Archive
2024
June
- cdk2024 #3: an unexpected downstream project
- Two meetings: ELIXIR Toxicology and FAIR4ChemNL
- New paper: FAIR assessment of nanosafety data reusability with community standards
May
- New paper: A template wizard for the cocreation of machine-readable data-reporting to harmonize the evaluation of (nano)materials
- New paper: From papers to RDF-based integration of physicochemical data and adverse outcome pathways for nanomaterials
- cdk2024 #2: publishing grant proposals
April
- cdk2024 #1: NWO Open Science grant for the Chemistry Development Kit
- Open Science Retreat #2: CiTO Nanopublications
March
February
January
2023
November
September
- Artificial intelligence for natural product drug discovery
- Using FAIR to select data for reuse
- Making BridgeDb Derby files with Groovy
- American Chemical Society Fall 2023 meeting
August
- Last post there / the Freebie model online
- Boiling points in Wikidata
- History, provenance, detail
- Blog planets: blogging about Debian, GNOME, Wikimedia, FSFE, and many more
July
- Archiving and updating my blog
- Universities and open infrastructures
- Journal Rankings
- Qeios, an open dissemination platform for research output
- Twitter exits FAIR and is no longer a dissemination solution
June
May
- Information Retrieval versus ChatGPT
- Paper: The FAIR Cookbook - the essential resource for and by FAIR doers
April
2022
November
- Finding Mastodon accounts with Wikidata (a few SPARQL queries)
- Wikidata script for SMILES, SMARTS, and CXSMILES depiction
- s/Twitter/Mastodon/g
August
March
2021
November
2020
July
- Bioclipse git experiences #2: Create patches for individual plugins/features
- Bioclipse git experiences #1: Strip away unwanted plugins
2017
December
November
2016
March
January
2015
April
2013
November
2012
February
2011
September
August
April
January
2010
October
September
August
- The Molecular Chemometrics Principles #3: stand on shoulders
- The Molecular Chemometrics Principles #2: be clear in what you mean
- The Molecular Chemometrics Principles #1: access to data
- Oxford… #2
- Oxford…
February
2008
October
2006
May
- Open Text Mining Interface and Bioclipse
- Four graph mining methods integrated in ParMol
- Nightly CDK builds now available
April
- Protein support in Bioclipse using Jmol and the CDK
- Download statistics for chemblaics components
- Postgenomic.com maps upcoming conferences
- The CDK data classes and change notifications
- Getting Jmol’s ‘cartoon on’ to work in Bioclipse
- Mining the KEGG pathway database with self-organizing maps
- Uncertainty in NMR based 3D protein models
- Free online ChemConf 2006 conference
March
- InChI’s in LaTex and CDK News
- The Cologne University BioInformatics Center (CUBIC)
- How to make money from Open Source scientific software
- The PDB protein database uses Jmol
- Open source in drug discovery
- More chemistry in KDE
- Classpath 0.90 makes the Jmol application run
- Progress with CMLRSS plugin for Bioclipse
February
- Open source Jmol taking over the world
- Hacking InChI support into postgenomic.com
- Novel QSAR and QSPR descriptors?
- BlueObelisk: OpenSource, OpenData and OpenStandards
- Blogging chemistry on blogspot.com
- Chemical reactions in CML
- Hot articles; mining the semantic web
- Kalzium Wins Award; Carsten Niehaus Interviewed
- An test suite for free, open source JVMs
- Tagging blog items
- A blog about bioinformatics, semantic web, comics and social networks.
- Skype on Kubuntu using a Tiptel USB telephone
- Dutch Google News themes messed up
- Open source Jmol hits student text book Biochemistry
January
- 1D NMR Spectra do not work in QSPR
- Trouble running the CDK JUnit tests with Cacao and Kaffe
- Free at last!
- USPTO considers open source software prior art
- Open Source Java tool chain: CDK compiles and JUnit tests run
- Kubuntu, XRandR and TV-OUT
2005
December
- The good, the bad and the ugly molecules
- Knoppix saves the day…
- Subset selection: mind the complexity
- StatCVS on CDK
- CDK Debug classes and fixing the ModelBuilder3D bug
- Math libraries for Java?
- Jumbo 5.0 and the CDK
- Jumbo 5.0 and CML support in CDK
- UML diagram of CDK module dependencies
- Planet Blue Obelisk website updates
- About JChemPaint’s future and todays 2.1.5 release
November
- KDE 3.5 is out
- Getting Started with Eclipse and the SWT
- A Blue Obelisk blog Planet
- Open Source Swing: Jmol renderer runs!
- Machine crash; SVN went along
- Bioclipse: the chemo-/bioinformatics workbench
- Open Source Swing: JChemPaint runs!
- The goal: a live chemblaics CD
- Back from the 1st GCC
- Going to the German Chemoinformatics Conference
- Scons and bksys for kfile_chemical
- When to stop including QSAR model variables…
- A R GUI: rkward
- Ubuntu Dapper will include chemistry features
- R/CDK install fails on GCC 4.0 systems
- Open Source data mining in chemoinformatics
- The annual Lunteren meeting
October
- CDK News
- kfile_chemical gets XYZ, Mol2, SMILES, VMD and GenBank support
- My birthday (31) and the Adsense
- More cdk.interfaces updates
- JChemPaint applet download size: 538kB
- Wrapping up…
- Viagra saves the environment
- CDK News 2.3 and InChI’s
- Jmol’s FAH team in Top 800
- InChI meta data with kfile_chemical
- CDK-Taverna fully recognized
- CIA statistics for Blue Obelisk
- Single PDFs for CDK News articles
- Chem-bla-ics