Décrypthon
Encyclopedia
Décrypthon is a project which uses grid computing
resources to contribute to medical research. The word is a portmanteau of the French word "décrypter" (to decipher) and "telethon".
", to gather (in a grid) the capacity of several supercomputers (500 Gflop) installed by IBM
in 6 French universities (Bordeaux 1, Lille 1, Paris 6 Jussieu, ENS
Lyon, Crihan in Rouen, Orsay) and/or individual personal computers via the World Community Grid
, itself a BOINC project. A dozen scientific projects selected through a call for tenders have been completed under the Décrypthon program.
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: 75,000 Internet users mobilized, billions of complex calculations performed, 550,000 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 17,000 directories.
All this in less than two months whereas it would have taken more than 1,170 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:
Three other teams from the IGBMC (Institut de génétique et de biologie moléculaire et cellulaire, Genomics Institute of molecular and cellular biology) 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.
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 .
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 “Décrypthon based” project on a grid of servers graciously provided by IBM at 6 partner universities.
In 2009, the french actor Thierry Lhermite becomes the patron of the Décrypthon.
, 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, 150,000 Internet users will be called upon and devoted for an entire year.
At the moment, HCMD is the running project which is on its second stage.
Grid computing
Grid computing is a term referring to the combination of computer resources from multiple administrative domains to reach a common goal. The grid can be thought of as a distributed system with non-interactive workloads that involve a large number of files...
resources to contribute to medical research. The word is a portmanteau of the French word "décrypter" (to decipher) and "telethon".
Description
Décrypthon is a technology platform providing the computational power required to process complex data in biology today, whose volume is multiplied by two every year. This thus allows, through technologies called "gridsGrid computing
Grid computing is a term referring to the combination of computer resources from multiple administrative domains to reach a common goal. The grid can be thought of as a distributed system with non-interactive workloads that involve a large number of files...
", to gather (in a grid) the capacity of several supercomputers (500 Gflop) installed by IBM
IBM
International Business Machines Corporation or IBM is an American multinational technology and consulting corporation headquartered in Armonk, New York, United States. IBM manufactures and sells computer hardware and software, and it offers infrastructure, hosting and consulting services in areas...
in 6 French universities (Bordeaux 1, Lille 1, Paris 6 Jussieu, ENS
École Normale Supérieure
The École normale supérieure is one of the most prestigious French grandes écoles...
Lyon, Crihan in Rouen, Orsay) and/or individual personal computers via the World Community Grid
World Community Grid
World Community Grid is an effort to create the world's largest public computing grid to tackle scientific research projects that benefit humanity...
, itself a BOINC project. A dozen scientific projects selected through a call for tenders have been completed under the Décrypthon program.
History
During the 2001 French Telethon, the AFM ("Association française contre les myopathies" / "French Association Against Myopathy") and IBMIBM
International Business Machines Corporation or IBM is an American multinational technology and consulting corporation headquartered in Armonk, New York, United States. IBM manufactures and sells computer hardware and software, and it offers infrastructure, hosting and consulting services in areas...
launched a call to mobilize Internet users: "Make your unused computer time available to research". Objective: Accomplish the first proteome
Proteome
The proteome is the entire set of proteins expressed by a genome, cell, tissue or organism. More specifically, it is the set of expressed proteins in a given type of cells or an organism at a given time under defined conditions. The term is a portmanteau of proteins and genome.The term has been...
mapping: all the proteins/molecules produced by cells.
This scientific, technological and human challenge was brilliantly taken up: 75,000 Internet users mobilized, billions of complex calculations performed, 550,000 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 17,000 directories.
All this in less than two months whereas it would have taken more than 1,170 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 Commissariat à l'Energie Atomique (CEA, Commission for Atomic Energy) Department of Life Sciences at Saclay (S Zinn-Justin and R Guérois) in association with A Poupon, from the National Center of Scientific Research (Centre Nationale de la recherche scientifique ou CNRS), Laboratory of yeast structural genomicsGenomicsGenomics is a discipline in genetics concerning the study of the genomes of organisms. The field includes intensive efforts to determine the entire DNA sequence of organisms and fine-scale genetic mapping efforts. The field also includes studies of intragenomic phenomena such as heterosis,...
