Systems-Biology

14th EMBL International PhD symposium: Overcoming Chaos - Networks in Life Sciences

Fri, 11 May 2012 15:05:22 +0900

Heidelberg, Germany

http://phdsymposium.embl.org/register

CHI's Twelfth Annual Structure-Based Drug Design

Tue, 24 Apr 2012 23:33:56 +0900

Royal Sonesta Hotel Boston
Cambridge, MA

www.healthtech.com/sbd

Job posting from The Microsoft Research - University of Trento

Tue, 24 Apr 2012 23:31:22 +0900

The Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI) is a dynamic, multicultural and multidisciplinary research center based in Northern Italy where scientists collaborate with the aim of improving the understanding of biological processes using programming languages. Along with advanced research programs, COSBI activities include many collaborations worldwide, and the development of solutions to academic and industrial partners.

COSBI is currently looking for highly motivated and experienced Junior Researchers / Post Doctoral Researchers:

Junior Researcher in Ad-Hoc Language Design and Implementation

Junior Researcher in Hybrid Symulation

Junior Researcher in Computational Systems Ecology

Junior Researcher in Molecular Nutrition

Junior Researcher in Static Analysis

Junior Researcher in Bioinformatics, Data Inference and Manipulation

Junior Researcher in the field of Compilation of concurrent languages on parallel architectures

The positions listed above require a PhD in bioinformatics, computational biology, computer science or molecular biology and some years of research experience in the specific field.

An extensive description of our Institute and of our vacancies currently available at COSBI are given at www.cosbi.eu/index.php/people/careers.

Learn more at www.cosbi.eu!

2012 IEEE International Conference on Bioinformatics and Biomedicine (BIBM12)

Mon, 16 Apr 2012 09:50:19 +0900

Philadelphia, PA, USA
http://www.ischool.drexel.edu/ieeebibm/bibm12/

Post-doctoral fellowship in molecular systems biology

Fri, 06 Apr 2012 11:14:26 +0900

The Molecular Systems Biology Group at the Center for Neuroscience and Cell Biology (CNCB) - University of Coimbra, is seeking highly motivated candidates for a post doctoral fellowship under the project PTDC/QUI-BIQ/119657/2010 - "Finding the naturally evolved design principles of prevalent metabolic circuits", funded by FCT/MCTES (PIDDAC) and co-funded by the European Fund for Regional Development (FEDER) through "COMPETE - Programa Operacional Factores de Competitividade (POFC)". Applicants of any nationality must have a Ph. D. degree, a documented strong mathematical and computational background, and a strong publication record in computational systems biology or related areas. Documented experience in mathematical modeling of biochemical processes is a preferential condition.

The object of activity will be the characterization of principles of quantitative design of metabolic network motifs through mathematical modeling, systems analysis and analysis of available experimental data.

The fellowship will have the duration of 12 months, eventually renewable for an additional 12 months, to start June 2012 (negotiable). The monthly salary (tax free) will be €1495, plus €750 yearly travel allowance, plus Social Security reimbursements.

Application deadline:

Applications can be submitted from April 2nd to May 4th 2012 indicating reference BPD1/PTDC/QUI-BIQ/119657/2010 and including all the following documents: motivation letter, curriculum vitae, publications list, copy of Ph. D. diploma/certificate, and contact information (email and phone) of at least three references.

Applications must be submitted by email to armindo.salvador @ gmail.com.

For further information please see http://www.eracareers.pt/opportunities/index.aspx?task=showAnuncioOportunities&jobId=29234&idc=1

SYSMED 2012 Conference

Thu, 05 Apr 2012 10:24:21 +0900

Carton House, Dublin, Ireleand
https://www.eventsforce.net/sbi/frontend/reg/thome.csp?pageID=56&eventID=1&eventID=1

PhD Student Scholarships in Bioinformatics/Systems Biology for Systems Biology

Thu, 29 Mar 2012 13:39:32 +0900

14 PhD research projects are offered within the JSMC Recruitment Call 2012/1 (see list at the following website).

http://www.jsmc.uni-jena.de/phd-program/fellowship-application/vacant-projects/

Job opportunities in Computational and Systems Biology

Thu, 29 Mar 2012 13:37:36 +0900

The Fondazione Edmund Mach, in Trentino, Italy, is pleased to inform you of the following open training and job opportunities:

15 Research positions in Computational and Systems Biology

- open until the 31st July 2012;

More information:
http://www.fmach.it/FEM_work_with_us

Daniele Barbacovi
Fondazione Edmund Mach
Via Mach 1, 38010 San Michele all'Adige (TN) - Italy
Phone +39 0461 615542 - Fax + 39 0461 615183

Doctoral candidate position (PhD student) Systems Biology/Database and Information Systems

Thu, 29 Mar 2012 13:29:43 +0900

Doctoral candidate position (PhD student)
Systems Biology/Database and Information Systems

Job offer opened: 26th of March, 2012

The junior research group „Simulation Experiment Management System" (SEMS) is looking for a PhD student. The offered contract is for a 40h/week, 3yrs, full time position (TVL-E13), starting from June 2012.

Area: Systems Biology, Database and Information Systems

Project objectives:
"Tools and concepts for Simulation Experiment Management in Systems Biology: Improving the production of simulation experiments through standard formats and management support" (SEMS)

Standardization efforts and the exchange of protocols to generate data in the life sciences have become a necessity for large scale projects and multinational collaborations. The data under consideration are highly context dependent and if the processes by which the data were generated are not sufficiently well documented, it becomes difficult to reproduce these results and to share and integrate results across projects. The same arguments apply to the generation of scientific results that are based on mathematical models and computer simulations. Systems biology is a scientific approach characterized by an iterative cycle of data-driven modelling and model-driven experimentation. The present project is to provide support for this iterative cycle through techniques and tools that improve and ease the working with simulation setups, in particular through better model version control.

Further information: www.sbi.uni-rostock.de/sems

Specific objectives for the PhD position:

The successful applicant for a PhD position will investigate methods and techniques for model version control. Models are here regarded as XML encodings of computational models of biological systems. Today, version changes on these models are not sufficiently stored, maintained, curated, classified and presented to the users of model databases. This project will enable model version control to ensure improved reusability of models in the computational biology field.

Main tasks
- Evaluation of existing version control techniques (XML and non-XML)
- Development of methods and concepts tailored to model version control in computational systems biology
- Development of an ontology of model changes
- Design and implementation of a database for the management of XML-encoded simulation descriptions & their integration with existing model data
- Data import, creation of sample XML files, prototype search interface

What we expect
- Experience with database systems and version control
- Experience with XML-data
- An interest in biological questions
- Good programming experience (preferred: Java)
- Good command of English
- Dedication & enthusiasm
- Master's degree or equivalent

What we offer
- International interdisciplinary training
- International working environment
- Participation at presentations & scientific group events
- An excellent preparation for a scientific career
- Equal opportunity employer

Applications should include standard documents (cover letter, curriculum vitae, diploma certificate, etc.) and be addressed to (postal or e-mail):

Dr. Dagmar Waltemath
Department of Systems Biology and Bioinformatics
Institute for Computer Science
Ulmenstrasse 69 (building 3, 3rd floor)
18057 Rostock, Germany
dagmar.waltemath(at)uni-rostock.de

BIOGEMMA is seeking A System Biologist/Bioanalyst

Wed, 21 Mar 2012 13:44:50 +0900

BIOGEMMA is seeking
A System Biologist/Bioanalyst

Biogemma is a leading European plant biotech company based in France, dedicated to research in genetics and genomics in field crops, for the improvement of native traits and the development of GM. You will be immersed in a multidisciplinary environment, where collaboration and search for innovation are crucial and permanent.

Role purpose:

Join the Genomic and Genetic Research Group, and participate to our gene candidate discovery process for plant traits and breeding by analyzing complex datasets in the context of biological pathways and omics data. Your main mission will be to responsible for the interpretation of large scale array-based data (genomics, transcriptomics, metabolomics) related to trait of interest (Yield, drought, nitrogen use efficiency...) and in relationship with quantitative genetic data. Identify and build biological networks and pathways that may help us in the understanding of such complex traits.

Primary responsibilities:

Analysis of transcriptomic/metabolomic data, genes networks, pathway analysis
Data-mining and experience with managing high throughput 'omics data as well as public repositories such as NCBI, PlexDb, Genevestigator...

Qualifications:

Experience in Biology, computational biology, Bioinformatics, preferably with a focus in large scale data analysis.
Experience with modern high-throughput 'omics data including sequence expression, genomic variation and metabolic profiling data is highly desired.

Required skills:

Experience with gene expression analysis and gene interactions networks.
Experience with pathway databases and softwares (Pathway studio...), analysis and visualization tools such as Spotfire, GeneSpring...
Tools of bioanalyst (UNIX, Blast, GGB, gene prediction, promoter analysis etc...)
Excellent interpersonal skills,
Excellent verbal and written communication skills in French or/ and English.

Application instructions:
Ref 12-GGC-001-CR is mandatory when submitting your application
Apply until 30 April 2012: rh @ biogemma.com

Additional information:
Temporary contract (15 months); position based in Chappes, France (63, Puy-de-Dôme). Starting date as soon as possible.

PyDSTool

Thu, 15 Mar 2012 09:43:45 +0900

PyDSTool is a sophisticated & integrated simulation and analysis environment for dynamical systems models of physical systems (ODEs, DAEs, maps, and hybrid systems). It supports symbolic math, optimization, continuation, data analysis, biological applications, among others.

http://pydstool.sf.net

Post-Doctoral Research Associate Position

Wed, 14 Mar 2012 12:38:44 +0900

Department of Chemical Engineering
University of Massachusetts
Amherst, MA

A post-doctoral research position is available in the laboratory of Professor Michael A. Henson in the Chemical Engineering Department at the University of Massachusetts. The research involves the development of microbial metabolic models and solid-state fermentation technology for the conversion of lignocellu-losic feedstocks into precursors for high-density hydrocarbon fuels. The project is funded by the Navy through a research subcontract from PSI Inc. Close interactions with microbiologists and engineers from PSI and the Navy will be required. Candidates with a Ph.D. in chemical engineering or a related eld and the following background are sought: (1) microbial and/or solid-state fermentation; (2) genome-scale metabolic modeling; and (3) metabolic engineering.

The position is available starting April 1, 2012 for a period of 12-18 months. A nine month extension is possible with satisfactory progress and availability of funds. The stipend and benets are competitive. Please send a letter of application, a curriculum vitae, and three letters of recommendation to:

Dr. Michael A. Henson
Professor, Director of the Center for Process Design and Control, and Co-
director of the Institute for Massachusetts Biofuels
Department of Chemical Engineering
University of Massachusetts Amherst
686 N. Pleasant Street
Amherst, MA 01003-9303
Phone: 413-545-3481
Fax: 413-545-1647
E-mail: henson @ ecs.umass.edu

CMSB 2012 10th International Conference on Computational Methods in Systems Biology

Wed, 14 Mar 2012 11:30:18 +0900

Royal Society, London, UK

http://www.brunel.ac.uk/cmsb2012

COMBINE 2012

Tue, 13 Mar 2012 11:30:25 +0900

The third annual COMBINE (COmputational Modeling in BIology' NEtwork) forum will be organised as a satellite of the 13th ICSB, Toronto, Canada

HARMONY 2012: The Hackathon on Resources for Modeling in Biology

Tue, 13 Mar 2012 11:28:25 +0900

Maastricht, The Netherlands
http://co.mbine.org/events/HARMONY_2012