April 2016 - BBClist - maillist.psb.ugent.be

REMINDER: BeMGI 2016-Brussels Meeting, Wednesday-13 April
by Marilou Ramos Pamplona 23 Sep '16

23 Sep '16

Dear BBC colleagues, We would like to remind you of the 2016 Annual Meeting of the Belgian Medical Genomics Initiative (BeMGI) entitled "From predisposing germline and somatic variants to disease-driving mechanisms.," which will feature the two keynote lectures: Genetic basis and mechanisms of Parkinson’s disease. Alexis Brice, MD Brain and Spine Institute Hôpital Pitié Salpêtrière Paris, France Search for predisposing factors in myeloid malignancies. Christine Bellanné-Chantelot, PhD Centre de Génétique Moléculaire et Chromosomique Groupe Hospitalier Pitié-Salpétrière Paris, France This meeting will take place on Wednesday (13 April 2016) from 12h00-17h30 at the Auditoire central 51E of UCLouvain Brussels campus (Avenue Mounier 51, 1200 Bruxelles, www.uclouvain.be/286287.html) The complete meeting info document with directions to the meeting venue, is available via: https://edc.ulg.ac.be/merci/BeMGI2016-Brussels_Meetin_d1f1ea81615957fe5c13_… The online meeting registration (http://bit.do/BeMGI2016register) is available until tomorrow noon (Tuesday, 12-Apr, 12h00). We kindly request all interested meeting participants to either register online by tomorrow noon or to register on site upon arrival at the meeting venue. See you soon in Brussels! Regards, The BeMGI network

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CPW2016 - Bioinformatics and computational pathology summit
by Yves Sucaet 29 Apr '16

29 Apr '16

CALL FOR ABSTRACTS: CPW2016 - Bioinformatics and computational pathology summit When? Saturday, September 3, 2016. Where? Den Hague, Netherlands (during ECCB2016) Website? http://cpw.pathomation.com Digital pathology is increasingly used to study biological processes and diseases as novel molecular probing and imaging techniques allow the measurement of single molecules in whole tissue sections. Resulting multi-gigapixel images can be viewed on a computer screen via dedicated software. However, automated analysis of such large-scale datasets is challenging and their combination with omics data is not trivial. This workshop wants to facilitate bridging opportunities between the bioinformatics and tissue image analysis communities. This first edition is organised as a full-day workshop during ECCB 2016 (http://www.eccb2016.org) KEYNOTE SPEAKERS: The following keynote speakers have already agreed to speak at the conference: Jeroen Van der Laak, UMC Radboud Jeffrey Fine, Magee-Womens Hospital of UPMC SUBMISSIONS: The conference solicits oral talks, posters, and proceeding papers contributions of original work or work that was recently accepted or published in a peer-reviewed journal or at a high level international conference. In the latter case, the publication reference should be clearly mentioned, and the abstracts should be checked mainly for relevance, rather than receive a full review. Conference proceedings will be published by the Journal of Pathology Informatics. The program committee will decide which contributions are selected for an oral presentation, and which ones are presented during a poster session. For submission instructions, please refer to https://www.fourwav.es/view/265/info/. SCOPE: Computational pathology exists at the interphase between bioinformatics, machine learning, and digital pathology (microscopy). Submissions from all topics of interest are welcome (non-exhaustive list): Machine learning and image analysis for quantification in digital pathology (in 2D & 3D), Novel approaches (e.g. spatial or graph-based methods) to extract high-level features (e.g. molecular networks or spatial expression patterns) from tissue images for systems pathology, Software development methodologies and tools to ease the exploitation of large tissue images and integration with omics data, Novel molecular imaging techniques on tissues (molecular pathology, next generation pathology) and their analysis challenges, e.g. in situ hybridization, mass spectrometry imaging of formalin-fixed paraffin-embedded tissues, mass cytometry, and other spectroscopy techniques (Raman,...)... Research applications on non-human model organisms KEY DATES: Submission deadline: May 31, 2016. Notification of acceptance: June 30, 2016. Conference: September 3, 2016. Organizing committee: Yves Sucaet, Vrije Universiteit Brussel, Belgium Jeroen Van der Laak, UMC Radboud, Netherlands Marius Nap, HistoGeneX, Belgium and Rigshospitalet Copenhagen, Denmark Zev Leifer, New York College of Podiatric Medicine, USA Yukako Yagi, Harvard Medical School & Massachusetts General Hospital, USA Raphaël Marée, Université de Liège, Belgium David Ameisen, IRIF, CNRS and Université Paris Diderot, France Paul Van Diest, UMC Utrecht, Netherlands

