Continuing on the trend of adding green chemistry features to apps, which started with a previous train of thought, a useful reference value for reactions is the Process Mass Intensity. As it happens, the Yield101 app is very well positioned to be the recipient of this upgrade.
cheminformatics
Web-accessible data for Green Solvents
This is the second blog post pertaining to the Green Solvents app, before it has been approved on the iTunes AppStore – except that this one is about the data. Actually it’s not really about the data at all – it’s about the method of delivering the data. Let me explain.
Looking at the Molecular Materials Informatics site, you might get the impression that the company only makes mobile apps, and that’s it. But in fact the company has quite an extensive stealth web strategy, which includes a project called MolSync, which has recently been harnessed to provide auxiliary cheminformatics support for MMDS. As well as back-end functionality, there is also a toolkit of user-facing cheminformatics widgets for various tasks.
MMDS with remote procedure calls: email SVG
Version 1.2.8 of the Mobile Molecular DataSheet has been submitted to the AppStore: with any luck, the new version will be available within a few days. The release schedule got moved forward a little bit because the previous version inadvertantly blanked out two of the icons on the main menu (oops). The new version introduces a significant new feature that has been in the works for some time: MMDS now makes use of remote procedure calls to provide some of its functionality. The first such feature to be exposed is the ability to generate SVG (scalable vector graphics) of images when sending molecules, reactions or datasheets via email. Continue reading
5 kinds of open: source, data, algorithms, formats and protocols
Over the years I have often found myself favourably inclined towards the principles of openness in the field of software in general, and scientific software in particular. While I use many open source products on a daily basis, and have personally contributed to the free software gestalt, openness comes in many different forms, and they are not all applicable to all situations.
Melting point prediction for MMDS by way of Open Notebook Science
As described in the UsefulChem blog, the Open Notebook Science WebServices project has been making good use of a collection of high quality, well curated physical property data, in particular: melting points. As many people have independently discovered, melting points have traditionally yielded poor results when subjected to attempts to use chemical descriptors to predict properties, as compared to other related physical properties, such as boiling point. It would seem, from recent results, that the reason for these poor results may well be primarily due to low quality data. As the data is cleaned up, the correlations improve.
These new results, which are based on open data, are made available to the world by way of webservices, and more recently, the functionality has been made available using the MMDS webservices protocol. MMDS (the Mobile Molecular DataSheet) uses an openly defined protocol which allows it to communicate with an arbitrary webservice. The Open Notebook Science physical property prediction service is now included in the default set of webservices offered to users of MMDS.
The real reason for junk chemical data
There is been a fair bit of chatter on the blogosphere lately about the perennial problem of low quality chemical data, e.g. chemical structures that do not adequately describe the material they claim to represent, messed up names, broken references, mistaken or underspecified accompanying data, etc.
This latest round of discussion seems to have been triggered by the recent publication of the so-called NCGC Pharmaceutical Collection, which not only claims to be definitive, but may in fact be unusually bad, such that even practitioners who have no illusions about the quality of data in general use are noticeably unimpressed (e.g. ChemConnector, In The Pipeline). While I haven’t personally examined the offending dataset, this is as good an occasion as any to weigh in with my long-held opinion on how things have gotten so bad that chemical data wranglers routinely expect between 5 and 20% of their source data to be junk.
An inline abbreviation mechanism for structure diagrams
One of the habits that most chemists engage in when they sketch out structures with a pen and paper is the use of abbreviations for certain kinds of functional groups. Using abbreviations saves a lot of wasted time and ink, and it is also a useful way to draw attention to the chemistry that is relevant to the subject at hand, and away from the spinach that is coming along for the ride. For example:
In this classical organic chemisty reaction, the phenyl groups of the Wittig reagent are abbreviated as Ph, and the unreactive alkyl chain is abbreviated as a molecular formula, because these groups are inert and not particularly exciting; the part that really matters is the reaction transform.
The current menagerie: MMDS, Reaction101, Yield101
As of the time of writing, the number of iOS apps published by Molecular Materials Informatics is about to grow to three, with the addition of Yield101, which is in the final stages of testing prior to submitting to the app store. All of these products are built around the same technology core, which includes, most importantly, a chemical structure diagram editor that is optimised for smartphone/tablet-sized devices. They also share a common visual theme and user interface style elements.
The apps, in chronological order of release are… Continue reading
Why have chemistry software on mobile devices?
As the founder of Molecular Materials Informatics, and the programmer/scientist who designed and built its mobile chemistry products, a sensible question to address is: what is the point of going to all this trouble to redesign the core user interfaces of chemical information software so that it works well on things like phones and tablets?
To many of the people who already own mobile devices and enjoy using them in preference to more conventional computing hardware, this question probably answers itself, but to many others, smartphones and tablets are just tools that have some role to play. Why does having apps to create, manage and exchange chemical data make sense – and why would somebody think that was enough of a business opportunity to justify quitting a great job and starting a new company? Continue reading
Inaugural post
Welcome to the Cheminformatics 2.0 blog. The name is an obvious riff on the “web 2.0” moniker: the subject relates to the design and use of chemical information software on such new-fashioned platforms as mobile devices and feature-rich client-heavy web pages, as well as other related modern paradigms such as cloud-computing and distributed storage of data and computational capacity.
Blogs that will be appearing under this label will have a much lower density of trendy buzzwords than the preceding paragraph. Rather the articles will be oriented toward describing recent progress toward building new products, or finding new uses for them. The theme is extension of chemistry software to areas that go beyond the traditional domain of workstation class computers.
Cheminformatics 2.0 