Chemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.

Maastricht University

Readers of my blog know I have been using the Citation Typing Ontology, CiTO (doi:10.1186/2041-1480-1-S1-S6). I allows me to see how the CDK is cited and used


. CiteULike is currently adding more CiTO more functionality, which they started


doing almost one and a half years ago.

CiTO / CiteULike: publishing innovation

I value ODOSOS


very high: they are a key component of science, and scientific research, though not every scientist sees these importance yet. I strongly believe that scientific progress is held back because of scientific results not being open; it’s putting us back into the days of alchemy, where experiments were like black boxes and procedures kept secretly.

Why ODOSOS is important

Craig James wants to make SMILES an open standard, and this has been received with much enthusiasm. SMILES (Simplified molecular input line entry specification) is a de facto standard in chemoinformatics, but the specification is not overly clear, which Craig wants to address. The draft is CC-licensed and will be discussed on the new Blue Obelisk blueobelisk-smiles mailing list.

SMILES to become an Open Standard

Paul Bracher and Joshua Finkelstein pointed my attention to a nice discussion in Nature on the future of chemistry, in What Chemists Want to Know, by Philip Ball. Paul and Joshua already reviewed it thoroughly, but I could not resist commenting in it too.

Organic chemists can now tune properties without changing the molecular structure??

An InChI (or see the FAQ) is a line notation for a molecular structure that was recently developed by the NIST and the IUPAC. Principally they can be applied to protein too (see below), but because proteins would give lenghty InChI’s and are quite well defined in terms of connectivity anyway, those can better be described by their amino acid sequence.

InChI's in LaTex and CDK News

Egon Willighagen

Just finished applying the latest spelling error fixes to CDK News 2.3


. Took me some three hours to finish it up the 12 pages, which has mostly to the need to recompile the PDF after each change to make sure that nothing in the layout got broken.

CDK News

Everyone of use knows that big pile of paper on your desk that contains the things we want to read, scan or just browse. I even have an electronic equivalent. Another pile contains leaflets and glossy folders from conferences, like the ACS meeting in Chicago. OK, going to get rid of those last ones, and will shortly put the links here. The first leaflet is from Chemistry Central, one of the open access publishers.

That big pile of paper...

Deepak blogged about screencasting for bio topics, concentrated at bioscreencast.com


of which he is co-owner. I guess it is like a YouTube for bioinformatics thingies. Jean-Claude picked this up very quickly (seen on Cb? At least I did.), and already uploaded a screencast, demoing JSpecView


written by Robert. I wonder if he will upload the screencasts he made for Bioclipse too?

Screencasts for life science informatics

Martin Szugat reported that a beta for BioJava 1.5 has been released. New features include: a new biojavax package with extension on the basic functionlity, such as the RichSequence.IOTools and the RichSequence object; a genetic algorithm library; features that allow manipulation of 3D structure files and objects; and non-HMM implementations of the NW and SW alignment algorithms.

BioJava 1.5 beta released

Some years ago we started the ELIXIR Toxicology Community. It has been an interesting journey, partly covered in this whitepaper). We started with interaction we had in several projects already, but particularly the potential. I see this.

Community activity #2: FAIRsharing

During the Open Science Retreat I organized a short session where we looking into typing citation intentions using a new nanopublication template. First, let’s describe nanopublications (originally used in doi:10.3233/ISU-2010-0613) a bit. Scholia gives a nice overview of (macro?)publications on the topic.

Open Science Retreat #2: CiTO Nanopublications

Jerven Bolleman

 et al.

recently published a great preprint about how to use RDF to give SPARQL queries context by linking it (semantically) with metadata. The context includes keywords, the SPARQL endpoint the query can be run against, and a human-oriented description of the query.

SPARQL examples: SIB model, software, and patches

Almost a year ago I started a position


with Peter Murray-Rust to work on Oscar for three months (see this overview of results; a paper by the full Oscar team (Sam, David, Dan, Lezan) is pending, and I’m really happy to have been able to contribute bits to the project). Since then, I have had little time :( That’s how it goes, with post-hopping, unfortunately. One thing I did do after that, was write a Bioclipse plugin.

