The Functional Bioinformatics (FBI) group led by Dr. Michael Sammeth at the CNAG in Barcelona (http://fbi.sammeth.net) is looking for talented candidates who are highly motivated for cutting-edge research in functional genomics and transcriptomics, involving data produced by the latest Next-Generation Sequencing (NGS) technologies.
The FBI group investigates functional aspects of expressed genes, as by their mutual interaction and regulation, to advance in the understanding how the information encoded in a single genome can give rise to a plethora of different cell types that together form an organism.
To achieve these ambitious goals, we employ results of state-of-the-art sequencing experiments applied to the transcriptome (RNA-Seq) and from Chip-Seq assays, most of them carried out at the CNAG (http://www.cnag.eu).
With currently twelve state-of-the-art Illumina HiSeq sequencing machines, the CNAG centre is becoming one of the major high throughput Sequencing Centers in Europe, participating in several consortia of networked projects such as the International Cancer Genome Consortium, and EUfunded projects such as READNA, ESGI, GEUVADIS and BLUEPRINT.

Responsibilities
The successful candidate will be involved in different projects and collaborations, and explore various aspects of data yielded by deep sequencing in order to advance in our understanding about functionality of genomic elements. To this end, the candidate will primarily apply established pipelines to RNASeq and Chip-Seq datasets.
Depending on the candidate’s profile, the FBI also offers the possibility to participate actively in the development of computational approaches for analyzing NGS data, based on the programs Flux Capacitor / Simulator, and Astalavista we have developed.

Candidate profile:
We are looking for a post-doctorate research fellow and a technician with a PhD/Master’s Degree in Biology, Bioinformatics, or related fields.
The CNAG operates a powerful Unix cluster with currently ~1000 cores and 2 Petabyte of disk space; therefore, a profound knowledge of common Unix commands is an essential pre-requirement for the candidate to be eligible. Candidates are also expected to possess a background that provided them with a general knowledge about the biological concepts of gene expression.
The successful candidate will employ statistical frameworks (e.g., the “R” platform) and scripting to pursue comparisons of experimental data. The FBI group already developed pipelines for the low-level data processing, and we support candidates who are interested in extending and improving these computational tools implemented in Java and Groovy.
In addition to these technical skills, we especially encourage candidates with preliminary experiences in genomics, transcriptomics, and/or the analysis of high throughput sequencing data to apply.

Conditions:
We offer a 2-year contract is offered with prospective starting date in june/july or september 2012. Salary will be determined according to the academical degree and experience of the candidate.

Application procedure:
Interested candidates should send their CV to msammeth@pcb.ub.es

Directores: Dr. D. Federico Morán Abad, Dr. D. Alfonso Valencia Herrera y Dr. D. Luis Vázquez Martínez.

Coordinador: Andrés Cañada Pallarés.

Fechas y horario: Del 9 al 27 de julio de 2012. Mañanas de 9:00 a 14:00 horas.

Nº de plazas: 20

Nº de créditos de libre configuración: 7,5 (sólo alumnos UCM)

Nº de créditos de grado: 3 (solo alumnos UCM).

Lugar de celebración: Universidad Complutense de Madrid.

Precio de la matrícula: 900 Euros.

Ayudas: Las de carácter general.

Perfil del alumno: El curso está abierto a doctores, licenciados o estudiantes de ciencias o ingeniería con cierta formación en biología molecular y conocimientos básicos de informática. El curso se impartirá en inglés en su totalidad (o al menos en una buena parte del programa), por tanto se requiere el conocimiento de este idioma.

Más información:

Web

PDF

Candidate requirements:
PhD after 1 Jan 2009
Bioinformatics and statistical knowledge is mandatory.
R or MATLAB programming skills would be valuable.

For further information, please contact:
Agustín Lahoz (agustin.lahoz@uv.es), including a CV.
Death line: 30 May de 2012.

http://www.eccb12.org/workshops#ws2

http://www.unbsj.ca/sase/csas/data/aimm2012/

Keynote Speaker
- Mauno Vihinen PhD, Professor of Medical Structural Biology (Lund). VARIATION ONTOLOGY: ontology for standardized, systematic description of effects and consequences of variations.

Important Dates
Abstract submission       June 15 2012
Full paper submission     July 1 2012
Acceptance notification   July 30 2012
Final manuscript             Aug 15 2012
AIMM2012 Workshop      Sept 9 2012

Workshop Themes

* Mutation Nomenclature, Databases and Metadata: Design, Content, Accuracy.
* Mutation Data Integration, Phenotype Ontologies, Semantic Services and Reuse.
* Semantic Integration and Interpretation of data linked to mutations and diseases
* Impacts of Mutations: Prediction and Bootstrapping.
* Extraction and grounding of mutations and impact annotations from scientific literature
* System Evaluations and Benchmarking

http://www.unbsj.ca/sase/csas/data/aimm2012/themes.html

http://www.unbsj.ca/sase/csas/data/aimm2010/themes.html

http://www.ebi.ac.uk/Rebholz-srv/aimm.html

*Submissions*

We invite workshop papers (3000 words / 8 pages) and demonstrations. Early Abstracts should be no more than 500 words. Manuscripts should be focused around a specific challenge with a biomedical context where they suggest a solution, demonstrate feasibility and possibly also a meaningful evaluation.

