SAR Table app: new life on the desktop

sartable_xmds1The SAR Table app originally came out in 2011 for iOS, and went from being a tightly focused product to an expansive showcase of cheminformatics technology. In recent years it has not received much attention, due to the fact that having all this functionality on a touchscreen turned out to be pushing further than an iThing is really meant to go. Now the core functionality is being ported to the XMDS desktop app.

When I was first dreaming up the SAR Table app (described in some detail in the official manual page), it was fully my intention to try to stay within the sweet spot of mobile app functionality: do one or two things well, and delegate anything else to other tools. The idea was to solve for the problem of curating molecules from the literature, in which a single paper often describes dozens of compounds in tables using an abbreviated format of scaffolds + substituents. This kind of thing, as an arbitrary example:

sartable_xmds2

It is very efficient for saving space, and is often effective as a human-to-human communication tool (with some epic counterexamples), but for purposes of turning these numbered compounds into a database of actual molecules, it’s a very painful task, and also very error prone. The SAR Table app was simultaneously designed to solve for this as well as the reverse problem, i.e. creating these tables out of molecules, and exporting a draft version to Microsoft Word.

Whether unfortunately or not, the sophisticated cheminformatics needed to make even this most basic functionality effective created an irresistable temptation to do more and more. Things like integration with searchable databases, matrix plots, automatic scaffold matching and model building and prediction pushed the capabilities of the app way too far forward. The technology part worked out rather well: whatever features could not be easily coded up locally on the app were delegated to custom web services, and the molecule sketching part had already been fine tuned with the pioneering Mobile Molecular DataSheet (MMDS) app. What didn’t work so well is the fact that working on a touchscreen device with limited input/output channels (i.e. no underlying filesystem in the same sense as a regular computer) is very… cramped, when applied to workflows that cannot be rolled into a canned series of routine steps.

For all of the times I toured around scientific gatherings showing off this tool to chemists, the feedback was entirely positive, but unsurprisingly tended to end with an inquiry as to whether this was going to be made available on a desktop platform anytime soon. I couldn’t argue with the sentiment, but at the time the platforms that I was building for were primarily a combination of mobile & cloud, and so that’s where any potentially innovative ideas first saw the light of day.

Fast forward to now, the XMDS project for macOS has been in long beta for awhile, and is slowly but surely racking up features that were previously dispersed through a collection of mobile apps. First the functionality of MMDS (molecular spreadsheet) was assimilated, and then the Green Lab Notebook (reaction editor), and now more recently the SAR Table functionality, with new features for handling the breakdown between scaffolds, substituents and constructed molecules:

sartable_xmds1

The data format is the same as used by the mobile app, i.e. the SARTable aspect extension to the native datasheet format. The user interface is integrated into the general purpose spreadsheet editor that XMDS uses. The scaffoldssubstituents and constructed molecules are largely just regular molecular structures, but they are specially maintained in order to keep the relationship that they have with each other, and also specially decorated to show how they related to each other.

Unlike the mobile app, the desktop version does not co-opt additional information about labels and activity values. The mobile app had to do this because the platform is not very conducive to a plugin approach (a mobile app kind of is a plugin, in a certain sense, and tends to be atomic), whereas XMDS allows many different aspects to be mixed together simultaneously. And so the scaffolding functionality is separate from the numeric assays, which can be handled by another method, e.g. the AssayProvenance aspect.

The scaffolding functionality that has been or will be wrapped into the XMDS app in the near future includes the various features that are relevant to content creation, and to convenient exporting of data and graphics (e.g. being able to drag vector art into a manuscript). This functionality does include some fancy cheminformatics like automatically matching scaffolds to molecules, which was a little bit awkward with the mobile SAR Table app because the algorithms were implemented by a webservice, but with the desktop product will be handled locally.

On the other hand, model building and advanced visualisation techniques are not on the short term roadmap for the XMDS app itself, because they are more the domain of content consumption, and will probably be coded up using a different technology base. This delineation is in part due to the fact that a content creation user experience is very labour intensive and really benefits from being painstakingly carefully integrated into the underlying operating system – every tiny detail matters – hence the choice to go with native macOS. On the other hand, manipulation and visualization of existing data puts more of a burden on the machine end of the equation, so it might as well be deployed as a cross platform product, such as via the web.

If you are interested in trying out these features, remember that the XMDS long beta programme is open to anyone who is willing to make the effort to send a polite email introduction. It does of course require that you have a Mac.

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