Jun
27
Isbjørn #2: added recursion and FOAF support
I added recursion and FOAF support (foaf:page, foaf:homepage, foaf:depiction). More to follow, including CHEMINF support for properties.
Jun
27
Spidering the Semantic Web for Linked Open Drug Data (a start)
Hacking up a quick Bioclipse plugin to spider the Linked Open Drug Data network for useful information.
Jun
25
CDK gatekeepers do not scale
Some six years ago, the Linux kernel development hit a critical point: the observations that Linus does not scale. The CDK is facing the same similar issues now. Recently, the amount of activity has gone up, and both Rajarshi and I seem to have had less time than normal. As you know, the CDK project uses peer review, but, unfortunately, the amount of peer reviewing is low. Part of this is perhaps due to peoples' inexperience with git, which makes the review harder than needed.
Jun
22
Depiction of chemical graphs
I read just now about the new ChEBI release and particular this nice drug with gold in it:
This is a wonderful structure!
Notice the InChI given for this structure below, which shows actually a charge-separated structure. And this InChI has a "/q;;+1". That suggests to me that only the gold is charged, and thus that the full structure is charged. That does not match the drawing.
Is that inconsistent? Yes.
This is a wonderful structure!
Notice the InChI given for this structure below, which shows actually a charge-separated structure. And this InChI has a "/q;;+1". That suggests to me that only the gold is charged, and thus that the full structure is charged. That does not match the drawing.
Is that inconsistent? Yes.
Jun
22
CDK 1.4.11: the changes, the authors, and the reviewers
The CDK 1.4 series is really getting into slower waters. With only one new feature anticipated, we still see bug fixes though, and I'm sure there are a few left to review.
For me, the most important patch is that of Kevin for finding the position of double bond positions, important when taking SMILES input (see SMILES, Bioclipse, double bonds and Finding where to put double bonds...).
For me, the most important patch is that of Kevin for finding the position of double bond positions, important when taking SMILES input (see SMILES, Bioclipse, double bonds and Finding where to put double bonds...).
Jun
21
SMILES, Bioclipse, double bonds
I wrote the other day about Finding where to put double bonds... and that Kevin and Klas were writing code to address that issue. Klas' code is more general, but yet unfinished. For the upcoming Bioclipse 2.6 (yes, it is really happening!), we settled for the Kevin's code for a post-processing after SMILES parsing.
Jun
9
200 nanomaterials in the database
Capturing the nanomaterial-property and nanomaterial-activity
(toxicology-related) spaces.
(toxicology-related) spaces.
Jun
8
Adding papers in Mendeley by DOI
I'm sure all the Mendeley users know that already, but you can very easily add papers by DOI (Add entry manually). Just click the looking glass icon.
Jun
5
Thousands of people do not want to be a bioinformatician
Shocking to see how many people want to learn how not to be a bioinformatician (doi:10.1186/1751-0473-7-3)!
If you want to learn how to become one instead, read our editorial in this first Open Research Computing special issue instead (doi:10.1186/1751-0473-7-2).
If you want to learn how to become one instead, read our editorial in this first Open Research Computing special issue instead (doi:10.1186/1751-0473-7-2).
Jun
3
Tax-paid research as innovation infrastructure
We pay tax to fund things we are a community have a need for: public transport, infrastructure to support industry, health care, etc. We also fund universities, because we've learned that an increased knowledge about the things around us, are good for the country too.
However, we typically leave in the middle what is good for the country. It is debatable.
However, we typically leave in the middle what is good for the country. It is debatable.
