Dec
21
BlueObelisk StackExchange: summary of the first month
The Blue Obelisk StackExchange (BOx) has seen a relatively good start, but the number of questions is dropping.
Dec
19
December wrap up. X-mas holidays at last!
Wow, I just saw it has been 17 days since my last post already :( That's a new record, I think! A lot has happened actually, but I have not had time to write up things. Actually, I have still have SWAT4LS coverage left to do :(
Latex
Anyway, one of the things our group has been up to in the last two weeks, is writing a book to support of the free, online Pharmaceutical Bioinformatics course.
Latex
Anyway, one of the things our group has been up to in the last two weeks, is writing a book to support of the free, online Pharmaceutical Bioinformatics course.
Dec
2
CDK 1.3.1: the changes
Two weeks ago, I released CDK 1.2.4. Anay reported fails with generating the JavaDoc from the packages, which I think I both fixed now; the uploaded 1.2.4.1 packages on SourceForge include these fixes.
The 1.2.4 release was soon followed by 1.3.1. Unfortunately, uploading the packages to to SourceForge over 3G with Chrome did not work well, so only finished that today. CDK 1.3.1 is the second release in the development branch, and brings in new functionality but also API changes.
The 1.2.4 release was soon followed by 1.3.1. Unfortunately, uploading the packages to to SourceForge over 3G with Chrome did not work well, so only finished that today. CDK 1.3.1 is the second release in the development branch, and brings in new functionality but also API changes.
Nov
25
SWAT4LS: wrapping up #1
It's already been five days since the SWAT4LS meeting (matching blog), and finally got around to writing up my personal summary. I very much enjoyed the Blue Obelisk dinner on Thursday evening with Nico, Duncan and Miguel (the CDK one).
Nov
20
SWAT4LS: "Linking Open Drug Data to Cheminformatics and Proteochemometrics"
Please find below the presentation I gave today at SWAT4LS:
Linking Open Drug Data to Cheminformatics and Proteochemometrics from Egon Willighagen
Linking Open Drug Data to Cheminformatics and Proteochemometrics from Egon Willighagen
Nov
20
Linking two Virtuoso instances to one Apache server
Virtuoso comes with its own web front end, but I did not want to make that public. Additionally, I actually have two instances running, one for the GNU FDL licensed NMRShiftDB data, and one for the CC0 ChemPedia and Solubility data sets.
So, I used Apache's proxy module linking to two Virtuoso instances. These two are set up by just duplicating a data based folder and to have it use two virtuoso.ini config files.
So, I used Apache's proxy module linking to two Virtuoso instances. These two are set up by just duplicating a data based folder and to have it use two virtuoso.ini config files.
Nov
19
ChemPedia RDF #1: the SPARQL end point
Well, you might spot a pattern here; yes, another chemical SPARQL end point (actually, it shares the end point with the Solubility data). This time around Rich's ChemPedia. Taking advantage of the CC0-licensed downloads, I have created a small Groovy script (using this JSON library) to convert the ChemPedia JSON into Notation3:import net.sf.json.groovy.JsonSlurper;
input = new File("substances.json")
json = new JsonSlurper().parse(input);
println "@prefix dc: <http://purl.org/dc/elements/1.
input = new File("substances.json")
json = new JsonSlurper().parse(input);
println "@prefix dc: <http://purl.org/dc/elements/1.
Nov
19
Open Notebook Science Solubility: the SPARQL end point
The Open Notebook Science Solubility challenge is an project crowd sourcing solubility of organic compounds in non-aqueous solvents. I have been working on RDF-ing this data: Solubility Data in Bioclipse #1 Solubility Data in Bioclipse #2: handling RDF Solubility Data in Bioclipse #3: Finding ChEBI IDs Solubility Data in Bioclipse #4: Finding ChEBI IDs (Again, but better) And this resulted in a joint chapter in the nice Beatiful Data book.
Nov
18
CDK 1.2.4: the authors
The CDK 1.2.4 changelog I posted earlier was directly created from git output. Git has many features which makes such thing simple. Here's a list of authors of the 1.2.4 change set:
56 Egon Willighagen 9 Rajarshi Guha 5 Stefan Kuhn 2 mark_rynbeek 1 Uli Köhler 1 Rajarshi Guha 1 Peter Odéus 1 Paul Turner 1 Miguel Rojas Cherto 1 Arvid BergThis is just the number of commits, and many of mine are logistic in nature.
56 Egon Willighagen 9 Rajarshi Guha 5 Stefan Kuhn 2 mark_rynbeek 1 Uli Köhler 1 Rajarshi Guha 1 Peter Odéus 1 Paul Turner 1 Miguel Rojas Cherto 1 Arvid BergThis is just the number of commits, and many of mine are logistic in nature.
Nov
18
CDK 1.2.4: the changes
Here is the changelog of CDK 1.2.4 which I am about to upload to SourceForge:
Fixed param name 743bad3 Updated the makefp3d target to work with the current build system bbb78ee Set up a branch for the 1.2.4 release 4801d79 Fixes bug 2898399. Updates to the SMARTS parser to handle proper matching for explicit hydrogens (including H, 1H, 2H and 3H). SMARTSQueryVisitor updated to take into account different isotopes of H. Also updated unit tests to take into account proper H matching.
Fixed param name 743bad3 Updated the makefp3d target to work with the current build system bbb78ee Set up a branch for the 1.2.4 release 4801d79 Fixes bug 2898399. Updates to the SMARTS parser to handle proper matching for explicit hydrogens (including H, 1H, 2H and 3H). SMARTSQueryVisitor updated to take into account different isotopes of H. Also updated unit tests to take into account proper H matching.
