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 »

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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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What’s in a name: Molecular Materials

I am presently attending the Gordon Research Conference: Computer Aided Drug Design meeting, having a wonderful time, and at this moment taking an afternoon break to relax and catch up on some work. This is one of my favourite properties of the GRC meeting format, because it means that it’s not necessary to be pretty much out of the loop for the entire week.

So far I’ve met and reacquainted myself with more scientists of my own particular species than I can count, and a recurring theme of the introduction/renewal process is taking turns to explain what we’re both doing these days. One part of this which seems a little incongruous is that the name of the company that I created is called “Molecular Materials Informatics”. Since the occasion is a conference that is exclusively devoted to the pursuit of drug molecules and a few related parts of life sciences, this requires some explanation. Read the rest of this entry »

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Inline abbreviations with XMDS

abbrev1Abbreviations are a common shorthand used by chemists to alleviate the tedium of drawing out structures by hand, and in many areas – including much of organometallic and inorganic chemistry – use of abbreviations is more or less essential to achieve any kind of visual clarity. This presents a challenge for cheminformatics, though, because there is no universal dictionary for abbreviations: different research groups use different shorthand notations for their own nefarious purposes. Now the beta version of XMDS is catching up to MMDS by adding the ability to conveniently define inline abbreviations, which are readable to humans in diagram form, but also completely well defined behind the scenes for the benefit of machines. Read the rest of this entry »

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Closing the collaborative loop: Bayesian models with XMDS, CDD Vault and MMDS

vaultexport13The CDD Vault web product has recently delivered on one of its promises: making models truly sharable to the community, including both open source and participating commercial products. Bayesian models can now be exported in a well documented and openly consumable format, which removes a major bottleneck in the creation and use of models for structure-activity predictions. Read the rest of this entry »

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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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