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Call for Applications for ECCB 2016 - deadline May 16
by Femke Francissen 29 Apr '16

29 Apr '16

*Call for Applications for ECCB 2016 - extended submission deadline: May 16* The European Conference on Computational Biology <http://www.eccb2016.org> (ECCB 2016) started a new initiative to promote application of computational biology in industry and other fields beyond academia. *What is the aim of the Applications track <http://www.eccb2016.org/calls/applications/>?* The aim of the track is to give a voice to those who apply computational biology in industry, clinics, governmental organizations, and other fields beyond academia. With advanced science and technology finding its ways everywhere, many clinicians, analysts, data scientists have more and more to share with scientists in academia. A plethora of scientists currently works outside of academia, and may not be interested or are sometimes restricted to publish, thus making themselves and their work invisible to the academic community. This track is a platform for presenting such applications, some of which may well be untraditional or otherwise not often heard at academic conferences. *Examples of submissions* Examples of submissions that we envision include computational applications, software, services, infrastructure or combinations of these that are developed for beyond-academia applications e.g. for pharmaceutical industry, biotech startups, clinics. Academic developments which do not have yet the beyond-academia component but have clearly outlined potential for it, are also welcome. *Dont't we already have applications presented at ECCB and other CB conferences? * Absolutely. Computational biology is by its nature about applying computational tools in biology. The difference of this track from many applied sessions at ECCB is bridge the academia and other applications fields of CB and to cross-disseminate both sides. This is an open track alongside the ELIXIR Applications track which is mainly devoted to the participants of ELIXIR. *I'm in academia, can I submit an abstract? * Yes, please do if you feel that A) your applications cross the boundaries of traditional academic science, or B) your developments are directly relevant beyond academia or have potential for it. *Read more about the review criteria and submission guidelines here: http://www.eccb2016.org/calls/applications/ <http://www.eccb2016.org/calls/applications/>* *Submission deadline: May 16, 2016* For questions about the Applications track, please contact: applications(a)eccb2016.org For other ECCB 2016 related questions contact: info(a)eccb2016.org ** **

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Benelux Machine Learning conference 12-13/9 in Kortrijk
by Katrijn Vannerum 29 Apr '16

29 Apr '16

CALL FOR ABSTRACTS: BENELEARN 2016 September 12-13, 2016. Kortrijk, Belgium http://www.kuleuven-kulak.be/benelearn/ Benelearn is the annual machine learning conference of Belgium and The Netherlands. It serves as a forum for researchers to exchange ideas, present recent work, and foster collaboration in the broad field of Machine Learning and its applications. The 25th edition will be co-organised by KU Leuven, UGent and the Flemish Supercomputer Centre at the Katholieke Universiteit Leuven, Campus Kortrijk (KULAK). In contrast to previous editions, the anniversary edition of Benelearn will be organised on two days, where the first day will feature a workshop on Big Data, including keynote speakers, a tutorial session, corporate presentations, and ample opportunity for networking. KEYNOTE SPEAKERS: The following keynote speakers have already agreed to speak at the conference: Jeff Ullman (Stanford University) Christian Blum (University of the Basque Country) Hugo Ceulemans (Janssen R&D) Greg Tsoumakas (Aristotle University of Thessaloniki) Emilia Barakova (Technische Universiteit Eindhoven) SUBMISSIONS: The conference solicits abstract contributions (2 pages max.) of original work or work that was recently accepted or published in a peer-reviewed machine-learning journal or at a high level international conference. In the latter case, the publication reference should be clearly mentioned, and the abstracts should be checked mainly for relevance, rather than receive a full review. The program committee will decide which contributions are selected for an oral presentation, and which ones are presented during a poster session (with spotlight presentations). Submissions related to Big Data analysis will preferably be presented on the thematic day. All accepted contributions will be published on the Benelearn website, but no copyright will be claimed. For submission instructions, please refer tohttp://www.kuleuven-kulak.be/benelearn/. SCOPE: Although we particularly encourage submissions related to learning from Big Data, submissions from all topics of interest within machine learning are welcome (non-exhaustive list): Kernel Methods Bayesian Learning Case-based Learning Causal Learning Ensemble Methods Computational Learning Theory Data Mining Evolutionary Computation Inductive Logic Programming Knowledge Discovery in Databases Online Learning Learning in Multi-Agent Systems Neural Networks Deep Learning Reinforcement Learning Robot Learning Feature Selection and Dimensionality Reduction Scientific Discovery Transfer Learning Statistical Learning Ranking / Preference Learning / Information Retrieval Computational models of Human Learning Structured Output Learning Learning for Language and Speech Media Mining and Text Analytics Learning and Ubiquitous Computing Applications of Machine Learning KEY DATES: Submission deadline: June 1, 2016. Notification of acceptance: July 1, 2016. Conference: September 12-13, 2016. Organizing committee: Celine Vens (KU Leuven) Patrick De Causmaecker (KU Leuven) Yvan Saeys (UGent) Ewald Pauwels (VSC) -- ====================================================================== Prof. dr. Yvan Saeys VIB Group Leader Data mining and modeling for biomedicine Inflammation Research Center, a VIB-UGent Department UGent Department of Internal Medicine, Respiratory Medicine (GE01) Technologiepark 927 , B-9052 Zwijnaarde , Belgium Tel : +32(0)9 331 37 40 Fax : +32(0)9 221 76 73 Mailto: yvan.saeys(a)ugent.be http://www.dambi.ugent.be ======================================================================

