One of the features that’s slated for the next major version of the Mobile Molecular DataSheet (MMDS) is integration with OpenPHACTS pharmacological assay data. The feature is not quite ready yet, but the user interface is taking form, and is almost functional. The basic idea is that you start with a datasheet, with some number of molecules. Then, select the assay lookup feature, and a webservice intermediary cross references each of the molecular structures to the OpenPHACTS service, to pull out every available pharmacology datum, in a form that’s ready to insert into your data sheet as a new column. Looking up the data is quite easy, since OpenPHACTS is preassembled and has a very no-nonsense API, but reconciling a large number of datapoints into one or several columns of numbers is an interesting user interface workflow challenge. Continue reading
cheminformatics
Aromaticity in cheminformatics
One of the frustrating things about being an academically trained bench chemist and a creator of cheminformatics software is having awareness of the number of chemical concepts that got mistranslated when they were turned into software products. This is principally due to the fact that being a research scientist and being a software engineer are two separate professions, each with their “10,000 hours” proficiency requirements. For this reason, most of the robustly engineered cheminformatics software was built by professional programmers, after having the scientific concepts conveyed by professional chemists.
Problem is, some of the concepts didn’t get explained properly, and one of the important ones is aromaticity. Continue reading
Linear pipelining operations with the Mobile Molecular DataSheet app
The next release of the Mobile Molecular DataSheet (MMDS) app will have a fairly major new feature: pipelining. First let me point out that it is not the grandiose feature that the name might suggest. Pipelining usually suggests a graphical layout tool allowing arbitrary nodes with multiple branches and huge volumes of data with sophisticated calculations at each step, and the new feature is much more constrained. But it is still useful, and intended to evolve into a midpoint compromise between power and simplicity. The system is engineered to provide linear pipelines (e.g. no branching, no alternative pathways, etc.): any number of datasheets can be jammed into the input funnel, but the outcome is always just a single resulting datasheet. The kinds of operations fit into 3 categories: filters, sorts and web operations. Filters are boolean logic clauses used to reduce the number of rows, sorts are are exactly what they sound like, and web operations are going to be implemented in a later iteration (keep reading for more about that). Continue reading
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. Continue reading
Multistep reaction viewing and editing: taking shape
The previous chemistry-related post described some of the issues involved in representing chemical reactions. The Green Lab Notebook app-in-progress needs to be able to express multistep reactions as a collection of highly marked up molecular components, and it also needs to be able to render them on demand, to a level of quality that is comparable to what a user might draw themselves, if they happened to be in total control over where everything is positioned. Drawing a multistep reaction algorithmically is not an entirely trivial task, though, since there are multiple opportunities for making judgment calls for how best to fit the scheme on a piece of paper to achieve close packing, aesthetic readability, and consistency across a series. Continue reading
Chemical reactions: the format matters (a lot)
The Green Lab Notebook (GLN) app, mentioned in the previous blog post, makes a strong point of capturing the cheminformatic data of each chemical reaction at the point of entry, i.e. the scientist who currently knows more about that reaction than anyone else in the universe needs to provide that information in a digitally hygienic and lossless form. Continue reading
Winter project: Green Lab Notebook
The Canadian winter has announced itself, coinciding with American thanksgiving. Apart from a lot more time indoors and a significantly increased consumption of heavy stout ales, it signifies time to hunker down and concentrate on product development for awhile. Continue reading
Dynamic similarity clustering in the Approved Drugs app
The Approved Drugs app is about to get a new update, which introduces a visual clustering feature. Initially, this is a bit of a novelty, but has a clear pathway toward a more sophisticated, high value offering. Continue reading
Mobile sketcher gets some lovin’
The next version of the Mobile Molecular DataSheet (MMDS) for iOS will come with a few new features for sketching out molecular structures, followed by each of the other apps that are based on the same core technology, as and when they are updated. While the sketcher codebase has been quite stable for awhile, on account of already being powerful enough to draw some very tricky structures perfectly & quickly, the to-do list has been collecting up ideas for improvements. Continue reading
Cheminformatics workflows using the mobile + cloud platform: NETTAB 2013
Yesterday I returned from a truly delightful trip to Europe, the primary purpose of which was to deliver a presentation to the 2013 NETTAB meeting. The slides are now available on slideshare:
http://www.slideshare.net/aclarkxyz/alex-clark-nettab-2013
For the benefit of the audience at the conference, I wanted to make sure that everyone present could easily access the apps that I was talking about, and so rather than handing out promotional codes on scraps of paper, I decided to simply drop the price of the non-free apps that I described in the presentation to zero for a few days. I didn’t tell anyone else about this, and figured that a few dozen people would accidently get a freebie or two. That’s not quite the way it worked out: in actuality more like a few tens of thousands of people got in while the going was good. Next time I pull a stunt like that, I might just shorten the window of opportunity a little bit, but if anyone out there is reading this, and you made the best of it, please consider popping by the iTunes AppStore and putting in a favourable review and/or rating!
Besides having the opportunity to meet a lot of bioinformaticians and semantic web experts (two adjacent fields that I have not been paying as much attention to as I should have), it certainly didn’t hurt that the conference was held at the Lido of Venice. This being my first time ever to visit any place along the mediterranean, I have to say the location is quite amazing. For a rustic colonial who doesn’t normally bother taking photographs, well lets just say I snapped several hundred of them in the Lido and main city of Venice. It’s one of those places that isn’t overhyped: it really is a must-see.
Nonetheless, there’s now a lot of work to catch up on. My list of cool ideas to try to prioritise was already pretty long, but many brainstorming sessions later, it’s grown a whole lot. So much to do, before or after the next trip, to the 9th German Conference on Cheminformatics.
Cheminformatics 2.0 