From Inge.Jonassen at ii.uib.no Mon Sep 2 08:55:44 2013 From: Inge.Jonassen at ii.uib.no (Inge Jonassen) Date: Mon, 2 Sep 2013 08:55:44 +0200 Subject: [SocBiN] 3 years senior engineer/programmer Bioinformatics position in Bergen Message-ID: <6312A673-7430-4E5D-968B-853148F89C0A@ii.uib.no> For more information, see http://www.jobbnorge.no/job.aspx?jobid=96054 Please submit your application through the link provided at the above web page. Deadline: September 8th. Inge -- Inge Jonassen, Prof PhD Computational Biology Unit Department of Informatics University of Bergen HiB N5020 Bergen Norway inge at ii.uib.no From Rolf.I.Skotheim at rr-research.no Mon Sep 2 16:04:11 2013 From: Rolf.I.Skotheim at rr-research.no (Rolf I. Skotheim) Date: Mon, 2 Sep 2013 16:04:11 +0200 Subject: [SocBiN] Centre for Cancer Biomedicine: Three bioinformatics postdoc positions available Message-ID: Three bioinformatics postdoc positions available At the Centre of Excellence, Centre for Cancer Biomedicine, we have three vacant postdoctoral positions, each a full-time position for three years. The work place will be at the Department of Cancer Prevention, Institute for Cancer Research, Radium Hospital, Oslo University Hospital, where each postdoc will be formally linked to one of the three research groups at the department. Research includes genetics and epigenetics of cancer, with particular focus on improving diagnostics and treatment of colorectal and prostate cancers. The lab has established various omics-technologies. For more info, see attached PDF. Rolf Skotheim Genome Biology Group Department of Cancer Prevention Institute for Cancer Research Norwegian Radium Hospital Oslo University Hospital P. O. Box 4953 Nydalen, 0424 Oslo Tel: +47 2278 1727 Fax: +47 2278 1745 http://www.radium.no/cancerprevention -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Oslo_UH_Postdocs_in_Bioinformatics.pdf Type: application/octet-stream Size: 242425 bytes Desc: Oslo_UH_Postdocs_in_Bioinformatics.pdf URL: From samuel.kaski at aalto.fi Tue Sep 3 22:09:16 2013 From: samuel.kaski at aalto.fi (Kaski Samuel) Date: Tue, 3 Sep 2013 20:09:16 +0000 Subject: [SocBiN] Postdoctoral positions in Computer Science in Helsinki, Finland Message-ID: <303D2BEE-F61A-40B3-95FF-5497A2D6596B@aalto.fi> [Includes computational biology. -Sami] POSTDOCTORAL POSITIONS IN COMPUTER SCIENCE IN HELSINKI, FINLAND Application deadline Sept 30, 2013, 3:00 p.m. EEST Topics include: Algorithms, Bioinformatics, Human-Computer Interaction, Information retrieval, Logic, Machine Learning, Networks, Statistical Data Analysis, etc. http://www.hiit.fi/postdoc-call-2013 Jobs are available at: Helsinki Institute for Information Technology HIIT, Aalto Univ and Univ Helsinki; Dept Computer Science, Univ Helsinki; Dept Information and Computer Science, Aalto Univ; Dept Computer Science and Engineering, Aalto Univ; Dept Mathematics and Statistics, Univ Helsinki. Why Helsinki? The collaborating Aalto University and University of Helsinki form a leading hub of computer science and modelling. Helsinki region is a safe, pleasant and attractive place to live in, with well-functioning services such as public transport etc. Finland has a comprehensive social security and health care system, including exceptionally good parental leaves, and children's day care services. Positions are offered in: Algorithm engineering (String Algorithms group) Algorithmic bioinformatics (Genome-Scale Algorithmics group) Automated reasoning and search, especially propositional logic (Computational Logic group) Computational astrophysics and/or data analysis (Computational Methods and Data Analysis for Astrophysics group) Computational biology and statistical methods in bioinformatics (Computational Systems Biology group) Computational creativity and data mining (Discovery group) Dynamic and large-scale networked systems (Data Communications Software group) Intelligent multimodal information access (Content-Based Image and Information Retrieval Group) Machine learning and neuroscience (Statistical Machine Learning group) Machine learning for structured data (Kernel Machines, Pattern Analysis and Computational Biology group) Machine learning methods for infectious disease epidemiology (Bayesian Statistics Group) Probabilistic modeling and machine learning (Complex Systems Computation group) Statistical machine learning (Statistical Machine Learning group) Analysing