From arne at bioinfo.se Tue Dec 3 13:47:08 2013 From: arne at bioinfo.se (Arne Elofsson) Date: Tue, 3 Dec 2013 13:47:08 +0100 Subject: [SocBiN] Full time bioinformatician position in Stockholm with a focus on web-development Message-ID: Bioinformatician with a focus on web-development Bioinformatician with a focus on web-development at the Department of Biochemistry and Biophysics with placement at the Science for Life Laboratory. Reference number SU FV-3647-13. Deadline for applications: January 15, 2014. The Science for Life Laboratory (SciLifeLab) is a collaboration between four universities in Stockholm and Uppsala: Stockholm University, the Karolinska Institute, the Royal Institute of Technology, and Uppsala University. The SciLifeLab is a national centre for large-scale biosciences with a focus on health and environmental research. The centre combines advanced technical know-how and state-of-the-art equipment with a broad knowledge in translational medicine and molecular biosciences. BILS (Bioinformatics Infrastructure for Life Sciences; http://bils.se/) is a distributed national infrastructure focused on research infrastructure in bioinformatics. BILS is supported by the Swedish National Research foundation. The aim of BILS is to provide bioinformatics support for users within life science. BILS is now recruiting a bioinformatics scientist to create and maintain stable, secure and user-friendly web-interfaces for methods developed by Swedish researchers. *Tasks* - Create and maintain user-friendly web frontends for the methods developed in Sweden related to protein structure prediction. - Create user-friendly web frontends with multiple accessible methods, including standard web-interfaces and computer based (REST) methods. - Improve existing source code to make it more robust, secure and easily accessible. - Simplify integration of different distributed resources. *Desired qualifications* The application should have a PhD in bioinformatics or a related subject. The applicant should have good knowledge in protein structure prediction or related areas. The applicant should be a skilled programmer. The applicant should be able to communicate with other developers as well as with end users. Applicants with skills from one or several of these areas are given priorities: - web development in HTML5, SOAP, and/or Ajax, - experience in programming languages, including Python, C, C++, - Linux system administration and - experience of distributed computing environments. The applicant should be able to work independently and to take his/her own initiatives. The applicant should also be service minded and be able to express him/her-self in English both orally and in written text. *Terms of employment* The position is full-time and is valid until further notice with a probationary period of six months. Starting date as soon as possible. The administration of the position and its placement will be handled at the Department of Biochemistry and Biophysics , Stockholm University. Stockholm University strives to be a workplace free from discrimination and gives equal opportunities for all. For application see: *http://www.su.se/english/about/vacancies/technical-and-administrative-personnel/bioinformatician-with-a-focus-on-web-development-1.157362 * Yours Arne ----------------------------------------- Arne Elofsson Science for Life Laboratory Tel:+46-(0)852481531 Stockholm University http://bioinfo.se/ Box 1031, Email: arne at bioinfo.se 17121 Solna, Sweden Twitter: https://twitter.com/arneelof Scholar: http://scholar.google.se/citations?user=s3OCM3AAAAAJ ORCID: 0000-0002-7115-9751 -------------- next part -------------- An HTML attachment was scrubbed... URL: From prash at bioclues.org Thu Dec 5 13:38:52 2013 From: prash at bioclues.org (Prash) Date: Thu, 5 Dec 2013 13:38:52 +0100 Subject: [SocBiN] Call for submissions on hypothetical and uncharacterized protein research: IWBBIO 2014@Spain Message-ID: Details at http://iwbbio.ugr.es/sessions_proposals.php *SS17**Annotation and Curation of Uncharacterized Proteins: Systems Biology Approaches* A hypothetical protein (HPs) is a protein whose existence is predicted but whether or not it is expressed remains uncertain. However, many HPs in the recent past have been known to be expressed in vivo. With various methods known to identify components in cell membrane, the functional significance of thousands of proteins especially those that do not have function, not expressed, unique or common among genomes is least understood. Apart from this, many HPs might turn out to be pseudogenes at a later point of