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 →

It’s been awhile since I posted, but this welcome gift shown to the right reminded me to do so: one of the outputs from the honeycomb clustering algorithm is featured on the Journal of Chemical Information and Modeling cover page, for an article driven by Sean Ekins. My main contribution was the diagram technique, which hadn’t been described in the literature before, but has been demonstrated within the Approved Drugs and PolyPharma apps.

What I have been actively working on these last couple months has involved another sabbatical at the Collaborative Drug Discovery mothership in the San Francisco Bay Area, helping out with a number of R&D projects, but most significantly the BioAssay Express. This is a project you will be hearing about more in the near future: it has been somewhat on the down-low so far, despite being implemented in the open, with the entire project being deployed to a public internet-facing website with no security of any sort. It’s all about describing bioassay protocols using well structured terminology, rather than the rather retro best practice of writing everything down in scientific English jargon. Stay tuned for more.

As mentioned in previous posts, the MolSync site has had a major redesign under the hood, and now it has been followed up with an aesthetic re-skinning. The presentable web content was always presented as somewhat of a placeholder, since the main purpose of the site was to expose certain cheminformatics and data hosting capabilities, in particular to boost the functionality of various mobile apps. Now that it is evolving into a site that provides user-facing functionality as well, it is time for a little bit more attention to detail on the design front. Continue reading →