ubiquitous sensor data (HIIT-Wide Focus Area) Interactive visualization (HIIT-Wide Focus Area) Affective computing and BCI (HIIT-Wide Focus Area) Intelligent user interfaces and/or recommender systems (HIIT-Wide Focus Area) Information retrieval (HIIT-Wide Focus Area) Machine learning and data analysis, especially information retrieval, HCI, text and context data (HIIT-Wide Focus Area) Probabilistic modeling and data analysis for bioinformatics (HIIT-Wide Focus Area) -- Samuel Kaski, Professor, Director Helsinki Institute for Information Technology HIIT Aalto University and University of Helsinki P.O. Box 15400, FI-00076 Aalto, Finland; http://www.hiit.fi/samuel.kaski Tel: +358 50 3058694, Fax: +358 9 47023277 From erik.kristiansson at chalmers.se Tue Sep 3 22:20:35 2013 From: erik.kristiansson at chalmers.se (Erik Kristiansson) Date: Tue, 3 Sep 2013 22:20:35 +0200 Subject: [SocBiN] =?iso-8859-1?q?Post-doc_position_in_bioinformatics_at_Ch?= =?iso-8859-1?q?almers_University_of_Technology=2C_G=F6teborg=2C_Sweden?= Message-ID: <52264493.30404@chalmers.se> Everyone, Another post-doc position in bioinformatics at Chalmers University of Technology, G?teborg, Sweden. Full details are available at http://www.chalmers.se/en/about-chalmers/vacancies/Pages/default.aspx?rmpage=job&rmjob=1318 Cheers, Erik -- -------------------------------------------------------------------------------- Erik Kristiansson, Assistant Professor Department of Mathematical Statistics Chalmers University of Technology, Sweden Email: erik.kristiansson at chalmers.se, Phone: +46 (0)31 772 3521 -------------------------------------------------------------------------------- From erik.kristiansson at chalmers.se Wed Sep 4 09:16:44 2013 From: erik.kristiansson at chalmers.se (Erik Kristiansson) Date: Wed, 4 Sep 2013 09:16:44 +0200 Subject: [SocBiN] =?iso-8859-1?q?Post-doc_position_in_bioinformatics_at_Ch?= =?iso-8859-1?q?almers_University_of_Technology=2C_G=F6teborg=2C_Sweden?= In-Reply-To: <52264493.30404@chalmers.se> References: <52264493.30404@chalmers.se> Message-ID: <5226DE5C.5020602@chalmers.se> And here is a working link: http://www.chalmers.se/en/about-chalmers/vacancies/Pages/default.aspx?rmpage=job&rmjob=1483 Cheers, Erik On 2013-09-03 22:20, Erik Kristiansson wrote: > Everyone, > > Another post-doc position in bioinformatics at Chalmers University of > Technology, G?teborg, Sweden. > > Full details are available at > http://www.chalmers.se/en/about-chalmers/vacancies/Pages/default.aspx?rmpage=job&rmjob=1318 > > > Cheers, > Erik > -- -------------------------------------------------------------------------------- Erik Kristiansson, Assistant Professor Department of Mathematical Statistics Chalmers University of Technology, Sweden Email: erik.kristiansson at chalmers.se, Phone: +46 (0)31 772 3521 -------------------------------------------------------------------------------- From coordinator at rth.dk Fri Sep 6 10:20:23 2013 From: coordinator at rth.dk (Betina Wingreen Jensen) Date: Fri, 6 Sep 2013 10:20:23 +0200 Subject: [SocBiN] Available PhD Fellowship in Computational RNA Biology Message-ID: <001001ceaad9$ef215f90$cd641eb0$@rth.dk> Dear Colleague, Center for non-coding RNA in Technology and Health in Copenhagen is inviting applications for a PhD position in Computational RNA Biology. We are looking for a person who will be able to join our group 1st October or soon thereafter. The position is for three years. Application deadline is 20th September 2013. For more information about the center, please http://rth.dk To see the full posting and online application procedure visit: www.offentlige-stillinger.dk/sites/cfml/kbhuni/kbhuniVis.cfm?plugin=1 &englishJobs=NO&nJobNo=215170&nLangNo=1 Please pass this email on to qualified students or people you think could otherwise be interested. Background Noncoding RNAs (ncRNAs) have shown to be a highly abundant class of genes which play numerous important roles in the cell. NcRNAs often contain RNA structure which plays a role in function, however, many RNAs do also function through their interactions to other ncRNAs. Job description The current project involves developing time and memory efficient algorithms to search for RNA molecules (of which some are genes) interacting with each other. Doing this on a scale involving a full genome is non-trivial due to the complexity of computational algorithms for RNA-RNA interactions. However, by employing