An article in the PRBB journal El.lipse on the work done by the CBBL.
Physicists, mathematicians, biochemists, biologists, computer technicians and pharmacists seven men and one woman. This is the profile of the Computional Biochemistry and Biophysics group of the GRIB, directed by Jordi Villà i Freixa since 5 years ago. The group makes simulations of several biochemical processes, and they also develop the computer programs needed for the simulations. These are always created as “Open Source” so they can be used by the rest of the community. The simulations can be at different levels, from individual molecules to groups of cells and tissues. For example, they simulate the interaction between proteins, complementing the experimental studies and based on fundamental principles, in order to predict which ones can interact amongst them and which mutations could prevent or help this interaction. This is the case of their collaboration with Paco Muñoz (UPF), with whom they study the effect of oxidative stress in the activity of certain enzymes and their possible relation to Alzheimer. In the other extreme, the group creates simulations of gene regulation networks during the development of the chicken otic placode and the interaction with morphogens that are differentially expressed within the tissue. This is done with Berta Alsina, also from the UPF.
The group participates in several European projects. On the one hand there is “QosCosGrid”, a project on distributed computing, a way of doing complex calculations from different independent machines connected within a unique network. “This way we don’t depend on a supercomputer, but joining what everyone has at home we can do very complex calculations”,says Villà.
“The problem with distributed computing is that these machines don’t know each other and they have difficulties communicating”, he continues. The aim of “QosCos Grid” is to solve these communication problems.
“BioBridge” is another of the European projects in which they work, a biomedical informatics initiative that aims to create a portal for the integration of genomic and clinical information using systems biology tools. The group uses COPD (Chronic Obstructive Pulmonary Disease) as a working case. The longterm aim is to find biomarkers, molecules that can predict if a person has more or less propensity to suffer COPD. Since this June, the laboratory is also part of the European Network of Excellence “Virtual Physiological Human” (VPH), in which other groups at GRIB, those of Ferran Sanz and Manuel Pastor, also participate. This network will help creating the necessary infrastructure to generate the first virtual human being. For this they must make integrated simulations of what happens within a cell, an organ or the whole organism. “The most important task is to develop standards of how to relate the information from groups working at different levels”, points out Villà. Within VPH, the group is in charge of making a pilot application on drug safety, in close collaboration with “Ramón y Cajal” researcher Gianni de Fabritiis and the other two groups from the GRIB, “Many drugs block specific heart ionic channels as a side effect. What we try to do is to make simulations at multiple scales, to see whether a drug could block these channels at the molecular level, and how would this affect at a supracellular level and at the level of the whole organism”, concludes Villà