2010

December

• The 100th Blue Obelisk 2006 paper citation
• Text mining chemistry from Dutch or Swedish texts
• Blogging as part of your workflow
• Converting JSON to RDF/XML with Groovy
• What should a free CC0 RDF hosting for scientists look like?
• My first encounter with Open Source cheminformatics
• Oscar: training data, models, etc
• Status update on BJOC analysis with Oscar and ChemicalTagger #3
• re: Commercial or Proprietary?
• Commercial or Proprietary?
• Re: Why I and you should avoid NC licences
• Open Research Computation, ORC, #openrescomp
• My talk at Imperial College
• Supramolecular chemistry
• Status update on BJOC analysis with Oscar and ChemicalTagger #2
• Status update on BJOC analysis with Oscar and ChemicalTagger
• Trust has no place in science #2
• How many hydrogen-bond acceptor groups does triazole have?
• Trust has no place in science
• What is 'hes'?
• Konqueror Web Shortcuts for CHEMINF
• ChemWriter, Google Chrome, and Many Eyes in Open Source

November

• Adding a new dictionary to Oscar
• Uppsala Status Report
• Installing Oscar
• More fails... (aka: no VR grant awarded)
• Why you have not heard me much about chemometrics recently...
• Oscar4 command line utilities
• TTT it is

October

• CiteULike CiTO Use Case #1: Wordles
• Calculating molecular descriptors with OpenTox
• Uninformative Blue Obelisk eXchange notification
• Algorithm or Model: OpenTox API quiz
• Oscar4 Java API: chemical name dictionaries
• CDK 1.2 to 1.4 API changes #2: implicit hydrogens
• CDK 1.2 to 1.4 API changes #1: creating objects with an IChemObjectBuilder
• Multiple unit test inheritance with JExample
• Really free chemistry books #2: @bookboon
• The Answer to: Are these organic molecules the same?
• Cb: New Blogs #14
• Oscar text mining in Taverna
• Royce Murray and Caveat Emptor
• Working on Oscar for three months
• Are these organic molecules the same?
• Mapping BioStar users onto the world map
• CDK Book in progress
• The 100th CDK 2003 paper
• RDFa support in CiteULike

September

• Visualizing data embedded in XHTML+RDFa
• Quo vadis, CDK?
• Using PubChem to create CDK unit tests
• Presentation at AstraZeneca
• Noel's chemical ASCII art
• The CDK 2003 paper is now cited 99 times
• A list of things I miss in CiteULike
• xournal: free annotator for PDFs
• Call for Papers: Thematic Series about RDF in Chemistry
• CDK 1.3.6: the changes, authors, and reviewers
• CDK 1.2.7: the changes, the authors, and the reviewers
• Pulling out data as JSON from XHTML+RDFa
• Second #acs_boston talk: teaching scientific communication
• Handbook of Chemoinformatics Algorithms
• Data duplication at Mendeley
• BioMed Central is going to support Open Data

August

• Added a Simile Timeline to my homepage
• Third #acs_boston talk: the Orbital Development Kit
• First #acs_boston talk: Linking RDF to cheminformatics and proteochemometrics
• Skyline of #Boston walking to the convention center at 6:45am #acs_boston
• #ACS_Boston #acsrdf2010 ? It's all about Open Standards!
• Specifying unit test dependencies with JExample
• The Molecular Chemometrics Principles #3: stand on shoulders
• The Molecular Chemometrics Principles #2: be clear in what you mean
• XHTML+RDFa: chemical examples
• XHTML+RDFa Template
• The Molecular Chemometrics Principles #1: access to data
• Cleaner CDK Code #8: the Java Naming Conventions and Camel Casing
• Oxford... #2
• Cleaner CDK Code #7: understand what the code is supposed to do
• Using Bioclipse to upload data to an OpenTox server
• Is there an Open Specification for structure normalization?
• Oxford...

