Searching public databases from mobile apps: better feedback

searchrtA few iterations ago, some of the flagship mobile apps from Molecular Materials Informatics (namely the Mobile Molecular DataSheet, SAR Table and MolPrime+) added an integrated feature for searching public databases by name and structure. The feature works through a webservice meta-layer that currently wraps PubChem and ChEBI.

The use case is very convenient, but one of the downsides for the presently available features is that the webservice connection is carried out as a single operation, with no feedback until the search is complete. From a user experience point of view, an operation with no progress indicator gives the impression of taking about 10x as long as one that provides useful feedback. Continue reading →

ACS redux

The American Chemical Society meeting in New Orleans (April 2013) is now all wrapped up – at least for me anyway, there may be some last vestiges of action still going on. It was a fun meeting, and even though I spent the entire time either talking shop or sleeping, the choice of city didn’t hurt. I managed to experience a number of the highlights while prowling around with gangs on fellow chemists.

My two presentations are now available online:

  • COMP division: Mobile + Cloud: A replacement for desktop cheminformatics? (slideshare, figshare)
  • CINF division: Pistoia Alliance AppStore: Apps for life sciences R&D (slideshare, figshare)

Also, I was thrilled to see the C&E Picks video feed include a large segment of the footage that I provided, which shows the SAR Table app in action, and the SPRESImobile app is in there too. Mobile apps for chemistry are making their way further up the food-chain!

MolPrime (iOS) due for an overhaul

molprime_changelogoThe MolPrime app is one of the first free apps from Molecular Materials Informatics. It was designed as a minimalist showcase for the powerful touch-based sketching technology of its older sibling, the Mobile Molecular DataSheet. It was put together in short order and, by the standards of the rest of the app suite, is a bit of an ugly duckling. Given that it has become quite popular, second only to ChemSpider Mobile in download count, it’s time revisit the aesthetic. Continue reading →

Publication-quality molecular rendering: behind the scenes

molrenderMy most recent publication is now available as early access, and is entitled Rendering Molecular Sketches for Publication Quality Output (Molecular Informatics, 2013). As the title suggests, the paper describes the process of turning a data representation of a molecular structure into a graphical figure that is suitable for the most aesthetically demanding circumstances (e.g. manuscripts, posters, etc.). If one were to start with a connection-table representation of a molecule, with well selected coordinates (e.g. a typical MDL Molfile, among others), the process of creating a perfect diagram seems pretty simple compared to everything that goes on up to that point, but actually it’s not. There is a great deal of information that has to be inferred before a great picture can be produced. The paper goes into a lot of detail, and describes all of the important algorithms necessary to bridge the gap. Continue reading →

SAR Table: colour coded activities for lookups

sartable_lookupThe SAR Table app is undergoing a number of enhancements to make it more suited for planning new compounds based on existing structure-activity relationships. A lot of this has to do with property prediction, model building and scaffold searching of public databases. One of the features slated for the next update is a bit more down to earth: presenting a indication of activities when selecting scaffolds or substituents for reuse. Continue reading →