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

GET_HOMOLOGUES for pan-genome analysis

Hola,

en el último número de Applied and Environmental Microbiology mi colega Pablo Vinuesa y yo publicamos un artículo describiendo el software GET_HOMOLOGUES, que tiene como abstract:

GET_HOMOLOGUES is an open source software package that builds upon popular orthology-calling approaches making highly customizable and detailed pan-genome analyses of microorganisms accessible to non-bioinformaticians. It can cluster homologous gene families using the bidirectional best-hit, COGtriangles or OrthoMCL clustering algorithms. Clustering stringency can be adjusted by scanning the domain-composition of proteins using the HMMER3 package, by imposing desired pair-wise alignment coverage cut-offs or by selecting only syntenic genes. Resulting homologous gene families can be made even more robust by computing consensus clusters from those generated by any combination of the clustering algorithms and filtering criteria. Auxiliary scripts make the construction, interrogation and graphical display of core and pan-genome sets easy to perform. Exponential and binomial mixture models can be fitted to the data to estimate theoretical core and pan-genome sizes, and high quality graphics generated. Furthermore, pan-genome trees can be easily computed and basic comparative genomics performed to identify lineage-specific genes or gene family expansions. The software is designed to take advantage of modern multiprocessor personal computers as well as computer clusters to parallelize time-consuming tasks. To demonstrate some of these capabilities, we survey a set of 50 Streptococcus genomes annotated in the Orthologous Matrix Browser as a benchmark case.

El  software  se puede descargar de http://www.eead.csic.es/compbio/soft/gethoms.php y también de http://maya.ccg.unam.mx/soft/gethoms.php y está escrito mayoritariamente en Perl, aunque contiene también trozos en R.

El manual del programa describe en detalle ejemplos de uso y está disponible en http://www.eead.csic.es/compbio/soft/manual.pdf .

Este paquete de programas se diseñó para el estudio de los pan y core-genomas de grupos de microorganismos, que es con lo que trabaja el grupo de Pablo fundamentalmente, y permite generar figuras como éstas:

Un saludo,

Bruno

Trucos para la biología computacional

Buenas,
hoy quiero invitaros a leer lo que nos cuentan dos bioinformáticos (Mick Watson y Nick Loman) sobre el trabajo y el aprendizaje de este oficio, publicado en Nature Biotechnology. Además de tocar temas más relacionados con el desarrollo de software (como el control de versiones) y la construcción de tuberías de análisis, el artículo repasa obviedades que no obstante conviene no olvidar, como

"knowledge of biology is vital in the interpretation of computational results"

 u otra más concreta:

 "Laboratory scientists wouldn’t dream of running experiments without the necessary positive and negative controls... tests are the computational biology equivalent".

El texto, breve, toca temas importantes como la elección apropiada de métodos en bioinformática, la validación de tu propio código y el que te descargaste de otros autores, y la búsqueda de opiniones expertas en foros como SEQanswers. Si te interesa, puedes seguir leyendo en http://www.nature.com/nbt/journal/v31/n11/full/nbt.2740.html?WT.ec_id=NBT-201311,
un saludo,
Bruno

Premio Nobel en biología computacional

Buenos días,
han pasado ya unos días desde el anuncio, pero hasta hoy no he caído en que sería buena idea hablar en este blog sobre el reciente premio Nobel de Química, que ha caído sobre los hombros de Michael Levitt, Martin Karplus y Arieh Warshel. He de reconocer que al último no le conocía, pero a los dos primeros les he leído, visto en congresos y escuchado mencionar muchas veces a lo largo de mi aprendizaje, sobre todo en la vertiente estructural de la bioinformática.

Martin Karplus es famoso por sus trabajos sobre dinámica de macromoléculas, a menudo apoyados por datos cristalográficos,  y por el desarrollo de CHARMM. Por tanto, creo que tiene un perfil muy fuerte en química.

Sin embargo, Levitt ha tenido un papel muy relevante en la bioinformática estructural y en el desarrollo de algoritmos, y por tanto creo que es justo decir que ha sido muy influyente en el desarrollo de nuestra disciplina. Prueba de ello es que participa en los consejos editoriales de revistas que han sido clave en nuestra área como Journal of Molecular Biology, PNAS y PLoS Computational Biology, y que ha participado como evaluador en CASP. Además, como recoge una reciente nota de la ISCB, sus propias palabras traen un poco de este premio a la biología computacional:

“It’s sort of nice in more general terms to see that computational science, computational biology is being recognized. [...] It’s become a very large field and it’s always in some ways been the poor sister, or the ugly sister, to experimental biology.”

