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

Egon Willighagen

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

This paper got published in July already, but I had not had the time yet to blog about this exciting work by Irini Furxhi and Ammar Ammar:

 A data reusability assessment in the nanosafety domain based on the NSDRA framework followed by an exploratory quantitative structure activity relationships (QSAR) modeling targeting cellular viability

(doi:10.1016/j.impact.2023.100475) The study has two sides to it: first, it looks into how far we

Using FAIR to select data for reuse

CASE OF DIABETES.

DR. CLANNY'S CASE OF DIABETES

SUGAR IN THE BLOOD OF DIABETIC PATIENTS.

Scholia, Scientometrics and Wikidata

Diabetes was already discussed in literature back in 1838-1839 (doi:10.1016/S0140-6736(02)96038-1, doi:10.1016/S0140-6736(02)96066-6, and doi:10.1016/S0140-6736(02)83966-6). These three papers show a short discussion.

Scholarly discussions through they eyes of CiTO (and Wikidata)

Kasabi was an innovative RDF publishing platform from around 2011. Shortlived, and maybe just too early. I published two open datasets there. One was ChEMBL-RDF (see these posts). The second was a small data sets called ChemPedia, a open science effort to crowdsource chemical names. This is still very much needed, and possibly Wikidata could fill that gap, but it would first need to be able to handle all labels as statements itself.

Kasabi archive at the Internet Archive

Update: this work is now described in this paper.

The Chemical Information Ontology: Provenance and Disambiguation for Chemical Data on the Biological Semantic Web

CiTO, the Citation Typing Ontology

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

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 2021-02

: this post is still the second-most read post in my blog. Welcome! Some updates: Ammar Ammar in our BiGCaT group has set up a new SPARQL endpoint. Please use and tweet. blog, or otherwise let others now how you use the ChEMBL RDF. Since this post I have blogged a lot more about ChEMBL.

 Update

: this work is now written down in this paper.

ChEMBL 09 as RDF

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

Last month I reported a few things I missed in CiteULike. One of them was support for CiTO (see doi:https://doi.org/10.1186/2041-1480-1-S1-S6), a great Citation Typing Ontology. I promised the CiTO author, David, my use cases, but have been horribly busy in the past few weeks with my new position, wrapping up my past position, and thinking on my position after Cambridge.

CiteULike CiTO Use Case #1: Wordles

AJCann posted a blog today about what he doesn’t like about Mendeley. Abhishek replied that he does not like people complain about one tool, instead of pointing out a good alternative. Mendeley has two alternatives, Zotero and CiteULike (there is also Connotea, but got behind in evolution).  Agreeing with @citeulike and @abhishektiwari, as a service provider any bad news is good news too: they provide opportunities to improve.

A list of things I miss in CiteULike

Molecular Chemometrics

I noted earlier this week that

 [d]uring the week [in Oxford
 
 
 ], someone (name and address is know at the editorial office) commented on the fact that my blog posts are somewhat difficult to follow;

The Molecular Chemometrics Principles #2: be clear in what you mean

The Bioclipse Workshop is in progress, and Ola is now leading a discussion about future releases and functionality. Proceedings are live updated, and presentation sheets will be available shortly.

The Bioclipse Workshop is in progress

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

Last night I upgraded the software behind Chemical


blogspace, to the version online on Google Code, though I needed the help from Eaun


to get paper titles correctly picked up for ACS journals.

Updated Chemical Blogspace Layout and Software

The Bioclipse Workshop has ended and, for just three days, turned out quite productive. We have first bits of scripting support for JavaScript using Rhino. At this moment the scripting plugin needs to explicit depend on plugins to be able to access their classpath, but we plan to solve that. An example script: // to have short identifiers Array = Packages.java.lang.reflect.Array; String = Packages.java.lang.String;

Bioclipse Workshop: short but productive

Chemical Markup, XML, and the World Wide Web. 6. CMLReact, an XML Vocabulary for Chemical Reactions

The Blue Obelisk mailing list has seen an interesting discussion on ambiguity in the term ‘open source’, triggered by a study by Beth Ritter Guth. For example, Jean-Claude Bradley performs ‘open source’ science (see his Useful Chemistry blog) who is not opposed to using closed source software, while the Blue Obelisk is about ‘open source’ software.

