GitHub simplifies code review and leaving comments

The workflow here is that the proposed patch gets uploaded to a GitHub branch or fork; the code reviewer is made aware of the patch, and goes to the commit page on GitHub, and hovers over the line numbers and clicks the ‘Add comment’ button and leaves a comment; the reviewer informs the author, and the author updates his patch. less than 1 minute read

Web 2.0 technologies in Student Assessment

Below should show up the wave (that is, if you have a Google Wave account), about a piece I am writing for a course on PhD Supervision I am following. The aim is to dig up old standards and how they apply to Web 2.0 technologies, including wikis, waves, blogs, source code repositories etc. less than 1 minute read

CIP rules #2: parsing @ and @@ from SMILES

I recently wrote about a project for a (partial) CIP implementation. This implementation is in place, and we are working towards setting up an extensive test suite. The data set we had in mind was available as SMILES and as MDL molfile. Now, the latter does not really specify the stereochemistry of the tetrahedral centers, and relies on wedge bonding. Actually, a few years ago Jonathan Brecher wrote up the IUPAC recommendation for the use of the wedge bond for chirality specification (doi:10.1351/pac200678101897), with 74 pages of rules and examples, like the following (copyright by authors or journal; I’m claiming fair use): less than 1 minute read

Wondering who will be the 100th Blue Obelisk eXchange user...

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Chem4Word goes Apache 2.0

Early March I reported about Konstantin’s JChemPaint-based chemistry plugin for OpenOffice, but there is (friendly) competition: Chem4Word. Being for Microsoft Word, the plugin only works on top of proprietary software, unfortunately; therefore, I cannot tell you if Chem4Word release is any good, but what Jim has showed me about a year ago, it is pretty cool. Another big difference is that Microsoft gave the Chem4Word a big grant, and Konstantin does not have such funding, AFAIK, and relies on community support. 1 minute read

CIP rules for stereochemistry

Uniquely identifying stereochemical enantiomers is an important aspect of data exchange of chemical structures. The simplest, most neglected solution is to pass around 3D models, but a lot of people like to stick to things like SMILES, or IUPAC names. Now, given that we want to uniquely represent the stereochemistry, we can use special rules. One example for enantiomers are the Cahn-Ingold-Prelog (CIP) rules. 3 minute read

ACS Liveblogging 1st Disclosures of Drug Candidates

Carmen liveblogged via her twitter account the disclosures of drug candidates at the past ACS meeting, and later aggregated the tweets in her blog. While many of her tweets made it into the FriendFeed room, the structure she drew up and shared did not make it. And until just know, I was not aware the had tweeted those too. The first twitpic she pushed was: less than 1 minute read