From marcela.davila at gu.se Tue Aug 5 09:12:15 2014 From: marcela.davila at gu.se (Marcela Davila) Date: Tue, 05 Aug 2014 09:12:15 +0200 Subject: [SocBiN] Swedish Bioinformatics Workshop 2014 In-Reply-To: <364E34EE94F5A44997F852280E71AC4601B7FB4FD0@GU-MBX06.ad.gumail.local> References: <364E34EE94F5A44997F852280E71AC4601B7FB4FD0@GU-MBX06.ad.gumail.local> Message-ID: <53E083CF.8070404@gu.se> Hi everyone, This year the SBW will be held in Gothenburg, don't miss the opportunity to interact with young researchers in the different areas of bioinformatics from all over the country. PS. Please forward this announcement email to interested colleagues, relevant mailing lists, etc. Attached you will also find a PDF flyer that you can print and put up on poster boards at your institution. Best, Marcela -- /Bioinformatics Core Facility The Sahlgrenska Academy at University of Gothenburg Box 413, 405 30 G?teborg Visiting address: Medicinaregatan 3B, Floor 1000 www.bioinformatics.cf.gu.se -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: SBW2014.pdf Type: application/pdf Size: 108124 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: sbw2014_flyer.pdf Type: application/pdf Size: 4123613 bytes Desc: not available URL: From Inge.Jonassen at ii.uib.no Mon Aug 11 09:49:53 2014 From: Inge.Jonassen at ii.uib.no (Inge Jonassen) Date: Mon, 11 Aug 2014 09:49:53 +0200 Subject: [SocBiN] Computational Biology PhD student positions in Bergen Message-ID: We have three open positions announced, see http://www.jobbnorge.no/en/available-jobs/job/103943/research-fellow-phd-candidate-in-computational-biology http://www.jobbnorge.no/en/available-jobs/job/104258/research-fellow-phd-candidate-in-computational-biology http://www.jobbnorge.no/en/available-jobs/job/103947/research-fellow-phd-candidate-in-computational-biology for more information. Please pass on to interested colleagues etc. Applications must be submitted through the jobbnorge web site in order to be considered. Deadline: August 15th Inge -- Inge Jonassen, Prof PhD Computational Biology Unit Department of Informatics University of Bergen HiB N5020 Bergen Norway inge at ii.uib.no -------------- next part -------------- An HTML attachment was scrubbed... URL: From roland.nilsson at ki.se Tue Aug 12 12:36:43 2014 From: roland.nilsson at ki.se (Roland Nilsson) Date: Tue, 12 Aug 2014 10:36:43 +0000 Subject: [SocBiN] Postdoc position at Karolinska Institutet Message-ID: <33690959AD0CD344837C8E67C93F40C27670C613@KIMSX01.user.ki.se> Dear all, we have an open position for a postdoctoral fellow in our group at Karolinska, involving integrative data analysis to study metabolic enzymes in cancer --- see attachment. Please forward to interested colleagues or relevant mailing lists! Many thanks in advance. Best regards, --------------------------------------------------------- Roland Nilsson, Ph.D roland.nilsson at ki.se Center for Molecular Medicine +46 722 334580 Karolinska Institutet Stockholm, Sweden www.nilssonlab.se -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: recruitment-ad.pdf Type: application/pdf Size: 78266 bytes Desc: recruitment-ad.pdf URL: From Erik.Bongcam at slu.se Wed Aug 13 14:34:28 2014 From: Erik.Bongcam at slu.se (Erik Bongcam-Rudloff) Date: Wed, 13 Aug 2014 12:34:28 +0000 Subject: [SocBiN] ALLBIO: ChIP- and DNase-seq data analysis workshop Message-ID: <5E8973A2-E0B7-48CB-B3FD-66B10EA47B72@slu.se> Dear all, Please note that registration for the international ChIP- and DNase-seq data analysis workshop is now open at http://www.csc.fi/english/csc/courses/archive/chipseq2014. The workshop covers several topics ranging from alignment and peak calling to motif detection and annotation. The program consists of a lecture day (18th of September), and several hands-on days that participants can choose from. This workshop is part of the FP7 AllBio project (http://www.allbioinformatics.eu), which kindly provides 15 travel bursaries of 500 euros for early stage researchers. The registration deadline is 21.8.2014. 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 Erik.Bongcam at slu.se Thu Aug 14 15:01:00 2014 From: Erik.Bongcam at slu.se (Erik Bongcam-Rudloff) Date: Thu, 14 Aug 2014 13:01:00 +0000 Subject: [SocBiN] New ALLBIO Workshop: Analysis of Cis-Regulatory Motifs from High-Throughput sequences Message-ID: ================================================================ -- ECCB 2014 Tutorial -- Analysis of Cis-Regulatory Motifs from High-Throughput sequences ================================================================ There are still some places available for this tutorial: ECCB Tutorial T01 Analysis of Cis-Regulatory Motifs from High-Throughput Sequence Sets Date: Saturday Sept 6, 2014 Place: Forum building of the Faculty of Medicine of Strasbourg Time: 9am ? 5.30pm (registration starts from 8am) Contact e-mail: mthomas at biologie.ens.fr More details: http://www.eccb14.org/program/tutorials/cis-r How to register: http://www.eccb14.org/registration Registration includes lunch & coffee breaks on the day of the workshop and the tutorial material (.pdf and/or print). ECCB Tutorial rates: 110 ? (academic) or 60 ? (student) ---------- Short description ---------- This tutorial aims at introducing the theoretical principles and giving practical skills to use specialized software tools to extract motifs from full-scaled NGS datasets (typically covering tens of Mb). --------- Teachers ---------- - Jacques van Helden, Aix-Marseille Universit? (France) - Morgane Thomas-Chollier, Ecole Normale Sup?rieure (France) - Carl Herrmann, University Heidelberg (Germany). - Alejandra Medina-Rivera, SickKids Research Institute, Toronto (Canada) ---------- Description ---------- Next Generation Sequencing led to the development of novel methods (ChIP-seq, FAIRE-seq, clip-seq, ) to acquire massive data about diverse signals involved in genome regulation and function (cis-regulation, chromatin conformation, RNA maturation, recombination, replication, ...). Extracting relevant information from the raw data requires not only specialized software tools, but also a good understanding of their principles and parameters. In this tutorial we will demonstrate how to analyze ChIP-seq data using the Regulatory Sequence Analysis Tools (RSAT, http://www.rsat.eu/), via their different ways of access: web-interface, command-line, and web-services. This tutorial aims at introducing the theoretical principles and giving practical skills to use specialized software tools to extract motifs from full-scaled NGS datasets (typically covering tens of Mb). ---------- Contents ---------- The tutorial will be organized in 2 half days: 1) Analysis of cis-regulatory elements with the Regulatory Sequence Analysis Tools (RSAT): methods and website utilization (http://www.rsat.eu/). 2) Using RSAT in command-line and via web services (SOAP/WSDL). Topics: - Motif discovery in NGS peak sets. - Impact of the background models. - Comparison between motifs. - Motif enrichment in peak sequences. - Evaluating the quality of motifs extracted from NGS peaks. - Building control sets to estimate the rates of false positives. ---------- Topics not covered ---------- Other steps for the analysis of ChIP-seq data (e.g. read mapping, peak calling, functional enrichment of peaks, other tools for pattern discovery and matching). ---------- Target audience ---------- The course is addressed to bioinformaticians and biologists. The afternoon will require being familiar with the Unix shell (Linux) and basic programming skills (Perl or Python) to implement clients for web services. ---------- In practice ---------- * Participants will need to bring their own laptop. * All command-line programs will be run on the IFB cloud platform (https://cloud.france-bioinformatique.fr/) managed by Christophe Blanchet (IBCP, Lyon, France). Each participant will be given a (free) account to access this cloud and thereby a fully functional virtual machine with RSAT. * Wireless internet will be available at the conference venue. * An indicative reading list will