Opensource Chemistry and Opensource Chemoinformatics

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??

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

Unit testing is important when developing source code. JUnit provides a library to facilitate this in Java, and Eclipse had the functionality to run JUnit tests. Even better, it allows you to run single JUnit tests, even in debug mode:    Just open the java class in your Package Explorer, right click on the JUnit method you want to run, then pick Run As or Debug As, and then JUnit test.

Running single JUnit tests in Eclipse

Joerg Wegner recently blogged about

 Chemogenomics: structuring the drug discovery process to gene families

by C.J. Harris and A. P. Stevens in Drug Discov Today (DOI: 10.1016/j.drudis.2006.08.013). This review article provides a nice overview of a trend in mathematical modelling of the interaction of small organic molecules with proteins, often referred to as QSAR.

Are chemogenomics and proteochemometrics the same?

Because I was struggling hard with default values for cdk.interfaces fields, I did not have time to write up the Bug Squash Party report for day 3 (see also day 1 and day 2). But here it is. Day 3   Kai worked hard on getting the cdk.interfaces API cleaned up, as agreed upon earlier. Christian added a test for the RMSD calculator (see getAllAtomRMSD()), and cleaned up his code a bit.

CDK Bug Squash Party - Day 3 and 4

Last week I attended the Open Science Retreat (#osr24nl) in a quite and relaxing region in North-Holland. The meeting was how I like all meetings to be (and I count myself lucky many of my meetings are like this): open, welcoming, constructive, diverse, and intellectually challenging. Not all scientific meetings are like this and it is easy to end up going to obligatory meetings where the discussions are of a different level.

Open Science Retreat #1: impressions

2023 has been a long year in which a lot happens. Two EU projects ended (RiskGONE and NanoSolveIT; more about that in a later post), our group leader Chris Evelo will retire this year, the ELIXIR Toxicology Community started (see this post), the new WikiPathways website launched (see this post), and a lot, lot more.

PhD Defences: Andra Waagmeester and Marvin Martens

Some time ago I blogged about the ChildResourceCreator extension point in Bioclipse and hinted as using that for PDB files. which contain 3D molecular models, sequences and bibliographic information.

Complex PDB documents using the Bioclipse ChildResourceCreator

Bernard Munos at Eli Lilly &amp; Co. wrote up a lengthy analysis on open source in drug discovery in Nature Reviews Drug Discovery: Can open-source R&amp;D reinvigorate drug research?

"Jmol and the CDK add powerful chemical capabilities", says Munos in Nature Reviews Drug Discovery

If you have read my previous post and visited that other blog, you might have noted the Technorati keywords


. Or tags, really, as explained in this rel=”tag” microformat. Adding them to blog items, will enable indexing by Technorati, one of the bigger blog search engines. So, from now on, you’ll see these tags in my items too, hoping they don’t get annoying.

Tagging blog items

R News just released a special issue on the use of the versatile statistics program R in chemistry. It features six articles amongst which one by Rajarshi Guha on the CDK-R bridge, and one by my supervisor and me on the use of self-organizing maps to cluster crystal structures.

R News special issue on chemistry

ケムインフォマティクスに虚空投げ runs a story on how to calculate geometrical properties of a 3D structure using CDK’s ForceFieldTools. This class contains a few methods to calculate distances between atoms and angles between bonds. This tools class is special as it uses vecmath GVector objects, which just contain atomic coordinates, likely suitable for extensive computation, as expected in CDK’s force field implementation.

Calculating geometrical properties with the CDK

We all know chemical space; Chemical blogspace (Cb) is different: it is the chemistry discussed in blogspace. Cb is build on the opensource software of Postgenomic.com which I bloged on before. The now running Cb aggregates 19 blogs and, like the original, extracts linked (cited or reviewed) articles from literature. The system is beta, but I am happy about it already that I mention it now.

