We have obtained 20,000 additional hours for the TNF project at BSC.
The last 2 days I was at the Course on Bioinformatics for Integrative Genomics organized by The Biomedical Genomics Group.
“The application of high-throughput technologies in medical genomics yields complex, multidimensional data sets that describe in detail the myriad changes that occur within individual cells and how these changes differ between patients, cells or conditions. Usually we want to use this data to answer some specific questions. For instance, which of the long list of mutations detected are likely to affect the function of the protein and which are probably neutral? Which of the genes affected by those mutations are already known to be involved in cancer or other diseases? Which pathways or biological processes are affected by the transcriptomic alterations detected in my experiment? Etc.
We need to apply bioinformatic approaches to answer these questions. This course provides theoretical and practical expertise in the field of bioinformatics for integrative genomics. Students are updated on the state of the art in the field and they become capable of handling and analyzing genomics data. Upon completion, the attendees are able to perform integrative analysis and interpret the results, in order to answer specific biological questions.
To achieve these objectives we will use three tools developed in our lab:”
Today, Dr. Luis F. Santamaría-Babi, researcher at Institute for Research in Biomedicine (IRB Barcelona) in the “Gene Expression Group”, gave as an interesting seminar on “Lymphocyte homing”.
CESCA (at present ‘Center for Scientific and Academic Services of Catalonia’; before known as the ‘Supercomputing Centre of Catalonia Consortium’) has accepted our new project on TNF signaling. This will provide us with 200,000 computational hours along this year.
I attended the Schrödinger Workshop at CESCA (Center for Scientific and Academic Services of Catalonia).
09:30 – Welcome
09:45 – Target structure prediction, refinement and characterization
12:30 – Lunch
13:30 – Virtual Screening part 1: Docking and post-docking processing
15:00 – Virtual screening part 2: Cheminformatics, pharmacophore and shape-based searching
17:00 – Summary
This was the Agenda of the Workshop:
I invited Jordi Villà-Freixa, group leader of the Computational Biochemistry and Biophysics lab (Research Unit on Biomedical Informatics, Parc de Recerca Biomèdica de Barcelona) to make a seminar at our Institute. It will take place this afternoon at General Hospital.
Molecular simulations and biochemical kinetics modelling are among the most computing demanding problems in biomedicine. In this talk I will introduce several improvements our group has been developing in the last years, and how they have been applied to a variety of questions proposed by our fellow experimentalists. However, an increasing demand for simple and multiplatform bioinformatics and simulations methods to tackle a variety of problems in biomedicine exists. Thus, the natural move of a research group to make its software widely spread is to create web portals and web services that habilitate others to use its tools in an easy way. We will show the concept of Activ8 as an extremely simple to use and absolutely expandable platform for building computational protocols on-line. Examples of its use will range from research to training.
María José is finishing her PhD studies and is going to make an stage at Paris. She leave many friends here and the farewell was very emotional. Ester Cantó has prepared an impressive comic strip as a present for María José representing the daily life at our lab.
Agustina García presented her last work on Multiple Sclerosis at CEM-Cat Seminars.
On February 25th, BSC (Barcelona Supercomputing Center) has published the list of accepted activities for the 1st period of 2011. Our project TNF alpha and Sphingosine 1-phosphate transduction systems in Multiple Sclerosis received 15,000 computational hours.