Breaking radio silence

This site hasn’t had a post for couple months, and there’s a reason for that: I’ve been out of town, doing some collaborative work on-site, but now things are getting back to normal. Read the rest of this entry »

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MMDS with a news cycle feed (and how to turn it off)

newscycle00The latest version of the Mobile Molecular DataSheet (for iOS: see AppStore) has a news ticker feature, which shows a rotating series of facts and links that are displayed along the bottom of the screen. The items include mentions of other related apps, as well as news from Molecular Materials Informatics, and articles from this blog. The functionality is the same as what originally appeared in the free MolPrime app. Read the rest of this entry »

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Structure queries: a bit of attention to editing

query02Using chemical substructures with query annotations is a cheminformatics trick that goes back a long way: by annotating the query structure with additional logical constraints, the utility of this functionality can be juiced up, by matching a variety of certain kinds of fragments, rather than literal pieces. The amount of work involved to implement such a system is quite evenly divided between providing the low-level algorithm for doing the matching, and providing a high-level editor for people to design the queries. One of the “TO-DO” features in the XMDS beta version has taken some steps toward fulfilling the latter. Read the rest of this entry »

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Visualisation of structure-activity models: fudging it with a widget

contrast_singleOne of the opinions (arguably of the educated variety) that I’ve been pushing for awhile now is the idea that when a model building or visualisation technique requires a user parameter in order to get the correct result, that is essentially an admission of partial failure. If the method really was so great, then it would be able to figure it out, because a parameter is an extra degree of freedom that the method has punted on. Now of course this is not a rule by any stretch of the imagination, and there are numerous exceptions, or grey areas between what’s a parameter and what’s an integral component of the source data. But sometimes a parameter really is just something that a method ought to know, but gives up and passes the burden on to the user – and that’s not necessarily a bad thing, as long as we admit it. Read the rest of this entry »

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XMDS and Mac OS X integration: drag’n’drop and previews

xmds_qlgen1 The OS X Molecular DataSheet (XMDS) app has been getting a bit more attention lately, after being interrupted by the summer conference season (slides, poster, slides & more slides) and the PolyPharma app (which is now submitted to the AppStore and waiting for approval). The next step that brings XMDS closer to being a finished product rather than a functional beta is deeper integration with OS X. Read the rest of this entry »


Some app housecleaning & ACS aftermath

front_polypharmaWriting this post from Boston as the American Chemical Society meeting winds down – by Wednesday evening most of the action is over – it has been a good one. My first talk (see slideshare) went without a hitch, which was not a foregone conclusion, since the second half involved a live demo of the PolyPharma app, which didn’t exist 2 weeks ago, is half finished, and consists mostly of brand new original code.

Besides a new app on the way and a busy month of conference presentations, there are changes afoot in the app lineup which will start to be noticed on the Molecular Materials Informatics product page shortly. For chemistry app users, there’s good news and bad news. The bad news is that some apps have been retired, and some more are slated for the glue factory in the near future. The good news is that all the rest of the flagship apps are now free, as of several days ago, and the intention is to leave them that way indefinitely. Read the rest of this entry »

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The PolyPharma app: a mash-up of ideas and technology

AppIcon_152Things have been a bit quiet around here lately, but there is a good reason: at the Gordon conference on Computer Aided Drug Design a couple of weeks ago, a confluence of ideas came together. With the opportunity to observe a series of talks and posters about what practitioners in the industry are interested in right now, and the chance to discuss my recent projects and gauge the level of interest, it all happened to coincide with a number of partially complete product explorations that have been sitting on the workshop floor, waiting for the right time and place to assemble release to the outside world. Read the rest of this entry »

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