Chemical blogspace

I hacked in a new extension point for Bioclipse yesterday, based on a proposal I made earlier. The new extension point (EP) is called ChildResourceCreator and allows creating child resources for a given IBioResource. One application where this is very useful is the CMLRSS application (earlier blog), or any RSS or Atom enriched with any other XML language.

Bioclipse gets a new extension point

Tobias commited Jumbo 5.0 to CDK CVS, so that the CDK is now again up to date with the latest CML library. Note that Jumbo 5.0 requires Java 5.0.  At first all JUnit tests seems to work, but apparently the CML2Writer tests were skipped because they were only run when Java 1.4 was found. I updated the test for the a appropriate Java version, and then it turned out that most tests fail.

Jumbo 5.0 and CML support in CDK

Bling! Bling!. Mark Wielaard announced the GNU Classpath 0.92 release, with the following changes:

 an alternative awt peer implementation based on Escher that uses the X protocol directly. Various ImageIO providers for png, gif and bmp images. Support for reading and writing midi files and reading .au and .wav files have been added. Various tools and support classes have been added for jar, native2ascii, serialver, keytool, jarsigner.

Classpath 0.92 has been released

I reported earlier


that the CDK has been updated in CVS to use CML from the new Jumbo 5.0. The transition actually involved a lot of changes in the CDK, some I would like to address in the following comments. One thing is that CML write support (not reading!) uses the new Jumbo library which requires Java 1.5. Thus, if Java 1.5 is not available, then CML writing should not be compiled. This is how this is done.

Jumbo 5.0 and the CDK

Mix one of the oldest and one of the latest computer technologies, and you get FoX (BSD license), a Fortran library for reading and writing Chemical Markup Language, and thus XML.

Fortran and XML: FoX reads and writes CML

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

In reply to interesting comments to my previous blog on Strigi and xAttr support in KDE4, I would like to suggest the following mockups, which I would find very useful. The deal with the ability to store keywords, for example, not but necessarily using xAttr. I have no idea on how to implement these mockups, so any help or pointers are appreciated.

KDE4 keyword support mockups

The Dutch version of the Google Summer of Code, Programmeerzomer.nl, announced today the five students participating. I was happy to see that Rob Schellhorn was selected with his project proposal for a Ghemical plugin for Bioclipse. Like in the Google original, both the student and the mentoring organization are funded, 3600 and 400 euro respectively.

Dutch Summer of Code sponsors a Bioclipse project

I started a spin-off blog earlier this week: kemistry desktop environment. It will deal with integration of chemistry on opensource desktops, with KDE as one of them. Today, it features an overview of earlier blogs on the subject in this new blog.

New chemistry-on-the-desktop blog

With some help, I got the kfile stream analyzer for Strigi working. This means that Strigi will now index the meta data fields defined by the kfile-chemical plugins. The problem why it was not working earlier, was that it segfaulted on every creation of KDE classes. That’s something I really hate about C/C++: the lack of stack traces, though valgrind was helpful. It turned out that adding the below line fixed all.

Strigi gets kfile plugin support

Peter Corbett from Peter Murray-Rust’s group at the Unilever Cambridge Centre for Molecular Informatics visited Christoph Steinbeck’s junior Research Group on Molecular Informatics at the CUBIC today, and spoke about the status of Oscar3, a chemistry text mining program with the Artistic License.

Text mining for chemistry using OSCAR3

Desktop searching has become a hot topic (some earlier


blogs


), now that years of data accumulated on ones hard disk: PDFs, OpenOffice.org documents, Latex manuscripts, old Java source code, digitized music, and a lot of chemical files. Well, on my hard disk that is. Unlike piles of paper, a computer could search this data, but due to the size an index is required. What’s KDE4 going to offer?

