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Pierre MARGUERITE's English Resume

Bioinformatics Scientist

Version Française

Personal Information

• Email:
• Sex: Male
• Nationality: French
• Age: 26
• Marital Status: Single

Education

• 2003-2004: Postgraduate degree in computer sciences specialising in bioinformatics (with honours) ("DESS BioInformatique", University of Lille, France).
• 2002-2003: Postgraduate degree ("DEA Informatique" (Systèmes et Communication), University of Grenoble, France).
• 2001-2002: Master's degree in Computer Science (with honours) ("Maîtrise d'informatique", option bioinformatique/biomathématiques, University of Grenoble, France).
• 2000-2001: Bachelor's degree (with honours) ("Licence d'Informatique", University of Grenoble, France).
• 1998 : "Baccalauréat Scientifique (S)" (French "A"-levels) specialising in Mathematics (Lycée du Grésivaudan, Meylan, France).

Skills and Qualifications

Computer Science

Information system modelling:	Z, ZSP, Merise methods (UML)
Programming languages:	C, C++, Pascal, Scheme, Ada, JAVA (JNI, RMI, SWING, J2EE), Prolog, Lustre, Perl
Web technologies:	HTML, XHTML, CSS, Java (JSP/Servlet, JaxB, JDBC), PHP, XML (XPATH), XSLT, SMIL, SOAP (AXIS)
Software and hardware Architectures:	assembler language (SPARC)
Databases (DBMS):	SQL - Oracle, PostgreSQL, MySQL
Operating systems:	UNIX, GNU/Linux, Microsoft Windows (95, 98, Me, 2000, XP)
Development tools:	Eclipse, Ant, Maven, JProbe
Component Applications:	Lifecycle, concepts and implementation
Algorithmics and techniques in distributed systems
Cluster architectures for high-performance computing
Middleware
User interface models
Neural Network

Bioinformatics/Biomathematics

Knowledge bases	genetic, genomic
Biostatistics: R	Microbiology
Data mining (Weka), annotation, phylogeny(Phylip)	Databases and software for bioinformatics: EMBL, UniGene, Swiss Prot, PIR, TrEMBL, UniProt, InterPro, SRS, BLAST, Fasta, ClustalW, Dialign, GeneMark, OrfFinder
Sequence analysis: homology search, pattern matching, gene prediction, multiple alignment, structures prediction	Microarray: MIAME, MAGE, MGED Ontology
proteomic, transcriptomics	Cellular Biology and Eukaryote Genetic
Biochemistry, enzymology

Foreign Languages

• Fluent in French: Mother's tonge
• Fluent in English: Working knowledge of English: two years living in Cambridge,U.K., Six months in Cambridge, United Kingdom, courses at various locations - King's College London, Cork English College (Eire), Scotland, Edinburgh, (summer 1999, 2000, 2001, 2002 and 2003).
• Basic German.

Professional experience

• Visualisation and Analysis of Molecular Sequences, Alignments and Structures Project -VAMSAS@EBI- at European Bioinformatics Institute (Cambridge, UK)
  Macromolecular Structure Database , EBI, Cambridge (United Kingdom)

  September 2005 - September 2007

  Skills: Java, UML, XML, XSLT, XML Schemas, Ant, Linux, Eclipse, TOMCAT, jsp, servelt, Log4j API, CASTOR API, AstexViewer@MSD-EBI, Soap web service (AXIS), Maven2, Perl, shell scripting, AJAX, Oracle, MSD API, Secondary structure matching (SSM)

  Part of the development team for the Visualisation and Analysis of Molecular Sequences, Alignments and Structures project (Vamsas), coordinator of the project at the EBI. The Vamsas project is a collaboration between the University of Dundee, Biomathematics & Statistics Scotland (BioSS) and the EBI. A key objective of this project is to simplify collaboration between the phylogeny and protein structure communities via the provision of easy to use tools for complex methods. We achieved this by adding significant new functions to three popular Java-based applications that span phylogenetics on DNA (TOPALi) protein sequence analysis and prediction (JalView) and visualisation of three-dimensional structure (AstexViewer@MSD-EBI). We developed a document exchange format (XML based), and an API to manipulate documents and interact between applications. I worked on the integration of the AstexViewer@MSD-EBI in the workflow. The analysis tool has been embedded in a Java multi-platform application provided several developed services, mainly accessible as soap webservices.

