From andrew.dowsey at manchester.ac.uk Wed Jul 2 20:15:17 2014 From: andrew.dowsey at manchester.ac.uk (Andrew Dowsey) Date: Wed, 2 Jul 2014 18:15:17 +0000 Subject: [SocBiN] Call for Abstracts - The 1st Unified Workshop on Proteome and Metabolome Informatics @ ECCB 2014 Message-ID: Abstract submission deadline: Monday July 14th Dear colleagues, We invite you to submit an abstract for oral or poster presentation at The 1st Unified Workshop on Proteome and Metabolome Informatics, to be held at ECCB 2014, Strasbourg, France on Saturday 6th September. This workshop will be of interest to all researchers in proteomics or metabolomics, whether at the wet-lab or informatics level. It will also be of relevance to systems modellers and network biologists who integrate proteomics and metabolomics data and who wish to gain a greater understanding of how upstream processing of this data is performed. The core aim for this workshop is for there to be an equal proportion of talks on proteome and metabolome informatics. In particular, we will prefer talks that already describe some synergy between the two fields. Speakers are advised to ensure metabolomics concepts are accessible to a proteomics audience, and vice versa. The agenda with invited speakers and further details is available from http://www.cadetbioinformatics.org/workshops/eccb14/ Here you can also find the abstract submission form and details for registering. The abstract submission deadline is Monday July 14th. Hope to see you in Strasbourg! The Organsing Committee, Andrew Dowsey Simon Rogers Rainer Breitling Richard Unwin Andrew Dowsey PhD Lecturer and CADET Bioinformatics Research Lead Institute of Human Development, The University of Manchester t: +44 161 701 0244 f: +44 161 701 0242 http://www.manchester.ac.uk/research/andrew.dowsey Centre for Advanced Discovery and Experimental Therapeutics (CADET) Central Manchester University Hospitals NHS Foundation Trust Oxford Road Manchester M13 9WL UK -------------- next part -------------- An HTML attachment was scrubbed... URL: From Carsten.Daub at ki.se Thu Jul 3 09:26:15 2014 From: Carsten.Daub at ki.se (Carsten Daub) Date: Thu, 3 Jul 2014 07:26:15 +0000 Subject: [SocBiN] Fwd: Postdoc opportunity in Tokyo References: Message-ID: <43700E52-3395-42B0-8CF4-584B5BA00FBD@ki.se> Dear colleague, I would be extremely grateful if you could forward this to anyone who might be interested. Have a nice day, Martin Martin Frith (http://www.cbrc.jp/~martin/, http://scholar.google.com/citations?user=b1hM6FsAAAAJ) is looking for a postdoctoral researcher to work with him in Tokyo for 2-3 years. The project is negotiable, but presumably some aspect of computational genomics. Strong skills in computational biology are necessary. Start date: any time between now and early 2015. Any queries feel free to contact martin at cbrc.jp. -------------- next part -------------- An HTML attachment was scrubbed... URL: From prash at bioclues.org Tue Jul 8 15:00:29 2014 From: prash at bioclues.org (Prash) Date: Tue, 8 Jul 2014 15:00:29 +0200 Subject: [SocBiN] (Call for) Late breaking submissions:Annotation and Curation of Uncharacterized Proteins: Systems Biology Approaches Message-ID: Annotation and Curation of Uncharacterized Proteins: Systems Biology Approaches Topic Editors: Prashanth Suravajhala , Bioinformatics.org and Bioclues.org Alfredo Benso , Politecnico di Torino, Italy Jayaraman Valadi , Shiv Nadar University , India Deadline for abstract submission: 12 Mar 2014 Deadline for full article submission: 15 Jul 2014 Submit Abstract Submit Manuscript - About - | - Info for Authors - | - Articles 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. More here: http://www.frontiersin.org/bioinformatics_and_computational_biology/researchtopics/annotation_and_curation_of_unc/2557 *Prashanth Suravajhala, PhD.