KDE desktop search: Kat, Strigi and Tenor

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

Together with Christoph, Christian and Jerome, I will be representing the Blue Obelisk movement on the first First Workshop on Chemoinformatics in Europe with the topic

 Research and Teaching

. Though I wonder what this theme excludes? Development? Can’t imagine that commercials companies will not be represented as usual. Moreover, it will likely include some bioinformatics too, unless you consider that to deal with sequences only.

Blue Obelisk in Obernai at Chemoinformatics in Europe

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

Geoff Hutchinson blogged about his OS/X ChemSpotLight, an indexing tool for chemistry documents. It’s like, but more advanced than, the kfile_chemical and Kat I have been working on (with others) for the KDE desktop (see earlier blog items).  ChemSpotLight currently does more than the KDE tools: it adds Spotlight comments. I assume these are like the Linux extended attributes, used for example by Beagle.

Molecular indexing on the KDE and OS/X desktops

Classpath 0.91 is released with 1.45 million lines of code and with 98.96% coverage of Java 1.4.2, and 99.82% of java.swing. Or, as Dave calls it: 0.91 rocks! JChemPaint runs again


(they fixed the XML parsing problem), and Jmol still runs

 ,


 but slow. I also tested Taverna which now also starts up, but has an XML parsing error too: Exception occured whilst loading RDFS!

Taverna runs with Classpath 0.91

November last year, I reported my plans


to develop a live CD with all our favorite chemo- and bioinformatics software. Bioclipse requires Java5 and sort of still depends on the Sun JVM (I will experiment with classpath-generics later), but is now distributable with operating systems.

A live life-sciences CD

Chemical Markup, XML, and the World Wide Web. 5. Applications of Chemical Metadata in RSS Aggregators

Timo Hannay blogged


in Nature’s Nascent blog


about the Open Text Mining Interface (OTMI), which is “a suggestion from Nature about how we might achieve text-mining and indexing purposes”. The idea is that each article has a link pointing to a machine readable file containing raw data about (and from?) the article.

Open Text Mining Interface and Bioclipse

Here are some quick download statistics for some of the chemblaics components. First Jmol. The new stable Jmol 10.2 was release just over a week ago, and this obviously boosted downloads, breaking the monthly download total of two earlier this year (source):    Statistics for the CDK include download numbers for the CDK library itself, but for JChemPaint, the CDK News, and several other packages too. Totals are at about 1/3rd of Jmol.

Download statistics for chemblaics components

Conference season is nearing. And just in time, Postgenomic.com


added a conferences map


showing locations of upcoming and recently finished conferences. Oh boy, do I want to set this up for chemoinformatics too! Postgenomic.com makes use of the rel=”conference” attribute


for the element.

Postgenomic.com maps upcoming conferences

On the Use of 1H and 13C 1D NMR Spectra as QSPR Descriptors

About two years ago a student started with me to work on the use of 1D NMR and IR spectra in quantitative structure-activity relationship (QSAR) work, with the goal to show that these spectra contain 3D information relevent to QSAR models. It is known that these spectra depend on the 3D conformation of the molecule.

1D NMR Spectra do not work in QSPR

While waiting for a Dragon calculation to finish (it does not work for molecules with more than 300 atoms!), I updated CDK’s build.xml to support gjdoc. The build script is now able to compile the custom doclets we use for creating the src/*.javafiles and others from the Java source files. And using gij I could also run CDK’s 1688 JUnit tests!

Open Source Java tool chain: CDK compiles and JUnit tests run

Relationships between Molecular Complexity, Biological Activity, and Structural Diversity

In a recent JCIM article, Schuffenhauer compares a few subset selection methods, and notes that some of them reduce the average complexity of the molecules. They put this in relation to other research that states that lead compounds with high complexity have higher activities. Recommended reading material for the holidays.

Subset selection: mind the complexity

Update

: Mark wrote up a blog post on the RDF that the ChEMBL team itself. Yesterday, the paper “The ChEMBL database as linked open data” (doi:10.1186/1758-2946-5-23) by Andra Waagmeester (@andrawaag), Ola Spjuth (@ola_spjuth), Peter Ansell (@p_ansell), Antony Williams (@chemconnector), Valery Tkachenko, Janna Hastings, Bin Chen (@binchenindiana), David J Wild (@davidjohnwild), and me appeared in the OA JChemInf journal.

