2011 redux

2011 has been a busy year for Molecular Materials Informatics, with new products, new features and new developments coming on hard and fast. 2012 begins tomorrow, and promises to keep up the same breakneck pace. This post is an executive summary of some of the news that was released over the year. Leaving out of course some of the projects that have yet to be unveiled.

At the beginning of 2011, there were just two products, with the same name: the Mobile Molecular DataSheet, or MMDS for short. Due to the rapidly shifting fortunes of mobile device platform makers, the iOS version for iPhone, iPod and iPad took centre stage in 2011, leaving the BlackBerry version behind. The iOS version was mostly feature complete by the beginning of 2011, having already added webservices access and reaction editing. Throughout 2011 the product has steadily matured, with a regimen of software updates adding minor and not-so-minor features, enhancements, bug fixes and ergonomic improvements.

At the beginning of 2011, there were two other apps making use of a package called MMDSLib, which is a library version of MMDS that can be embedded into other iOS apps. In 2011, six new iOS apps using this library for core functionality were created and released: Reaction101, Yield101, Green Solvents, MolPrime, ChemSpider Mobile, MolSync and SAR Table, with more on the drawing board or already in development.

The Reaction101 app, co-designed with Eidogen-Sertanty, got off to an exciting start: Apple featured the app, and have used the app to promote the educational potential of the iOS platform. Green Solvents proved to be an interesting foray into the world of green chemistry, and some of the ideas made their way into the Yield101 app (e.g. calculation of process mass intensity). The MolPrime app introduced limited structure-searching interaction with the popular ChemSpider portal, which initiated a discussion leading to the creation of the ChemSpider Mobile app on behalf of the Royal Society of Chemistry.

While the original MMDS app has always had strong features for sending and receiving chemical information in the form of structures, reactions and tables of data, using a single mobile device as the resting point for data is not always the ideal way to fit into a workflow. The MolSync app was conceived to deal with this: the app accesses chemical data on a remote file hosting service (currently just Dropbox, but more services are planned), and provides editing, viewing, file conversion and graphics creation services. More importantly, these remotely stored chemical documents can be explicitly synchronised with the MMDS app, and it can be done in a way that takes advantage of the collaborative sharing features of Dropbox.

The app lineup has started to take on a distinctive shape: the Mobile Molecular DataSheet (MMDS) is the grand-daddy app, which provides a superset of mobile cheminformatics functionality. The rest are descendents from this core technology, which focus on a limited feature set for a specific workflow, by trimming, repackaging, and adding new functionality when necessary. The most recept app – SAR Table – exemplifies this: its purpose is to generate tables representing a series of structures, based on a few scaffolds, and associating these fragments with the corresponding whole molecule, and activity data. It can be used to prepare manuscripts, or enter data from existing publications, and is designed to make this process as quick and painless as possible.

2011 also included the first official scientific presentation from Molecular Materials Informatics, at the American Chemical Society meeting in Anaheim in March. Two peer-reviewed papers came out in the scientific literature: Mobile apps for chemistry in the world of drug discovery (Drug Discovery Today) and The Case for Zero-Order Bonds and Explicit Hydrogen Counting (Journal of Chemical Information and Modeling). Two more papers were submitted in December, and are awaiting review. A fifth paper was submitted and unfortunately rejected, so was released as a whitepaper instead (Reaction101 and Yield101: Two mobile apps for chemistry with pedagogical value, free download: PDF).

Social media has become a more integral part of communication, including the creation of the blog that you are currently reading – http://cheminf20.org, as well as regular and continual news, updates and articles written in a more impersonal style on the main company website, http://molmatinf.com. Both of these sites have RSS feeds, and Twitter (@aclarkxyz) is a good way to keep an eye on new developments. There is a LinkedIn company page, a Facebook company page, a description for each app on SciMobileApps, and more recently I have my own personal wiki page on ScientistsDB.

2011 has seen a continuation and extension of collaborative projects and idea sharing, particularly with Steven Muskal and Maurizio Bronzetti (@MauriBrz) of Eidogen-Sertanty, who are the other half of the Reaction101 and Yield101 apps, as well as other to-be-announced projects. Collaboration on numerous interesting projects with Sean Ekins (@collabchem) and Antony Williams (@chemconnector) started out with ChemSpider, Green Solvents, various wiki pages and joint publications, with plenty more ideas on the drawing board. A short-but-sweet joint project with the Open Notebook Science project produced a new webservice interface to their cutting-edge melting point calculation service.

A little side-tracking adventure involved the addition of mini-games to the two free apps: Conway’s Life for MolPrime, and Chemical Tiles for Green Solvents.

Not all of the new products were mobile apps. A whole new cheminformatics stack has been gradually built up over the last 2 years, all coded in Java. In 2011 this software graduated to being ready to provide practical value, and was introduced by way of a new web server, accessible at http://molsync.com. This is not to be confused with the MolSync app – they have the same name because their features are expected to converge, but for now they are two different things. The server provides some important cheminformatics functionality for the mobile apps, including reading ChemDraw and Chemical Markup Language (CML) files, exporting extended MDL Molfiles, creating SVG graphics, and creating Microsoft Word and Excel documents using the OOXML format (i.e. .docx and .xlsx files), which contain high quality vector graphics representations of molecules and reactions.

The molsync.com website also provides some user-facing functionality which allows chemical content to be rendered and transcribed, and also combines with the MolSync app to allow chemical data to be tweeted – from within the app, when the content is stored in a public Dropbox folder. There is also a not-very-secret experimental project to produce a chemical structure sketcher that runs in a web browser (i.e. JavaScript), but leverages the server for heavyweight functionality. The interface is a hybrid superset of the mobile interface that was pioneered by MMDS, and the conventional desktop sketcher tools that every chemist is already familiar with.

It’s been a busy year. Next year will see all kinds of new developments, some of which are already underway, and just waiting for the right moment to announce.

 

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