Tools




Seminars, events & talks

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)

Sunday, 3rd October, 2010, 14h - 15h

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

Sunday, 3rd October, 2010, 12h - 13h

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

Sunday, 3rd October, 2010, 15h - 16h

Multimodel description of the human lungs (workshop on multiscale simulations - 2nd Barcelona School on Biomedical Informatics)

The respiratory system realizes the transfer of oxygen from the outside air to the alveolar membrane, through which it diffuses onto the blood. As pure diffusion is far from being sufficient to realize that transfer, most of it is of advective type, and this advection is triggered by inflation-deflation cycles of the paremchyma.
The mechanical part of the lungs can then be seen as a tree-like domain (conducting airways) embedded in an elastic medium. The flow in the upper part is inertial (incompressible Navier-Stokes equations), whereas inertia can be neglected for deeper branches (Stokes equations), which allows to use Poiseuille’s law for each branch, and consequently Darcy like equations on the corresponding subtrees. We aim at addressing the delicate issues in terms of theory, numerics, and modelling, raised by the coupling of those models (Navier-Stokes, Darcy equations on a network, elasticity equations).

Speaker: Bertrand Maury(Université Paris Sud)

Room PRBB Auditorium

Sunday, 3rd October, 2010, 16h - 17h

Multiscale modelling and simulation of drug-induced effects on the heart (workshop on multiscale simulations - 2nd Barcelona School on Biomedical Informatics)

In 1962, Denis Noble published the first mathematical model of a cardiac cell action potential based on the Hodgkin-Huxley formulation.
Since then, computational cardiac electrophysiology has developed into a mature discipline in which advanced computational, mathematical and engineering techniques are used to investigate heart rhythm mechanisms in health and disease.
The causes of cardiac arrhythmias are numerous and include disease, mutations and also drug-induced abnormalities in ionic properties. Of particular concern for regulatory agencies, pharmaceutical industry and society is the fact that certain drugs, in particular those not designed to affect the heart, can exhibit cardio-toxicity (i.e. unwanted side effects), which can put patients with otherwise healthy hearts at risk of developing lethal arrhythmias. In this presentation, we will describe the state-of-the-art in multiscale modelling and simulation of ventricular electrophysiology,and we will illustrate their use in the investigation of drug-induced abnormalities in heart rhythm mechanisms. The ultimate goal of the research described here is to contribute to the improvement of the diagnosis and treatment of cardiac arrhythmias to reduce the burden
they impose to society.

Speaker: Blanca Rodríguez (Oxford University)

Room PRBB Auditorium

Sunday, 3rd October, 2010, 11h - 12h

Multiscale modelling and simulation, lessons learned from COAST (workshop on multiscale simulations - 2nd Barcelona School on Biomedical Informatics)

A few years ago, within the COAST project, we started to develop a multiscale model of a challenging VPH application, namely in-stent restenosis (ISR). This resulted in a multiscale modelling paradigm that we coined Complex Automata (CxA). CxA models can be implemented using our Multiscale Coupling Library and Environment (MUSCLE). I will introduce the main ideas behind CxA, propose a taxonomy of multiscale models, and try to indicate the lessons learned for VPH type of applications. Multiscale modelling is one thing, but actually executing your multiscale models on computers is quite another ball game. I will show the example of a MUSCLE implementation of a simplified multiscale model for in-stent restenosis. Tightly coupled three dimensional multiscale models will usually require computing power beyond the desktop. This gave rise to the paradigm of Distributed Multiscale Computing, which is currently under development in the MAPPER project.

Speaker: Alfons Hoekstra (University of Amsterdam)

Room PRBB Auditorium



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