"DECRYPTHON" APPEAL TO INTERNET USERS
During the 2001 Telethon, the AFM and IBM launched a call to mobilize Internet users: "Make your unused computer time available to research". Objective: Accomplish the first proteome mapping: all the proteins/molecules produced by cells.
This scientific, technological and human challenge was brilliantly taken up: 75000 Internet users mobilized, billions of complex calculations performed, 550000 proteins mapped. It is a library for comparing proteins from different species of living organisms (animal, plant, human). It contains nearly 2.2 million files divided into 17000 directories.
All this in less than two months whereas it would have taken more than 1170 years to achieve with a single computer! Each computer contributed about 133 hours, or more than 10 million hours of calculations in total. Twenty-one IBM servers have hosted all the solutions and data throughout the operation.
Following this success, in 2003 the AFM launched a call for tenders to promote the use of this knowledge base. Four projects were selected:
This scientific, technological and human challenge was brilliantly taken up: 75000 Internet users mobilized, billions of complex calculations performed, 550000 proteins mapped. It is a library for comparing proteins from different species of living organisms (animal, plant, human). It contains nearly 2.2 million files divided into 17000 directories.
All this in less than two months whereas it would have taken more than 1170 years to achieve with a single computer! Each computer contributed about 133 hours, or more than 10 million hours of calculations in total. Twenty-one IBM servers have hosted all the solutions and data throughout the operation.
Following this success, in 2003 the AFM launched a call for tenders to promote the use of this knowledge base. Four projects were selected:
- A project was proposed by two teams from the CEA Department of Life Sciences at Saclay (S Zinn-Justin and R Guérois) in association with A Poupon, from the CNRS, Laboratory of yeast structural genomics from the University of Orsay. This project aimed to study the relationships between structure and function of proteins that reduce the risk of genetic abnormalities in humans and yeast.
Three other teams from the IGBMC in Illkirch, J Laporte and J-L Mandel, A Pujol and J-L Mandel, G Bey, F Sirockin, F Plevwniak and O Poch proposed three projects of increasing complexity. - The first project involved the identification and characterization of proteins implicated in several neuromuscular diseases, as well as the prediction of protein domains and tissue-specific functions.
- A second project involved the analysis of proteins of a cellular organelle, the peroxisome, which is involved in many essential metabolic functions.
- The third project, at the scale of an organism, was to identify new potential therapeutic targets in Vibrio cholerae and Diabac (Bacterial diarrhoea) organisms involved in diarrhoeal diseases
"DECRYPTHON" THE PROJECT OF A HANDFUL OF FASCINATED ROLE-PLAYERS
Two projects were selected in 2003/2004. The aim was to demonstrate the feasibility of a program with its own grid before making it available to all teams, to set up the grid, and to test its operation. Both projects were successfully carried out on the grid and beneficially for their calculations.
PROJECT OF O. POCH, G. DELEAGE ET AL (IGBMC/IBCP, STRASBOURG/LYON)
The objective of this project is twofold: to develop an analytical description grid of proteins with known mutations, and develop a predictive tool to facilitate the understanding of these mutations in human disease.
A picture of the team involved in the MS2PH project in Strasbourg: from left to right, Olivier Poch, Anne Friedrich, Luc Moulinier, and Raphael Bolze, in front of The Institute of Genetics and Molecular and Cellular Biology (IGBMC) in Illkirch.
The Decrypthon team has been strengthened. Since February 2005, Hoan Nguyen joined the group in Strasbourg in order to develop a relational database to integrate and query all the accumulated knowledge.
A picture of the team involved in the MS2PH project in Strasbourg: from left to right, Olivier Poch, Anne Friedrich, Luc Moulinier, and Raphael Bolze, in front of The Institute of Genetics and Molecular and Cellular Biology (IGBMC) in Illkirch.
The Decrypthon team has been strengthened. Since February 2005, Hoan Nguyen joined the group in Strasbourg in order to develop a relational database to integrate and query all the accumulated knowledge.
PROJECT OF C. BRANLANT, F. LECLERC, Y. GUERMEUR ET AL (CNRS UMR 7503 AND 7567/LORIA, NANCY)
To synthesize a protein, the gene (present in the DNA molecule) transports into the cell a code involved in a process that has been called "splicing".
This project proposes to analyze the links between splicing defects and genetic diseases.
The analysis of mutations in genes in individuals suffering from genetic diseases and the consequences of splicing should provide fundamental data for understanding these diseases. This study should enable the development of therapies based on splicing repair involving, for example, exon skipping.