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 (Institut de génétique et de biologie moléculaire et cellulaire, Genomics Institute of molecular and cellular biology) 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 organelleOrganelleIn cell biology, an organelle is a specialized subunit within a cell that has a specific function, and is usually separately enclosed within its own lipid bilayer....
, the peroxisomePeroxisomePeroxisomes are organelles found in virtually all eukaryotic cells. They are involved in the catabolism of very long chain fatty acids, branched chain fatty acids, D-amino acids, polyamines, and biosynthesis of plasmalogens, etherphospholipids critical for the normal function of mammalian brains...
, 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 choleraeVibrio choleraeVibrio cholerae is a Gram-negative, comma-shaped bacterium. Some strains of V. cholerae cause the disease cholera. V. cholerae is facultatively anaerobic and has a flagella at one cell pole. V...
and Diabac (Bacterial diarrhoea) organisms involved in diarrhoeal diseases
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 .
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 “Décrypthon based” project on a grid of servers graciously provided by IBM at 6 partner universities.
In 2009, the french actor Thierry Lhermite becomes the patron of the Décrypthon.
Projects
- 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, DNADNADeoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
or ligands.
- Project of Christophe Pouzat and Pascal Viot (CNRS UMR 8118, Université René Descartes, Paris V). Parallelization of a Monte Carlo methodMonte Carlo methodMonte Carlo methods are a class of computational algorithms that rely on repeated random sampling to compute their results. Monte Carlo methods are often used in computer simulations of physical and mathematical systems...
to sort action potentials: improving a tool for basic research in neuroscienceNeuroscienceNeuroscience is the scientific study of the nervous system. Traditionally, neuroscience has been seen as a branch of biology. However, it is currently an interdisciplinary science that collaborates with other fields such as chemistry, computer science, engineering, linguistics, mathematics,...
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/ENSÉcole Normale SupérieureThe École normale supérieure is one of the most prestigious French grandes écoles...
Lyon). Data mining of animal transcriptomes to annotate the neuromuscular processes of the human genomeGenomeIn modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....
. 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 (LIFLLaboratoire d'Informatique Fondamentale de LilleThe Laboratoire d'Informatique Fondamentale de Lille , is a computer science research laboratory of Lille University of Science and Technology , in Lille, France...
– 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/ENSÉcole Normale SupérieureThe École normale supérieure is one of the most prestigious French grandes écoles...
Lyon). Integration of multiple approaches of functional genomicsGenomicsGenomics is a discipline in genetics concerning the study of the genomes of organisms. The field includes intensive efforts to determine the entire DNA sequence of organisms and fine-scale genetic mapping efforts. The field also includes studies of intragenomic phenomena such as heterosis,...
to understand the muscle.
Help Cure Muscular Dystrophy (HCMD)
In 2007, the project of Alessandra Carbone’s team launched its preparatory phase on the worldwide and public grid, the World Community GridWorld Community Grid
World Community Grid is an effort to create the world's largest public computing grid to tackle scientific research projects that benefit humanity...
, by calculating the interactions of 336 proteins. It is now publicly known as "Help Cure Muscular Dystrophy
Help Cure Muscular Dystrophy
Help Cure Muscular Dystrophy is a distributed computing project that runs on the BOINC platform. It is a joint effort of the French muscular dystrophy charity, L'Association française contre les myopathies; and L'Institut de biologie moléculaire et cellulaire .-Project purpose:Help Cure Muscular...
" (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, 150,000 Internet users will be called upon and devoted for an entire year.
At the moment, HCMD is the running project which is on its second stage.
| Date | Position computed | Received workunit | Completion |
|---|---|---|---|
| 05/11/09 | 0 | 0 | 0.00% |
| 01/15/10 | 16 697 552 861 | 10 810 355 | 12.13% |
| 05/07/10 | 28 965 307 201 | 16 586 055 | 21.04% |
| 02/04/11 | 78 226 996 848 | 33 088 783 | 56.83% |
| 05/16/11 | 96 053 905 758 | 39 184 254 | 69.78% |