Course on Bioinformatics for Integrative Genomics

The last 2 days I was at the Course on Bioinformatics for Integrative Genomics organized by The Biomedical Genomics Group.


Course Description
“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:”


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CEM-Cat Seminar: Luis F. Santamaría-Babi

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”.

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Computational hours for the TNF project

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.

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Schrödinger Workshop

I attended the Schrödinger Workshop at CESCA (Center for Scientific and Academic Services of Catalonia).

This was the Agenda of the Workshop:

  • 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
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    VHIR Seminar: Jordi Villà-Freixa

    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.

    Abstract:
    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.

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    María José leave our lab

    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.


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    CEM-Cat Seminar: Agustina García

    Agustina García presented her last work on Multiple Sclerosis at CEM-Cat Seminars.

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    LAB Seminar: Ignasi Buch

    Ignasi Buch, PhD student at the Research Unit on Biomedical Informatics (Barcelona Biomedical Research Park, PRBB) and an important collaborator on the Soluble Guanylate Cyclase project, presented his last work in our lab today. Part of the presentation has been recently accepted for publication in PNAS (Buch I, Giorgino T, De Fabritiis G. Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations. Proc Natl Acad Sci U S A. 2011; 108:10184).

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    Computational hours in BSC

    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.

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    Article in Teraflop


    The journal of the Supercomputing Centre of Catalonia Consortium (CESCA) has just published a presentation of our new line of research. You can read this brief comment in the last page of Teraflop number 110 (December 2010). Two of my projects are now running in CESCA supercomputers: TNF alpha receptor type I (the subject of the presentation in Teraflop) and Soluble Guanylate Cyclase. Altogether, CESCA has provided me until now with more than 100,000 computational hours. Impressive, isn’t it?

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