Bioclipse-Oscar4 - Text mining in Bioclipse

I use Google Analytics to analyze the visitors of my blogs and of Planet Blue Obelisk too. Now, for the past couple of weeks, the webpage of the Journal of Chemical Information and Modeling is showing up as refering site: What is going on here ?!?! This is really no fake, but cannot find an actual link when I visit the journal webpage either…

 Update

: When looking at the logs, it becomes even weirder.

The JCIM is linking to Planet Blue Obelisk??

The second Programmeerzomer and the second summer of code for me, will end tomorrow with a presentation of Niels on his new JChemPaint code. The summer is over before you know it. One of the goals was making the JChemPaint editor Swing independent and more easy to integrate with SWT widgets. So, I hacked up the last bits of Bioclipse code.

SWT View with the new JChemPaint

Some days ago, I started added boiling points to Wikidata, referenced from Basic Laboratory and Industrial Chemicals (wikidata:Q22236188), David R. Lide’s ‘a CRC quick reference handbook’ from 1993 (well, the edition I have). But Wikidata wants pressure (wikidata:P2077) info at which the boiling point (wikidata:P2102) was measured. Rightfully so. But I had not added those yet, because it slows me and can be automated with QuickStatements.

Boiling points in Wikidata

I’ve just uploaded kfile_chemical 0.9


. It has new translations for ES and DA, and plugins for InChI files. It will extract the InChI string as meta data (and will thus be used by the KDE desktop search Kat


, and the InChI version number. Thinking about this, it might be useful to extract all layers as meta data, so that one can search on chemical formula and even connectivity, and find all matching structures.

InChI meta data with kfile_chemical

Not so long ago, it was decided that KDE 4.0 will use SCons as a configuration and building tool, instead of the autotools and make: the common ./configure &amp;&amp; make &amp;&amp; make install which has served the open source community very well for so long. SCons is different in several ways.

Scons and bksys for kfile_chemical

The role of a university is manifold. Being a place where people can find knowledge and the track record how that knowledge was reached is often seen as part of that. Over the past decades universities outsources this role, for example to publishers. This is seeing a lot of discussion and I am happy to see that the Dutch Universities are taking back control fast now.

Universities and open infrastructures

A bit over a year ago I got introduced to Qeios when I was asked to review an article by Michie, West, and Hasting:

 “Creating ontological definitions for use in science”

(doi:10.32388/YGIF9B.2). I wrote up my thoughts after reading the paper, and the review was posted openly online and got a DOI. Not the first platform to do this (think F1000), but it is always nice to see some publishers taking publishing seriously.

Qeios, an open dissemination platform for research output

When last week in a large (and relevant) Dutch research event ChatGPT came up, and that this was going to change the world. Even the critiques came up, but were effectively disregarded with “these methods get better very quickly”. This is not untrue, but not really true either. I murmur “not even wrong”. I know how hard it is to get computers to find meaningful patters; I did a PhD in this in the early 21st century.

Information Retrieval versus ChatGPT

I think that if you want to make your knowledge FAIR, you should use an open license and RDF. Simple. Now, not everything is knowledge. A lot of data is, but a lot more is not, think raw data. Using RDF to explain a protein sequence is still something that makes me feel uneasy. However, first, you need to make RDF, you need to make assumptions explicit, you need to decide on meaning. Making RDF is not easy.

Paper: The FAIR Cookbook - the essential resource for and by FAIR doers

This is a series of two posts repeating some content I wrote up back in the Bioclipse days (see also this Scholia page). They both deal with something we were facing: restructuring of version control repositories, while actually keeping the history. For example, you may want to copy or move code from one repository to another.

