BioAssay Express: models mixing assays & compounds

baesian1The latest experimental feature of the BioAssay Express project involves taking all of the curated assays (3500 so far) and their corresponding compounds from PubChem (hundreds of thousands of unique structures) and feeding them all into one giant Bayesian model. Rather than the usual approach of modelling compound ⟹ activity separately for each assay, this approach takes advantage of the fact that the semantic annotations that describe the assay can be used like fingerprints. The model is therefore compound + assay activity, which means that it is possible to lump together everything that is known about screening compounds against assay protocols. Continue reading

SAR Table app: new life on the desktop

sartable_xmds1The SAR Table app originally came out in 2011 for iOS, and went from being a tightly focused product to an expansive showcase of cheminformatics technology. In recent years it has not received much attention, due to the fact that having all this functionality on a touchscreen turned out to be pushing further than an iThing is really meant to go. Now the core functionality is being ported to the XMDS desktop app. Continue reading

BioAssay Express: finding assays (and doing stuff with them)

bae_find04The BioAssay Express project has been moving forward at a solid pace: several important new features have been added or improved for locating assays and inspecting them, with an eye toward performing some sophisticated analysis and model building. This is motivated by the fact that we have curated quite a few assays (~3,500) which is sufficient reason to start putting real effort into figuring out what we can actually do with this high quality professionally annotated data. Continue reading

Green Solvents app: complete facelift

greensolv_dev1Way back when, I threw together an app called Green Solvents, which got started anachronistically from a tweet by Sean Ekins (which I misinterpreted, but it got the conversation started, so all is well). Since mid-2011, the app hasn’t had much attention, but that has now changed: it has been rewritten and given a much more modern look. The overhauled version is live on the iTunes AppStore, and is free to anyone with an iThing. Continue reading

BioAssay Express: now with molecules

bae_mol1In the previous post, I introduced the BioAssay Express project, which is based on the idea that when assay protocols are described using semantic annotations rather than just scientific text, a whole realm of software analysis becomes possible. Whenever there’s a bioassay experiment protocol at hand, chances are there are also some molecules with activity measurements not far away: which is the subject of this article. Continue reading