New Paper: "The ChEMBL database as linked open data"

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

The “Emerging practices for mapping and linking life sciences data using RDF” (doi:10.1016/j.websem.2012.02.003) is now available online, where I contributed a section on the original workflow for creating ChEMBL triples, and contributed to the section about open licensing, referring to CCZero and the Panton Principles. Happy reading!

"Emerging practices for mapping and linking life sciences data using RDF"

Userscripts for the Life Sciences

Web of Science is my de facto standard for citation statistics (I need these for VR grant applications), and defines the lower limit of citations (it is pretty clean, but I do have to ping them now and then to fix something). The public front-end of it is Researcher ID. There is an Microsoft initiative, which looks clean but doesn’t work on Linux for the nicer things, but the coverage of journals is pretty bad in my field, giving a biased

My Google Scholar Citations profile arrived

Some time ago, the brilliant GitHub people gave me the following tip. Rajarshi is lazy, and might find it interesting. By appending .patch to the commit URL, a commit can easily be downloaded as patch. That way, developers can easily download it with wget or curl and apply it locally with git am, without having the fetch the full repository.

GitHub Tip: download commits as patches

I have blogged about two Molecular Chemometrics principles so far: McPrinciple #1: access to data McPrinciple #2: be clear in what you mean Peter’s post #solo10: Green Chain Reaction; where to store the data? DSR? IR? BioTorrent, OKF or ??? gives me enough basis to write up a third principle:

 Molecular Chemometrics Principles #3

: We make scientific progress if we build on past achievements. Sounds logical, right?

The Molecular Chemometrics Principles #3: stand on shoulders

Yesterday I arrived in Oxford, after a 3.5 hour bus transfer from London Stansted. Long, boring ride (though I might have seen a few red kites


, but seeing that they were near extinct, I am wondering what other large bird of prey has strong split tail like a swallow). Showed once more that the UK infrastructure has hardly changed since the 19th century. Enjoying an undergraduate room at one of the colleges.

Oxford...

CompLife’06 started today in Cambridge, UK. About 80 people are attending the meeting, and topics range from systems biology to QSAR. This evening there was a free software session mostly focussing on opensource software.

CompLife'06 - Day 1

I plan to do a daily coverage of the Chemistry Development Kit Bug Squash Party (BSP). While Stefan was working hard to get the wiki machine back online after a hard-disc crash, Rajarshi, Miguel and me have been working hard. Miguel started to work on missing JUnit tests for bugs reported on SourceForge and Rajarshi fixed PMD, JavaDoc and other problems.

CDK Bug Squash Party - Day 1

Like yesterday I will give short overview of things done at the Chemistry Development Kit Bug Squash Party (BSP). I think Stefan was the only to fix and close a bug report yesterday.

CDK Bug Squash Party - Day 2

Trepalin et al. published in Molecules the article

 A Java Chemical Structure Editor Supporting the Modular Chemical Descriptor Language (MCDL)

(open access PDF). The applet is about 250kB (though the article mentions 200kB) in size and downloadable from the MCDL project on SourceForge (license: Public Domain). The article compares the applet with the JChemPaint applet and notes that their applet is much smaller.

Small java applet for 2D structure drawing

With chemometrics in mind (QSAR, data mining, …), I have started working on matrix support in Bioclipse, because the matrix is the important step between (bio-)molecular content and statistical analysis. I implemented this such that the actual matrix implementation can be freely chosen, that is, bc_statistical provides a IMatrixImplementation extension point.

Matrix support in Bioclipse

Recent Developments of the Chemistry Development Kit (CDK) - An Open-Source Java Library for Chemo- and Bioinformatics

Recent Developments of the Chemistry Development Kit (CDK)
 
 
 - An Open-Source Java Library for Chemo- and Bioinformatics

(green OA) discusses (reasonably) recent additions to the CDK. It appeared in issue 17 of this years Current Pharmaceutical Design volume, after being too long in the queue after being accepted; but I am happy that it is out now.

