Expertise
Hub members Have many expertise, covering most of the fields in bioinformatics and biostatistics. You'll find below a non-exhaustive list of these expertise
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Related people (7)
Fabien MAREUIL
After a Master degree in Genome Analysis and Molecular Modeling at Denis Diderot University, I did a PhD in NMR / bioinformatics at Denis Diderot University, where I worked on the development and use of a software named DaDiModO which uses SAXS data and RDC/NMR data to calculate models of structural proteins. After a postdoc aiming to adapt ARIA software to allow execution on computing grid in the Structural Bioinformatic Team at Institut Pasteur in collaboration with IBCP, I joined CIB/DSI Team where I was responsible for the development of bioinformatics projects and the deployment, maintenance and evolution of the Pasteur Galaxy server. I joined the Hub/C3BI team in 2017 as research engineer where I’m involved in several projects such as structural bioinformatics, softwares and web development. I am also in charge of the maintenance of the Galaxy Pasteur instance.
KeywordsData managementGalaxyStructural bioinformaticsWeb developmentDatabaseProgram developmentScientific computingDatabases and ontologiesWorkflow and pipeline developmentGrid and cloud computing
Organisms
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Projects (15)
- Development of a secure API for ARIAweb(Benjamin BARDIAUX - Structural Bioinformatics) - In Progress
- Development of a web server to calculate functional binding sites using Deep Learning(Olivier SPERANDIO - Structural Bioinformatics) - In Progress
- A pipeline to detect correlated evolution on phylogenetic trees(Eduardo ROCHA - Microbial Evolutionary Genomics) - In Progress
Bertrand NÉRON
Activities Contact for any subject related to IFB. Help scientists to develop new tools (architecture, design, implementation). animate the Python Working Group at pasteur . O|B|F (http://www.open-bio.org/) member. Skills Strong programming experience in Python. Software architecture and design. NoSQL DataBase (MongoDB, CouchDB) XML/YAML continuous integration (github/travis-CI/readthedocs, gitlab/gitlab-CI) containers (Docker, Singularity) linux (Gentoo, Xubuntu) IFB developer Main projects on the campus Mobyle http://Mobyle.pasteur.fr Mobyle: a new full web bioinformatics framework IntegronFinder (ongoing project) MacsyFinder (ongoing project) githubaccess to my projects on github Teaching Unix (Unix-I , Unix-II) Python . Education 2002 Phd in Molecular and cellular biology. “Rôle de deux protéines QN1 et PATF impliquées dans l’arrêt de prolifération des cellules de la neurorétine aviaire au cours du developpement”. 2001 “Informatique En Biologie” course (Pasteur)
KeywordsData managementDatabaseProgram developmentScientific computingDatabases and ontologies
Organisms
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Projects (11)
Louis JONES
retired
KeywordsSystems Biology
Organisms
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Projects (0)

Johann DRÉO
As a senior research engineer, I have explored many corners of computer science and artificial intelligence. I can most notably help you on the following topics. Skills Decision support systems Boxes and arrows design and implementation of decision-aid software (web-based as well as native interfaces and backends), visualization and diagrams (how to summarize complex data/concepts in a visual way), integration of third-party modules (how to design API to use external services, how to integrate software that does not really want to be integrated). Automated decision A black-box with a black-box inside score function modelling (how to design a metric defining a quality for a solution to a decision problem, while maintaining good mathematical properties), optimization problem modelling (how to design a formal model of a decision problem to be automatically solved by a computer), solving automated configuration problems (how to set parameters of a complex system so as to maximize its performances), Scientific computing Lego blocks and arrows efficient algorithmics (how to cope with combinatorial explosion or curse of dimension when implementing complex algorithms), highly modular software architectures (how to structure your code to allow efficient —and automated— exploration of your ideas), modern C++ (how to program with C++ using —almost— the same concepts than in Python), shell scripting (how to use the existing Unix tools to —very— efficiently automatize any task). Artificial Intelligence search heuristics, metaheuristics or evolutionary computation (how to solve hard optimization problems), design of experiments for randomized algorithmics (how to design experiments involving modern AI, using rigorous statistics), automated planning (how to compute shortest paths, and more generally optimize sequences of actions), semantic graph mining (how to find patterns in an ontology).
KeywordsAlgorithmicsData Visualization
Organisms
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Projects (0)