be available a few weeks before the tutorial. * The hands-on will be organized in a cookbook mode: we will distribute protocols explaining the steps to solve selected test cases. * For the practicals, we ensure that there is no need to transfer data from the conference room to the servers. ---------- Funding ---------- This tutorial is funded by the ALLBIO project (http://www.allbioinformatics.eu/), whose goal is to establish the link between bioinformatics and biologist communities who express uncovered needs for other fields than human genomics (microbial, plant, livestock). -------------- next part -------------- An HTML attachment was scrubbed... URL: From rune.linding at gmail.com Thu Aug 14 16:10:18 2014 From: rune.linding at gmail.com (Rune Linding) Date: Thu, 14 Aug 2014 16:10:18 +0200 Subject: [SocBiN] =?utf-8?q?Announcing_Keystone_Symposia=E2=80=99s_2015_Co?= =?utf-8?q?nference_on_=E2=80=9CThe_Biological_Code_of_Signaling=3A?= =?utf-8?q?_A_Tribute_to_Tony_Pawson=E2=80=9D?= Message-ID: *Announcing Keystone Symposia?s 2015 Conference on ?The Biological Code of Signaling: A Tribute to Tony Pawson?* Submit an abstract and register today for Keystone Symposia?s conference on ?*The Biological Code of Signaling: A Tribute to Tony Pawson*,? taking place January 11?16, 2015 at Sheraton Steamboat Resort in Steamboat Springs, Colorado, USA. Organized by *Tony Hunter* of The Salk Institute and *Rune Linding* of the University of Copenhagen, the four-day conference will: - Focus on the role of post-translational modifications (PTMs), modular protein domains and signaling networks as driving forces of human evolution and disease; - Explore how the dysregulation of protein interaction networks leads to new signaling states critical for disease processes in, for instance, cancer, such as tumor progression or drug resistance; - Educate the next generation of investigators who may not have had the privilege of knowing Tony Pawson and his groundbreaking work. Scholarships are available to students and postdoctoral fellows. Short talks on the program will be selected from submitted abstracts. *Deadlines:* - Scholarship Application and Discounted Abstract ? September 23, 2014 - Abstract ? October 15, 2014 - Discounted Registration ? November 12, 2014 *To register and for more information, **please visit www.keystonesymposia.org/15F1 and for a flyer, visit http://www.keystonesymposia.org/index.cfm?e=Web.Meeting.Flyer&MeetingID=1365 * -------------- next part -------------- An HTML attachment was scrubbed... URL: From marcela.davila at gu.se Mon Aug 18 13:26:47 2014 From: marcela.davila at gu.se (Marcela Davila) Date: Mon, 18 Aug 2014 13:26:47 +0200 Subject: [SocBiN] Fwd: FW: Annons, bioinformmatiker In-Reply-To: References: Message-ID: <53F1E2F7.3030405@gu.se> Info to be spread. Position in bioinformatics at VGR, Sahlgrenska hospital. Best regards, Frida -------------------------------- Frida Abel, Docent Gothenburg University Sahlgrenska Academy Dept. Clinical Genetics/Genomics Core facility Box 413 405 30 G?teborg Visiting address: Medicinaregatan 5A Phone: +46 (0)31 786 3478 Cell phone: +46 (0) 709-126134 Email: frida.abel at gu.se Web address: www.cf.gu.se/Genomics -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Annons, bioinformatiker.pdf Type: application/pdf Size: 702731 bytes Desc: not available URL: From prash at bioclues.org Mon Aug 18 13:34:46 2014 From: prash at bioclues.org (Prash) Date: Mon, 18 Aug 2014 13:34:46 +0200 Subject: [SocBiN] Deadline Extended /Call for Submissions: Annotation and Curation of Uncharacterized Proteins Message-ID: What: Annotation and Curation of Uncharacterized Proteins: Systems Biology Approaches Deadline for abstract submission: 12 Mar 2014 Deadline for full article submission: 20 Jul 2014 Extended deadline for full article submission: More here: http://www.frontiersin.org/Bioinformatics_and_Computational_Biology/researchtopics/Annotation_and_Curation_of_Unc/2557 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 that have