time and the use of these proteins remain mis-conducive. To circumvent the problem, several methods to easily screen functional candidates among many hypothetical proteins, use of feature selection algorithms and testing the efficacy of these proteins in terms of precision and accuracy using stochases have widely been covered. With experimental procedures for HP function prediction being low throughput by nature, there has been a need to precisely know their functions for a better understanding of the underlying biological mechanism. We would invite authors interested in these niche areas of annotating uncharacterized proteins and functional genomics for their contribution in any of the following areas, not just limited to the following but to a broader purview: - Computational flow for the functional annotation of uncharacterized proteins using motif discovery, sequence and structural similarity, structural homology, hypothome (interactome of hypothetical proteins) or combination of data from highly similar non-interacting proteins (Similactors). - Predictive approaches based on Gene Ontology (GO). - Feature selection and machine learning methods. - Diseasome approaches. *Organizers: Prof. Alfredo Benso *, Department of Control and Computer Engineering, Politecnico di Torino (Italy) *Dr. Prashanth Suravajhala *, Founder of Bioclues.org and Director of Bioinformatics.org Prashanth Suravajhala, PhD. Homepage: http://www.bioinformatics.org/wiki/Prash Linkedin: http://dk.linkedin.com/in/prashbio "Scientific research is one of the most exciting and rewarding of occupations." ~Frederick Sanger -------------- next part -------------- An HTML attachment was scrubbed... URL: From nicosia at dmi.unict.it Thu Dec 5 18:56:56 2013 From: nicosia at dmi.unict.it (Giuseppe Nicosia) Date: Thu, 5 Dec 2013 18:56:56 +0100 Subject: [SocBiN] 1st announcement: Synthetic and Systems Biology Summer School: Biology meets Engineering and Computer Science, Taormina - Sicily, Italy June 15-19, 2014 Message-ID: <4844AFBD-7667-4BAC-B94F-C76F752DEB7E@dmi.unict.it> ______________________________________________________ Call for Participation (apologies for multiple copies) ______________________________________________________ Synthetic and Systems Biology Summer School: Biology meets Engineering and Computer Science Taormina - Sicily, Italy, June 15-19, 2014 W: http://www.taosciences.it/ssbss2014/ E: ssbss at dmi.unict.it *Application Deadline: February 15 2014* Recent advances in DNA synthesis have increased our ability to build biological systems. Synthetic Biology aims at streamlining the design and synthesis of robust and predictable biological systems using engineering design principles. Designing biological systems requires a deep understanding of how genes and proteins are organized and interact in living cells: Systems Biology aims at elucidating the cellular organization at gene, protein, cell, tissue, organ and network level using computational and biochemical methods. The Synthetic and Systems Biology Summer School (SSBSS) is a full-immersion course on cutting-edge advances in systems and synthetic biology with lectures delivered by world-renowned experts. The school provides a stimulating environment for doctoral students, early career researches and industry leaders. Participants will also have the chance to present their results (Oral presentations or Posters) and to interact with their peers. *List of Speakers* Uri Alon, Weizmann Institute of Science, Israel Jef Boeke, Johns Hopkins University, USA Jason Chin, MRC Laboratory of Molecular Biology, UK Virginia Cornish, Columbia University, USA Angela DePace, Harvard University, USA Paul Freemont, Imperial College London, UK Tanja Kortemme, University of California San Francisco, USA Giuseppe Nicosia, University of Catania, Italy Sven Panke, ETH, Switzerland Rahul Sarpeshkar, MIT, USA Ron Weiss, MIT, USA Other speakers will be announced soon. School Directors Jef Boeke, Johns Hopkins University, USA Giuseppe Nicosia, University of Catania, Italy Mario Pavone, University of Catania, Italy Giovanni Stracquadanio, Johns Hopkins University, USA Short Talk and Poster Submission Students may submit a research abstract for presentation. School directors will review the abstracts and will recommend for poster or short-oral presentation. Abstract should be submitted by February 15, 2014. The abstracts will be published on the electronic hands-out material of the summer school. W: http://www.taosciences.it/ssbss2014/ E: ssbss at dmi.unict.it -- Giuseppe Nicosia, Ph.D. Associate Professor Dept of Mathematics & Computer Science University of Catania Viale A. Doria, 6 - 95125 Catania, Italy P +39 095 7383048 E nicosia at dmi.unict.it W http://www.dmi.unict.it/nicosia ----------------------------------------------------------- From Erik.Bongcam at slu.se Fri Dec 6 12:48:54 2013 From: Erik.Bongcam at slu.se (Erik Bongcam-Rudloff) Date: Fri, 6 Dec 2013 11:48:54 +0000 Subject: [SocBiN] ALLBIO: RNA-seq data analysis workshop in Finland 8.