Mathias - Administrateur système LINUX
Ref : 070829V001-
75015 PARIS
-
Administrateur système, Développeur, Ingénieur de production (48 ans)
-
Freelance
Since May 2006 : Research Associate, Computational Biology & Mass Spectrometry : Institut Pasteur, Paris, France. Research in the field of proteomics.
May 2005 – May 2006 : Post-doctoral fellow at the Ecole Normale Supérieure, Paris, France.
Vertebrate Genomics: identification and analysis of the syntenic regulatory zones in newly sequenced eucaryotic genome-sequences. Implementation of heuristic approaches – data mining.
May 2004 – May 2005 : Post-doctoral fellowship at the University Basel, Basel-stadt, Switzerland.
Yeast Genomics: identifiation of regulatory syntenic sequences in newly available yeast genomic sequences. Imple- mentation of computationally efficient data-mining and analysis tools – sequence analysis.
March 2004 : Ph.D in Computer Science, Laboratoire bordelais de Recherche en Informatique (LABRI, University of Bordeaux I, France), and Institut National de Recherche en Informatique et Automatique (INRIA Rocquencourt, France). PhD thesis: “Algorithms and statistical metrics for assessing the significance of functional motifs in biological regulatory sequences.” – Promotors: Dr. M. Régnier, Prof. Dr. S. Dulucq).
January – April 2000 : Course of “Informatique pour la Biologie” (computer science applied to biological problems), Institut Pasteur, Paris, France.
June 2000: M.Sc in the Laboratory of Protein Biochemistry and Protein Engineering, University of Ghent, Belgium. Master’s thesis, undertaken in the laboratory of Biochemistry, microbiology and physiology, entitled: “Cloning and expression of the Chlorobium limicola forma thiosulfatophylum cytochrome c-551 gene and its influence in the thio- sulfate comsuming gene-cluster” – Promotors: Prof. Dr. J. Van Beeumen, Dr. ir. F. Verté.
June 1997: B.Sc. Biology, University of Ghent, Belgium.
Teaching
January 2008 – April 2008 Course of “Informatique pour la Biologie” (computer science with biology-related applications ).
Institut Pasteur, Paris France.
October 2002 – January 2003 Assistant teacher, computer science, University of Marne la Vallée.
April 2002 & April 2003 Assistant teacher, computer science, Ecole Centrale de Paris:
Pratical statistics – probabilities in bioinformatics.
Supplémentaire Course in prediction of protein 3D-structure and fonction
Computer skills
- Unix: C, C++, Java, Perl, Awk, Lisp, R, GPU parallell programming using C/CUDA, OpenMP, C++ Pthreads.
July ’08 & Sept ’09: (Advanced) Object Oriented Programming in C++ (Orsys, la Défence, Paris, France)
- Conception and software development: Eclipse – Cvs, Svn – MySql DB – project management with Redmine
(Ruby-gems) - Institut Pasteur.
Examples of developped software:
• JAVA: MascotDatReader – analysis and interpretation of mass spectrometry - Mascot search results (version 0.01 using the MascotDatFile library; version 0.02-0.05 using the MatrixScience MsParser). Collaboration Univ. Evry, France.
• JAVA: MaldiTool – analysis and interpretation of LC/Maldi-MS data for quantification. Collaboration Univ. Tuebingen, Germany.
• JAVA: Madi2Orbi – reformatting tool for Maldi-MS data for input compatible with Orbitrap analysis tools. CollaborationUniv. Tuebingen, Germany.
• C++: multiple alignment of LC-MS/MS experiments. Visualisation of results. Institut Pasteur.
• PERL: Comparison through alignment of genomic sequences for detection of syntenic regions using homology. Ecole Normale Supériere & Univ. Basel.
• ANSI-C: counting and statistical analysis of genomic regulatory motives. Inria and Univ. Bordeaux I, France.
- Hardware management, installation, updating and maintenance of High-Performance Computing servers and user-workstations: Linux RedHat, Mac-OSX, FreeBSD 8.x./9.0, SunOS 5.11/OpenSolaris/OpenIndiana b147. Network Security. Cluster Management tools: PBS/SGE, Pvfs2.
- Maple and Mathematica for symbolic computing,
- Unix (Linux, BSD, Mac-OS X, SunOS) System Administration.
- Windows environments and application suites (MS-Visual Studio 08, Ms-Office suite).
Languages :
• French–English–Dutch: read–spoken–written.
• German: good level
• Spanish: notions.