions. The data quality is very high, and there are some very fun tools to use. In fact, they were one of the earliest tutorials we did years back (but of course we have updated since). If you aren’t already familiar [...]
I wish I had more time to go into this paper in more detail–but I wanted to let you know that the paper is out there now. It came in my recent Nature Methods in paper version, and if I wasn’t crazy busy on a very cool project that we hope to launch this week [...]
The Comparative Toxicogenomics Database (or CTD) is an excellent database to find information on chemical-gene-disease interactions. It is a manually curated database of chemical-gene interactions, chemical-disease and gene-disease associations. At your fingertips you can find information about chemicals, interacting gnees, inferred diseases, pathways, references and news. It’s worth a look. And you can use Google [...]
OpenHelix today announced the availability of a new tutorial suite on MINT, a highly used database of protein-protein interactions, and an update to the Reactome tutorial. MINT is a collection of molecular interaction databases that can be used to search for, analyze and graphically display molecular interaction networks from a wide variety of species. Reactome [...]
My Bio SmartBrief newsletter today had a reference to a paper in a rather…um…obscure journal. Maybe it is just something I have missed over the years, but the Journal of the Royal Society Interface has really just never come across my desk before. Nevertheless, Wired seems to think this software is finally meeting our needs [...]
Bioinformatics.org is a great organization and web site (disclosure: I’ve taught an online course with them ) and they regularly have online course in the field of bioinformatics that are more in the theory and analysis area of bioinformatics (where ours is more in the use and access of resources). If you need bringing up [...]
MINT, the Molecular INTeraction Database, is so much fun to use. I know–there is high-quality curated information from the scientific literature. And that’s the real point. But quite frankly, I just love to examine the protein-protein interactions in the MINT viewer. In this brief (about 3 minutes) exploration of some of the high-level features of [...]
In the previous post I briefly mentioned a paper coming out of the Bork lab at EMBL. The lab just made public a new tool: STITCH, “a resource to explore known and predicted interactions of chemicals and proteins.” This is a sister project to STRING, a great tool for exploring the interactions of proteins
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