Bioclipse git experiences #1: Strip away unwanted plugins

Bioclipse git experiences #2: Create patches for individual plugins/features

SWAT4LS was once again a great meeting. I doubt I will find time soon enough to write up notes, but at least I can post the eNanoMapper poster I presented, which is available from F1000Research:

The SWAT4LS poster about eNanoMapper

I previously wrote about the JavaScript Object Notation (JSON) which has become a de facto standard for sharing data by web services. I personally still prefer something using the Resource Description Framework (RDF) because of its clear link to ontologies, but perhaps JSON-LD combines the best of both worlds. The Open PHACTS API support various formats and this JSON is the default format used by the ops.js library.

Programming in the Life Sciences #20: extracting data from JSON

Now that I have wrote out the goals, what they students will practically do, and how to get started with the Open PHACTS platform, I will list how we will assess the students: a presentation on the second day, outlining the project and work plan, working source code at the end of the cour se, a final presentation, showing the results and conclusions. Primarily, they will be judged on their acquired programming skills.

Programming in the Life Sciences #3: the assessment

Kasabi is a new, RDF hosting service by Talis. It’s still in beta, and I have been testing their beta service with the RDF version


I created of ChemPedia Substances (the now no longer existing cool web service from MetaMolecular to draw and name organic molecules). Kasabi makes the RDF data available via a few APIs, depending on the APIs selected by the uploader. I picked all five of them, just to see how things work.

ChemPedia-RDF #2: Kasabi

One of the goals of my project in Cambridge


is to make Oscar available as Taverna plugin (source code, Hudson build). I have progressed somewhat, but still struggling with getting the update site working.

Oscar text mining in Taverna

There was some talk about the history of chemoinformatics toolkits by Noel and Andrew, which made me wonder on the exact history of Jmol and JChemPaint.

JChemPaint history: CML patches in 1999

Julio and Gert placed their ICCS 2011 work


online, and today I was going through old CDs (see From the archives: Chemical Web, and the CDK in 2004 and Chiral Molecules: how cool is the SEM picture?). I also ran into my ICCS 2005 poster, and because that too was before I started blogging, I never posted it online.

From the archives: my ICCS 2005 poster

Part of the scientific program of the ICCS 2022. Now that most speakers confirmed their talk by registering for the conference, it was time to upload the preliminary scientific program of the International Conference on Chemical Structures (#2022ICCS ).

Part of the scientific program of the ICCS 2022.

The International Conference on Chemical Structures scientific program is online!

Later this year the ninth International Conference on Chemical Structures (ICSS) conference will be held in the Netherlands. I had the pleasure of joining this meeting, I think, eight years ago, when I was doing my PhD in Nijmegen. Mind you, I did not

 attend

the conference;

The 9th International Conference on Chemical Structures (ICCS)

On the 7th International Conference on Chemical Structures


Jeroen Kazius


has a poster


on finding discriminative substructures, that is, molecular fragments which can be discriminate between two acitivity classes. The software is released as Gaston


, is written in C++ and has the GPL license. Later I encountered MoSS


which has the same goal, but uses a different algorithm.

Open Source data mining in chemoinformatics

I wish I could say I remember the first citation to one of my research articles. I do not. But I do remember the excitement to see why someone was citing my research. What I do remember is that I got a comment around the same time along the lines of this:

 “why would anyone cite your article if they can download the results for free?”

(about open science cheminformatics research). Other times.

Niche papers and citation intentions

The last week before the winter break Serious Request took place. We started an action around WikiPathways and we collected 877 euro for the MetaKids Foundation. In total there were 2612 actions, many of which brought in a lot more. We ended up in position 928.

Serious Request: the results

If you are into openscience chemistry or chemistry blogging, then you probably heard of Rich Apodaca’s Depth-First blog. Rich started blogging in 2006


but this is not how I discovered his work originally.

Richard L. Apodaca

In August I reported about 2D depiction of (CX)SMILES in Wikidata via linkouts (going back to 2017). Based on a script by Magnus Manske, I wrote a Wikidata gadget that uses the same CDK Depict (VHP4Safety mirror) to depict the 2D structure in Wikidata itself:    Note the depiction of the undefined (CIP) stereochemistry on two atoms. Thanks to Adriano and John for working that out.