Pre-submission enquiries and variations to the deadlines above may be made in consultation with the Chris Baker bakerc@unb.ca

* Author instructions can be obtained by sending an email to bmcmutations@gmail.com an automated reply  will be sent and complete submissions should be uploaded to Easychair:https://www.easychair.org/conferences/?conf=aimm2012

Journal Special Issue

A special issue in a biomedical scientific journal will be produced of the best contributions to the Workshop Proceedings. Papers have to address genuine themes relevant to the: Annotation, Interpretation and Management of Mutations (see below)*

Workshop Organizers / Special Issue Editors

-  Christopher J. O. Baker – University of New Brunswick, Canada
-  Dietrich Rebholz-Schuhmann, European Bioinformatics Institute, UK

The 12th Workshop on Algorithms for Bioinformatics (WABI 2012)

http://algo12.fri.uni-lj.si/?file=wabi

September 10-12, 2012, Ljubljana, Slovenia

Key dates
Submissions deadline: May 18th
Notification to authors: June 10th
Final version due: June 22nd

WABI 2012 will be part of ALGO 2012, hosted by the University of Lubljana. WABI is sponsored by the European Association for Theoretical Computer Science (EATCS), and the International Society for Computational Biology (ISCB).

Scope
All research in algorithmic work in bioinformatics, computational biology and systems biology. The emphasis is mainly on discrete algorithms and machine-learning methods that address important problems in molecular biology, that are founded on sound models, that are computationally efficient, and that have been implemented and tested in simulations and on real datasets. The goal is to present recent research results, including significant work-in-progress, and to identify and explore directions of future research.

Topics
Original research papers (including significant work-in-progress) or state-of-the-art surveys are solicited in all aspects of algorithms in bioinformatics, computational biology and systems biology including, but not limited to:
*      Exact and approximate algorithms for sequence analysis, gene and signal recognition, alignment and assembly, molecular evolution, structure determination or prediction, gene expression, molecular pathways and network, proteomics, functional genomics, and drug design.
*      Methods, software, and dataset repositories for development and testing of such algorithms and their underlying models, as well as high-performance computing approaches to computationally hard learning and optimization problems.
*      Novel approaches to analyzing and modeling next-generation sequence data, including sequence assembly, population genomics, metagenomics, metatranscriptomics and ncRNA sequencing.

Call for Papers
Submissions must be formatted in LaTeX using the Springer LNCS style and must not exceed 12 pages. Each paper must contain a succinct statement of the issues and of their motivation, a summary of the main results, and a brief explanation of their significance, all accessible to non-specialist readers. All submissions must be made online, through the EasyChair submission system (http://wwweasychair.org/conferences/?conf=wabi2012). You need to register on that web site before submitting; you may update your submission(s) up to the last minute. A standard PDF file must be received by 23:59 (GMT) on May 18, 2012 in order for your submission to be considered. In case of problems, authors may, by prior arrangement, email a PDF file to the chairs, Ben Raphael and Jijun Tang.

Simultaneous submission to another conference with published proceedings is not permitted, but simultaneous submission to a journal is allowed, provided that the authors notify the program chairs; if published in a journal, such a contribution will be published as a short abstract in the WABI proceedings.

Proceedings
Proceedings will be published in the Springer series Lecture Notes in Bioinformatics; papers will be allotted 12 pages.
Previous proceedings of WABI appeared in LNCS/LNBI volumes 2149 (Aarhus 2001), 2452 (Rome 2002), 2812 (Budapest 2003), 3240 (Bergen 2004), 3692 (Mallorca 2005), 4175 (Zurich, 2006), 4645 (Philadelphia 2007), 5251 (Karlsruhe 2008), 5724 (Philadelphia 2009), 6293 (Liverpool 2010), and 6833 (Saarbrucken 2011).

By arrangement with the Editor-in-Chief, selected papers from WABI will be invited for an extended publication in a special issue of the BMC Algorithms for Molecular Biology.

————————————————————————–
Jijun Tang
Co-Chair, WABI 2012
Associate Professor
Department of Computer Science and Engineering
University of South Carolina, USA

Several international senior scientists will give general lectures and hands-on sessions on their topics within the field of protein evolution.  Around 20 students (Master and early PhD level) will have the opportunity to join the summerschool and present their work in short oral presentations.  In addition, there will be plenty of time for discussion with senior scientists about the students’ projects and other questions.  Deadline for application is May 1st, 2012.  More information on the summerschool can be found on our website:http://www.eeslmu.de/eeswiki/Summer_school_2012

La CCSSS12 tendrá lugar entre el 2 y el 31 de Julio en las instalaciones del CESGA (Santiago de Compostela). El programa formativo de la escuela se compone de varios cursos teórico-prácticos centrados en las áreas de Computación y Cálculo Científico. Los alumnos dispondrán además de tutorías personalizadas atendidas por el profesorado y el personal técnico del CESGA.

Información detallada sobre la escuela (profesorado, cursos, precios, etc) e inscripción en la dirección:

http://www.cesga.es/SummerSchool2012

Cualquier duda puede contactar con nosotros en la dirección de correo ccsss12@cesga.es y en el teléfono 981-569810.

Un cordial saludo,

Carmen Cotelo Queijo
Centro de Supercomputación de Galicia (CESGA)
Avda. de Vigo s/n. Campus Vida
15705 – Santiago de Compostela. SPAIN