no functional annotations, 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 remains mis-conducive. To better understand the problem many different areas have been investigated, from methods to screen functional candidates among many hypothetical proteins using feature selection algorithms, to the application of statistical methods to test the efficacy of these proteins annotations in terms of precision and accuracy. With experimental procedures for HP function prediction being low throughput by nature, there is a strong need to precisely know their functions for a better understanding of the underlying biological mechanisms associated with them. We encourage authors interested in protein annotation research to contribute in any of the following areas: 1. 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). 2. Predictive approaches based on Gene Ontology (GO). 3. Feature selection and machine learning methods. 4. Diseasome approaches. *Prashanth Suravajhala, PhD.* Wiki: http://www.bioinformatics.org/wiki/Prash Linkedin: http://dk.linkedin.com/in/prashbio *1. Is it the truth? 2. Is it fair to all concerned? 3. Will it build goodwill and better friendships? 4. Will it be beneficial to all concerned?* *"The Rotary.Org's Four-Way Test" of the things we think, say or do."* [image: Join Rotary Community Corps] -------------- next part -------------- An HTML attachment was scrubbed... URL: From Merja.Oja at vtt.fi Mon Aug 18 15:37:37 2014 From: Merja.Oja at vtt.fi (Oja Merja) Date: Mon, 18 Aug 2014 13:37:37 +0000 Subject: [SocBiN] Position for a metabolic modeller at VTT (Espoo, Finland) Message-ID: <8DC448DDE49D7542BA4169D11F2DEBE4283AACE4@VTTMAIL3.ad.vtt.fi> Dear all, We have an open position for a metabolic modeller at VTT (Espoo, Finland) VTT is seeking a candidate with a PhD or MSc degree and competence in several of the following: metabolic modelling, analysis of systems biology data, microbial bioprocess engineering, biochemistry, and/or industrial biotechnology. The task will be metabolic modelling of eukaryotic micro-organisms in bioprocess conditions. In addition, the position includes processing of systems biology, genomics and metabolomics data with bioinformatics methods, and creation of mathematical models from systems-wide data. The candidate is expected to develop VTT's competence in computational biology connected to microbial production processes. MSc applicants are expected to extend their studies towards a PhD while working at VTT. VTT has its own graduate study program. The job announcement and the electronic application form can be found from: https://irec2prodext.vtt.fi/vacancies/5064. DL for applications August 31st, 2014. Best regards, Merja Oja -- VTT Technical Research Centre of Finland Synthetic Biology Team E-mail merja.oja at vtt.fi Phone +385-(0)20-722 5022 Fax +358-(0)20-722 7071 Address (Tietotie 2) PL 1000 02044 VTT, Finland Web www.vtt.fi -------------- next part -------------- An HTML attachment was scrubbed... URL: From marcela.davila at gu.se Tue Aug 19 13:18:19 2014 From: marcela.davila at gu.se (Marcela Davila) Date: Tue, 19 Aug 2014 13:18:19 +0200 Subject: [SocBiN] Fwd: Fwd: FW: Annons, bioinformmatiker In-Reply-To: <53F1E2F7.3030405@gu.se> References: <53F1E2F7.3030405@gu.se> Message-ID: <53F3327B.2070608@gu.se> Info to be spread. Position in bioinformatics at VGR, Sahlgrenska hospital. Best regards, Frida -------------------------------- Frida Abel, Docent Gothenburg University Sahlgrenska Academy Dept. Clinical Genetics/Genomics Core facility Box 413 405 30 G?teborg Visiting address: Medicinaregatan 5A Phone: +46 (0)31 786 3478 Cell phone: +46 (0) 709-126134 Email:frida.abel at gu.se Web address:www.cf.gu.se/Genomics -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Annons, bioinformatiker.pdf Type: application/pdf Size: 702731 bytes Desc: not available URL: From albin at binf.ku.dk Fri Aug 22 08:15:26 2014 From: albin at binf.ku.dk (Albin Sandelin) Date: Fri, 22 Aug 2014 09:15:26 +0300 Subject: [SocBiN] PhD position in