Green Lab Notebook app now available on iTunes

gln_rxneditAfter somewhat more delay than I would have liked, the Green Lab Notebook (GLN) app is now live and available on the iTunes AppStore. The feature set that made its way into version 1.0 was crafted to ensure that editing of multistep reaction experiments and automatic calculation of green chemistry metrics are fully functional, and that importing and exporting features are complete enough to be effective. Read the rest of this entry »

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Publishing with PeerJ: first paper and first impressions

Spoiler: the experience of publishing a manuscript with PeerJ was very positive. My first paper published with them just arrived online: Fast and accurate semantic annotation of bioassays exploiting a hybrid of machine learning and user confirmation. This is a summary of the work that I was doing in San Francisco for the first half of summer 2014 (with Collaborative Drug Discovery), and it describes a hybrid machine learning/interactive method for marking up bioassay data, which is an optimised compromise between the two extremes of methods for taking plain text and turning it into semantically rich markup. Read the rest of this entry »

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Summer of 2014: roundup

Things have been a little quiet on this blog lately, as well as the Molecular Materials Informatics website, and indeed in the secret laboratory: and there is a perfectly good explanation for that – I’ve been away. For the last few months I’ve been quietly roosting in San Francisco, working on an interesting and exciting project at the bay area HQ of Collaborative Drug Discovery. Not wanting to put out any spoilers, but the beans will be spilled very soon via PeerJ, which should be releasing a paper with my name on it very soon indeed.

I left San Francisco a couple of weeks ago, which unfortunately means I didn’t get to attend the ACS meeting that many of you are heading towards right about now, but there is a perfectly good explanation for that, too: at the end of last month, I turned 40, and decided to celebrate this milestone by returning to my home country of New Zealand, which I have not been back to for a long time. It was a delightful trip, albeit too short: after having been away from my normal home (in Montreal) for more than 4 months, the things-to-do list was piling up quite high, as it tends to do. Read the rest of this entry »

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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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