Wikidata script for SMILES, SMARTS, and CXSMILES depiction

There was a lot of Open Science news this week. The announcement of the Google Dataset Search was one of them:    Of course, I first tried searching for “RDF chemistry” which shows some of my data sets (and a lot more):    It picks up data from many sources, such as Figshare in this image. That means it also works (well, sort of, as Noel O’Boyle noticed) for supplementary information from the Journal of Cheminformatics.

Also new this week: "Google Dataset Search"

If you are a scientist you have heard about the ORCID identifier by now. If not, you have been focusing on groundbreaking research and isolated yourself from the rest of the world, just to make it perfect and get that Nobel prize next year.

Chemistry Central and the ORCID identifier

Debugging is the process find removing a fault in your code (the etymology goes further back than the moth story, I learned today). Being able to debug is an essential programming skill, and being able to program flawlessly is not enough; the bug can be outside your own code.

Programming in the Life Sciences #19: debugging

I have outlined the scope of the six-day course: the students will learn to program while hacking on the Open PHACTS’ Linked Data API (LDA). The first step is to get an account for the LDA. I have already done that to save time. But these are the steps to take. You go to https://dev.openphacts.org/signup:    You then approve the account via your email account and you are set. The account is needed to get an API key.

Programming in the Life Sciences #2: accounts and API keys

Update: this work is now described in this paper .

Update

: this work is now described in this paper


. Last week, ChEMBL 13 was released, with even more data, data fixes, etc. Since my RDF for ChEMBL 09


my workflow has become more solid and uses more common ontologies, started using more common ontologies and ontologies I just like, such as CHEMINF and CiTO.

ChEMBL 13 as RDF

Six month was not quite the amount of time I anticipated between the third and fourth edition, but I finally managed to upload edition 1.4.7-0 of my Groovy Cheminformatics book. The first three editions sold 37 copies, including two for myself.

Groovy Cheminformatics 4th edition

About two weeks ago, the ChemConnector blog reported an InChIKey collosion


detected by Prof. Goodman


. Unlike the previous collision, this one was based solely on the graph and not on stereochemistry. The two molecules both have the InChIKey OCPAUTFLLNMYSX-UHFFFAOYSA-N: The compounds are really different, the molecular formulas are C

 50

H

 102

O and C

 57

H

 114

O respectively.

InChIKey collision: the DIY copy/pastables

Update

: the fourth edition


is out. I am starting to get the hang of this publishing soon, publishing often thing, and just uploaded edition 1.4.1-0 of the Groovy Cheminformatics


book. The cover is the same (with one typo fix), and the content is 20 pages thicker. True, six of those pages are isotope masses of all natural isotopes.

Groovy Cheminformatics 3rd edition

The two earlier posts in this series showed screenshots of results of Oscar, but the title also promised results by Lezan’s ChemicalTagger. Sam helped with getting the HTML pages online via the Cambridge Hudson installation. Where Oscar find named entities (chemical compounds, processes, etc), ChemicalTagger finds roles, like solvent, acid, base, catalyst. Roles are properties of chemical compounds in certain situations.

Status update on BJOC analysis with Oscar and ChemicalTagger #3

Well, you might spot a pattern here; yes, another chemical SPARQL end point (actually, it shares the end point with the Solubility data). This time around Rich’s ChemPedia. Taking advantage of the CC0-licensed downloads


, I have created a small Groovy script (using this JSON library) to convert the ChemPedia JSON into Notation3: import net.sf.json.groovy.JsonSlurper;

ChemPedia RDF #1: the SPARQL end point

Linus’ law:  Rich of MetaMolecular works on Open Source and closed source cheminformatics solutions. ChemWriter is one product he is working on which uses JavaScript and SVG (two Open Standards), and recently asked feedback on the new version.

ChemWriter, Google Chrome, and Many Eyes in Open Source

RDF and SPARQL are two really useful Open Standards. Bioclipse-RDF is a plugin for Bioclipse that provide RDF functionality, among which using remote SPARQL end points. The MyExperiment team has set up an excellent RDF front end. For example, this is my MyExperiment account in RDF. The storage gets updated once every day (at this moment), but I’m sure that will become more often in the future.