* Linkedin: http://dk.linkedin.com/in/prashbio ?Be who you are and say what you feel, because those who mind don?t matter and those who matter don?t mind.? -Theodor Seuss Geisel [image: Join Rotary Community Corps] -------------- next part -------------- An HTML attachment was scrubbed... URL: From Erik.Bongcam at slu.se Tue Jul 8 15:18:53 2014 From: Erik.Bongcam at slu.se (Erik Bongcam-Rudloff) Date: Tue, 8 Jul 2014 13:18:53 +0000 Subject: [SocBiN] ALLBIO: five-day course "Metagenomic Methods for Microbial Ecologists" Message-ID: <47224A9F-5FB6-458A-B072-CF836FBB6D73@slu.se> Dear colleague, Metagenomics has quickly become one of the most important discovery tools in microbial ecology. Metagenomics is a powerful tool to study the organisms in microbial communities, that has numerous applications in many areas of biomedical science. By bypassing the need for laboratory culturing, this technology can unlock the massive uncultured microbial diversity, enabling the microbial component of specific environments to be surveyed, discover new organisms, and explore the dynamic ecology of microbial populations under changing conditions. The high throughput nature of metagenomics means that huge datasets are generated, and in order to extract biological information from these data, advanced bioinformatics and statistical tools are indispensable. >From 15-19 September 2014 we organize a five-day course at NIOO-KNAW in Wageningen. Participants will get hands on experience in the analysis and treatment of metagenomic data, including preprocessing and quality filtering, data handling and submission to public archives, annotation, multivariate statistical analyses, and metagenome assembly. On the last day of the course, 19 September 2014, we are organizing an Environmental Metagenomics Symposium which will bring together renowned scientists in microbial ecology and bioinformatics, who will present their recent explorations of the microbiota of different environments. Moreover, we will welcome the presentations of several students of the metagenomics course held in the week leading up to this symposium. Together, this will be an exciting opportunity to see the latest advances in environmental metagenomics from young talents as well as established leaders in the field. The symposium is open for everyone interested in environmental metagenomics. Attending the symposium is free of charge, but registration by email is required. All information about the programmes of course and symposium and about registration can be found in the attached pdf. Our website will be available soon: https://nioo.knaw.nl/en/metagenomics-course. The organization of course and symposium has been made possible with the generous support of AllBio. If you are interested in participating in either the course or the symposium, please mark your calendar! You can also indicate your interest in participating by sending an email to Barbara van Kampen (Barbara.vanKampen at radboudumc.nl). You will then be notified when registration is open. Best regards, Bas Dutilh (Utrecht University & Radboudumc) Eiko Kuramae (NIOO-KNAW) Celia van Gelder (Radboudumc) -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Environmental Metagenomics Course and Symposium.pdf Type: application/pdf Size: 254584 bytes Desc: Environmental Metagenomics Course and Symposium.pdf URL: From Erik.Bongcam at slu.se Fri Jul 11 13:26:06 2014 From: Erik.Bongcam at slu.se (Erik Bongcam-Rudloff) Date: Fri, 11 Jul 2014 11:26:06 +0000 Subject: [SocBiN] =?windows-1252?q?The_Dual_Benefit_of_Bioinformatics_Trai?= =?windows-1252?q?ning_=96_Empowering_Life_Scientists_and_freeing_more_tim?= =?windows-1252?q?e_for_your_research?= Message-ID: Dear colleagues, Besides our work in research, many of us are also involved (in greater or lesser extent) in helping out / training / collaborating with our colleague researchers in the life sciences. We are organising a one-day workshop on on 7 September 2014, as a satellite event of ECCB'14 in Strasbourg, France, entitled: The Dual Benefit of Bioinformatics Training ? Empowering Life Scientists and freeing more time for your research The workshop will be a forum to hear from the bioinformaticians themselves about their experiences and perspectives in ?helping? life scientists in their bioinformatics tasks, being asked to collaborate or do the actual analysis for projects. How do they cope with this challenge (both time-wise and content-wise)? Are there best approaches, methodologies and even further existing materials and efforts