Jekyll2026-07-18T13:36:15+00:00https://chem-bla-ics.linkedchemistry.info/feed/by_tag/career.xmlchem-bla-icsChemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.Egon WillighagenThesis and copyright transfer2009-05-04T00:00:00+00:002009-05-04T00:00:00+00:00https://chem-bla-ics.linkedchemistry.info/2009/05/04/thesis-and-copyright-transferMy thesis was released slightly over a year ago in print form. The electronic form has not yet, which has social and legal barriers. Like many before me, I made the mistake to publish in journals that require me to reassign copyright. Combine that with the custom to publish papers in your thesis as is, which means reduction of work for the manuscript committee, as they can know which chapters have undergone peer-review in the form they are present in the thesis too. (The layout is different, as I integrated them into the thesis design.)

So, my thesis has six chapters which I cannot redistribute. I am still happy having published in the Journal of Chemical Information and Modeling (formerly JCICS), and still review papers for that journal; it still is the main forum in cheminformatics, but recently challenged .

I have come to the conclusion that copyright transfer will not be my author choice in the future, and the ACS AuthorChoice still seems to require copyright transfer, if I do not misunderstand the legal talk.

So, if you like a copy of those six chapters, send me an email requesting the a print copy of my thesis from my defense (I still have a few around). (Alternatively, donate to my project to make these chapters AuthorChoice, but the ACS charges quite some money, and Google Adsense is not compensating for that quite yet.)

]]>Egon WillighagenThings to do…2009-04-29T00:00:00+00:002009-04-29T00:00:00+00:00https://chem-bla-ics.linkedchemistry.info/2009/04/29/things-to-doI know I am lagging behind things… been busy and did not have time to reply to everyone yet. Some TOREPLY’s go back more then a month. Sorry about that!

Some of the things on my TODO list (in random order): Bioclipse2 bug fixes, CDK patch reviewing (e.g. vflib), look at the Jmol-CDK bridge and bring it into action in Bioclipse2, RDF for PubChem, convert the Woordenboek Organische Chemie data into in RDF, RDF for NMRShiftDB, align with ChemAxiom, publish about the Bioclipse2 RDF feature, finish the MetWare paper, write a metabolomics feature for Bioclipse2, finish the pKa prediction in the CDK, write 100% coverage CDK 2 CML 2 CDK, implement atom parity stereochemistry from SMILES and/or MDL molfiles, use supervised SOMs in QSAR, user supervised SOMs in proteochemometrics, study variable influence on supervised SOM models, make my thesis Open in the Radboud University library repository (excluding the papers I no longer have copyright on), update the QSAR and algorithm ontologies in OWL, create a web page with life ONS solubility RDF, create an ONS solubility Bioclipse2 feature, study the CDK fingerprint performance compared to the new PubChem fingerprint, make Chemical blogspace aware of the ChemSpider widget, interest people for an unconference in Stockholm or Uppsala, move house, learn to Swedish, get a driver license, implement a memory more-efficient CDK interfaces implementation, promote XMPP services which are better than SOAP, and write more papers, work on CMLSpect for metabolomics, finish the CDK book, finally get a grant application approved, read up with literature and summarize in blog, port the Jmol UFF force field code to the CDK, analyze atom typing in the CDK against PubChem and StarLite, compile strigi-chemistry again KDE 4.2.2, finish egonw.github.com homepage, … you know the regular list of things to do.

If you happen to be a masters student interested in doing a internship/practical here in Uppsala (unpaid, but you will learn so much), just email me.

]]>Egon WillighagenMoved to Sweden: Post-doc in the Bioclipse group of Prof. Jarl Wikberg2008-09-24T00:00:00+00:002008-09-24T00:00:00+00:00https://chem-bla-ics.linkedchemistry.info/2008/09/24/moved-to-sweden-post-doc-in-bioclipseThe reason why I have not been able to blog much lately, is that my family and I have been moving to Uppsala/Sweden, where I’ll start a postdoc in the group of Jarl Wikberg @ BMC @ Uppsala University, where I’ll work on chemoinformatics in drug design, and the use of CDK and Bioclipse in particular.

More blogging when I have more frequent internet access again…

]]>Egon WillighagenMoving to Sweden: Improving CDK support in Bioclipse2008-07-04T00:00:00+00:002008-07-04T00:00:00+00:00https://chem-bla-ics.linkedchemistry.info/2008/07/04/moving-to-sweden-improving-cdk-support This autumn I will end my current post-doc position at Plant Research International in the Applied Bioinformatics group and at Biometris (both part of Wageningen University) funded by the Netherlands Metabolomics Center (lot’s of vacancies), where I had a good time, and collaborated in several projects within the NMC with much pleasure.