Bioclipse and SPARQL end points #2: MyExperiment

Nature Chemistry just released the first issue with a few free papers, like

 Asymmetric total syntheses of (+)- and (-)-versicolamide B and biosynthetic implications

by Miller et al. (DOI:10.1038/nchem.110). Now, we’ve seen the Royal Society of Chemistry’s Project Prospect (see RSC: the first publisher to go semantic!) and ChemSpiders recent ChemMantis system which enriches the papers with machine readable representations of the

Nature Chemistry improves publishing chemistry: a detailed analysis

In this series I will introduce the technologies behind my FOAF network. FOAF means Friend-of-a-Friend and  My FOAF file (draft) will give you details on who I am, who I collaborate with (and other types of friends), which conferences I am attending, what I published etc. That is, I’ll try to keep it updated. BTW, FOAF is a RDF language.

My FOAF network #1: the FOAFExplorer

A bit over two years I posted my first blog item, Chem-bla-ics


, introducing the topic of my blog. In January this year I explained why I like blogging


.

My blog turned 2

Via SciFoo Planet


(from Partial immortalization


) I learned about TouchGraph Google (Peter brought it into Chemical blogspace). It’s cool, though not open source. Here’s the touch graph for my blog: As you can see, plenty of blogspot bloggers around me, among which, in purple, Useful Chemistry. Funny thing is, each time I repeat the Google search, the output is different. Oh, and make sure to drag one of the halos around;

Touchgraphing my blog

Peter wondered if data should be stored centralized or decentralized, when Deepak blogged about Freebase and Metaweb. Now, I haven’t really looked into these two projects, but the question of centralized versus decentralized is interesting. It’s MySQL versus the world wide web; it’s the PubChem compound ID versus the InChI;

Centralized or decentralized?

RDF might be the solution we are looking for to get a grip on the huge amount of information we are facing. microformats, and RDFa, are just solutions along the way, and Gleaning Resource Descriptions from Dialects of Languages (GRDDL) might be an important tool to get the web RDF-ied. One important aspect of RDF is that any resource has a unique URI.

RDF-ing molecular space

Making something FAIR is hard, particularly when you do more than making something findable. We’ve seen before that making something usefully findable requires deep indexing, and already that continues to be difficult, because we are not seeing it enough. So, when I thought convert a paper led by Hoet’s lab in Leuven into machine-actionable RDF to make it FAIR, I gravely underestimated the amount of work.

New paper: From papers to RDF-based integration of physicochemical data and adverse outcome pathways for nanomaterials

Peter is writing up a 1FTE grant proposal


for someone to work on the question how automatic agents and, more interestingly, the blogosphere are changing, no improving, the dissemination of scientific literature. He wants our input.

How the blogosphere changes publishing

I arrived in Chicago yesterday afternoon. Much warmed than the cold Chicago the ACS promised me, so my winter coat was really not necessary. Is this global warming? Or was the ACS simply wrong? Anyway, very foggy indeed, just like the Chemistry World blog wrote:    There were several other Dutch chemists on the plane, among which a few formed postdocs from Nijmegen, who I knew from the time I was still a M.Sc. student in organic chemistry.

Arrived in Chicago...

That’s why blogging works! I reported last Friday on using my Wii for reading


Scintilla and Postgenomic.com. Alf replied: Ah, the trick word: TCP windows scaling.

Scintilla and Postgenomic.com on Linux 2.6.17+

My current jobs description is to speed up metabolomics data analysis, and finally got around to making a first relevant workflow for Taverna, using the webservices just posted over at ChemSpider:    I uploaded the source to MyExperiment, so anyway can play with it. There is much to improve, such as using CDK-Taverna for further analysis of the results.

Metabolomics workflows in Taverna

Right at this moment I am listening to Andrew Hopkins from Dundee on chemical opportunities in system biology, at the Cytoscape conference in Amsterdam


. Anyone who wants to meet up over lunch or coffee break?

