American Chemical Society meeting: Autumn 2018 Boston

ACS time is sneaking up on us, as it tends to do: in about 2 months from now – August 2018 – a large proportion of the world’s chemistry community will be converting in Boston, including myself. This particular city is probably my favourite venue, simply by virtue of being such a massive hub for various forms of chemistry and derived industries, such as small molecule drug discovery.

My presentation will be on the Wednesday:

Paper ID 2972556 / CINF 150
Title Bringing assay protocols into the age of informatics
Session Drug Discovery: Cheminformatic Approaches
Section Division of Chemical Information
Time 1:30pm, Wednesday 22 August 2018

As for the last couple of meetings, I will be presenting aspects of the BioAssay Express project, on behalf of Collaborative Drug Discovery. Our team has been quietly expanding in numbers and working hard making the product more powerful and more polished, so there are lots of new features to talk about!

Bond Artifacts: cheminformatics and aesthetics for inorganic structures

bondartifact1Cheminformatics for inorganic/organometallic compounds is the perennial afterthought that oft appears in the future work section, but never seems to get implemented: exotic bond types can be drawn in a way that is pleasing to other inorganic chemists but meaningless to computers, or in some cases vice versa, but never both. This article explores an approach to achieving such harmony. Continue reading

TypeScript and Electron for desktop & web apps (e.g. SketchEl2)

ts-electron-1This is rare post that is not directly related to chemistry or informatics, even though the screenshot to the right suggests otherwise. Probably the most exciting trends in software is that the web runtime has finally matured into a development target that is somewhat on par with native options, and that is a huge breakthrough for people who want to code up their product just once. I’m going to describe some of the getting started issues & gotchas that I went through with getting SketchEl2 to work using Electron, TypeScript and Visual Studio Code. Continue reading

BioAssay Express: converting annotations into prose

The BioAssay Express project is about describing bioassay protocols using machine readable annotations (which are URIs that have been appropriated from semantic web dictionaries). Because almost all currently existing bioassay protocols are represented as text, much of the focus has been on finding ways to streamline the annotation process. Thinking forward to the future, however, we anticipate that once this technology is widely deployed, scientists will find it easier to annotate new protocols using our templates and web-based interface than to write up many pages of prose using a wordprocessor.

For this reason, we are experimenting with running the process in reverse: converting the nicely structured semantic web annotations to scientific English, so that the biologist doesn’t have to do. Continue reading