  Ownership or active involvement in the following projects, among others:

  MSDGrouping: (Development)

  Application for protein analysis, grouping of proteins per similarity by sequence or structure. Based on the analysis of well known external analysis tools. Runs on a PC farm, to improve performance and have job executions in parallel. A series of shell script runs analysis tools, treats their output and generates an XML output (including Perl scripts, Java tools). Data can be accessed either through the standard Web interface, command line or SOAP web service (using one of the various APIs available for SOAP, including C++, JAVA, Python, Perl, …) Technologies: Java, Unix, tcsh shell scripting, Perl, Oracle DB, Jsp/Servlet, (X)HTML, Apache Tomcat cluster, Apache Axis, LSF, Unix, XML schema, XSL transformation, Eclipse, CASTOR API.

  MSDMapping: (Development)

  Application for protein analysis, provided mapping between protein structures and entries from external biological databases against the MSD database. Uses the functionalities of the Oracle 9i database (pl/SQL, functions). The available data are the positions for MSD entries, so uses functions to determine position for corresponding PDB entries. Data accessible either through the standard Web interface, or SOAP web service (using one of the various APIs available, including C++, JAVA, Python, Perl …) Technologies: Oracle 9i, pl/SQL (functions), Java, DB, Jsp/Servlet, Apache Tomcat cluster, Apache Axis.

  MSD-API: Maintenance.

  The service provided an access to a range of web-services for end-user to the MSD database and the internal analysis tools, using SOAP protocol. The Service can be accessed using one of the various APIs available, including C++, JAVA, Python, Perl … Technologies: GSOAP, Lisp, C++, Oracle DB

Other Training

2003-2004

• Facilitating Standardization and Exchange of Microarray Layout at European Bioinformatics Institute (Cambridge, UK)
  Microarray Informatics Team, EBI, Cambridge (United Kingdom)

  Six-month placement (May 2004 - November 2004)

  Referee: Alvis Brazma

  Skills: Java (JAXB), UML, XML, XSLT, XML Schemas, Ant, Linux, MAGE-stk, Eclipse, DAML+OWL / OWL, jxl API, Log4j API, Latex

  Resources: Master's thesis, Master's presentation in French, Friday seminar talk.

• Bioinformatics project: Retrospective analysis of microarray data
  plate forme de génomique fonctionnelle -- inserm U459 unit, Lille (France)

  Referee: Pierre-Marie Danzé

  Skills: R, MIDAS (TIGR Microarray Data Analysis System)

• Informatics project: administration and visualisation tool for Ligand database

  develop an administration and visualisation tool for Ligand database (Reactions in Biological Pathways) from KEGG bank

  Skills: UML, PostgreSQL, Perl, JAVA, JDBC, JSP and XML

  Resources: Project presentation, project report in French.

• Generic Database consultation tool

  Skills: Java, Java Swing, PostgreSQL JSP and Servelt

2002-2003

• Middleware Deployment in Large Heterogeneous Environments
  Sardes Project, L.S.R., INRIA Rhône-Alpes, Grenoble (France)

  Nine-month placement during postgraduate DEA cursus at INRIA Rhône-Alpes, in "Logiciels, Systèmes, Réseaux" (L.S.R.)

  Referees: Emmanuel Cecchet, Philippe Laumay

  Skills: software laboratory, Java

  Dea Presentation 2eme Version

2001-2002

• Automatic Computer Configurations in Cluster Intranet Environments
  APACHE Team (INRIA), I.D., ENSIMAG, Grenoble (France)

  Study and research placement, followed by a Summer placement of nine weeks in the "Informatique et Distribution" (I.D.) laboratory of ENSIMAG within the APACHE team (INRIA)

  Referees: Philippe Augerat, Wilfrid Billot

  Skills: C, Latex, Doxygen, SLP protocol

2000-2001

• Design work on "Tablut"

  Design work on "Tablut", a game application under Ada language (Bachelor of Information Science project)

  Skills: Ada

Activities and Interests

• Communication Project: Participation in Téléthon 2003 in Lille (televised fundraising event for myopathy sufferers).
• Treasurer of the TATABOX association (bioinformatics student association).
• Full clean driver's license.
• European First Aid Certificate (A.F.P.S) - (BEPS)

Posters

• New components to MIAMExpress - easing submission and visualization of MIAME compliant experiments.
  Catherine Leroy, Pierre Marguerite, Bhuwan Tiwari, Niran Abeygunawardena, Sergio Contrino, Anna Farne, Ele Holloway, Gaurab Mukherjee, Helen Parkinson, Tim Rayner, Philippe Rocca-Serra, Susanna-Assunta Sansone, Ugis Sarkans, Alvis Brazma and Mohammadreza Shojatalab Abstract