Congreso BIFI2014 y taller internacional de bioinformática

Hola,

la próxima semana el laboratorio estará en dos eventos simultáneos:

http://bifi.es/events/bifi2014

http://congresos.nnb.unam.mx/TIB2014

1) los Talleres Internacionales de Bioinformática TIB2014, donde Carlos Pérez Cantalapiedra participa como profesor en el "Taller 2: Bioinformática para análisis de datos de secuenciación masiva (NGS)". Este evento tiene lugar en el campus UNAM en Cuernavaca, Morelos, México. Aprovecho para señalar que, entre otras muchas herramientas y utilidades para el manejo de datos NGS, Carlos empleará dos programas desarrollados en el laboratorio, uno escrito en C++ y otro en Perl:

•  split_pairs: efficient kseq-based program to sort and find paired reads within FASTQ/FASTA files, with the ability to edit headers with the power of Perl-style regular expressions
•  split_blast: Perl script to take advantage of multi-core CPUs for doing BLAST searches that fit in RAM, del que ya hablamos en este blog

2) la IV International Conference BIFI 2014, en Zaragoza, España, donde el laboratorio presenta varios pósters y una charla sobre trabajo reciente.

Nos vemos allí, un saludo,

Bruno

New release of GET_HOMOLOGUES

Dear users,
today we are announcing a new release of the GET_HOMOLOGUES package (20140110) that includes an updated version of compare_clusters.pl, which now performs as explained in the manual, including option -T for creating a parsimony pangenomic tree. The download links to get this code are as usual:

http://www.eead.csic.es/compbio/soft/gethoms.php

and

http://maya.ccg.unam.mx/soft/gethoms.php

Please let us know of any other bugs that you might encounter, we appreciate your comments,
many thanks,

Bruno Contreras and Pablo Vinuesa

Bioinformatician NGS Best Wishes for New Year

This year we didn't have Christmas greeting in the blog, and I received an email from Santa Claus asking for it. So we'll wish the best for New Year... (remember about the free NGS course in Zaragoza in January 2014)

Curso NGS en Zaragoza (30-31 Enero 2014)

Hola,
nuestro colega Miguel Pérez-Enciso impartirá los días 30-31 de Enero (30, mañana y tarde; 31, mañana) un curso básico de análisis de datos NGS en el Salón de actos de la facultad de veterinaria de la Universidad de Zaragoza, invitado y organizado por Luis Varona. El curso es gratuito y no requiere inscripción.

El horario será:
jueves   30: 11-14H y 16-18H
viernes  31: 10-13H


Si consigo un enlace con el material del curso lo pondré aquí, de momento no sé mucho más que lo que aparece en el propio material que Miguel usa (http://www.icrea.cat/Web/OtherSectionViewer.aspx?key=1403&titol=2012):

"This is a short introductory course for NGS analyses.
The course assumes no knowledge on NGS data or data analyses, rather to the contrary, if you have experience , you will be disappointed. It is not yet a hands-on course, I will rather present the material theoretically but I am open with help in the analyses. I assume you are a computer illiterate biologist but that you have realized that you need computers in daily life. You are willing to:

Analyze by yourself the data
Willing to learn linux and perl or similar (python ...)
The main topics covered are:
FASTQ format and sequence quality (Phred score and fastqc software)
A simple pipeline: BWA + Samtools
Visualization: IGV
Identifying SNPs: Samtools
Annotating SNPs: ensembl vep.pl
Identifying structural variants
RNAseq: tophat + cufflinks
Population genetics: pools and individuals
Association studies with sequence: IBSeq

All topics are treated at very beginners level and superficially (check accompanying slides)"

Feliz año a todos,
Bruno

ofertas de postdoc en Bioninformática (Dic2013)

Hola,
comparto información de ofertas de trabajo en bioinformática que nos han llegado, hasta luego,
Bruno

1.

"We are looking to recruit a young, post-doctoral researcher for work on: Development and application of bioinformatic analysis methods for identification of biomarkers to assess the efficacy of TGF-β RI inhibitors in vivo"

http://www.genxpro.info/contact_us/Open_Positions/

2.

"[..]The Computational Biology Group of the Luxembourg Centre for Systems Biomedicine seeks a highly-skilled Postdotoral Fellow to work on an exciting project on reconstruction and analysis of an integrated gene regulatory network model to elucidate key mechanisms of cellular reprogramming. The model will rely on the integration and mining of diverse transcriptomics and epigenomics data of different cell types from the Central Nervous System. The

Postdoctoral Fellow is expected to supervise a Ph.D. student working on this project. Both of them are expected to collaborate with other members of the CBG to develop a computational methodology aiming at designing, in-silico, cellular reprogramming events, with a focus on the nervous system. This project will be carried out in collaboration with Prof. Noel Buckley’s lab at Kings College London.

Requirements of the ideal candidate:
• Ph.D. degree in Bioinformatics, Computer Science, Biology or a related discipline
• Strong computational skills
• Prior experience in mathematical modelling of biological networks, especially in network inference and analysis
• Excellent working knowledge in English.

We offer:
• Full contract for three years with possibility of renewal
• Opportunity to supervise a Ph.D. student working on the project
• Opportunity to do applied research to medical problems within a highly dynamic research institution (LCSB) and in collaboration with internationally recognized partners
• An exciting international environment
• A very competitive salary

For further information, please contact:
Prof. Dr. Antonio del Sol
E-mail: antonio.delsol@uni.lu

Applications should contain the following documents:
• A detailed curriculum vitae
• cover letter mentioning the reference number
• description of past research experience and future interests
• name and addresses of three referees

All applications should be sent preferably in electronic version until December 31 st, 2013 to the following address:
Luxembourg Centre for Systems Biomedicine (LCSB)
University of Luxembourg
7, avenue des Hauts-Fourneaux
L-4362 Esch-sur-Alzette
Tel: +352-466644-6982 (Office)"

http://wwwen.uni.lu/lcsb/people/antonio_del_sol_mesa