Cytoscape in Amsterdam

Jim reported about SPECTRa being in the news and ./ about Toward a 3D Search Engine. These two items have in coming that they deal with the article

 Ultrafast shape recognition for similarity search in molecular databases

by Ballester and Richards (DOI:10.1098/rspa.2007.1823). The NewScientist wrote up their angle on it, with a quote from Henry Rzepa.

Fast molecular similarity with a new 3D shape descriptor

Jörg’s PhD book

 Data Mining und Graph Mining auf molekularen Graphen - Chemoinformatik und molekulare Kodierungen für ADME/Tox-QSAR-Analysen

has a dump of the JavaDoc of the GroupContributionPredictor in JOELib (Figure 3.2, page 43). There are two nice things to the shown JavaDoc: 1. it has links to Wikipedia; 2. it has a Further Reading section. Now, the CDK already links to a bibliography for some time now.

Pimp my JavaDoc

Slashdot reported on D-Wave’s recent demo of their 16-qubit quantum computing system. Video’s of the demo can be watched on Google Video. The second video demonstrates the use of the machine in similarity searching:    Now, that screenshot does look like Jmol. The companies website does not give the answer, though Scott mentions C and Java front end software.  So, let’s ask the source: Dear dr. Rose, is it Jmol what we see in that demo?

Is that Jmol in that D-Wave demo?

The last twelve months or so, I have been doing two jobs (excluding hobbies of mine, such as Chemical blogspace): my postdoc in the group of Christoph Steinbeck on computer aided structure elucidation, and finishing my PhD.

Writing up my PhD introduction chapter...

Days #3 and #4 of the CDK Workshop have been quite busy indeed, and I have not been able to summarize them so far. After a rather interesting day #2


, the third day was the last one with scheduled presentations. Kai Hartmann showed how he used the CDK in his systems biology research, and contributed the code he wrote to predict Gibbs energies based on fragment contributions.

CDK Workshop - Days #3 and #4

Yesterday I blogged about how to include the new del.icio.us tagometer on a www.blogger.com blog


, just like Improbulus did last December as I discovered later. Felix asked me how it could be done on the new www2.blogger.com template system.

The del.icio.us tagometer on www2.blogger.com

Recently, a second beta of Java 6 was released, which triggered a patch for the Debian java-package package. It was a Bioclipse bug report today, however, which made me patch my java-package setup and install the beta. So, next thing was to try to get the CDK compile with the Java 6 beta.

CDK and the Java 6 beta

I have heard that bioinformatics is ahead of chemoinformatics. However, I discoverd that this is not necessarily the case, while preparing for a homology modeling course I gave this week at the CUBIC. Open Access is really no issue there, with open access journals and many open access databases. But it is different when it comes down to open source software.

Bioinformatics: Open Source or Open Access??

Yesterday I installed the Eclipse Web Tools Platform again, and now succesfully, using the Eclipse update mechanism, on my Kubuntu dapper eclipse install. Because it has a validating XML editor, the one last thing I still needed jEdit for. (I do miss the vertical selection feature of jEdit, though.) It signals me of errors, and allows autocompletion.

XML validation on Eclipse with Web Tools Platform

BioMed Central is setting up a new peer-reviewed, open access journal Source Code for Biology and Medicine. It will

 “encompass all aspects of workflow for information systems, decision support systems, client user networks, database management, and data mining”

. Basically, anything that fits into chem-bla-ics. (Thanx to Werner, for pointing me to the website!) The ‘source code’ aspect is the interesting thing of this new journal.

New open access journal Source Code for Biology and Medicine

On my way back from the Taverna workshop I visited Nature HQ, as Ian reported about on Nascent. It was a (too) short meeting, but very nice to meet Euan (finally;

Lunch at Nature HQ (with Euan, Joanna, Ian and Ålf)

Earlier I reported about postgenomic.com


, and needed some diversion from my manuscript work (could no longer think straight about the article I’m working on). So time for some reading up on new technologies. Timing was perfect, because the source code of postgenomic.com got just uploaded to SourceForge SVN.