plant enhancer bioinformatics/transcriptomics Message-ID: Dear all We have a fully paid PhD position in Copenhagen - please share! Full application link: http://jobportal.ku.dk/phd/?show=675563 PhD scholarship in Plant Transcriptomics The Department of Biology, University of Copenhagen, is recruiting a PhD student for a 3-year project to work on plant transcriptomics. The starting date is November 1, 2014 or as soon as possible thereafter. The project is jointly supervised by Professor Albin Sandelin and Associate Professor Peter Brodersen at the Section for Bioinformatics and RNA Biology. The groups are housed in Copenhagen Biocenter in central Copenhagen, Denmark (http://www.biocenter.ku.dk/). Project The main focus of the project is to use high-throughput sequencing techniques and computational analyses to generate cell-type specific maps of transcription initiation sites and enhancer activity in Arabidopsis (for examples of our current work, see Andersson et al. (2014), Nature 507, 455?461 and Poulsen et al. (2013) Plant Cell 25: 22-37). The main task will be computational analysis of sequencing data, but construction of libraries for sequencing will also be part of the work. Qualifications We are seeking highly motivated individuals with a Master?s degree in bioinformatics or equivalent, with additional understanding of experimental molecular biology from courses at the bachelor or master level, and an interest in laboratory work. We strongly require documented experience in a programming script language such as Python or Perl, linux/unix systems, statistics using R and high-throughput data analysis. Experience in transcriptomics data analysis and mining is a big advantage. Fluency in spoken and written English is a strong requirement. Albin Sandelin Professor, PhD Section for Computational and RNA Biology, Department of Biology & Biotech Research and Innovation Centre, Copenhagen University Ole Maaloes Vej 5, DK2200, Copenhagen N, Denmark tel +45 224 56668 albin at binf.ku.dk skype albinsan -------------- next part -------------- An HTML attachment was scrubbed... URL: From coordinator at rth.dk Wed Aug 27 08:44:53 2014 From: coordinator at rth.dk (Betina Wingreen) Date: Wed, 27 Aug 2014 08:44:53 +0200 Subject: [SocBiN] PhD fellowship in Systems Biology Message-ID: <000d01cfc1c2$687b7010$39725030$@rth.dk> Dear Colleague, We have an open PhD position in Systems Biology and are looking for a person to join our team from January 2015. The position is for three years. The application deadline is 2015-09-21. Background: The use of model animals, such as mouse, pig and monkey is essential in the development of both treatments of human diseases as well as test of drugs. Obviously, it is important that genes and gene networks are as similar to human as possible for the specific disease in question. In spite of the many efforts, no systematic effort has been made to match which animal model is the most suitable in a given disease context. Job description: Methods to search for various degrees of conservation between human and model animals with respect to a range of features will be developed. These will include pathways, gene conservation and gene expression and in all cases include coding as well as non-coding and RNA structured genes and regulatory elements. Adding layers such as disease and tissue associations data for the individual model animals will be compared with human to search for which animal is the best match in a given disease to the corresponding data from human. Thus, the work spans broadly and also involve processing high-throughput data and implementing efficient computational methods for the comparisons. The full posting and online application procedure, can be found on http://jobportal.ku.dk/phd/?show=683497. 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 University of Copenhagen Groennegaardsvej 3 1870 Frederiksberg C Denmark Phone: +4535334704 Mob: +4521510932 -------------- next part -------------- An HTML attachment was scrubbed... URL: