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

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BioAssay Express: selecting molecules & plotting against assays

bae_assaygrid7Since the BioAssay Express project added molecules to supplement the annotated assays, we have been able to explore various interesting visualisation techniques. One of the obvious options is to plot a table with assays on one axis and compounds on the other, and look for insights regarding which molecules light up the various different screens. 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