July

• CDK 1.2.6: the changes and the authors
• An Ubuntu Blue Obelisk meta package
• My worst cited paper: supervised self-organizing maps
• Script logs as HTML+RDFa: mix free text reporting with CSV
• Amazon, the Kindle edition is more expensive than the paperback??
• Setting up a local Semantic MediaWiki with RDFIO and SPARQL support
• RDFaDev: HTML+RDFa development with FireFox
• A new CDK default fingerprinter?
• Cb: New Blogs #13
• Aggregating my blogs on this blog using labels

June

• Program for the RDF symposium at the American Chemical Society fall meeting
• Critical mass for Open Notebook Science wikis by prepopulation with RDF data
• All CrystalEye data available as PDDL
• Looking at your statistical models...
• QSPR modeling with signatures
• My OpenTox Workshop contribution: The Lost Slides
• I’m just a sucker with no self esteem
• CDK-JChemPaint #6: rendering atom numbers
• And now for something completely different...

May

• My OpenTox Workshop contribution: Linking explicit and implicit knowledge
• CDK 1.3.5
• PMD code checking: checking for programming against CDK interfaces
• Cleaner CDK Code #6: set the CDKException's cause Exception
• CKAN 1.0: A major contribution to Open Knowledge
• Cleaner CDK Code #5: develop against interfaces
• Three ACS-RDF sessions
• My favourite chemistry things
• How to use GitHub for [CDK|Bioclipse] code review
• GitHub simplifies code review and leaving comments
• Web 2.0 technologies in Student Assessment
• CIP rules #2: parsing @ and @@ from SMILES

April

• Wondering who will be the 100th Blue Obelisk eXchange user...
• Chem4Word goes Apache 2.0
• CIP rules for stereochemistry
• ACS Liveblogging 1st Disclosures of Drug Candidates
• CDK-JChemPaint #5: the Groovy-JChemPaint repository
• CDK-JChemPaint #4: embedding the renderer into a Swing panel
• BitTorrents for Science
• CDK-JChemPaint #3: rendering parameters
• CDK-JChemPaint #2: rendering reactions
• CDK-JChemPaint #1: rendering molecules
• New Blue Obelisk Exchange online at Shapado.com
• OpenTox Virtual Seminar, Thursday April 1, 11.00 CEST

March

• Cleaner CDK Code #4: inheriting JavaDoc from super classes and interfaces
• ACS Boston: RDF Symposium update
• CDK-Taverna paper published
• Updated my blog template
• Cleaner CDK Code #3: run the PMD tests
• Oxford, August 2010: eCheminfo Predictive ADME & Toxicology 2010 Workshop
• Cleaner CDK Code #2: String.contains() and logger messages
• RDF-powered QSAR wizard: SPARQL end points providing wizard content
• Cleaner CDK Code #1: List<IAtom> and the for-each loop
• OOChemistry 0.1 released: call for participation
• CDK 1.3.3: the changes
• RDF, Jena, Bioclipse, Eclipse, Zest #2: icons and an extension point

February

• Dutch contribution to the Crystallography Open Database at risk?
• What IF or Article Level Metrics does not tell you...
• Further statistics on the papers citing the CDK
• Wordle of the titles of the 20 most recent papers citing the first CDK article (as identified by WoS)
• Open Data: the Panton Principles
• Citing the Chemistry Development Kit
• Google Scholar allows downloading as BibTeX
• JChemPaint in OpenOffice.org! Cheers to Konstantin!
• Bioclipse understands ontologies: note how the InChI is not part of the RDF graph
• ChEMBL RDF #1:SPARQL end point
• RDF, Jena, Bioclipse, Eclipse, Zest: Mashups
• Average time on Site: chem-bla-ics
• UU Cheminformatics Journal Club
• CDK 1.3.2: the changes
• Google Translation in Gmail in action
• Journal of Chemical Information and Modeling 50th Anniversary

January

• Validating MDL SD files and Symyx molfiles with the CDK
• CDK 1.2.5: the changes
• Semantic Web features in Bioclipse 2.2
• Semantic Chemistry with the Resource Description Framework
• Extracting RDF from Chem4Word documents
• Installation HOWTO for CDK-Taverna 0.5.1.1 in Taverna 1.7.2
• Warren DeLano and the future of PyMOL
• Very cold in Uppsala!