Bioinformatics engineer - Web developer

Experience

LBCMCP, CNRS UMR5088, Université Paul Sabatier (Toulouse, FR)

Full time position: Bioinformactics engineer.

Working on a Qt/C++ framework named GeneHuggers for easing the developement of bioinformatics applications.

Sanger Institute (Cambridge, UK)

Full time position: Bioinformactics engineer, senior software developer.

Working in the High Troughput Gene Targeting (HTGT) bioinformatics team related to the European Conditional Mouse Mutagenesis programme (EUCOMM) and the KnockOut Mouse Project (KOMP). These projects aim to provide a public resource of thousands of lacZ-tagged, conditional mutations in mouse ES cells by 2011.

Fig.: Targeting vector (DNA construct) that gets inserted in mouse genome through ES cells

• Creation of a web application and its webservice interface for handling data of these projects:
  • Study of the scientific method used in the lab (gene knockout).
  • Study of the existing LIMS from which data are retrieved to load the application's database.
  • Conception of data models and implementation of a web application along with its webservice interface (REST)
  • Creation of a Biomart to provide a quick and read-only access to the data
  • Creation of a DAS adaptor to display genes annotations in Ensembl
  • Technologies used: Ruby on Rails, Biomart, Perl, SQL (Oracle, MySQL)
• Quality Control and reporting on gene knockout designs.
• Support and maintenance of the LIMS application.

Publication: The IKMC web portal: a central point of entry to data and resources from the International Knockout Mouse Consortium

Sibio (Paris, FR)

Full time position: Bioinformatics engineer, web developer.

Development of a web-based LIMS (Laboratory Information Management System) software:

• Database modelisation, server-side and client-side development of the whole software:
  • Workflow implementation: database modelisation, algorithms, graphical edition (drag & drop)
  • Display of biological samples tracking: parent and child relationships (tree view), attached files and images, storage spaces, etc.
  • Simple creation of custom analysis tables
  • Simple to complex forms management
• Use of latest web technologies:
  • Django: high-level Python Web framework that encourages rapid development and clean, pragmatic design. It lets you build high-performing, elegant Web applications quickly.
  • JQuery: fast and concise JavaScript Library that simplifies HTML document traversing, event handling, animating, and Ajax interactions for rapid Web development.
• Knowledge of sample traceability and Quality standards
• Constant communication with users for improving the software
• Management of a student (Master) during 6 months
• Screenshots:

LIMSI CNRS (Orsay, FR)

Internship: protein-protein docking

Worked with a PhD student on protein-protein interactions (docking) and complex visualisation:

• Study on existing viewers (UCSF Chimera, Pymol, etc.)
• Development of a Pymol plugin to handle manipulation of proteins designed with a Voronoï transformation.
• Re: Julie Bernauer (PhD), Christine Martin (PhD)

Banque de France (Paris, FR)

Internship: application development

Worked in the financial department for developing an analytics application:

• Analysis of current system and users expectations
• Conception and development of a light solution for retrieving data from a database, processing and displaying results in spreadsheets (Pie charts, tables, etc.).

Skills

Biology, bioinformatics and biostatistics

• Cell biology, molecular biology, genetics, structural biology
• Gene annotation, gene sequencing
• Data mining, text mining
• Statistical inference, statistical test

Programming languages

• Ruby on Rails, Django, JavaScript (JQuery), AJAX, HTML, CSS
• Ruby, Python, Java, Perl, C++, C
• R, Scilab

Development environment

• OS: Mac OS X, Linux (Ubuntu), Windows XP
• Tools: Textmate, Eric4, Scite, Eclipse IDE
• Databases: PostgreSQL, MySQL, sqlite
• Web server: Apache
• Revision control system: subversion (svn), git

Education

University Paris 11, France

Master degree in bioinformatics and biostatistics

University Paris 5, France

Associate's degree in computer science

Languages

• French: mother tongue
• English: read, written, spoken

Activities and sports

Activities

• Member of ISCB (International Society for Computational Biology) - France group. The association aims to build a community of young bioinformatics people in France. It is mainly designed for students who need basic to advanced information on bioinformatics, technical help, find a PhD or a job, etc.
• Cooking: main activity in my spare time
• Cinema

Sports

• Tennis (played for 8 years)
• Football (played occasionally)