Always-on R/S and E/Z stereo labels with XMDS

xmds_stereo1The most recent addition to the OS X Molecular DataSheet (XMDS) desktop app is calculation of stereochemistry labels as-you-edit, using the Cahn-Ingold-Prelog (CIP) designations (R/S, Z/E). The labelling can be switched off with a menu option, but since most people use software with its factory settings, this is more or less equivalent to having it hardcoded permanently. Read the rest of this entry »

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Aspects and XMDS: higher order metadata for datasheets

xmds_aspect1Recent progress on the OS X Molecular DataSheet (XMDS) app, which is currently in beta, has involved the inclusion of aspects into the user interface for editing datasheets. The core format that the XMDS desktop app, as well as all the rest of the products from Molecular Materials Informatics, is the datasheet, which is a tabular format made up of rows and columns: like a spreadsheet, except that the columns are strongly typed, so you can’t just abuse it and put in whatever you want wherever you want. The minimalistic table datastructure can be supplemented by any number of aspects, which are directives that impose higher order layers of interpretation, which are often composed of multiple columns (e.g. a chemical reaction which cobbles together multiple molecules for its reactants, reagents and products). One of the fun software engineering challenges has been to make these complex representations fit seemlessly into the grid-based “spreadsheet” editor upon which XMDS operates. Read the rest of this entry »

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XMDS ready for beta phase

xmds_hubThe OS X Molecular DataSheet (XMDS) desktop app is now ready for beta testing. And by beta testing, I mean the minimum viable product is done and ready to be used for actual cheminformatics tasks. You can sign up anytime: all it takes is an email (, a Mac with Yosemite-or-later (v10.10), and a Dropbox account. And you get to keep using the app for as long as you want, even after the beta testing programme is wrapped up. Read the rest of this entry »

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Literature how-to for structure:activity Bayesian models (and open source)

bayesianA two-pack of publications in Journal of Chemical Information and Modeling is now available: Bayesian the first, and Bayesian the second. Both papers are open access, so by all means go read them instead of this blog post. The first paper details the implementation of a variation of the classic naive Bayesian method that is suitable for use with structure-derived fingerprints such as ECFP6 and FCFP6. The text goes into some detail about how it is implemented, to the point of including pseudocode, which complements the fact that the source code is available as part of the Chemical Development Kit (CDK), conveniently and concisely coded up in a single source file. The intention is quite unashamedly to tell you everything you need to know to build the algorithm from scratch, should you be so inclined; and if not, to understand every little detail about how the open source software works. The second paper goes into some more detail about how to use this kind of (“Laplacian-modified”) Bayesian model, including a calibration method, and an extensive study carried out by extracting thousands of model-ready datasets from the ChEMBL database. Read the rest of this entry »

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Honeycomb clustering in Approved Drugs app: sneak preview

honeycomb1Work is currently underway on a novelty feature that will first be exposed within the Approved Drugs app: honeycomb clustering, which is a greedy visualisation technique that is remarkably effective for examining how a particular chemical structure relates to a collection of compounds. Read the rest of this entry »

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XMDS and dragging content into other Mac apps

xmdsdrag1One of the things that one must become accustomed to when using a Mac regularly is that drag’n’drop is actually an effective way to get real work done. Two main use case scenarios are considered: getting graphics images of molecules into presentation tools (e.g. Pages or Keynote), and getting raw data into another cheminformatics tool (e.g. uploading an SDfile to a browser-based application). Both of these are now functioning in the pre-alpha version of XMDS  (the OS X Molecular DataSheet), which essentially brings it to demo-ready status. Read the rest of this entry »

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Summer conference schedule

I’ve been out of the spotlight for awhile as far as scientific conferences go, but this summer-of-2015 it’s all back in form, with three in a month long window:

If you’re going to be attending any of these, perhaps I will see you there. If not, the materials will be going up on slideshare shortly thereafter…


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