that we can use, share and expand to tackle several of these topics and challenges, some of which are probably shared across many Institutes and groups worldwide? We invite you to share your experiences with us and encourage you to send in an abstract for a talk. We will be receiving abstracts for talk contributions until August 1. You will find all the information about this workshop at: http://www.eccb14.org/program/workshops/dbbt. We are looking forward to meet several of you at the workshop and/or at ECCB! Best regards Celia van Gelder (NL) Also on behalf of: Patricia Palagi (CH) Vicky Schneider (UK) Michelle Brazas (CA) -------------- next part -------------- An HTML attachment was scrubbed... URL: From arne at bioinfo.se Tue Jul 15 17:33:43 2014 From: arne at bioinfo.se (Arne Elofsson) Date: Tue, 15 Jul 2014 17:33:43 +0200 Subject: [SocBiN] 8 Assistant proferssorships in Stockholm/Uppsala Message-ID: Discover the Future - 8 Leading Positions at SciLifeLab Share with others: ------------------------------ To further strengthen its unique research environment SciLifeLab is looking to recruit eight outstanding young group leaders. SciLifeLab is a Swedish national center for molecular biosciences with focus on health and environmental research. The center combines frontline technical expertise with advanced knowledge of translational medicine and molecular bioscience. SciLifeLab is a joint effort between Karolinska Institutet, KTH Royal Institute of Technology, Stockholm University and Uppsala University. SciLifeLab was established in 2010 and appointed a national center in 2013. Today, approximately 1,500 people work at the center's two sites in Stockholm and Uppsala. Karolinska Institutet - Two positions as Assistant Professor in Biomedical Sciences KTH Royal Institute of Technology - Assistant Professor in Systems Biology - Assistant Professor in Computational Biophysics Stockholm University - Assistant Professor in Structural Biochemistry - Single particle cryo-electron microscopy - Assistant Professor in Molecular Bioscience - Gene-environment interactions Uppsala University - Assistant Professor in Molecular Medicine - Assistant Professor in Biodiversity Informatics 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 magali.michaut at iscb.org Sat Jul 26 11:55:54 2014 From: magali.michaut at iscb.org (Magali Michaut) Date: Sat, 26 Jul 2014 11:55:54 +0200 Subject: [SocBiN] Junior PI meeting @ECCB: still time to register! Message-ID: ** Registration deadline: August 1 ** Date of the meeting: 7 September 2014 http://www.eccb14.org/program/satellite-meetings/jpi Transitioning from Post-doc to (junior) PI is a major step in the scientific career ladder bringing new challenges to the scientist. Key among these challenges is moving from a single project-based responsibility to being responsible for the projects of students, technicians, and postdocs. On top of this, the researcher is expected to be a successful grant writer, a human resources manager, an engaging speaker, etc. In this meeting we aim to bring together scientists who have recently started or wish to start their own research group. This meeting will serve as a platform for building a community of junior PIs within the broader field of Computational Biology. The meeting will consist of (scientific!) speed-dating, short presentations and round-table discussions. Speakers: Sampsa Hautaniemi, University of Helsinki Lennart Martens, Ghent University, VIB Oliver Kohlbacher, University of T?bingen Sebastian Schultheiss, Computomics Alice C. McHardy, University Duesseldorf (ECCB keynote) Organizers: Virginie Bernard, Curie Institute, Paris, France Magali Michaut, Netherlands Cancer Institute, Amsterdam, the Netherlands Lennart Martens, Ghent University and VIB, Belgium Theodore Alexandrov, University of Bremen, Germany; University of California San Diego, USA Sponsor: F1000 Research We hope to see you in France in September! COSI JPI: http://cosi.iscb.org/wiki/JPI:Home contact: jpicontact at iscb.org ISCB COSIs: http://www.iscb.org/iscb-cosis -------------- next part -------------- An HTML attachment was scrubbed... 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