-10.1.2014 In-Reply-To: <4844AFBD-7667-4BAC-B94F-C76F752DEB7E@dmi.unict.it> References: <4844AFBD-7667-4BAC-B94F-C76F752DEB7E@dmi.unict.it> Message-ID: RNA-seq data analysis workshop in Finland 8.-10.1.2014 Please note that registration for the international RNA-seq data analysis workshop is now open at http://www.csc.fi/english/csc/courses/archive/rnaseq2014. The workshop covers several aspects of RNA-seq data analysis, ranging from quality control, assembly and alignment to differential expression analysis and miRNA-mRNA integration. Particular emphasis is given to comparison of different analysis tools. The program consists of two lecture days and four optional hands-on sessions. The workshop is part of the EU FP7 funded AllBio project. Best regards, Eija Eija Korpelainen, Ph.D Product Manager Application services, Bioinformatics CSC - IT Centre for Science P.O.Box 405, FIN-02101 Espoo, Finland Phone +358 50 381 9726 -------------- next part -------------- An HTML attachment was scrubbed... URL: From magali.michaut at iscb.org Fri Dec 20 19:18:18 2013 From: magali.michaut at iscb.org (Magali Michaut) Date: Fri, 20 Dec 2013 19:18:18 +0100 Subject: [SocBiN] Postdoc/PhD in computational cancer biology at the Netherlands Cancer Institute (Amsterdam) Message-ID: <65CEB238-4F59-45F9-9F61-90C20EE4FB8C@iscb.org> Postdoc/PhD in computational cancer biology: Prediction of response to neoadjuvant chemotherapy == Who we are == Located in Amsterdam, The Netherlands Cancer Institute (NKI) is the only Dutch Comprehensive Cancer Centre. Excellent basic, translational, and clinical cancer research is performed to give the best possible cancer treatment to patients. This environment attracts bright and ambitious scientists from all over the world. Research in the Computational Cancer Biology (CCB) group roughly centres around three core topics, all rooted in large-scale data analysis: characterization of oncogenic molecular alterations, tumour subtyping, and personalized treatment. The CCB group participates in unique collaborations with molecular biologists and clinicians. == Project outline == Neoadjuvant chemotherapy is widely used in all subtypes of breast cancers. However, only a small subset (~10%) of patients with luminal breast cancer achieve pathological complete response. We previously identified genes of which expression levels are associated to chemotherapy resistance. In this project, we aim to i) better understand the molecular alterations of luminal breast cancers (e.g. role of the genes identified, association with BRCAness); ii) develop practical routine predictive tests to tailor neoadjuvant chemotherapy for luminal breast cancer. To do that, we will leverage in-house (DNA and RNA sequencing data from 500 biopsies) and published data (METABRIC, TCGA) on primary luminal breast cancer together with a large collection of cell lines available via our collaboration with the Wellcome Trust Sanger Institute and the Cancer Systems Biology Centre at NKI. The successful candidate will be in charge of building computational models to achieve the aims as outlined above. == Who you are == We need an ambitious, motivated and skilled computational biologist to run this project. - Highly motivated postdoc or PhD candidate - Holding a degree in bioinformatics or computer science - Experienced in cancer biology and clinical applications - Proficient in common bioinformatics scripting and programming languages (e.g. R, python) - Experienced in analysing high-throughput genomic data (e.g. DNA and RNA sequencing) - Able to communicate effectively with scientists from various backgrounds - Speaking and writing English fluently == Interested? == Please contact Lodewyk Wessels, tel. +31 20 512 7987 or e-mail: l.wessels at nki.nl. When applying, please ensure you include a CV, list of publications and the names and addresses of at least two people that can be approached as references. Also see ccb.nki.nl for further information. == Closing date == 1 February 2014 -------------- next part -------------- A non-text attachment was scrubbed... Name: NKI_CCB_KWF_Luminal_2013.pdf Type: application/pdf Size: 257685 bytes Desc: not available URL: