Presentation about the Green Lab Notebook at ICCE2014 Toronto

icceglnSlides for a talk about the upcoming Green Lab Notebook (GLN) app, which was presented this morning at the International Conference on Chemistry Education (ICCE2014) in Toronto. The short presentation describes how the field of green chemistry can be brought closer to both students and professional chemists with the assistance of an accessible and easy to use mobile app. The presentation was given by Holly Hampson, since I’m currently situated much further away from the event.

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On the myth of chemical structure format conversion

There has been a lot of work, many products, and plenty said on the topic of converting chemical structures from one format to another, and a number of well used and highly regarded packages (e.g. OpenBabel) that specialise in providing this capability. Less well discussed, it would seem, is that when it comes to connection-table formats used to encode chemists’ sketches of molecules, there are no software packages and no two formats for which a round trip conversion can be reliably carried out without losing information, even if the chemical entities being expressed fall within the applicable domain of both formats. Read the rest of this entry »

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Microsoft Word app and vector-drawn molecular graphics

msword_ipadLike a few hundred million other people, I was curious to see what the newly released Microsoft Word for iPad app was capable of. One feature in particular is of great interest to me: the rendering of DrawingML graphics. It does not go without saying by any means that the app will abide to its own (very complex) format specification, but I am pleased to report that it does.

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The Green Lab Notebook project: where it’s at

gln_snap20140324Last week I was at the American Chemical Society meeting in Dallas, which was incidently a particularly enjoyable gathering. I presented two talks, one of which described some of the latest developments of the Green Lab Notebook project (for slides, see slideshare and figshare). After having given a couple of talks about this as yet unfinished app, it’s time to start the run-down checklist for what goes into a minimum viable product.

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What to expect from me at the Dallas ACS 2014

coverACS2014Like many (or most) chemists in North America, the twice annual American Chemical Society (ACS) mega-meeting is an important calendar event in spring & autumn. Its primary value proposition is networking, but it also provides an important source of stretch goals. I’ll be presenting two talks, one on Monday about electronic lab notebooks, and the other on Tuesday, about cloud computing. Read the rest of this entry »

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Green Lab Notebook: more on balancing & green metrics

gln_greensteps1Recent blog posts (here & here) have chronicled the experiment editor for the Green Lab Notebook (GLN) app-in-progress. The green chemistry metrics and some interesting stoichiometry/equivalents/balancing issues for multistep reactions have been grappled with. Read the rest of this entry »

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Open source ECFP/FCFP circular fingerprints in CDK

circular_rocAs of now, the latest version of the popular open source Chemical Development Kit (CDK) has its own implementation of the highly regarded ECFP and FCFP classes of chemical structure fingerprints (sometimes referred to as circular or Morgan fingerprints). While the general recipe for this kind of fingerprint has been available for awhile, and there are a number of implementations in various different toolkits, this one distinguishes itself in several ways: it has been implemented as closely as possible to the description of the original definition (without having access to the trade secrets that were left out of the paper); it includes resolution of chiral centres; it is freely available as open source Java code; and, last but not least, the algorithm is designed to be as portable as possible, with no major dependencies on specific programming languages or cheminformatics toolkits. Read the rest of this entry »

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