Décrypthon is a project which uses

grid computing Grid computing is the use of widely distributed computer resources to reach a common goal. A computing grid can be thought of as a distributed system with non-interactive workloads that involve many files. Grid computing is distinguished fro ...

resources to contribute to medical research. The word is a

portmanteau In linguistics, a blend—also known as a blend word, lexical blend, or portmanteau—is a word formed by combining the meanings, and parts of the sounds, of two or more words together.

of the French word "décrypter" (to decipher) and "

telethon A telethon (a portmanteau of "television" and "marathon") is a televised fundraising event that lasts many hours or days, the purpose of which is to raise money for a charitable, political or other cause. Most telethons feature heavy solicitatio ...

Description

Décrypthon is a technology platform providing the computational power required to process complex data in biology. It allows, through technologies called " grids", to gather (in a grid) the capacity of several supercomputers (500 Gflop) installed by

IBM International Business Machines Corporation (using the trademark IBM), nicknamed Big Blue, is an American Multinational corporation, multinational technology company headquartered in Armonk, New York, and present in over 175 countries. It is ...

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 World Community Grid (WCG) is an effort to create the world's largest volunteer computing platform to perform scientific research that benefits humanity. Launched on November 16, 2004, with proprietary Grid MP client from United Devices and add ...

, itself a

BOINC The Berkeley Open Infrastructure for Network Computing (BOINC, pronounced rhymes with "oink") is an open-source middleware system for volunteer computing (a type of distributed computing). Developed originally to support SETI@home, it became the ...

project. A dozen scientific projects selected through a call for tenders have been completed under the Décrypthon program.

History

During the 2001 French

Telethon A telethon (a portmanteau of "television" and "marathon") is a televised fundraising event that lasts many hours or days, the purpose of which is to raise money for a charitable, political or other cause. Most telethons feature heavy solicitatio ...

, the AFM ("Association française contre les myopathies" / "French Association Against Myopathy") and

launched a call to mobilize Internet users: "Make your unused computer time available to research". Objective: Accomplish the first

proteome A proteome is the entire set of proteins that is, or can be, expressed by a genome, cell, tissue, or organism at a certain time. It is the set of expressed proteins in a given type of cell or organism, at a given time, under defined conditions. P ...

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 coordinated 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 The French Alternative Energies and Atomic Energy Commission, or CEA ( French: Commissariat à l'énergie atomique et aux énergies alternatives), is a French public government-funded research organisation in the areas of energy, defense and sec ...

(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

genomics Genomics is an interdisciplinary field of molecular biology focusing on the structure, function, evolution, mapping, and editing of genomes. A genome is an organism's complete set of DNA, including all of its genes as well as its hierarchical, ...

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 disease A neuromuscular disease is any disease affecting the peripheral nervous system (PNS), the neuromuscular junctions, or skeletal muscles, all of which are components of the motor unit. Damage to any of these structures can cause muscle atrophy and we ...

s, as well as the prediction of protein domains and tissue-specific functions. *A second project involved the analysis of proteins of a cellular

organelle In cell biology, an organelle is a specialized subunit, usually within a cell (biology), cell, that has a specific function. The name ''organelle'' comes from the idea that these structures are parts of cells, as Organ (anatomy), organs are to th ...

, the

peroxisome A peroxisome () is a membrane-bound organelle, a type of microbody, found in the cytoplasm of virtually all eukaryotic cells. Peroxisomes are oxidative organelles. Frequently, molecular oxygen serves as a co-substrate, from which hydrogen perox ...

, 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 ''Vibrio cholerae'' is a species of Gram-negative bacteria, Gram-negative, Facultative anaerobic organism, facultative anaerobe and Vibrio, comma-shaped bacteria. The bacteria naturally live in Brackish water, brackish or saltwater where they att ...

'' and bacterial

diarrhea Diarrhea (American English), also spelled diarrhoea or diarrhœa (British English), is the condition of having at least three loose, liquid, or watery bowel movements in a day. It often lasts for a few days and can result in dehydration d ...

organisms involved in diarrhoeal diseases Two projects were selected in 2003/2004. Both projects were successfully carried out on the grid and provided useful calculations. Following the success of these two projects, an agreement was signed in May 2004 between the AFM, the CNRS and IBM formalizing the then named “Décrypthon based” project on a grid of servers donated by IBM at six partner universities. In 2009, the French actor

Thierry Lhermitte Thierry Lhermitte (; born 24 November 1952) is a French actor, director, writer and producer, best known for his comedic roles. He was a founder of the comedy troupe ''Le Splendid'' in the 1970s, along with, among others, Christian Clavier, Géra ...

becomes the patron of Décrypthon.

Projects

*Project coordinated by Alessandra Carbone (

Inserm The (Inserm, ) is the French National Institute of Health and Medical Research. History and organisation Inserm was created in 1964 as a successor to the French National Institute of Health. Inserm is the only public research institution ...

Unit 511,

Université Pierre et Marie Curie Pierre and Marie Curie University ( , UPMC), also known as Paris VI, was a public research university in Paris, France, from 1971 to 2017. The university was located on the Jussieu Campus in the Latin Quarter of the 5th arrondissement of Paris, ...

). 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 Deoxyribonucleic acid (; DNA) is a polymer composed of two polynucleotide chains that coil around each other to form a double helix. The polymer carries genetic instructions for the development, functioning, growth and reproduction of al ...

ligands In coordination chemistry, a ligand is an ion or molecule with a functional group that binds to a central metal atom to form a coordination complex. The bonding with the metal generally involves formal donation of one or more of the ligand's ...

. *Project of Christophe Pouzat and Pascal Viot (CNRS UMR 8118,

Université René Descartes Paris Descartes University (), also known as Paris V, was a French public university located in Paris. It was one of the inheritors of the historic University of Paris, which was split into 13 universities in 1970. Paris Descartes completely merg ...

, Paris V). Parallelization of a

Monte Carlo method Monte Carlo methods, or Monte Carlo experiments, are a broad class of computational algorithms that rely on repeated random sampling to obtain numerical results. The underlying concept is to use randomness to solve problems that might be ...

to sort action potentials: improving a tool for basic research in

neuroscience Neuroscience is the scientific study of the nervous system (the brain, spinal cord, and peripheral nervous system), its functions, and its disorders. It is a multidisciplinary science that combines physiology, anatomy, molecular biology, ...

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 A genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding genes, other functional regions of the genome such as ...

. 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 The National Institute for Research in Digital Science and Technology (Inria) () is a French national research institution focusing on computer science and applied mathematics. It was created under the name French Institute for Research in Comp ...

, 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

to understand the muscle.

References

External links

* {{DEFAULTSORT:Decrypthon Grid computing projects Muscular dystrophy organizations