BitTorrents for Science

The idea has been lingering in the air for a long time now: sharing large science data sets using bittorrent. Over the past couple of years I have seen a lot of science related software being distributed over torrents, and the use in open source in general is abundant. Given a good network of so-called seeders, download times go down dramatically, and the overall energy consumption goes down too, as data has to follow a much shorter path.

3 minute read

CDK-JChemPaint #3: rendering parameters

OK, one last CDK-JChemPaint tutorial for today (see #1 and #2). Rendering wasn’t as much fun, if you could not tune it to your needs. JChemPaint has long had many rendering parameters, and one by one we are converting them to the new API. The following code is an modification to the first example, and adds some code to list all rendering parameters for the three used generators:

1 minute read

CDK-JChemPaint #2: rendering reactions

I posted earlier today a Groovy script to render molecules with CDK-JChemPaint 8. Now, the new JChemPaint rendering engine also contains the functionality to render reactions. So, I can also do:

1 minute read

CDK-JChemPaint #1: rendering molecules

I reported earlier that the CDK-JChemPaint patch is now a clean add-on from the CDK releases. This means that you download cdk-1.3.4.jar and cdk-jchempaint-8.jar separately, put them in your class path, and get started with, for example, Groovy:

1 minute read

New Blue Obelisk Exchange online at Shapado.com

StackOverflow has served as very well in the past couple of months with the Blue Obelisk Exchange. The BOx was taking advantage of a beta project of StackOverflow, and users of that program can switch to a payed plan after the beta phase was over. That moment is nearing, but the pricing model is just unrealistic for us. There were also some comments on the Blue Obelisk using proprietary software (see Stackoverflow not open source — not a problem?).

less than 1 minute read

OpenTox Virtual Seminar, Thursday April 1, 11.00 CEST

Today I gave a presentation of my research, the CDK, Bioclipse, and recent RDF work:

less than 1 minute read

Cleaner CDK Code #4: inheriting JavaDoc from super classes and interfaces

When you write a class implementing an interface or extending a super class, it is often the case that the API is identical. It would be nice to inherit the JavaDoc documentation, which is possible.

less than 1 minute read