PRBB Technical Seminars

in Computational Genomics

A brief introduction to latex for writing papers

Feb 26

Posted by admin in Uncategorized

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

Jan 27

Posted by admin in Sequencing, Tools

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

Jan 18

Posted by admin in Sequencing, Tools

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

Dec 3

Posted by admin in Tools, python

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

Nov 9

Posted by admin in Statistics, Tools

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

Oct 7

Posted by admin in Web, python

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

Jul 6

Posted by admin in Uncategorized

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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Accessing BioMart using R and Bioconductor

May 29

Posted by admin in Bioconductor

Ensembl is a database that contains genomes and their annotation of different species.

Biomart is a tool to extract data from Ensembl in different formats.

Another possibility despite the web api in perl, is a package from Bioconductor called biomaRt.

It allows to mine and retrieve data from Ensembl without leaving the environment of the script. It eases automatic data retrieval and aids in creating reproducible work flows. The subsequent analysis of data is therewith easier and it is not necessary to download loads of different tables.

Sonja Haenzelmann, from Functional Genomics, will give a talk about how to use the R package biomaRt the following Tuesday, June 2nd at 11h in room 473.10 of PRBB.

The slides are here.
And the R example is here.

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Writing pipelines using Makefiles

May 19

Posted by admin in Workflows

Makefiles are a great tool to organize pipelines of shell commands, and to keep track of the different programs and options executed over our data files.

It is really an essential tool for any bioinformatician working with scripts or unix commands, and a requirement to understand more complex systems like taverna and other workflow building softwares.

Giovanni Marco Dall’Olio, from Biologia Evolutiva, will talk us about how to use Makefiles to create pipelines.

And at the end there will be a brief presentation by Christian Pérez-Llamas, from Biomedical Genomics, of the pipeline used in a real project called IntOGen where a lot of calculations are needed to analyze data.

The slides are available at http://www.slideshare.net/giovanni/makefiles-bioinfo

More information on GNU Make at http://www.gnu.org/software/make/manual/make.html

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Introduction to Python for Bioinformatics

Apr 21

Posted by admin in python

For those of you that are interested in reviewing the slides or couldn’t come to presentation here you have the slides:

http://www.slideshare.net/giovanni/introduction-to-python-for-bioinformatics

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