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03 May 2010

My new position at INSERM/UMR915

I'm pleased to announce that I've started a new position as a postdoc in Nantes/France at INSERM/U915 , the Thorax Institute for 3 years. The Institute is face up to the Loire and works in close collaboration with the neighboring Hotel-Dieu Hospital.

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My team is led by Dr Richard Redon who worked at the Sanger institute on the Copy Number Variations . I'll be part of a project studing the genetics of the Brugada Syndrome using NGS. I'm just starting on this technology so I'm currently learning how to use all those new tools such as R, MAQ, SAMTOOLS , BWA , etc.... biostar.stackexchange.com has been a useful source of information here.

I applied for this position a few days before leaving to Biohackathon 2010 and I started to work in the lab on April 1st. I've been said that my professional network has been of help to get this job, especially Jan Aerts (my new best friend ! ;-) ) (thanks Jan !) who worked with Dr Redon at the Sanger Insitute.

More to come... ! :-)

That's it

Pierre

23 April 2009

A Tag Cloud for my Resume.

I'm revising my CV as I'll move to Nantes and I wanted to create a Tag Cloud to illustrate my resume. Paul and Richard suggested to use wordle to generate the cloud but I wanted to generate it on the fly, for any language, whenever I want, etc...
so I stored my skills in a RDF file which looks like this:

<?xml version="1.0" encoding="ISO-8859-1"?>
<!DOCTYPE rdf:RDF [
          <!ENTITY info "plum">
          <!ENTITY bio "blue">
          <!ENTITY other "lightgray">
          <!ENTITY devtool "magenta">
          <!ENTITY devlang "darkRed">
          <!ENTITY os "purple">
          <!ENTITY database "orange">
          ]>
          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns="http://ontology.lindenb.org/tagcloud/">
                  <Tag rdf:about="https://javacc.dev.java.net/">
                          <weight>25</weight>
                          <label>Javacc</label>
                          <title xml:lang="en">JavaCC is a parser/scanner generator for java</title>
                          <title xml:lang="fr">Un generateur de parser pour java</title>
                          <color>magenta</color>
                  </Tag>
 (...)
                  <Tag rdf:about="http://en.wikipedia.org/wiki/Awk">
                          <weight>25</weight>
                          <label>Awk</label>
                          <title>Awk</title>
                          <color>darkRed</color>
                  </Tag>

                  <Tag rdf:about="http://en.wikipedia.org/wiki/GNU_bison">
                          <weight>25</weight>
                          <label>Lex/Yacc</label>
                          <title>Lex/Yacc & Flex/Bison</title>
                          <color>magenta</color>
                  </Tag>
 (...)
          </rdf:RDF>

Advantages: I can store the labels for various languages, use xml entities like <!ENTITY devlang "darkRed"> to quickly change a color, etc...

This XML file is then transformed with the following XSLT stylesheet

http://code.google.com/p/lindenb/source/browse/trunk/src/xsl/tagcloud2html.xsl

And (tada !) here is the result

Waves... :-)

(And the icing on the cake : it is a RDFa output).

Note: Pawel Szczesny did great job for his CV too.

Pierre

06 April 2009

Go West !

After one year at the Center for the Study of Human Polymorphisms I will follow my wife in Nantes (France) on September 1st 2009. Hum... that is not the right period to find a new occupation, so I hope I'll find a new job there (related to science or to the semantic web). Wanna hire me? Here is my profile on LinkedIn.

Nantes Image via wikipedia

01 September 2008

I'm not looking for a job anymore: Welcome at the CEPH

Today was my first day as a bioinformatician at the Center for the Study of Human Polymorphisms (CEPH http://www.cephb.fr/en/cephdb) and I want to thank my former colleagues Christine K and Philippe Gesnouin (philguess on twitter/FF ) who helped me to find this position. It's a short term contract (one year).

The CEPH is localized in Paris near the St-Louis Hospital and the "Place de la République" it maintains a database of genotypes for genetic markers that have been typed on the CEPH reference family resource for linkage mapping (Genomics 6: 575-577, 1990; Science 265: 2049-2054, 1994). The CEPH works works in conjunction with the National Center of Genotyping (CNG/Evry) where I also worked height years ago and both centers are managed by Dr Mark Lathrop. One of my first objective is to develop a set of tools around OPERON with the help of his author, Mario Foglio.

As far as I've understand operon today (I may be wrong), it is a C program handling a large set of genotypes (among other things...) using BerkeleyDB as a storage engine (I blogged about BerkeleyDB a few posts ago). It seems that using this strategy, the genotypes can be quickly accessed using something like fseek(table,sizeof(genotype_t)*(sample_count*marker_index+sample_index),SEEK_SET).

As a java programmer, I wish I could write a wrapper around the Operon C API, that would be useful to embed this model in a web container (servlet, jsp) or to write a Swing interface. My first ideas to achieve this are:
* using JNI (Java Native Interface, allows to call C from java) to write a java wrapper around the C API
* reading the data in the berkeleyDB files using the BerkeleyDB Java API.
* ...

That's it for tonight.

Pierre

10 June 2008

I'm looking for a job !

Hi all,
I've just given my letter of resignation to my current employer , thus I'll be free from my professional obligations on September 1st and from now on I'm looking for a new fascinating job combining biology and informatics near Paris, France. This blog is a proof of my passion and my motivation for this area of interest. Recruiters can contact me via e-mail ( plindenbaum at yahoo fr ) and consult my resume on linkedin at http://www.linkedin.com/in/lindenbaum.

Pierre Lindenbaum PhD

Après avoir remis ma lettre de démission à mon employeur actuel, je serai libre de mes obligations professionnelles à compter du 1er septembre 2008. Je suis donc à la recherche de toute opportunité d'emploi combinant la biologie et l'informatique dans la région de Paris. Ce blog étant une preuve de ma passion et de ma motivation pour ce sujet. Les recruteurs intéressés par mon profil peuvent consulter mon CV sur linkedin http://www.linkedin.com/in/lindenbaum et me joindre par mail à "plindenbaum at yahoo fr"

Pierre Lindenbaum PhD

07 November 2007

JOBS 20071106

Programmer to install and maintain genome database software:
http://www2.recruitingcenter.net/clients/CalTech/publicjobs/controller.cfm?jbaction=JobProfile&Job_Id=13989&esid=az

Bioinformatician/Biostatistician position at the Centre for Molecular Oncology, Institute of Cancer
Immediate opening for a highly motivated Bioinformatician/Biostatistician with strong numerical skills and a track record of the analysis of high throughput technologies.
http://webapps.qmul.ac.uk/hr/vacancies/jobs.php?c=0&format=full

05 November 2007

Job@Novartis 20071105

Position Title Research Investigator II/Bioinformatics
Work Location Switzerland - Basel
Company/Legal Entity Switzerland Novartis Pharma AG, Basel
Functional Area Research
Job Type Full Time
https://xjobs.brassring.com/2057/asp/tg/cim_jobdetail.asp?jobId=602151&PartnerId=13617&SiteId=5049&type=mail&JobReqLang=140&recordstart=1&JobSiteId=5049&JobSiteInfo=602151_5049&gqid=0

02 November 2007

job@swissprot 2007-11-02

The Swiss-Prot group at the Swiss Institute of Bioinformatics (SIB) in Geneva (Switzerland) is looking for a Java developer.

See http://www.isb-sib.ch/infos/careers_070625.htm for more details.

YOKOFAKUN