Así que estamos de enhorabuena, verdad?
Un saludo, Bruno

Añadido el 15/11/2013:
http://www.sciencedirect.com/science/article/pii/S0022283613006943

Añadido el 04/12/2013:
http://www.pnas.org/content/110/49/19656.extract.html

What does an SNP look like?

So about to use samtools pileup or mpileup? Would you like to take a look at the file, instead of going straightforward for the BCF and bcftools automation?

Ok! this is what an SNP looks like!

contig_100029   698     C       39      .$.....,.,,,,.,,,.,.,..,......,,,,,,.,,^S. 
contig_100029   699     A       38      .....,.,,,,.,,,.,.,..,......,,,,,,.,,. 
contig_100029   700     A       38      .....,.,,,,.,,,.,.,..,......,,,,,,.,,. 
contig_100029   701     C       39      TTTTTtTttttTtttTtTtTTtTTTTTTttttttTttT^ST       
contig_100029   702     A       40      .....,.,,,,.,,,.,.,..,......,,,,,,.,,..^S,     
contig_100029   703     G       41      .....,.,,,,.,,,.,.,..,......,,,,,,.,,.,.,       
contig_100029   704     G       42      .....,.,,,,.,,,.,.,..,......,,,,,,.,,.,.,^S.   

I have ommited the last column (read base qualities).

And what about a reference skip? Maybe want to see an spliced alignment? Here you are!

contig_100029   516     T       43      ,,,.,,...,.,,.................,.,,,,.,,,.,^S.   

contig_100029   517     A       43      ,,,.,,...,.,,.................,.,,,,.,,,.,.     

contig_100029   518     G       43      ,,,.,,...,.,,.................,.,,,,.,,,.,.  

contig_100029   519     A       43      ,,,.,,...,.,,.................,.,,,,.,,,.,.     

contig_100029   520     G       43      ,,,.,,...,.,,.................,.,,,,.,,,.,.    

contig_100029   521     G       43      <<<><<>>><><<>>>>>>>>>>>>>>>>><><<<<><<<><>     

contig_100029   522     T       43      <<<><<>>><><<>>>>>>>>>>>>>>>>><><<<<><<<><>     

contig_100029   523     G       43      <<<><<>>><><<>>>>>>>>>>>>>>>>><><<<<><<<><>     

contig_100029   524     A       43      <<<><<>>><><<>>>>>>>>>>>>>>>>><><<<<><<<><>    

.    .    .    .    .    .    .    .    .    .    .    .    .    .    .

.    .    .    .    .    .    .    .    .    .    .    .    .    .    .

.    .    .    .    .    .    .    .    .    .    .    .    .    .    .

contig_100029   651     C       43      <<<><<>>><><<>>>>>>>>>>>>>>>>><><<<<><<<><>    

contig_100029   652     A       43      <<<><<>>><><<>>>>>>>>>>>>>>>>><><<<<><<<><>     

contig_100029   653     G       43      <<<><<>>><><<>>>>>>>>>>>>>>>>><><<<<><<<><>     

contig_100029   654     G       44      ,,,.,,...,.,,.................,.,,,,.,,,.,.^S, 

contig_100029   655     G       44      ,,,.,,..$.,.,,............$.....,.,,,,.,,,.,., 

contig_100029   656     C       42      ,,,.,,..,.,,................,.,,,,.,,,.,.,     

contig_100029   657     G       42      ,,,.,,..,.,,................,.,,,,.,,,.,.,     

Who wants an IGV when you can scroll up and down seeing how things pile down and up?
An it is memory efficient, right?
You just have to grep or awk filter your region of interest!

Do you want me to explain about columns?

1st: reference_name

2nd: position in reference

3rd: base on reference

4th: depth, or number of bases pilling-up over this reference position

5th: each symbol comes from a read, with some exceptions. Lets look at it:

"." and ",": matches! one in fwd strand, "," in reverse.

"$": end of read. Followed by mapping symbol of that read base ("." or "," for example). So, 2 symbols.

"^": start of read. Followed by mapping quality of the read (the MAPQ field in SAM format) and the mapping symbol of that base ("." or "," for example).

">" "<": reference skip. That is, the read still maps, but no in these reference bases. So probably an spliced alignment with part of the read aligning before the ">" and part after that. ">" fwd strand, "<" reverse.

6th: (not shown, just working with HQ bases ;)

Looking for more information? Ask please!