Month: January 2014

Which platform to build software for?

For most of the desktop computing era (ca. 1980-2010) software creators have had to grapple with decisions of which operating systems to build their software for. This century, any desktop application with a user interface has been a choice of Windows/Linux/MacOSX, with relative importance being dependent on the industry. Since mobile devices turned into real computers, and HTML5 found its way onto mobile browsers, the decision has moved up a level: software creators now have to start by deciding which meta-platform, i.e. desktop, mobile or web. And it’s not always an easy choice. Continue reading →

Sneak preview: MMDS lookup of assays via OpenPHACTS

openphacts_assay1One of the features that’s slated for the next major version of the Mobile Molecular DataSheet (MMDS) is integration with OpenPHACTS pharmacological assay data. The feature is not quite ready yet, but the user interface is taking form, and is almost functional. The basic idea is that you start with a datasheet, with some number of molecules. Then, select the assay lookup feature, and a webservice intermediary cross references each of the molecular structures to the OpenPHACTS service, to pull out every available pharmacology datum, in a form that’s ready to insert into your data sheet as a new column. Looking up the data is quite easy, since OpenPHACTS is preassembled and has a very no-nonsense API, but reconciling a large number of datapoints into one or several columns of numbers is an interesting user interface workflow challenge. Continue reading →

Aromaticity in cheminformatics

One of the frustrating things about being an academically trained bench chemist and a creator of cheminformatics software is having awareness of the number of chemical concepts that got mistranslated when they were turned into software products. This is principally due to the fact that being a research scientist and being a software engineer are two separate professions, each with their “10,000 hours” proficiency requirements. For this reason, most of the robustly engineered cheminformatics software was built by professional programmers, after having the scientific concepts conveyed by professional chemists.

Problem is, some of the concepts didn’t get explained properly, and one of the important ones is aromaticity. Continue reading →