2008
December
- Editing and Validation of CML documents in Bioclipse
- 11 Years of Debian
- State of CDK 1.2.0...
- Peer reviewed Cheminformatics #2: Code review for the Chemistry Development Kit
- Cheminformatics Benchmark Project #1
- Who says Java is not fast?!?
- Short variables and lack of comments...
November
- Parallel building the CDK
- Software is a Method (Meme)
- Scripting JChemPaint
- Solubility Data in Bioclipse #1
- Re: Open Source != peer review
- Finding the commit that causes the regressions...
- Open{Data|Source|Standards} is not enough: we need Open Projects
- Next generation asynchronous webservices #2
- EMBRACE workshop in Uppsala
October
- Next generation asynchronous webservices
- Embedding Gists in blogs
- Bioclipse2 Scripting #1: from SMILES to a UFF optimized structure in Jmol
- Git-Eclipse integration
- Bugzilla Eclipse IDE integration: Mylyn
- GitToDo support for Freemind: graphical mapping of important things on my schedule
- Chemical Editing...
- Chem-bla-ics turns 3!
- Chemoinformatics p0wned by cheminformatics... #2
- Jmol 11.6 RC 18 in Bioclipse
- pKa prediction, or, how to convert a JCIM paper into Java
- Who likes my FriendFeed posts most...
- JChemPaint history: CML patches in 1999
- Cherry-picking commits from CDK trunk: how to make a reasonable commit message
September
- Git mirror for the CDK
- Moved to Sweden: Post-doc in the Bioclipse group of Prof. Jarl Wikberg
- FriendFeed for the Chemistry Development Kit
- CDK development with branches using Git
- Ubiquity fun: entering semantic markup as easy as running a Ubiquity command
- Ubiquity fun: resolving DOIs
August
- Creating CMLReact from UsefulChem Ugi Reactions
- UgiChem2CML
- Science Blogging 2008 London was Cool!
- Leaving to Science Blogging 2008 London
- MetWare screenshot: propagating XML Schema data types
- MetWare screenshot: spectrum support #2
- MetWare screenshot: spectrum support
- Profiling the CDK atom typer
- Scientific progress is a primary human need
- Mapping Peoples Interest: Google Insight Search
- "The End of Theory: The Data Deluge Makes the Scientific Method Obsolete"
- Online, multiplayer metabolomics game!
July
- CDK Literature #5
- Molecular QSAR descriptors in the CDK
- Commercial QSAR modeling? Sorry, already patented...
- Peer reviewed Chemoinformatics: Why OpenSource Chemoinformatics should be the default
- Metabolomics needs you
- Going to Science Blogging 2008: London
- Chemoinformatics p0wned by cheminformatics...
- SVN commit hooks down for CDK and Bioclipse
- Moving to Sweden: Improving CDK support in Bioclipse
June
- The CDK Community: Developers, Members, and Users
- The SWT JChemPaint (viewing) widget
- Graphical overview of my bookmarks
- Recovering full mass spectra from GC-MS data #2
- Recovering full mass spectra from GC-MS data
- Good Scientists Pimp there Research (was: Damn, I'm boring...)
- Finding differences between IChemObjects #2
- Finding differences between IChemObjects
May
- Development of the new JChemPaint
- Metware Status Report
- John Wilbanks replies to the ChemSpider/OpenData discussion
- Does ChemSpider really violate Open Data with CC SA?
- Re: What should a Nature Chemistry paper look like?
- Wicked chemistry and unit testing
- Comparing JUnit test results between CDK trunk/ and a branch #2
April
- MetWare, SKOS and Java Server Faces
- JChemPaint for Bioclipse2
- Blog Comments? No, Peer Reviews!
- Comments on 'Rethinking software access'
- More CDK-Ruby users...
- Quality Publishing: EndNote versus InChIs
- Open Access / Open Data leads to added value
- "Make all research results CC-BY"
- The MetWare developers meeting in Halle
- The CDK/Metabolomics/Chemometrics Unconference results
- Legal Advice Needed: the NIH restricting access to our CC-licensed research results
- T plus 51 hours: a short photo impression
- T plus 18 hours: dr and preparing for the afterparty, umm ^w^w^w, CDK/Metabolomics/Chemometrics unconference
- T minus 26 hours: defending open source chemoinformatics (and more)
March
- CDK Module dependencies #2
- Be in my Advisory Board #3: JChemPaint widgets?
- My FOAF network #5: SPARQL-ing my network
- My FOAF network #4: Tabulating my publications
- Sugammadex: the molecular condom
- My FOAF network #3: My publications
- The Chemical Object Identifier; or, the freedom to identify chemicals
- My FOAF network #2: XSLT for a HTML GUI
- Metabolomics Ontologies: SKOS-ified the ArMet specification
- Jane, find me interesting journals, please.
- TODO: April 2nd, defend my PhD work
February
- Where's the maize genome torrent?!?
- CDK is now available from your nearest Debian mirror
- CDK close to entering Debian
- Simple, Open Bug Track System: social bookmarking
- Performance: C, C++, C#, Java, Perl and Python
- Defining Development Goals: LaunchPad complements SourceForge
- 10000 CDK commits!