chem-bla-ics: May 2014

International Conference on Chemical Structures 2014

This Sunday the International Conference on Chemical Structures starts. If you aren't joining, it is important you know how to keep track of things online. First, follow the #iccs2014 hashtag on Twitter, and use the hashtag on any social platform. For example, I will bookmark papers mentioned in presentations on CiteULike. And slides that speakers put online, as well as coverage of other kinds, I'll link on Lanyrd. If you want to know what to expect, read this abstract book. And, of course, if you are attending the meeting, you can still join the online discussion.

May

Pathway analysis for Malaria research

A recurrent theme in my blog is that an easy way to support Open Science is to just join the show. You do not have to contribute a lot to have some impact. Of course, sometimes what you do has more impact than other times. Sometimes something with initially little impact gets high impact later. This is hard to predict, but maybe as well as the stock exchange.

May

Jean-Claude Bradley, Blue Obelisk award winner

There are nowadays a lot of people talking about Open, about open access, open data, open source. In fact, some discussion on Twitter resulted in the realization that it is highly unlikely that any scholar has not taken advantage of Open in some way in their research in the last few years. However, this is mostly due to people whom actually do, not by those who talk about it or use it.

One of the few people in chemistry who did both promoting Open and doing Open was Jean-Claude Bradley.

May

Changes in CDK 1.6 #5: the SMILES generator

I won't say much about this, as John already did. It's much faster, more functional that what the CDK had before. Some things to keep in mind, which I ran into when proofreading my Groovy Cheminformatics with the CDK book. Importantly, make sure to read the SMILESGeneration documentation, as it many new cool options, and like much of the new CDK code, performance was a goal and it therefore is faster.

May

Changes in CDK 1.6 #4: IsotopeFactory and Isotopes

A major CDK API change happened around the IsotopeFactory. Previously, this class was used to get isotope information, which it gets from an configurable XML file. This functionality is now available from the XMLIsotopeFactory class. However, to improve the speed of getting basic isotope information as well as to reduce the size of the core modules, CDK 1.6 introduces a Isotopes class, which contains information extracted from the XML file, but is available as a pure Java class.