Hacking InChI support into postgenomic.com

I was very pleased to read today that Kalzium, one of the projects that participate in the Blue Obelisk, got awarded! Cheers, Carsten!

Kalzium Wins Award; Carsten Niehaus Interviewed

A recent report by the Dutch RIVM,

 PFAS in the blood of the Dutch population

(doi:10.21945/RIVM-2025-0094), writes that seven PFAS compounds are found in blood samples of all tested people. Another nine compounds are found in at least 1-in-10 people. Because there is relevant data in the report on the 28 studied PFAS compound, I wanted to have the report more FAIR than it is on the website. Why this report?

PFAS in the blood of the Dutch population

One of the things I had not fully figured out up to today, was how to configure my Kubuntu system to easily view DVDs on our TV, using my NVIDIA’s TV-OUT. I’ve seen xorg.conf files that define a X11 server for the monitor and a second for the TV, and files that use TwinView. Now, I did not really like the way first option worked, so tried the second.

Kubuntu, XRandR and TV-OUT

OK, just back from the first German Chemoinformatics Conference, which I enjoyed very much. A rather interesting program, and lots of interesting posters too. You can read the programme online, and will not spend too many words on that (at least not now). But what I will do is point out some interesting posters here. One poster was on the Molecular Query Language (MQL) by Ewgenij Proschak from Frankfurt.

Back from the 1st GCC

There are many ways to contribute to opensource software (OSS), programming only being one of them. I develop OSS, but use OSS too. For example, I am a big user of the Linux kernel, the KDE desktop, Kubuntu, Debian (I have unstable in a chroot), Firefox, Eclipse, Classpath, and many, many others. What these have in common, is that I generally have no time to look into the source code of these projects.

Being a good opensource user

Most Dutch chemists have their annual Lunteren meeting, so do I. Lunteren is a small village on the Veluwe where nothing much can be done, except for listening to the presentations. I participate in the Lunteren meeting for analytical chemists, i.e. HPLC, MS, GC and all their combinations upto and including HPLC/MS/MS, and since a few years the Lab-on-a-Chip stuff.

The annual Lunteren meeting

I have started using branches for non-trivial patches, like removing the HückelAromaticityDetector, in favor of the new CDKHückelAromaticityDetector


. I am doing this in my personal remove-non-cdkatomtype-code branch, where I can quietly work on the patch until I am happy about it. I make sure to keep it synchronized with trunk with regular svn merge commands.

Comparing JUnit test results between CDK trunk/ and a branch

Jerome Pansanel contributed new patches for kfile_chemical; on Monday actually, but I have been busy with other things, among which a presentation I have to give next Monday for some 100+ analytical chemists. The patch adds support to KDE for five new chemical MIMEs: XYZ, Mol2, SMILES, VMD and GenBank. Therefore, I just released a new version (0.10), and added an announcement to Freshmeat.net.

kfile_chemical gets XYZ, Mol2, SMILES, VMD and GenBank support

Today is my 31st birthday, nearing half-point now (statistically seen). Also, by now I should have had my scientific moment of glory, otherwise I can forget that Nobel prize. Oh well, forget it.  Have you seen those small advertisements on this page (RSS users, please visit the website :)? Funny links they give. The system is very nice btw: it awaits google indexing of the blog and then decides which ads are relevant.

My birthday (31) and the Adsense

Yesterday I had some spare time before going to a meeting about the Woordenboek Organische Chemie, so I was boldly going where no one has went before: getting the CDK module core independent of the data module.

More cdk.interfaces updates

A good functional molecular editor is of much important to the chemical web. There are a few small download sized editors around. JChemPaint has been available as applet for some time now, but the download size has been large. The situation has improved considerable over the past months, and the download size upon which the applet now shows up in your webbrowser is down to 538kB. A live demo is available from www.chemistry-development-kit.org.

JChemPaint applet download size: 538kB

Less then three months before the end of my contract of my PhD project. And not nearly done yet. Weekends are now spend on wrapping up bits of experimental research into something like a coherent article. And even lot’s of calculations to do to answer the open questions. FreeMind is helping me organize thoughts. Opensource chemoinformatics is a welcomed diversion now and then.

