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Seminars, events & talks

Friday, 25th March, 2011, 11:00-12:00

Computational Biophysics

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

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

Evolutionary Genomics

Are microsatellites junk?

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

Room 473.10_ Aula

Wednesday, 16th March, 2011

Computational Biophysics

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

Thursday, 3rd February, 2011, 11:00

Evolutionary Genomics

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

Wednesday, 2nd February, 2011, 12:00-13:00

Computational Biophysics

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)

Wednesday, 26th January, 2011, 12:00 pm

GPCR drug discovery

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 for an example) and support for the PhyloXML and NeXML formats. Some ETE examples can be found at

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

Friday, 21th January, 2011, 11:00 AM

Computational Biophysics

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

Wednesday, 20th October, 2010, 11:00

Computational RNA Biology

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)

Monday, 4th October, 2010, 14h - 15h

Computational Biochemistry

Elements of Multiscale nonstandard simulation techniques (workshop on multiscale simulations - 2nd Barcelona School on Biomedical Informatics)

Standard mathematical models of complex dynamical biological processes include elements of ordinary differential equations to capture, for example, biochemical kinetics coupled with continuum partial differential equations models that represent spatial elements such as transport and motion. However, there is increasing interest in nonstandard simulation techniques that capture, for example, discrete stochastic subcellular behaviour or spatial heterogeneity in media via the concept of fractional derivatives. My challenge in 50 minutes is to give an overview of some of the important multiscale modeling and simulation issues associated with these nonstandard approaches.

Speaker: Kevin Burrage (Oxford University and QUT, Brisbane, Australia)

Room PRBB Auditorium

Monday, 4th October, 2010, 12h - 13h

Computational Biochemistry

How Local Network Oscillations lead to Functional Networks during Rest (workshop on multiscale simulations - 2nd Barcelona School on Biomedical Informatics)

Spatiotemporally organized spontaneous low-frequency (< 0.1 Hz) fluctuations have been revealed by the blood-oxygenation level-dependent (BOLD) fMRI signal during rest. Indeed, in the absence of a task, significant correlations between distinct anatomical regions are found. These correlations, referred to as functional connectivity (FC), yield large-scale maps constituting so-called resting-state networks (RSNs). Furthermore, direct measurements of the neuronal activity have revealed similar large-scale correlations, particularly in the slow fluctuations of the power of local field potential gamma frequency range oscillations. Nevertheless, the origin of this highly structured slow dynamics and its relationship with neural activity, particularly in the gamma frequency range, remains largely unknown. To address these questions, we defined a model of brain neural activity taking into account the long range connectivity together with their corresponding conduction delays and instantiating sustained gamma oscillations in the dynamics of its local nodes. We apply the model to the macaque and human measured structural connectivity. In the human case, we search for parameters such that the model best reproduces the human empirical FC obtained at the same nodes. The best agreement is found in a region of the parameter space where the network is globally in an incoherent state but where partial clusters of nodes tend to synchronize. Inside such clusters, the BOLD signal between nodes is found to be correlated, instantiating then RSNs. Between clusters, patterns of positive and negative correlations are found, as in experiments. These results are found to be robust to a number of model parameters.

Speaker: Gustavo Deco (Universitat Pompeu Fabra)

Room PRBB Auditorium

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