Recent Developments of the Chemistry Development Kit

We're living in a 3D world

Crystal structure of the essential N-terminal domain of telomerase reverse transcriptase

Earlier I already reported that student text books were picking up Jmol as 3D viewer. Now, Nature Structural &amp; Molecular Biology reports (DOI:10.1038/nsmb0206-93) that they picked it up too, using FirstGlance in Jmol (thanx Peter, for reporting this on the Blue Obelisk mailing list!). And, thanx Eric, for acknowledging the hard work of the Jmol developers.

Open source Jmol taking over the world

This is the best news I heard in weeks! The US Patent and Trade Offfice spoke with open source representatives about ways to deal with open source software as prior art. Apparently, their problem was how to be sure about release dates of open source, and authoritative sites like SourceForge.net, FreshMeat.net help a lot here, which extensive logging of releases.

USPTO considers open source software prior art

Method for the computational comparison of crystal structures

This sunday starts the first German Chemoinformatics Conference


in Goslar. It’s an interesting programme


, with presentations on the InChI, PubChem, 25 years of chemoinformatics, the chemical semantic web, and much more. Among these presentations is mine, on comparing crystal structures (PDF


) and deducing cell parameters. But I’m having a poster on QSAR too.

Going to the German Chemoinformatics Conference

I reported earlier how to I uploaded the ChemPedia (RIP) data onto Kasabi. But for ChEMBL-RDF I have used the pytassium tool, not just because it has a cool name :) I discovered yesterday, however, that I did not write down in this lab notebook, what steps I needed to take to reproduce it. And I just wanted to uploaded new triples to the ChEMBL-RDF data set on Kasabi.

ChEMBL-RDF: Uploading data to Kasabi with pytassium

I cannot find the bug report just now, but the CDK has an open problem with change even notification, where the nonotify classes still caused change event to be sent around. This was because the nonotify classes extended in a wrong way the data classes. So, I worked today on copying the data class implementations into a new implementation, not extending the data classes, while removing the listener code: the

 silent

module.

Data, Nonotify, or Silent?

The meetings in and around Oxford were great! I already wrote that the Predictive Toxicology workshop was brilliant (see Oxford… #1


) and Oxford… #2


), but I also very, very much enjoyed meeting up with Dan and Nico! During the week, someone (name and address is know at the editorial office) commented on the fact that my blog posts are somewhat difficult to follow; that is, it’s often not clear why I am posting what I am posting.

The Molecular Chemometrics Principles #1: access to data

SMARTCyp: A 2D Method for Prediction of Cytochrome P450-Mediated Drug Metabolism

The Predictive Toxicology


meeting is over. It was a great meeting, by any standard. Very much recommended, and many thanx to Barry for the organization! The meeting was a true workshop, with a mix of presentations and getting work done. I participated in a group that looked at mutagenicity of potential anti-malaria drugs from the datasets of GSK and Novartis recently release as Open Data.

Oxford... #2

The announcement of the Panton Principles


is the


big news today, though Peter already spoke about them in May last year (see coverage on FriendFeed and Twitter). The four principles list in their short versions: When publishing data make an explicit and robust statement of your wishes. Use a recognized waiver or license that is appropriate for data.

Open Data: the Panton Principles

Google has set up a new search enginge specifically for source code: /* Code Search */. Important difference with their normal search engine is that it allows restricting your search by programming language, license and filename and package. I have not been able to figure out how to use ‘package’ yet, but the others are pretty clear.

Google's new search engine: /* Code Search */

Day 5 was formally the last day (see also the summaries of day 1, day 2 and day 3/4) of the Chemistry Development Kit Bug Squash Party (BSP). Miguel uploaded the last bits of his CDK PDBPolymer to CML to CDK PDBPolymer roundtripping functionality (closing a bug and a feature request in one go). Have not tested this first hand yet, but looking forward to playing with this bit of code.

