2013 redux

The year is almost over, which means it’s time for a blog post summarising all that went on as pertains to my entrepreneurial experience, in year 4 of the existence of Molecular Materials Informatics, Inc. First of all, it has been a turbulent year. Before I made the jump from a comfortable job to a new company with a bag of crazy ideas, I consumed a lot of literature about what to expect at the helm of a tech startup, and the universal opinion was that it’s a manic depressive roller coaster ride, with euphoric highs and devastating lows. I can now report that these prophecies are starting to ring true! Due to the unusual trajectory (single founder, no dependencies on hired talent, anticipated market doesn’t actually exist yet) things just hummed along quietly for the most part, until this year. While I’m not at liberty to blog about any of the details, I can focus on specific milestones, which are all part of the public record.

In terms of travel and conferences, this has been quite an active year. Starting with the American Chemical Society meeting in New Orleans, two talks delivered: Mobile+Cloud: a viable replacement for desktop cheminformatics? and Pistoia Alliance App Strategy. The first talk described a workflow sequence of chemical structure + data that used mobile apps for the interface and cloud services for the heavy calculations (with a strong focus on the SAR Table app), while the second described the Pistoia Alliance‘s work in progress to build out an app strategy in support of life sciences. Unfortunately the times almost overlapped, so I had to rush out and gatecrash the second session, but such is life.

On a more local note, I delivered a short presentation to the inaugural Montreal Hacking Health meeting, about the Open Drug Discovery Teams (ODDT) project. While my own scientific interests are a couple of steps away from the health arena, most of the technology that I build gets used for drug discovery, and the ODDT app is an unusual project for me because it has a foot in that particular door.

The high point of the summer was a very welcome invitation to give a talk at the Gordon Conference on Visualisation in Science & Education. I have not posted slides for this talk, in order to respect the spirit of the conference (i.e. you really did need to be there), but it described in detail how the various apps that I’ve created are useful to students in an educational context, and focused on all of the useful visualisation techniques and their increased availability due to the mobile platform. For the occasion, I accelerated my stretch goal of finishing the Living Molecules app. It was my first time at a Gordon Conference, and I am pleased to report that the format is awesome. I don’t think I’ve ever been to a week long conference and gotten to the end wishing that it would continue on for another week; normally no matter how great a conference is, I end up feeling rather burned out and looking forward to getting home and unpacking all of the new ideas.

The next stretch goal was to get ready to present a workshop tutorial at the NETTAB conference in Venice, Italy. The conference normally has a bioinformatics focus, which is not quite what I do, but in order to get as close as possible to the domain, I put in a significant amount of background work to put together a cheminformatics workflow that tied together mobile apps, cloud services and original desktop-based algorithms to kickstart a scaffold-oriented discovery project. The slides are quite long, as befits a 2-hour long presentation.

Cutting it a bit close for time (by my standards, anyway), a fortnight after I got back to Montreal I was on another plane to present at the German Chemical Society chemoinformatics conference. This was a high honour indeed, and so I went with the stretch goal approach once again, by promising to talk about my electronic lab notebook app, called the Green Lab Notebook. The only catch is that the app is not actually finished, and so I had to fast track the development efforts in order to have a story ready in time. As I mentioned during the presentation, the app is about 1/3 finished, 1/3 based on technology waiting to be migrated from existing apps and 1/3 just not done yet. Since the conference, these ratios have improved a little toward the minimum viable product stage!

2013 has been a good year for me in terms of published papers, with 5 of them hitting the metaphorical shelves:

  • Sean Ekins; Alex M. Clark; Antony J. Williams: “Incorporating Green Chemistry Concepts into Mobile Chemistry Applications and Their Potential Uses”, ACS Sustainable Chemistry and Engineering 1, 8-13 (2013) link
  • Sean Ekins; Alex M. Clark; Antony J. Williams: “Cheminformatics workflows using mobile apps”, Chem-Bio Informatics Journal 13, 1-18 (2013) link
  • Sean Ekins; Chris L. Waller; Mary P. Bradley; Alex M. Clark; Antony J. Williams: “Four disruptive strategies for removing drug discovery bottlenecks”, Drug Discovery Today 18, 265–271 (2013) link
  • Sean Ekins; Alex M. Clark; Malabika Sarker: “TB Mobile: a mobile app for anti-tuberculosis molecules with known targets”, Journal of Cheminformatics 5, 13 (2013) link
  • Alex M. Clark: “Rendering Molecular Sketches for Publication Quality Output”, Molecular Informatics 32, 291-301 (2013) link

For most I can thank my repeat-offending collaborators Sean Ekins and Antony Williams. These papers describe a number of products that we have been working on together, as well as overall trends. As is often the case, the process of getting these papers published is sometimes a story in itself. Our paper in ACS Sustainable Chemistry and Engineering was originally sent elsewhere, as Sean Ekins describes, which I think the original recipients probably regret since it turned out to be quite popular and well read.

My single-author paper that came out in Molecular Informatics also had the dubious distinction of being rejected without review by its original destination, which made me rather angry. Since I was documenting high value proprietary software that’s relevant at the end of the day to every chemist who ever uses a computer, with no corresponding financial remuneration, I put it on the shelf for awhile and moved on to other things. After getting a tip that Molecular Informatics is run by a more agreeable editing team, I dusted it off and sent it in. It’s very dry, technical and detailed, so only a few people can benefit directly, but no less important for that. I am personally a big fan of publishing scientific algorithms in the literature, firstly because it is a good way to carry out shameless self-promotion while still doing a good deed for the community as a whole; and secondly, it is an effective way of ensuring that some [censored] can’t patent it. Apologies to any [censored] out there who own software patents, but I will state publicly that I hope that every single one of them gets invalidated by patent law reform in as long as it takes for ink to dry.