However, personal circumstances strengthened an older wish of me and my family to seek the adventure of living abroad, and a vacancy was available in the group of Prof. Wikberg. So, we are moving to Sweden. There, I will extend my research on effectively combining chemoinformatics (sometimes misspelled as cheminformatics ;) and chemometrics, as I did in my PhD, which fits well with the development of proteochemotrics methodology and Bioclipse as platform to transform scientific hypotheses into data queries.

]]>Egon WillighagenA new job: post-doc at the WUR on MS based structure elucidation2007-06-19T00:20:00+00:002007-06-19T00:20:00+00:00https://chem-bla-ics.linkedchemistry.info/2007/06/19/new-job-post-doc-at-wur-on-ms-basedOn July 1st I will start a post-doc in Wageningen, The Netherlands at the WUR. More precisely, with a post-doc in the group of Prof. Van Eeuwijk at Biometris, cooperating with the group of Prof. Hall at Plant Research International (PRI), within the framework of the new Netherlands Metabolomics Center. The topic will be structure elucidation using mass spectral data originating from the experimental department of PRI, and will be a nice follow up on the work on SENECA I have been doing last year in the group of Dr. Christoph Steinbeck at the CUBIC.

]]>Egon WillighagenEx-CUBIC get-together2007-04-27T00:00:00+00:002007-04-27T00:00:00+00:00https://chem-bla-ics.linkedchemistry.info/2007/04/27/ex-cubic-get-togetherYesterday and today I was in Cologne to meet with other ex-CUBIC researchers from Christoph’s research group on chemoinformatics (and with Alexandr). Not all former group members where there, but on the other hand we were complemented with Pascal:

(Yes, the sun was very bright :)

The program was consisted of a couple of group things, like making a short list of articles to write up in the next few months. Yesterday evening ended in a very nice Biergarten called the Altenberger Hof.

]]>Egon WillighagenThe Cologne University BioInformatics Center (CUBIC)2006-03-25T00:00:00+00:002006-03-25T00:00:00+00:00https://chem-bla-ics.linkedchemistry.info/2006/03/25/cologne-university-bioinformaticsAs of April 3, I will be working as postdoc in the group of Christoph Steinbeck at the Cologne University BioInformatics Center, or simply CUBIC, for a year. Though no exact plans have been decided upon, the work will include CDK, CML, ontologies, Bioclipse, semantic web technologies, Jmol, and other interesting things. Research areas will at least include QSAR, but I hope to touch bits of bioinformatics too.

]]>Egon WillighagenGoing to the German Chemoinformatics Conference2005-11-11T00:00:00+00:002005-11-11T00:00:00+00:00https://chem-bla-ics.linkedchemistry.info/2005/11/11/going-to-german-chemoinformaticsThis 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.

I’ll arrive on saturday afternoon in Goslar, so leave a message at the conference hotel if you want to meet up, and talk about my work, or yours, or the CDK, KDE, JChemPaint, Jmol, kfile_chemical, Kat/Chemistry, BlueObelisk, Eclipse, R, or whatever else… I plan to have a modest german meal and one or two beers in the evening.

BTW, after Belém (Lissabon), Sintra, Boppard, Kinderdijk, Hoorn and Cologne, it’s the 7th UNESCO world heritage site I’m visiting in just 14 months! Can’t we just have conferences in Hawaii and sorts, like they do in other fields?? Oh, wait, we do: EuroQSAR is on a cruise boat.

]]>Egon WillighagenWrapping up…2005-10-23T00:00:00+00:002005-10-23T00:00:00+00:00https://chem-bla-ics.linkedchemistry.info/2005/10/23/wrapping-upLess 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. Working on some easy-to-fix CDK bugs yesterday, like the QueryAtomContainer now correctly updated for the recent cdk.interfaces changes . Fixed now. I also touched a lot of code when updating the FSF address in the LGPL license notice, and when I modified the construction of CDKException ’s to set the causing Throwable. Also helped out Carsten a bit with adding his data from Kalzium to the Blue Obelisk data repository .

Another nice diversion is The Battle for Wesnoth. Just got killed, though.

]]>Egon Willighagen