MolPress: more interactivity & reaction importing

molpress_interactive00After a bit of inattention, the MolPress project has received some important new features: chemical objects are rendered within the editor itself, and there’s a better onboarding process for bringing in reactions. Continue reading


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