The last two posts introduced molecules and collections being embedded into a WordPress document. Now the range of datatypes has been extended to include reactions, which can be rendered as schemes – or tabular forms indicating all of the components that go into a multistep reaction, with associated stoichiometry and quantity information. Continue reading →

The previous post introduced the insertion of molecules into a WordPress document. Now the plugin goes one further: collections of data – either simple tables of structures, text & numbers, or higher order datasets like scaffold breakdowns – can now be inserted into a blogpost. As with molecular structures, the prevailing philosophy is to have the data encoded in machine readable format and dynamically converted into something visual at the time of presentation. Continue reading →

Something I started thinking about recently is the idea of mixing high end cheminformatics tools with generic blogging software, to achieve a reasonable compromise in the electronic lab notebook area. It turns out that writing a WordPress plugin really is as easy as the documentation claims, and hooking it up to my work-in-progress web toolkit is also rather straightforward. Continue reading →

The 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 →

Since 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 →

The 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 →