In terms of new apps to be released, 2013 was in fact a bit of a slow year: Living Molecules came out, which is a free app that behaves like a QR code reader for molecular content. Like a lot of the apps that preceded it, the use case/business model is more of a collection of many possible ideas rather than a focused plan. A big part of the motivation is that I wanted to try my hand at building something with an augmented reality component to it, and tying that into cheminformatics. So if you see a Living Molecules glyph printed out on a poster at a conference, you can whip out your iThing, point the camera at the glyph, and have the app look up the content and display it. Once you’ve captured the data, you can import it in its raw cheminformatics form, so the molecules, reactions and data are usable for whatever nefarious purposes you have in mind. The alternative would be to take a photograph of the poster, then go home and draw the molecules and type in the data yourself.

All of the apps in the Molecular Materials Informatics collection have gone through a number of updates, some of them adding a lot of functionality. The SAR Table app in particular has bulked up on so much functionality that the documentation lags pretty far behind (a to-do for 2014). iOS 7 was a bit of an annoyance due to changing of some API capabilities in a fairly arbitrary way, which meant that each app needed to get a bit of re-tuning. In actual fact it inspired some refactoring of the underlying codebases. In the 3.5 years since I started building iOS apps, the language (Objective-C) and its framework have matured significantly (as to why Apple chose an immature language to start with, is a different story). And of course my own proficiency with these has increased significantly, and a number of experimental ideas did not work out quite as expected, and some temporary stopgaps needed to be expanded out. For example, the importing methodologies for the Mobile Molecular DataSheet app were good enough when the app came out, but were long out of date.

Also, the touchscreen-optimised molecule drawing interface has plateauxed out and matured, but there have been some ideas on the drawing board for awhile that finally got implemented: new drawing gestures have been added in.

In terms of documenting the company focus, the word “cloud” gets used a lot more often, because the user-facing mobile apps have been stacking up increasing amounts of powerful functionality by leveraging supporting webservices. Based on an all-new cheminformatics toolkit (written in Java, referred to as com.mmi, on account of the namespace hierarchy), these services have been slowly but steadily building out. The most noticeable recent improvements are scaffold assignment, model building and database searching. The latter is based on a module called MetaSearch, which is a very simple API used by apps which farms out the hard work to PubChem, ChEBI and ChemSpider. The results are combined and reconciled by the middleware to provide a unified front (each search engine has its own ways of doing things), and this becomes particularly useful when searching for scaffolds with the SAR Table app. The service also started importing vendor information from PubChem, which is almost a stub for planned future functionality. Quite a few extensions are planned for the near future (e.g. OpenPHACTS integration), but haven’t quite hit the top of the priority queue just yet.

Happily, the Royal Society of Chemistry recognised the work done by three apps, and decided to sponsor them: Green Solvents, Lab Solvents and Open Drug Discovery Teams. And for that matter, the ChemSpider Mobile apps for iOS and Android continue to be downloaded frequently.

The SPRESImobile app, produced for InfoChem in collaboration with Eidogen-Sertanty, got a major new feature: reaction searching, which allows either or both sides of a chemical reaction to be (partially) specified in order to carry out several types of searches. There is a new feature in the works, too, but that will have to wait until next year because it got delayed slightly.

The previously mentioned Green Lab Notebook app is still vapourware, but it continues to march on toward its minimum viable product state. If all goes well it will come out early-to-mid 2014, or at the very least I will have some new screenshots to show, because I’ll be talking about it at the next ACS meeting in Dallas, Texas. I am also working on a collaboration to produce an educational app, which should hopefully be unveiled in the coming months.

My open source SketchEl got a few improvements, including the MDL Molfile extensions for nonorganic molecules (described in the literature), and the ability to share content on molsync.com. While I like to support open source as much as possible, there aren’t enough hours in the day to give this particular project the attention it deserves, but I do use it myself on a daily basis, so it does need to live up to a certain minimum standard of maintenance.

Some of the not-so-fun events of public record that happened during 2013 include the (luckily temporary) banning of my YouTube account for the heinous crime of posting a demo of how to draw the structure of viagra using a mobile app. It looks like everything has been fully reinstated, but for a week it looked like my company’s presence on the world’s most popular video sharing site had been erased from the history of the internet. A cautionary tale if ever there was one.

Some kind of market milestone was probably achieved the day that the ChemDraw app appeared in the iTunes AppStore, if only for the marketing dollars and endorsement value. When the T-rex of the desktop market migrates its flagship product to mobile and spends a lot of money telling people about it, a certain category of progress indicators can be checked off. The creators decided (perhaps wisely) to not even bother with an iPhone version, and so the literal porting of the standard molecular drawing interface from mouse/bigscreen to touch/mediumscreen joins about a dozen other preceding products, and brings little if anything to the table technologically. But it’s nice to see people taking the platform seriously.

Problems with industry understanding of cheminformatics continue to persist, and there should be some more publications coming out next year to incrementally try to help with that. The distinction between drawing molecules for use as printable diagrams, and drawing molecules for being understood by computer algorithms, continues to cause confusion and corrupt the data people use. All products from Molecular Materials Informatics prioritise digital purity first and foremost, and then try to do as fantastic a job as possible with creating diagrams. But that causes friction when chemists want and expect to be able to skip the preservation of digital meaning and get straight to the diagram creation.

Overall, this blog post covers about half of the excitement of 2013. The rest will either show up as some interesting development in 2014, or evaporate away never to be spoken of again. Also, this particular blog – Cheminformatics 2.0 – has continued to be the primary location for breaking news about new features and development. The official company site, molmatinf.com, gets its content refreshed in a much less timely manner.

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