Wrapping up...

CDK News


2.3 is scheduled for this month, and origanally planned to be distributed on the CDK5AW event. So, it’s a bit late. But the editorial process is converging… I realized that I forgot to mention the requirement for InChI’s whenever molecules are given.

CDK News 2.3 and InChI's

The Jmol FAH team


has just entered the Top 800 of most active Folding@Home


teams. And they started monitoring contributions on a user level. Thus, I can now see how active I am within the team. And so can you! Join the team, and let’s get into the Top 500!

Jmol's FAH team in Top 800

After asking about it, Tom explained me how Taverna can pick up the apiconsumer.xml file from jars: just copy it into the root directory of the jar package. Easy as that.  So, users now only need to copy the cdk-taverna.jar into the taverna-workbench-1.3/lib/ directory and have a nice chemoinformatics workbench environment. I’ll upload the jar to CDK’s project page right now.

CDK-Taverna fully recognized

I have just enabled CIA


statistics for the Blue Obelisk SVN


: /stats/project/cdk/blueobelisk


. It’s done by using the ciabot_svn.py


client script and hooked into the $REPOS/hooks/post-commit hook on the SVN server. The client script is slightly hacked to hard code the module name, which otherwise did not show up on the chat channel.

CIA statistics for Blue Obelisk

This new blog will deal with chemblaics in the broader sense, and will not be restricted to research in this field in which I am involved personally. Chemblaics (pronounced chem-bla-ics) is the science that uses computers to address and possibly solve problems in the area of chemistry, biochemistry and related fields. The general denomiter seems to be molecules, but I might be wrong there.

Chem-bla-ics

Tuesday promised to be an interesting day: an interesting ‘Scientific Communication’ CINF session in the morning and early afternoon. And, rather important to me, the Blue Obelisk dinner that night, just after another CINF party, where I chatted with a few others about options of a chemistry equivalent of the Google Summer of Code;

ACS Chicago - Day #3

About a year ago Pedro wrote a Greasemonkey script to add comments from PostGenomic.com to table of contents of scientific journals. Noel extended it with support for Chemical blogspace (see also this earlier item). Now, the later website is maintained by me, and I extended the aggregator software with molecule support, for example to show

 hot

molecules on the frontpage (at some point my patches will be backported into mainstream.

Cb comments for InChI's

Now that we have the communication working with the Open PHACTS LDA, it is time to make a nice GUI.

Programming in the Life Sciences #5: converting the results into HTML

I am still an avid user of RSS/Atom feeds. I use Feedly daily, partly because of their easy to use app. My blog is part of Planet RDF, a

 blog planet

. Blog planets aggregate blogs from many people around a certain topic. It’s like a forum, but open, free, community driven.

Blog planets: blogging about Debian, GNOME, Wikimedia, FSFE, and many more

Some time ago Rajarshi Guha introduced R bindings for the CDK (see his CDK News articles), and today I tried to install his rcdk package that makes it happen. However, it requires SJava which compiled fine on other machines, but not on my AMD64 machine. The problem seems to be related to the GNU GCC 4.0 compiler I have installed.

R/CDK install fails on GCC 4.0 systems

Blogs come and go. Sometimes they move from one location to another. However, blogs have not been systematically archived, perhaps for work by efforts by OpenLaboraty.

Archiving blogs

As promised


, here is my list of submission for the Open Laboratory 2007: Open Data is critical for Reproducible Research


If you ever made something fluoresce after you did a reaction with a transition metal… One For the Brave Fun with singlet oxygen SMILES and Aromaticity: Broken?

My Open Laboratory 2007 submissions

A good number of years ago, a colleague and I explored if we could get access to the Retraction Watch Database, but we could not afford it. We have been using data on retractions for curate our databases, like WikiPathways. A database should not contain knowledge based on (only) a retracted article. Wikidata, btw, has a small number (499) of statements supported by retracted articles.

chem-bla-ics

Single PDFs for CDK News articles