Tools

Seminars, events & talks

Thursday, 31th March, 2011, 11:00-12:00

QM and MM Methods: Obtaining an Atomic and Electronic View of Nature

We will present our recent method development to map electronic and atomic coordinates for complex biological processes. 1) The atomic detailed mechanism of long range conformational changes remains a great challenge. Many biologically relevant processes, involving large domain motions or quaternary rearrangement, occur in the millisecond time scale, out of the reach of Molecular Dynamic techniques. PELE (Protein Energy Landscape Exploration), combines protein structure prediction techniques with a metropolis algorithm and is capable of fast mapping the slow motion energy landscape. 2) Electron transfer is one of the simplest but crucial reactions in biochemistry present in almost. Mixed quantum mechanics molecular mechanics methods (QMMM) offer a valuable computational tool for understanding the electron transfer pathway in protein-substrate and protein-protein complexes. By selectively turning on/off different residues in the quantum region, we have developed a novel approach capable of obtaining the electron pathway for short and large range interactions.
Short Cv. Past: PhD 1999 Autonomous University of Barcelona August 2000-August 2003, Postdoctoral Researcher, Columbia University Chemistry Department, New York City, NY (USA) August 2003- July 2006: Assistant Professor, Washington University in St. Louis, School of Medicine, Biochemistry & Molecular Biophysics (USA) Current: ICREA Professor, Life Science Department at the Barcelona Supercomputing Center and Adjunct Professor at Washington University in St. Louis (USA) Advice editor for Biophysical Chemistry, Elsevier Group.

Speaker: VíCTOR GUALLAR - ICREA - Barcelona Supercomputing Center

Room 473.10 PRBB

Wednesday, 30th March, 2011, 11:00

HeT_A_pi1, a piRNA target sequence in the Drosophila telomeric retrotransposon HeT-A, is extremely conserved across copies and species

Speaker: Natalia Petit- Evolutionary Biology, UPF

Room 473.10_Aula

Thursday, 24th March, 2011, 11:00-12:00

Computational methods to solve the crystallographic phase problem

Given the phase problem, determining an initial model from the diffraction data (phasing) is a bottleneck in crystallography. Ab Initio phasing of macromolecular structures with no heavy atoms has been limited to cases with up to around 1000 atoms in the asymmetric unit, diffracting to atomic resolution. Both the size and resolution barriers have been overcome in the case of several previously unknown structures. Proteins with a few thousand atoms, diffracting to 2Å have been solved through a combination of location of model fragments such as poly-alanine alpha-helices with the program PHASER and density modification with the program SHELXE. Given the difficulties in discriminating correctly positioned fragments, the method has to test many putative groups of fragments in parallel, thus calculations are performed in a grid. The method has been called after the Italian painter Arcimboldo, who used to compose portraits out of fruits and vegetables. In the case of our program, most collections of fragments remain a “still-life”, but some are correct enough for density modification to reveal the protein’s portrait. The same methodology can be used to build a protein out of shredded fragments from a low homology or NMR model where conventional molecular replacement has failed.
Short CV,
Chemistry degree in 1987, University of Zaragoza, Dr. Rer. Nat. University of Zaragoza in 1992, Product Research Scientist at the European Research Center in Brussels with Procter & Gamble for 15 months. Moved for a HCM postdoc at the University of Göttingen (Germany) and stayed for an Habilitation (German Higher Doctorate) at (1996-2001) with Prof. Sheldrick, and as C2 leading an independent research group. Moved to Barcelona in September 2003 joining the IBMB-CSIC as ICREA Research Professor.

Speaker: Isabel Usón - Molecular Biology Institute of Barcelona (IBMB)

Room Seminar Xipre (PRBB) - 1st Floor, room 173.06

Wednesday, 23th March, 2011, Thu, Mar 24, 2011 11:00 AM - Thu, Mar 24, 2011 12:00 PM

Are microsatellites junk?

Speaker: Alice Ledda - Evolutionary Genomics. Biomedical Informatics. IMIM-UPF

Room 473.10_ Aula

Tuesday, 15th March, 2011

What single molecule recording tells us of the activation of synaptic channels: the case of glycine receptors

Speaker: Lucia Silvilotti, University College London

Room PRBB room Xipre 1st floor

Wednesday, 2nd February, 2011, 11:00

The genome of an albino gorilla”

Speaker: Javier Prado - (Marques-Bonet´s lab) - Genómica de Primates. Institut de Bilogia Evolutiva (UPF-CSIC)

Room 473.10_Aula

Tuesday, 1st February, 2011, 12:00-13:00

Protein simulations at constant pH. Sometimes a pKa is not a pKa.

Speaker: Adrian Roitberg (University of Florida. Gainesville, USA)

Room Seminar room 173.06 (1st Floor)

Tuesday, 25th January, 2011, 12:00 pm

Analysis and manipulation of phylogenomic data using ETE

ETE is a python programming library that assists in the automated manipulation, analysis and visualization of phylogenetic trees. It allows to read trees in Newick format and operate with them as very intuitive python objects, providing advanced methods to locate nodes, browse tree topology, annotate branches, or manipulate node connections. In addition, ETE provides a fully customizable system for tree visualization. Users can visualize trees interactively or write their own python functions to create tree images in PDF or SVG format.

Although ETE is mainly focused on phylogenetic analysis (i.e. connectors to the phylomeDB database, orthology and paralogy detection, tree reconciliation) it can be also used to deal with any type of data that can be represented as a hierarchical tree. For instance, microarray clustering results are phylogenetic profiles are well supported.

Starting from version 2.1, ETE will provide a new module to add interactive phylogenetic trees within web pages (see http://phylomedb.org/?q=search_tree&seqid=Phy00085K5_HUMAN for an example) and support for the PhyloXML and NeXML formats. Some ETE examples can be found at http://ete.cgenomics.org/examples

With this short tutorial I will introduce the most basic functionality and the potential use of the different ETE modules. A comprehensive practical course on ETE and related tools is scheduled by the beginning of March 2011.

Speaker: Jaime Huerta Cepas. Comparative Genomics Group. Bioinformatics & Genomics Programme. CRG

Room room 470 Sem 2

Thursday, 20th January, 2011, 11:00 AM

The modulation of the endocannabinoid system by membranes

Speaker: Enrico Dainese, University of Teramo, Italy.

Room PRBB room UPF (3ª planta) 300.08/350.08

Tuesday, 19th October, 2010, 11:00

Analyzing Chip-Seq mapped reads with Pyicos and bash: Command-line real time examples.

When provided with some files with mapped reads coming from a Chip-Seq experiment, lots of the work has already been done. Extracting the biological information from them should be an easy job, right? Surprisingly, lots of bioinformaticians are finding that the methods and software packages proposed for the analysis of this kind of data doesn’t fit their particular needs. Because these experiments have gone through a long process and they commonly targets a particular Protein-DNA interactions, this last step normally takes longer than expected. Moreover, the technical difficulties of dealing with read files that can be on the Gigabyte-Scale, the different formats used by different laboratories and tools and the novelty of the field are extra headaches for the researcher performing this kind of analysis. This seminar is designed as an introduction where I will work in real-time with a sample dataset, showing how to use bash and Pyicos, a novel toolbox for the analysis of mapped reads coming from Deep Sequencing experiments.

Speaker: Juan Gonzalez-Vallinas-Regulatory Genomics Group, GRIB

Room PRBB room 173.06-183.01 (Xipre)

Site Information