The first part of the project consisted of establishing a database of splicing sites for different human genes. The software to analyse the splicing sites was rewritten to be implemented on the Decrypthon grid.
In this photo, part of the team of the alternative splicing analysis project: from left to right: Yann Guermeur, Fabrice Leclerc, and Raphaël Bolze in front of the Lorrain Laboratory for Computer Research and its Applications (LORIA) in Nancy.
Raphaël Bolze, Science PhD student at the Ecole Normale Superieure (ENS) of Lyon, performs algorithm applications on the grid (and ‘gridification’ and portage) for both teams.
This project proposes to analyze the links between splicing defects and genetic diseases.
The analysis of mutations in genes in individuals suffering from genetic diseases and the consequences of splicing should provide fundamental data for understanding these diseases. This study should enable the development of therapies based on splicing repair involving, for example, exon skipping.
The first part of the project consisted of establishing a database of splicing sites for different human genes. The software to analyse the splicing sites was rewritten to be implemented on the Decrypthon grid.
In this photo, part of the team of the alternative splicing analysis project: from left to right: Yann Guermeur, Fabrice Leclerc, and Raphaël Bolze in front of the Lorrain Laboratory for Computer Research and its Applications (LORIA) in Nancy.
Raphaël Bolze, Science PhD student at the Ecole Normale Superieure (ENS) of Lyon, performs algorithm applications on the grid (and ‘gridification’ and portage) for both teams.
"DECRYPTHON" THE NATIONAL SCIENTIFIC PROGRAM
Following the success of these two projects, an agreement was signed on May 2004 between the AFM, the CNRS and IBM formalizing the then named “Decrypthon based” project on a grid of servers graciously provided by IBM at 6 partner universities.
During this period 6 new projects have been completed or are still in progress:
During this period 6 new projects have been completed or are still in progress:
- Project coordinated by Alessandra Carbone (Inserm Unit 511, Université Pierre et Marie Curie). Large-scale investigation of protein-protein, protein-DNA and protein-ligand interactions leading to drug targeting. This project seeks to develop computer tools to identify at the protein surface, interaction sites with other proteins, DNA or ligands.
- Project of Christophe Pouzat and Pascal Viot (CNRS UMR 8118, Université René Descartes, Paris V). Parallelization of a Monte Carlo method to sort action potentials: improving a tool for basic research in neuroscience and diagnosis of neuromuscular diseases. This project aims to automate the processing of neuronal signals recorded by doctors to detect any malfunctioning of neurons in the brain or motoneurons that control muscle fibres.
- Project coordinated by Marc Robinson-Rechavi (Faculty of Biology and Medicine at the University of Lausanne/ENS Lyon). Data mining of animal transcriptomes to annotate the neuromuscular processes of the human genome. This project will allow to identify exactly which genes should be expressed (or are incorrectly expressed) in muscle cells, essential information to understand neuromuscular diseases.
- Project coordinated by E-K. Talbi (LIFL – Laboratory of Basic Computer Science in Lille, USTL, CNRS, INRIA, Villeneuve d'Ascq). Conformational sampling and docking on Grids: Application to neuromuscular diseases. The aim is to predict, by calculation, the nature and type of bonds of the molecules involved in the functioning of the normal cell, and to develop research “in silico” (by calculation), the means to interfere with the normal or pathological physiological processes - and therefore to rationally develop medication.
- Project coordinated by F. Relaix and O. Poch (Institute of Myology, Paris - IGBMC, Illkirch). Large-scale identification of transcriptional networks during myogenesis. This project aims to identify the molecular mechanisms of transcription in the development of muscle.
- Project coordinated by M. Robinson-Rechavi and L. Schaeffer (Faculty of Biology and Medicine at the University of Lausanne/ENS Lyon). Integration of multiple approaches of functional genomics to understand the muscle.
"DECRYPTHON" THE INTERNATIONAL SCIENTIFIC PROGRAMME
In 2007, the project of Alessandra Carbone’s team launched its preparatory phase on the worldwide and public grid, the World Community Grid, by calculating the interactions of 336 proteins. It is now publicly known as “Help Cure Muscular Dystrophy” (HCMD).
In 2009, after using the experience gained in the first phase, the second stage of the project has been launched on the World Community Grid. To accomplish this immense project, 150000 Internet users will be called upon and devoted for an entire year.
> View publications.
In 2009, after using the experience gained in the first phase, the second stage of the project has been launched on the World Community Grid. To accomplish this immense project, 150000 Internet users will be called upon and devoted for an entire year.
> View publications.