efficient filtering strategies and simplified models this becomes feasible. A further goal in the project is also to develop efficient design of interfering RNAs, which subsequently can be used in the design of knockdown experiments. Qualification requirements The applicant should hold professional as well as personal skills and qualifications as stated below: ? A master degree in computational biology, computer science, bioinformatics, or similar. ? Strong experience with algorithm development. ? Strong experience with Perl or Python (or similar). ? Strong experience with C or C++. ? Possess good interpersonal skills. ? Be excellent in English, writing and speech. The following are not formal requirements, but emphasis will be given to candidates fulfilling these criteria: ? Formal training in suffix arrays. ? General knowledge about RNA structure and folding, RNA gene search algorithms, and algorithms for structural alignment of RNAs and RNA-RNA interactions. ? Insight in statistics. ? Cover Letter applying for and detailing your motivation and background for applying (max. one page). ? CV incl. education, research experience, programming skills and other skills relevant for the position. ? Diploma and transcripts of records (BSc. and MSc.). If the MSc. degree is from a foreign university, it must be documented that it is on a level equivalent with a Danish MSc. ? Other information for consideration, e.g. list of publications (if any). ? Personal Recommendations. ? A maximum of 3 relevant scientific works (e.g. peer reviewed papers) which the applicant wishes to be included in the assessment. ? If the applicant has another nationality than Danish and doesn?t have English/ American as native language, a TOEFL (+TSE) (minimum score 560 pts. (paper based) or 83 pts. (internet based)) or IELTS (minimum score 6.0 pts.) official certificate is mandatory. With best wishes, Betina -- Betina Wingreen Jensen Scientific and Administrative Coordinator Center for non-coding RNA in Technology and Health Department of Veterinary Clinical and Medical Sciences Faculty of Health and Medical Sciences University of Copenhagen Groennegaardsvej 3 1870 Frederiksberg Denmark Phone: +45 353 34704 -------------- next part -------------- An HTML attachment was scrubbed... URL: From hhu at bio.ku.dk Mon Sep 9 15:08:29 2013 From: hhu at bio.ku.dk (Henriette Husum Bak-Jensen) Date: Mon, 9 Sep 2013 15:08:29 +0200 Subject: [SocBiN] Vacancy: Bio-Computing facility manager Message-ID: <64F55C0283E3A6469EA63E5B3F796A1B63F602@mailserver11.akizci.ku.dk> The Dept. of Biology at University of Copenhagen is looking for a person who can establish and develop the IT-infrastructure, system administration (Linux) and support / perform bioinformatics analysis and other types of bio-computing, in a brand new Bio-Computing Facility. Please send this advert to people who you think would be interested in this position. Link to job advertisement https://ssl1.peoplexs.com/Peoplexs22/CandidatesPortalNoLogin/Vacancy.cfm ?PortalID=3417&VacatureID=599215&Vacancy=Facility%20manager%20for%20New% 20Bio-Computing%20facility#top Sincerely, Henriette Husum Bak-Jensen, Ph.D. Research Manager Section for Computational and RNA Biology (SCARB) Dept. of Biology, University of Copenhagen Ole Maaloes Vej 5, DK-2200 Copenhagen Ph: +45 35321386 Email: hhu at bio.ku.dk www.bio.ku.dk /binf -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.gif Type: image/gif Size: 2501 bytes Desc: image001.gif URL: From prash at bioclues.org Thu Sep 19 13:00:56 2013 From: prash at bioclues.org (Prash) Date: Thu, 19 Sep 2013 13:00:56 +0200 Subject: [SocBiN] Yes, you heard it right! There isn't publication charge for IJCB accepted articles anymore! Message-ID: Forwarded message: Courtesy: Bioinformatics.org In collaboration with Bioinformatics.org, Bioclues has launched a new journal. International Journal for Computational Biology (IJCB)aims at the sharing of novel research ideas that reveal various characteristics of biological systems through computational approaches. The journal accepts articles on all aspects of computational biology from all over the world* with no publication charge and no production charge*. In order to ensure the dispersion of knowledge and ideas without hindrances, the journal assures free access to all its publications and will be available to use for non-commercial purposes. The manuscripts submitted to