A portal site for systems biology.

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!

posted 2012.04.24

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. 

posted 2012.04.06

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

posted 2012.03.29

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 

posted 2012.03.29

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

posted 2012.03.29

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.

posted 2012.03.21

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 benets 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

posted 2012.03.14

JUNIOR SCIENTIST (M/F) - BIOINFORMATICS/BIOSTATISTICS
Ref. 2011/1339

We are a member of the Helmholtz Association of German Research Centres, a leading Europe-wide association focusing on environmental health. The international research network "Helmholtz Virtual Institute of Complex Molecular Systems in Environmental Health" (HICE) investigates the effect of anthropogenic aerosols on biological systems, applying state-of-the-art analytical techniques, in order to obtain detailed information on molecular mechanisms of effect. In the framework of this interdisciplinary research project, the cooperation group Comprehensive Molecular Analytics as well as the Institute of Biomathematics and Biometry, University of Rostock, in cooperation with the Chair of Systems Biology and Bioinformatics (SBI) and the Institute for Mathematics, also located at the University of Rostock, are seeking a Junior Scientist (m/f) in Bioinformatics/Biostatistics.

Description
• Establishment and leadership of a junior research group
• Explorative data analysis of highly complex data sets
• Combination of exposure data with biological response data
• Graphic presentation of scientific data sets
• Statistical design of experiments and data management
• Supervision of PhD students
• Proactive participation in the acquisition of third party funds

Qualifications
• Successful completion of a university degree and a PhD in the areas of bioinformatics, biostatistics and/or biomathematics
• Extensive experience with data derived from scientific measurement procedures are an advantage
• Strong team skills
• Excellent knowledge of English

Work Environment and Compensation
• Innovative, well-equipped and scientifically stimulating surrounding with further training opportunities
• Initial short-term employment contract until 31 December 2014 with a standard public service salary (TVöD EG 13). In case of a positive project evaluation, an extension for another two years in the framework of the project is possible.

Application deadline: 30 March 2012.
Please send your application to Dr. Juergen Schnelle-Kreis at juergen.schnelle @ helmholtz-muenchen.de.
Further information is available at:
http://www.helmholtz-muenchen.de/en/career-and-education/ 

posted 2012.03.01

The Center for Genome Dynamics (www.genomedynamics.org) is an NIGMS National Center for Systems Biology housed at The Jackson Laboratory. The Center embraces a systems approach to genetics, with an emphasis on rodent models of complex disease-related phenotypes. Center investigators have interests in computation, mathematical modeling and statistics, with a shared focus on the genetics of complex traits within the Center's collaborative and cross-disciplinary environment.

The Jackson Laboratory (www.jax.org) in Bar Harbor, Maine, USA, offers a unique research and training environment characterized by scientific collaboration, unparalleled mouse resources and outstanding core services within a spectacular setting adjacent to Acadia National Park.  The Jackson Laboratory's postdoctoral program ranks among the nation's top - voted #2 in a poll of postdocs conducted by The Scientist (2009).
 
Applicants should have a PhD (or equivalent degree) in a quantitative field such as computer science, statistics, applied mathematics or in the biological sciences but with a strong quantitative background. Applicants must demonstrate a commitment to solving biological problems. Successful applicants must have good communication skills.  Experience with scientific programming languages including java, c/c++, ruby, perl, or R is recommended. Work within the center is highly interdisciplinary, and applicants must demonstrate a desire to develop skills in new areas of science and in building strong collaborations.

Apply online at www.jax.org/careers (Job ID 2311). The Jackson Laboratory is an EOE/AA employer. 

posted 2012.02.07

Department of Health and Human Services
National Institutes of Health
National Heart, Lung and Blood Institute

Postdoctoral positions are immediately available in the Theoretical Cellular Physics Section of Biochemistry and Biophysics Center at the National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD. Applicants should have PhD in theoretical chemistry, physics, applied math or engineering. Candidates with theoretical modeling experiences in biophysics and strong computational skill are highly desirable. Projects would utilize sophisticated statistical mechanics techniques to investigate mechanochemical couplings in various cellular processes, including membrane mechanics, cytoskeleton dynamics and reaction networks. All the projects would be in extensive and close collaborations with experiments. For more information, see: http://www.lobos.nih.gov/tcps/index.shtml

Appointment and salary are dependent on experience. Applicants should submit, in a PDF file, a letter of interest, curriculum vitae, and three letters of reference to: Dr. Jian Liu at jian.liu @ nih.gov

HHS and NIH are Equal Opportunity Employers. Applications from women, minorities and persons with disabilities are strongly encouraged.

