2009
December
- BlueObelisk StackExchange: summary of the first month
- December wrap up. X-mas holidays at last!
- CDK 1.3.1: the changes
November
- SWAT4LS: wrapping up #1
- SWAT4LS: "Linking Open Drug Data to Cheminformatics and Proteochemometrics"
- Linking two Virtuoso instances to one Apache server
- Open Notebook Science Solubility: the SPARQL end point
- ChemPedia RDF #1: the SPARQL end point
- CDK 1.2.4: the authors
- CDK 1.2.4: the changes
- BlueObelisk StackExchange (.com)
- Call for Collaboration: JavaDoc validation with OpenJavaDocCheck
- New Bioclipse Features: Kabsch Alignment, RMSD Distance and Tanimoto Simarlity Matrices
- Milestones...
- Bioclipse Manager for MyExperiment.org
October
- Maintaining patches is fixing patches
- CrossRef writes up RSS usage recommendations
- Work in Progress: an Open DocCheck replacement
- PMD 2.4.5 installed in the CDK 1.2.x branch
- SPARQL end points, Jena and bif:contains
- NMRShiftDB RDF #3: Bio2RDF
- Where are the CDK 1.3.1 and 1.2.4 releases ?!?
- VR.se funded research to be OA as of 2010
- Keeping my Bioclipse repositories in sync with upstream
- CDK Molecules in RDF
- Google Wave Invite: but you need to work on the CDK and the CDKitty robot
- Processing the ChEBI MDL SD file with the CDK
September
- Extension point for running JUnit tests in a RCP Application instance?
- JChemPaint update: merging of patches and CDK statistics
- My HTML+RDFa homepage
- Really free chemistry books
- VRMS meme: how much non-free software are you running?
- Bioclipse, RDF and defeasible reasoning
- Open Chemical Data #1: NMRShiftDB
- The Art of Programming: do not leak implementation details
- Updated Bioclipse SDK: the Eclipse 3.5 version
- NMRShiftDB RDF #2: Some statistics
- NMRShiftDB RDF #1: Spectra by InChI
- NMRShiftDB enters rdf.openmolecules.net #2: SPARQL end point with Virtuoso
- Open Knowledge: Reproducibility in Cheminformatics with ODOSOS
- Google Wave robot for CDK functionality
August
- Reminder: my talk in Frankfurt on Monday; Want to meet up?
- PLoS ONE and Chemical blogspace: About no Impact yet
- Bioclipse and SPARQL end points #2: MyExperiment
- The Social Web does not wait for Bioclipse... here comes Google Wave
- Bioclipse enters the social web
- Bioclipse and SPARQL end points
- Making Bioclipse Development easier: the New Manager Wizard
- "LAST CALL: XEP-0244 (IO Data)"
- Searching PubChem from within Bioclipse
- ChemSpider fail #1: SMILES
- Running Bioclipse Plugin Unit tests: solving the XPCOM error
- Dear Advisory Board: which QSAR descriptors would you like to see implemented in the CDK?
- JChemPaint-Primary being picked up...
July
- Maintaining the JChemPaint-Primary patch
- Things to check before you consider submitting a (final) CDK patch #1
- New Blogs #11
- New Blogs #10
- Updating my bioclipse.qsar fork with Ola's main branch
- ELN vendor: "The Open Source stuff just works better"
- Bioclipse moving to GitHub: CIA hooks enabled
- JChemPaint-Primary moving to Git
- Bioclipse-JChemPaint #2
- Knowledge Management - Ontologies
- Bioclipse for CDK Developers #2
June
- Making patches; Attribution; Copyright and License.
- JChemPaint hack session at Uppsala
- Michel Dumontier at Uppsala University
- The Dr Who's of Life Sciences
- Bioclipse-JChemPaint
- No, PDFs really do suck!
May
- Bioclipse beta5: really the last one now
- Open Data: license, rights, aggregation, clean interfaces?
- ChemSpider and the RSC: where next?
- Which feature must I install for org.eclipse.zest?
- PubChem-CDK
- Nomination of the CDK for a SF Community Award
- /me is having Bioclipse/XMPP/RDF fun
- Thesis and copyright transfer
April
- New FriendFeed layout, but there is a fix...
- Things to do...
- CDK Workshop 2009 #3
- My CDK Workshop 2009 Course Material #2
- CDK Workshop 2009 #2
- CDK Workshop 2009 #1
- My CDK Workshop 2009 Course Material
- Downloading Domoic Acid from PubChem
- CDK 1.2.1 Released
- Bioclipse2 Scripting #3: XLogP calculatation using a XMPP CDK cloud service
- Multiple inheritence for content types?
- Rednael, CDK Git for Rajarshi's patches, PubChem SDF
- Groovy CDK and the Keyword List
- "Open Knowledge: Reproducibility in Cheminformatics with Open Data, Open Source and Open Standards"
- Nature Jobs - Google Map mashup
- CDK - The Documentation
March
- StARlite talks in Uppsala; Helena's Open Chemogenomics thesis
- Highlighting Console output in Eclipse with Grep Console
- Journal of Cheminformatics: I hope the Instructions to the Authors improve
- Preferential positions of phophate counter ions
- Nature Chemistry improves publishing chemistry: a detailed analysis
- NMRShiftDB enters rdf.openmolecules.net
- Autogenerating CML bindings for XMPP services with XMLBeans
- Bioclipse: a powerful Jmol application
- Open NMR data: raw curves and annotated peak lists
- Open Data versus Capatalism?
- Solubility Data in Bioclipse #4: Finding ChEBI IDs (Again, but better)
February
- Solubility Data in Bioclipse #3: Finding ChEBI IDs
- RDF for chemistry
- Solubility Data in Bioclipse #2: handling RDF
- Bioclipse2 Scripting #2: searching PubChem
- DBPedia enters rdf.openmolecules.net
- Bioclipse for CDK Developers #1
- Blogger Degrading...
- DBPedia: lookup and autocomplete of chemistry
- CDK 1.2 Release Candidate
- Where can I host my experimental data? Open Submission Chemistry Databases #1
- Why can't SourceForge just remember me?
- YouTube for Chemistry
January
- MetWare presentation at Metabolomics Workshop
- Statistics on the Development Community
- Details behind the "Calling XMPP cloud services from Taverna2"
- Calling XMPP cloud services from Taverna2
- RSC now allows Jmol in main text of publication... well, almost
- Bioclipse and Gist integration
- Editing and Validation of PubChem XML documents