IJCB should not have already been published in any journal or other citable form. Before the submission of manuscript the corresponding author must ensure that all authors have read and agreed to its content. Submission to IJCB implies that all the reproducible materials described in the paper, including raw data, additional results and the supplementary data will be freely available to everyone to use them for non-commercial purposes, if they wish. For promoting development and use of open source software, manuscripts in which software is the core of the result, authors should ensure that methods are described in sufficient detail for reproducibility. The journal is also committed to ensure that research work published in the journal is free from bias that might arise during review process The journal attempts to publish the research articles that consist of computational methods that are original and offer insights into important biological processes thereby expected to significantly contribute to the field of computational biology. Journal considers research articles describing improved or routine computational methods, models, software and databases for publication depending upon its scope and usefulness to the scientific community. *SUBMIT YOUR MANUSCRIPT TODAY * ** or click this link: http://bioinformatics.org/journals/ijcb/index Thank you and looking forward Managing Editors: Jeff W. Bizzaro, M.Sc. (PhD) Tiratha Raj Singh, PhD. Prasad Siddavatam, PhD. Pritish Varadwaj, PhD. Huy Vuong, PhD. Editor-in-Chief: Achuthsankar S. Nair, PhD. International Journal for Computational Biology (IJCB) URL: http://www.bioinformatics.org/journals/ijcb or http://www.ijcb.bioclues.org International Journal for Computational Biology A peer reviewed open access journal (ISSN 2278 ? 8115:Online): -------------- next part -------------- An HTML attachment was scrubbed... URL: From coordinator at rth.dk Tue Sep 24 14:23:30 2013 From: coordinator at rth.dk (Betina Wingreen Jensen) Date: Tue, 24 Sep 2013 14:23:30 +0200 Subject: [SocBiN] Extended deadline for PhD Fellowship in Computational RNA Biology Message-ID: <009001ceb920$e107f450$a317dcf0$@rth.dk> Dear Friends and Colleagues, We have extended the application deadline until 8th October 2013 for our PhD Fellowship in Computational RNA Biology. Please pass this email on to qualified students and people who can distribute it further, and for a full posting see the attached pdf or go to: http://www.offentlige-stillinger.dk/sites/cfml/kbhuni/kbhuniVis.cfm?plugin=1 &englishJobs=NO&nJobNo=215170&nLangNo=1 Best wishes, Betina -- Betina Wingreen Jensen Scientific and Administrative Coordinator Center for non-coding RNA in Technology and Health Department of Veterinary Clinical and Medical Sciences Faculty of Health and Medical Sciences University of Copenhagen Groennegaardsvej 3 1870 Frederiksberg Denmark Phone: +45 353 34704 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: PhDinCompRNABiol.pdf Type: application/pdf Size: 56677 bytes Desc: not available URL: From prash at bioinformatics.org Wed Sep 25 12:22:50 2013 From: prash at bioinformatics.org (Prash) Date: Wed, 25 Sep 2013 12:22:50 +0200 Subject: [SocBiN] (Submit your LATE BREAKING abstract TODAY) BSB'13: Speakers Announced: Dr. Bruno Gaeta and ... Message-ID: Conference URL: http://www.bioinformatics.org/wiki/Bioinformatics_to_Systems_Biology_2013#Speakers_and_Program ** *Important Dates First announcement and CfP: July, 2013. Announced Conference dates: October 11-12, 2013. Registration starts: September 1, 2013. Submission deadline: September 30, 2013. Deadline for applications for virtual hubs: September 30, 2013. Preliminary Program: Announced on September 25, 2013. About the conference The first virtual conference on "Bioinformatics to Systems Biology" took place on November 16, 2007, online at the Bioinformatics Organization. The previous conferences BSB'12 ,BSB'11 ,BSB'10, BSB'08and BSB'07were received very well. The most recent conferences BIFX13 ,BIFX12, Bifx'11 Afbix '09 , BSB'08 ~Bioinformatics to Systems Biology 2008ignited a spark in the audience across the world through four keynote talks as well as other virtual presentations and posters. The conference brought together over 140 attendees both directly and indirectly across the globe. The BSB series including this year's Bioinformatics to Systems Biology 2012 (BSB ?12), is aimed at students and those