posted 2012.01.30

The University of Luxembourg is looking for the newly established Luxembourg Centre for Systems Biomedicine (LCSB) for a Doctoral Candidate (PhD student) in Systems Biochemistry Ref.I1C-DIR-COM-11ICOO Fixed-term contract 3 years, 40h/week renewable once Student and Employee status The PhD student will be a member of the highly interdisciplinary research centre, integrating experimental biological and computational biology approaches in order to develop the foundation of a future predictive, preventive and personalised medicine. Area: Biochemistry/Medical Biochemistry/Neurochemistry. Mission: Experimental determination of metabolic flux and concentration is a critical tool for developing understanding of the physiological state of a cell. Using isotopically labeled substrates with different labeling patterns, experimental techniques are used to measure the mass isotopomer distributions of select metabolites. Estimation of metabolic flux is by integration of mass isotopomer distributions with an isotopomer (isotope isomer) mapping model, that traces the path of each isotopomer through a metabolic network. Recently an algorithm for automated generation of draft genome-scale isotopomer mapping models has been developed. The latest reconstruction of human metabolism (Recon 2.0) is a stoichiometric model of a generic human cell. It is necessary to tailor Recon 2.0 to represent the metabolic capabilities of a particular cell type of interest. Extensive manual curation of neurochemical experimental data is necessary to tailor Recon 2.0 to accurately represent the metabolism of a normal neuron. A tailored stoichiometric model of a dopaminergic neuron, that also represents atom transitions for each reaction, would be an invaluable resource for estimation of metabolic flux and concentration in cultured dopaminergic cell lines. Tasks: To address the aforementioned challenges, the PhD project objectives are: Reconstruction of a tailored stoichiometric model of a normal dopaminergic neuron by literature review. Manual curation of an existing algorithmically created draft isotopomer mapping model of Recon 2.0 to retain only biochemically realistic atom transitions. Biological interpretation of whole cell metabolic flux and concentration data in normal and diseased dopaminergic neuronal cells toward a deeper understanding of Parkinsonism pathogenesis. Profile: A broad and deep knowledge of metabolic biochemistry e.g. M.Sc. level Medical Biochemist, Biochemist, Neurochemist. Excellent English writing and speaking skills. Offer: Contribution to an international, interdisciplinary project: Dr. Karsten Hiller, LCSB, Dr. Ronan Fleming, Center for Systems Biology, University of Iceland (CSBUI).International interdisciplinary training: In the first year, a 6 month training period in metabolic network reconstruction & modeling at the CSBUI. The University of Luxembourg offers competitive salaries and is an equal opportunity employer. Application: All applications (in English) should contain the following documents: A detailed curriculum vitaeCover letter mentioning the reference number. List of publications. Description of past research experience and future interests. Name and addresses of three referees Please send your electronic applications until the Feb 3rd 2012 to the following address: katrin.effenberger@uni.lu

posted 2012.01.19

Application End:  Saturday March 31 2012

The Laboratory of Computational Systems Biology at the Faculty of Informatics, Masaryk University is currently expanding its research team and is looking for highly motivated and talented individuals to a three year-fixed term post.

The position is available to participate in a project focused on parameter estimation in computational systems biology.

A central challenge in computational modeling of biological systems is the determination of the model parameters. Typically, only a fraction of the parameters (such as kinetic rate constants) are experimentally measured, while the rest are often fitted. The fitting process is usually based on experimental time course measurements of observables, which are used to assign parameter values that minimize some measure of the error between these measurements and the corresponding model prediction.

The goal of our research is to develop effective, fast, and scalable methods, techniques and tools for automated parameter estimation for computational analysis of biological systems. Our approach considers a generalized form of the problem provided that traditional fitting to experimental measurements is enhanced by considering several explicit hypotheses about expected behavior of the system. We employ computer science approaches, methods and techniques as known from the analysis of computer systems (like model checking) to fit parameters according to the expected behavior.
Requirements

Candidates must hold a PhD degree (or equivalent) awarded after 1 April 2008, should be highly motivated and have either a strong background in systems biology, molecular biology, cell biology or biochemistry OR a strong background in informatics or computational modeling and an interest in biological systems. Candidate must have excellent analytical skills, and strong interpersonal and communication skills.

The deadline for applications is March 31, 2012. The gross salary is about 2200 EUR per month. The post is available from 1 September 2012, but the precise starting date is negotiable.

Interested candidates should email their CV, list of publications, brief statement of interest and career goals, names and contact information for 3 references contained in one single PDF file to:

Prof. Lubos Brim
Masaryk University Brno
Faculty of Informatics
Botanicka 68a, 602 00 Brno
Czech Republic
Email: brim at fi dot muni dot cz

posted 2012.01.05