An interview with Alessandra Carbone
Decrypthon's "Help Cure Muscular Dystrophy" project is entering its second phase. During one year, 150000 Internet users will be asked to make the computational power of their computers available to research.
Interview with Alessandra Carbone, Decrypthon project coordinator at the University Pierre and Marie Curie.
Decrypthon, the program initiated in 2001 and extended in 2005 by the AFM in partnership with IBM, the CNRS and universities1, aims to accelerate research in genomics and proteomics of genetic diseases through a technology that allows the sharing of extensive computations between thousands of university computers or Internet users (grid computing). At the beginning of May, it launched the second phase of its project ‘Help Cure Muscular Dystrophy’ (HCMD,) coordinated by Alessandra Carbone of the University Pierre and Marie Curie2. This project aims to determine the interactions that exist between 2280 proteins, of which a hundred are known to be directly involved in neuromuscular diseases. Thanks to this “shared computing”, implicated in the largest computing grid distributed in the world (the World Community Grid which relies on Internet users), researchers hope to identify how these proteins establish partnerships and derive new therapeutic strategies for myopathies, but not exclusively, because as Alessandra Carbone stated, “among the 2280 proteins, some may also be linked to diseases of the brain or heart.”
Before attempting to identify these interactions, the researchers had to carry out preliminary work. Initially, “we worked with 168 protein complexes to calibrate the device,” says Alessandra. This first calculation phase lasted 26 weeks instead of 14 centuries and 89 years of calculations that would have been necessary on an average PC. The second phase of the project could then begin. It aims to “observe” the proteins in three dimensions and to “test” them, two by two. One is fixed, while thanks to computers, the researchers make the second one “move” to determine the positions in which the two proteins interact. If the task seems simple at the level of two proteins, for thousands of proteins, it is enormous. With only one computer, testing all potential sites of interaction with a single pair of proteins requires a few weeks of calculations. But studying the 2280 proteins of the project would require…several centuries of calculations. Hence the interest of shared computing, which will allow the execution of these calculations in about a year, a more realistic human time scale.
1. Bordeaux 1, Lille I, Pierre et Marie Curie, Orsay, Rouen, ENS Lyon
2. (Unit CNRS FRE3214)
Interview conducted by Françoise Dupuy Maury
Interview with Alessandra Carbone, Decrypthon project coordinator at the University Pierre and Marie Curie.
Decrypthon, the program initiated in 2001 and extended in 2005 by the AFM in partnership with IBM, the CNRS and universities1, aims to accelerate research in genomics and proteomics of genetic diseases through a technology that allows the sharing of extensive computations between thousands of university computers or Internet users (grid computing). At the beginning of May, it launched the second phase of its project ‘Help Cure Muscular Dystrophy’ (HCMD,) coordinated by Alessandra Carbone of the University Pierre and Marie Curie2. This project aims to determine the interactions that exist between 2280 proteins, of which a hundred are known to be directly involved in neuromuscular diseases. Thanks to this “shared computing”, implicated in the largest computing grid distributed in the world (the World Community Grid which relies on Internet users), researchers hope to identify how these proteins establish partnerships and derive new therapeutic strategies for myopathies, but not exclusively, because as Alessandra Carbone stated, “among the 2280 proteins, some may also be linked to diseases of the brain or heart.”
Before attempting to identify these interactions, the researchers had to carry out preliminary work. Initially, “we worked with 168 protein complexes to calibrate the device,” says Alessandra. This first calculation phase lasted 26 weeks instead of 14 centuries and 89 years of calculations that would have been necessary on an average PC. The second phase of the project could then begin. It aims to “observe” the proteins in three dimensions and to “test” them, two by two. One is fixed, while thanks to computers, the researchers make the second one “move” to determine the positions in which the two proteins interact. If the task seems simple at the level of two proteins, for thousands of proteins, it is enormous. With only one computer, testing all potential sites of interaction with a single pair of proteins requires a few weeks of calculations. But studying the 2280 proteins of the project would require…several centuries of calculations. Hence the interest of shared computing, which will allow the execution of these calculations in about a year, a more realistic human time scale.
1. Bordeaux 1, Lille I, Pierre et Marie Curie, Orsay, Rouen, ENS Lyon
2. (Unit CNRS FRE3214)
Interview conducted by Françoise Dupuy Maury
The Help Cure Muscular Dystrophy - phase II project is investigated by the "departement d'Informatique et Génomique Analytique, FRE3214 CNRS UPMC"
