Archive
2025
March
- New preprint: “BioHackEU24 report: ORCID and ROR identifiers in BioHackrXiv reports”
- cdk2024 #5: Chemistry Development Kit User Group Meeting - Day 2
- cdk2024 #4: Chemistry Development Kit User Group Meeting - Day 1
- One Million IUPAC names
February
January
- s/BiGCaT/Translational Genomics/g
- Niche papers and citation intentions
- Blog updates
- Serious Request: the results
- ISAAC Chrome Extension
2024
December
- FAIR blog-to-blog citations
- Archiving blogs
- Serious Request: “WikiPathways in actie voor MetaKids”
- Richard L. Apodaca
November
- Version of record, and what Open Access must learn from Open Science
- SPARQL examples: SIB model, software, and patches
- Mastodon, RSS, BlueSky
October
- Additional files, data, datasets, databases, and published data
- New paper: The Virtual Human Platform for Safety Assessment (VHP4Safety)
- NASA Transform to Open Science (TOPS) Open Science 101
September
- Patents, societal impact, and sustainability
- Better Publishing
- Adding citations between existing articles in Wikidata
August
- Scholia configurability
- Kasabi archive at the Internet Archive
- Scholarly discussions through the eyes of CiTO (and Wikidata)
- CiTO updates: Wakefield and WikiPathways
July
- New paper: “Discovering life’s directed metabolic (sub)paths to interpret human biochemical markers using the DSMN tool”
- GoatCounter, Rogue Scholar and more new things
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
October
August
May
April
March
2021
November
August
February
2020
July
- Bioclipse git experiences #2: Create patches for individual plugins/features
- Bioclipse git experiences #1: Strip away unwanted plugins
2019
March
2018
December
November
September
2017
December
November
October
2016
December
March
January
2015
April
January
2014
November
- Programming in the Life Sciences #20: extracting data from JSON
- Programming in the Life Sciences #19: debugging
- Programming in the Life Sciences #17: The Open PHACTS scientific questions
August
February
- Slow publishing innovation: SMILES in ACS journals
- Elsevier’s new text mining initiative is a step sideways
2013
November
October
- Programming in the Life Sciences #9: APIs and Web Services
- Programming in the Life Sciences #11: HTML
- Programming in the Life Sciences #10: JavaScript Object Notation (JSON)
- Programming in the Life Sciences #8: coding standards
- Programming in the Life Sciences #7: theory
- Programming in the Life Sciences #6: functions
- Programming in the Life Sciences #5: converting the results into HTML
- Programming in the Life Sciences #4: communication from within HTML
- Programming in the Life Sciences #3: the assessment
- Programming in the Life Sciences #2: accounts and API keys
- Programming in the Life Sciences #1: a six day course
May
2012
April
March
February
January
2011
November
October
September
August
July
April
February
January
2010
December
- Text mining chemistry from Dutch or Swedish texts
- Converting JSON to RDF/XML with Groovy
- Oscar: training data, models, etc
- Status update on BJOC analysis with Oscar and ChemicalTagger #3
- ChemWriter, Google Chrome, and Many Eyes in Open Source
November
October
- CiteULike CiTO Use Case #1: Wordles
- Oscar4 Java API: chemical name dictionaries
- Oscar text mining in Taverna
- Working on Oscar for three months
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
2009
November
September
August
March
2008
October
April
January
2007
December
November
October
- One Billion Biochemical RDF Triples!
- My blog turned 2
- Bob improved the POV-Ray export of Jmol
- More QSAR in Bioclipse: the JOELib extension
- Open Data Misconception #1: you do not get cited for your contributions
- Lunch at Nature HQ (with Euan, Joanna, Ian and Ålf)
- ChemSpider: the SuSE GNU/Linux of chemical databases?
- Why ODOSOS is important
- CompLife2007, Utrecht/NL. Day 1 and 2
- Taverna Workshop, Day 1 Update
- Taverna Workshop, Hinxton, UK
- How the blogosphere changes publishing
September
- SMILES to become an Open Standard
- Google’s view in history
- re: ACS RSS feeds are messed up
- Tuning Google Results?
- SWT View with the new JChemPaint
- Tagging Molecules: a mashup of Connotea and RDF
- ACS RSS feeds are messed up
- Why plain QSAR is not enough for me…
- Outscoring old science
- New InChI software beta: license issues resolved and InChIKey
- Double-charging your readers: quite unacceptable indeed
- A JChemPaint Hack-a-thon
August
- NXClient on Ubuntu Gutsy
- XCMS on Ubuntu Feisty
- JChemPaint too: PNG embedded connectivity tables
- Automatic Classification of thousands of Crystal Structures
- Dapagliflozin: the molecular structure
- Operator 0.8 released: a new Sechemtic user script
- Touchgraphing my blog
- Centralized or decentralized?