in the research community who fall under broader disciplines of bioinformatics and systems biology. The BSB ?12 conference will include invited keynote talks within sub-disciplines of these two exciting fields. Ample time will be set aside for discussion during the presentation of participants. In the coming days, we will be adding a lot of information to this website that will provide you with detailed information on BSB ?12.This conference is organized jointly with Bioclues.org About Bioinformatics.Org Bioinformatics Organization(Bioinformatics.Org) has over 35,000 members and currently hosts over 400 projects that are related to Bioinformatics and Computational Biology. The Organization also offers online interactive tutorials on several relevant topics. The tradition of virtual conferences at Bioinformatics.Org dates back to Bioinformatics to Systems Biology 2007(BSB'07). * *Prashanth Suravajhala, PhD.* *http://dk.linkedin.com/in/prashbio/* "Effectively, change is almost impossible without industry-wide collaboration, cooperation and consensus." ~ Simon Mainwaring -------------- next part -------------- An HTML attachment was scrubbed... URL: From paolo.dm.romano at gmail.com Fri Sep 27 10:33:10 2013 From: paolo.dm.romano at gmail.com (Paolo Romano) Date: Fri, 27 Sep 2013 10:33:10 +0200 Subject: [SocBiN] NETTAB 2013 Scientific Programme available on-line Message-ID: <524542C6.50202@gmail.com> NETTAB 2013 Semantic, Social, Mobile applications for bioinformatics and biomedical laboratories October 16-18, 2013, Lido of Venice, Italy http://www.nettab.org/2013/ Last Call for Participation Dear all, the Scientific Programme of the NETTAB 2013 Workshop is available on-line at: http://www.nettab.org/2013/progr.php A PDF copy is also available for downloading from: http://www.nettab.org/2013/docs/ScientificProgramme.pdf Please note: - 10 high quality works selected for oral presentation - 2 industrial technological talks - 2 Best Poster Awards assigned through a poll among all participants - parallel open group discussions on topics selected by participants - the joint event BioInfoVen (Meeting on Bioinformatics in the Veneto Region) Keynote talks: - Facilitating Scientific Discovery through Crowdsourcing and Distributed Participation, Antony Williams, RSC - Semantic technologies for the automation of research in biomedicine, Ross King, University of Manchester - SCIMOBS; the million minds approach revisited in mobile context, Barend Mons, LUMC & NBIC, NL Titles of selected oral presentations: + Mobile applications driven by Open PHACTS semantic web technology + TagCurate: Crowdsourcing the verification of biomedical annotations to mobile users + Genome interpretation and annotation + The OntoGene literature mining web service + Sprints, Hackathons and Codefests as community gluons in computational biology + Taverna Mobile: Taverna workflows on Android + Bio-GraphIIn: a graph-based, integrative and semantically-enabled repository for life science experimental data + An ontology based query engine for querying biological sequences + The representation of biomedical protocols + The role of parallelism, web services, and ontologies in bioinformatics and omics data management and analysis Industrial technological talks: + New publishing opportunities for digital life science + Extracting more value from data silos: Using the semantic web to link chemistry and biology for innovation Tutorials: - Semantic Web for Life Sciences: vision, aims, tools, platforms, Andrea Splendiani, IntelLeaf, UK, & DERI, IE - Open PHACTS and NanoPublications, Christine Chichester, Swiss Institute of Bioinformatics, CH - Standards for Web Applications on Mobile: current state and roadmap, Dominique Haza?l-Massieux, W3C/ERCIM, FR - Mobile applications for life sciences: perspectives, limitations, and real examples, Alex Clark, MMI, Inc, CDN Registration is now open. Register on-line and take profit from on-line registration fees. Check the registration form to see if you are entitled to the reduction for supporting Societies (e.g., ISCB, EMBnet, and many other). I'm looking forward to meeting you soon. Best regards. Paolo Romano -- Paolo Romano Bioinformatics Group Biopolimers and Proteomcis Service IRCCS AOU San Martino IST Genova, Italy -- Paolo Romano Bioinformatics Lab, Biopolimers and Proteomics Service IRCCS AOU San Martino IST, Genova, Italy Email: paolo.dm.romano at gmail.com