CDK Bug Squash Party - Day 5

EDITORIAL

An Experiment in Crystal Structure Prediction by Popular Vote

There are a number of links I wanted to blog about, but never really had time for yet. Here’s a short review of a them. Bio::Blogs is a series of summary/review articles of bio related blogs, and definately worth putting in your aggregator. Maybe someone is interested in setting up a Chemo::Blogs for chemistry blogs? My del.icio.us (social bookmarking) network informed me about HTML Slidy, an XHTML based PowerPoint replacement.

Chemo::Blogs #1

Experimental data checker: better information for organic chemists

Chemical Archeology (see Christoph’s comment) is the process of extracting chemical information from old journal articles. Some time ago, Peter Corbett from the group of Peter Murray-Rust visited the CUBIC to talk to us about Oscar3 which can do just that. That day, we already hooked OPSIN into Bioclipse


. Oscar3, however, is capable of more then the name2structure of OPSIN (see also 10.1039/b411033a;

Chemical Archeology: OSCAR3 to NMRShiftDB.org

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

Recently, a new generation of Chemical Markup Language CML users seem to hit the learning-curve-wall; there seems to be a niche in explaining the use of CML, so here goes. My new (third) blog will discuss frequently and less frequently asked questions about the use of CML.

CML Explained

Something I have not completely comfortable with about the CDK in the past, is the way Atom’s are constructed:   IAtom carbon = new Atom("C");  Not that it is horrible code, but the CDK has an Element too. Why not reuse that?

new Atom(Elements.CARBON);

Technorati is nice in several ways, one being the feature to set up a watchlist. I have set watches on

 chemoinformatics, Jmol, Bioclipse

and a few more. This allows me see the latest blog items on these topics. Often, the point to Asian blogs, mostly Chinese and Japanese, which I mostly find hard to read.

BlueObelisk components in Japanese

The Eclipse Rich Client Platform (RCP) is very powerfull, and takes a lot of architectural things of your hand when developing a bio- and chemoinformatics GUIs. Bioclipse is based on it. One thing the RCP offers is a Help View which works with plain (X)HTML files, and one neat feature is the context help. It is help shown in the Help View when one focused on a specific GUI element.

Context help in Bioclipse

David Strumfels posted news about the Useful Chemistry CMLRSS feed


. He explains how this feed can be accessed using Jmol and Bioclipse. The latter are accompanied by two AVI movies: one about creating a new OPML file, and one about accessing the CMLRSS file from the OPML.

AVI movies of CMLRSS howto in Bioclipse

Just wanted to make sure this news made it to the Blue Obelisk Planet too: David Strumfels reported that he extended MS-Excel with CDK functionality


. I wonder how difficult it would be to do this with Kspread or Gnumeric?

A chemistry extension for spreadsheet(s)

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

Joerg Wegner


mentioned in his blog the graph mining program ParMol


which integrates four mining algorithms: MoSS (aka MoFa) and Gaston, which I mentioned in November last year


, and FFSM and gSpan, which I did not know about yet. ParMol provides a common interface to the four different algorithms and is, like the four mining modules, licensed GPL.

Four graph mining methods integrated in ParMol

Rajarshi Guha


has set a nightly build service


for the Chemistry Development Kit (CDK). The output is pretty, but information rich: it includes results for the JUnit test, DocCheck, and PMD. The compiled jar and the corresponding JavaDoc can be downloaded, offering a cutting edge distribution for users.

Nightly CDK builds now available

I have not blogged for about a week now, and been too busy with other things, like finishing my PhD articles/manuscript, my new job at the CUBIC where I continued the work on proper protein support in Bioclipse using the CDK and Jmol: The latter involves getting the CdkJmolAdapter


, the interface between the CDK and Jmol, updated for changes


since the Jmol as 3D viewer for CDK


article in CDK News


, the open

chem-bla-ics

Uncertainty in NMR based 3D protein models