- Molecular Connectivity Tables in Images
- Molecules in Wikipedia without InChIs
- Molecules in Wikipedia
- Excel messes up your data analysis :)
July
- RDF-ing molecular space
- Further Bioclipse QSAR functionality development
- OSRA: GPL-ed molecule drawing to SMILES convertor
- Screencasts for life science informatics
- The CDK data model #1
- The Open Science Notebook 10 years ago
- CDK Literature #2
- Inter- and Extrapolation: the NMR shift prediction debate
- That big pile of paper…
- Standing on the shoulders of … the Blue Obelisk
- Atom typing in the CDK
June
- Chemical RDFa with Operator in the Firefox toolbar
- QSAR plugin for Bioclipse getting in shape
- Test File Repository and RelaxNG
- Nature should host our Electronic Lab Notebooks
- Archiving spectra: use InChI and CML
- A new job: post-doc at the WUR on MS based structure elucidation
- Quality of Chemical Database
- Using Wikipedia to recognize Molecules in Blogspace
- Payed summer jobs in chemoinformatics
- Janocchio: Jmol and CDK based 1H coupling constant prediction
- Preprint servers: the CPS failed, how will Nature Precedings do?
- Scientific Literature: searching, ranking, storage
- A Blue Obelisk corner in Chemical Blogspace
- Finding email with Strigi in .tar backups
May
- ChemRank: ranking scientific literature
- Weka Decision Trees to Java Conversion
- The JCIM is linking to Planet Blue Obelisk??
- Numbers are copyrighted?
- Added my hCard to my blog
- Microformats in chemistry…
- Preparing a Chemoinformatics workshop
- Cb comments for InChI’s
April
- Ex-CUBIC get-together
- Bioclipse now allows QSAR descriptor selection
- CDK 1.0: a milestone after 7 year of development
- Clustering web search results
- CUBIC period is over
March
- ACS Chicago - Day #3
- ACS Chicago - Day #2
- ACS Chicago - Day #1
- Arrived in Chicago…
- Chicago (Bulls), here I come!
- Pipelining chemical information with Yahoo Pipes
- What is dapagliflozin?
- Fast molecular similarity with a new 3D shape descriptor
February
- Nature Network v2: cannot create a new group
- Invisible InChI’s
- Pimp my JavaDoc
- Is that Jmol in that D-Wave demo?
- Writing up my PhD introduction chapter…
- CDK Workshop - Days #3 and #4
- RSC: the first publisher to go semantic!
January
- CDK Workshop - Day #2
- OSMB2007 Day #1: venture capital, scientific blogger and Kepler
- Blogging and the Press
- Open Source Meets Business 2007
- CDK Literature #1
- Why do I blog?
- The del.icio.us tagometer on www2.blogger.com
- The del.icio.us tagometer on Blogspot.com
- Chemical blogspace is getting more chemical
- Chemistry in HTML: JavaScript from the server
2006
December
- Modern chemistry in the CDK: beyond the two-atom bond
- Updated Chemical Blogspace Layout and Software
- Chemistry in HTML: Greasemonkey again
- SMILES, CAS and InChI in blogs: Greasemonkey
- Counting constitutional isomers from the molecular formula
- Molecular Chemometrics
- Including SMILES, CML and InChI in blogs
- H-index in chemoinformatics
- The power of big numbers
- Chemo::Blogs #2
November
- Code coverage: making sure your code is tested
- German Conference on Chemoinformatics 2006: Day 3
- German Conference on Chemoinformatics 2006: Day 1 and 2
- Organic chemists can now tune properties without changing the molecular structure??
- When is open source chemoinformatics successful?
- Chemical Blogspace updates
- Bioclipse Workshop: short but productive
- The Bioclipse Workshop is in progress
October
- Opensource Chemistry and Opensource Chemoinformatics
- Running single JUnit tests in Eclipse
- Being a good opensource user
- Are chemogenomics and proteochemometrics the same?
- Google’s new search engine: /* Code Search */
- Bioinformatics: Open Source or Open Access??
September
- CompLife’06 - Day 1
- CDK Bug Squash Party - Day 5
- CDK Bug Squash Party - Day 3 and 4
- CDK Bug Squash Party - Day 2
- CDK Bug Squash Party - Day 1
- Chemo::Blogs #1
- Complex PDB documents using the Bioclipse ChildResourceCreator
- “Jmol and the CDK add powerful chemical capabilities”, says Munos in Nature Reviews Drug Discovery
- Chemical Archeology: OSCAR3 to NMRShiftDB.org
- BioJava 1.5 beta released
- Calculating geometrical properties with the CDK
August
- R News special issue on chemistry
- Chemical blogspace
- Bioclipse gets a new extension point
- CML Explained
- Small java applet for 2D structure drawing
- Classpath 0.92 has been released
- Fortran and XML: FoX reads and writes CML
- new Atom(Elements.CARBON);
- BlueObelisk components in Japanese
- CDK and the Java 6 beta
July
- Context help in Bioclipse
- Matrix support in Bioclipse
- AVI movies of CMLRSS howto in Bioclipse
- New chemistry-on-the-desktop blog
June
- KDE4 keyword support mockups
- Text mining for chemistry using OSCAR3
- Strigi gets kfile plugin support
- Dutch Summer of Code sponsors a Bioclipse project
- KDE desktop search: Kat, Strigi and Tenor
- A chemistry extension for spreadsheet(s)
- Recent Developments of the Chemistry Development Kit
May
- Blue Obelisk in Obernai at Chemoinformatics in Europe
- Molecular indexing on the KDE and OS/X desktops
- XML validation on Eclipse with Web Tools Platform
- A live life-sciences CD
- Taverna runs with Classpath 0.91
- New open access journal Source Code for Biology and Medicine
- 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
- A 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