BIBEX, high performance exploration for bibliographic databases

June, 15th 10:30 room 473.10

logo_bibexBibliographic exploration is important for the management, preservation and creation of IP. Questions like “who is the most significant authority in a specific knowledge area?”, “who is a suitable reviewer for a given paper?”,  “what is the seminal paper in a specific topic?” or “how it is the social network of a researcher?” are questions that many researchers and managers from Academia and industry would like to have responded in a few seconds. This would save them time for other more creative and productive tasks within their organizations.

BIBEX is an innovative software for the exploration of bibliographic and documental repositories. It allows answering those queries and other more sophisticated ones in a fast and synthetic way over huge amount of data. BIBEX stems from the last five years of research and development at UPC, turning our product into a marketable technology, commercialized by Sparsity technologies, a spin out company of UPC. Our technology has been supported and is being used by the Ministry of Science and Innovation of Spain, and by Generalitat de Catalunya.

BIBEX solves, for the first time, those complex queries in very fast execution times for billions of objects in a database. It is based on a technology also developed at UPC, the DEX graph database management system, which has also been used in many other different application areas, like fraud detection, cancer analysis, social network analysis and recommendation systems.

Speakers: JOSEP LLUIS LARRIBA PEY (DAMA-UPC) / PERE BALETA FERRER (SPARSITY TECHNOLOGIES)

More information on www.dama.upc.edu

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Biana: a software framework for compiling biological interactions and analyzing networks

May, 5th at room 470. Javier García-García, UPF

The analysis and usage of biological data is hindered by the spread of information across multiple repositories and the difficulties posed by different nomenclature systems and storage formats. In particular, there is an important need for data unification in the study and use of protein-protein interactions. Without good integration strategies, it is difficult to analyze the whole set of available data and its properties. We introduce BIANA (Biologic Interactions and Network Analysis), a tool for biological information integration and network management. BIANA is a Python framework designed to achieve two major goals: i) the integration of multiple sources of biological information, including biological entities and their relationships, and ii) the management of biological information as a network where entities are nodes and relationships are edges. Moreover, BIANA uses properties of proteins and genes to infer latent biomolecular relationships by transferring edges to entities sharing similar properties. BIANA is also provided as a plugin for Cytoscape, which allows users to visualize and interactively manage the data. A web interface to BIANA providing basic functionalities is also available. The software can be downloaded under GNU GPL license from http://sbi.imim.es/web/BIANA.php. BIANA’s approach to data unification solves many of the nomenclature issues common to systems dealing with biological data. BIANA can easily be extended to handle new specific data repositories and new specific data types. The unification protocol allows BIANA to be a flexible tool suitable for different user requirements: non-expert users can use a suggested unification protocol while expert users can define their own specific unification rules.

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Integration of biological annotations and networks using Cytoscape (hands on tutorial)

Cytoscape is a widely used open-source software for visualization and analysis of networks. There is a wide range of plugins available facilitating the analysis of biological networks (protein-protein interaction networks, biological pathways etc). This hands on tutorial will give a short introduction to Cytoscape and will focus on the integration of biological annotations with networks.

Date and place: April 6th, 15h in room 470 of PRBB

Speaker: Anna Bauer-Mehren Integrative Biomedical Informatics Laboratory

Requirements: People should bring their laptops with Cytoscape verision 2.6.3 installed. Cytoscape can be downloaded here.

The slides will be available after the talk. Material needed for the tutorial will be available shortly before the tutorial on http://ibi.imim.es.

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A brief introduction to latex for writing papers

Latex is an open source text document markup language broadly used among scientists. We propose a hands on two hours tutorial to show the basic features of this language. Everything you need is just your notebook!
If your laptop is mounting linux check that you have the latex compiler and one of the most used editors (kile, texmaker, lyx).

If your laptop is a mac you can get everything you need to follow the tutorial here: http://guides.macrumors.com/Installing_LaTeX_on_a_Mac.

If you are a windows user, please send a mail to aledda@imim.es and we will provide you with a live CD with all the tools.

Any further question can be addressed to aledda@imim.es.

The workshop will be given by Alice Ledda, PhD student at Evolutionary Genomics lab and Inma Tur, PhD student Functional Genomics, GRIB

Download the course material.

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GEM hands on

February 2nd at 11h in room 473.10 of PRBB, Paolo Ribeca from Genome Bioinformatics, CRG.

GEM is a set of tools for mapping and analysing next-generation sequencing data.

This seminar will be a continuation, more practical with use cases, on the tutorial that was presented in the previous seminar.

You can download binaries from http://gemlibrary.sourceforge.net

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GEM tutorial

January 19th at 11h in room 468 of PRBB, Paolo Ribeca from Genome Bioinformatics, CRG is going to present a tutorial on how to use GEM, a set of tools for mapping and analysing next-generation sequencing data.

The project is hosted in Sourceforge at http://gemlibrary.sourceforge.net

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Reading and plotting CSV files with python and pylab

The latest releases of the numpy and scipy libraries for python have seen the introduction of a nice system to read CSV files and plot their content with pure python, in a way similar to R and other data management programming languages, along with a new data structure, the recarray, to contain data in a matrix-like object.

This tutorial will be a short introduction to the numpy/scipy/pylab system, along with some live examples.

After the talk on Python, an alleged self-declared python expert will try to answer to any doubt or problem you may have with python programming. you can bring your code on a usb card, or your laptop, or just prepare a question, and we will try to solve it all together.

December 9th at 11h in room 473.10 of PRBB, Giovanni Marco Dall’Olio from Biologia Evolutiva, CEXS-UPF.

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Tools and challenges for ChIP-seq data analysis

In the last couple of years new-generation sequencing technologies have allowed researchers to study protein-DNA interactions in a genome-wide manner, at a cost much reduced than array-based technologies, and without the need of previous knowledge on binding sites. Increasing amounts of this type of data are being made available through public databases or individual research, and this gives a great opportunity to extract new knowledge at a bioinformatics level.

Here the main challenges that the analysis of this type of data poises will be exposed and discussed, as there is not yet a single valid method to do so. Also a prototypical pipeline will be shown, along with some downstream analysis examples.

No laptop is needed for this seminar, but an active participation will be much appreciated.

November 10th at 11h in room 473.10 of PRBB, Alba Jené Sanz from Biomedical Genomics Group.

The slides can be accessed at http://www.slideshare.net/ajene/20091110-technical-seminar-chipseq-data-analysis

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Fast and efficient web development with Django

Next October, 13th at 11h in room 473.10 of PRBB, Juan Ramón González-Vallinas will show us how to create web application very fast and efficiently using Django.

It’s not necessary to bring the laptop.

More about Django at http://www.djangoproject.com/

The slides will be published after the talk.

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Cloud computing introduction

In the last few years there has been a steady growth and tendency towards a new powerful approach to IT management: Cloud computing.

The focus of this talk is to give some basics and insights on these flourishing technologies while trying to use them on common bioinformatics problems.

Roman Valls, from esCERT-UPC, has experience on grid systems administration and recently he has started to focus on bioinformatics.

The talk will be the following Tuesday, July 7th at 11h in room 473.10 of PRBB.

The slides are published here.

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