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Junior assistant position at Ghent University
by Tim De Meyer 28 Apr '16

28 Apr '16

Dear colleagues, we have a job opening for a junior assistant at the Dept. of Mathematical Modelling, Statistics and Bioinformatics of Ghent University (Faculty of Bioscience Engineering). The candidate should have a particular interest in omics and bioinformatics research and education and is expected to pursue a PhD. More information about the position and the application procedure can be found here: https://edit.ugent.be/nl/vacatures/aap/voltijds-assistent-17/ https://edit.ugent.be/en/work/vacancies/assisting/full-time-junior-assistant -10/ Please forward to potentially interested candidates, thanks! Best regards, Tim De Meyer Dr. Ir. Tim De Meyer, Associate Professor Bioinformatics Institute Ghent Nucleotides 2 Networks (BIGN2N) BIOBIX Lab. of Bioinformatics and Computational Genomics Dept. Mathematical Modelling, Statistics and Bioinformatics Faculty of Bioscience Engineering - Ghent University Campus Coupure, A, Coupure Links 653, B9000 Ghent, Belgium <mailto:Tim.DeMeyer@UGent.be> Tim.DeMeyer(a)UGent.be +3292645987 www.bigN2N.be www.biobix.be cid:image007.jpg@01D08CC7.326402A0

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'STATS COURSE - DNA taxonomy using R'
by Oliver Hooker 28 Apr '16

28 Apr '16

"Advances in DNA taxonomy" Instructors - Prof. Ziheng Yang and Dr. Diego Fontaneto This course will run from 8th – 11th August 2016 at SCENE Field Station, Loch Lomond national park, Scotland http://prstatistics.com/course/advances-in-dna-taxonomy-dntx/ Course content is as follows Day 1 • Introduction to DNA taxonomy • The applied ecological approach and the theoretical evolutionary approach. • What is needed to perform DNA taxonomy. • How to get data. • Phylogenetic reconstruction using distance-based and parsimony methods. • Introduction on NJ, UPGMA, parsimony; when and why they can be used for DNA taxonomy. • Computer practical. Day 2 • Phylogenetic reconstructions • Using Maximum Likelihood with computer practical on Maximum Likelihood. • Using Bayesian Inference with computer practical on Bayesian Inference. Day 3 • Single-locus DNA taxonomy. • Most commonly used methods Rationale and use for fixed threshold, ABGD, K/theta, PTP, GMYC with computer practicals. • Other methods, Haplowebs, bGMYC, etc. with computer practicals Day 4 • Multi-locus DNA taxonomy with computer practicals Please email any inquiries to oliverhooker(a)prstatistics.com or visit our website www.prstatistics.com Please feel free to distribute this material anywhere you feel is suitable Upcoming courses - email for details oliverhooker(a)prstatistics.com ADVACNING IN STATISTICAL MODELLING USING R (May) TIME SERIES MODELS FOR ECOLOGISTS AND CLIMATOLOGISTS USING R (May) INTRODUCTION TO PYTHON FOR BIOLOGISTS (May) GENETIC DATA ANALYSIS USING R (August) BIOINFORMATICS USING LINUX (August) INTRODUCTION TO BAYESIAN HIERARCHICAL MODELLING (August) PHYLOGENETIC DATA ANALYSIS USING R (October) MODEL BASED MULTIVARIATE ANALYSIS OF ECOLOGICAL DATA USING R (October) LANDSCAPE (POPULATION) GENETIC DATA ANALYSIS USING R (October) APPLIED BAYESIAN MODELLING FOR ECOLOGISTS AND EPIDEMIOLOGISTS (October) Dates still to be confirmed - email for details oliverhooker(a)prstatistics.com STABLE ISOTOPE MIXING MODELS USING SIAR, SIBER AND MIXSIAR USING R INTRODUCTION TO R AND STATISTICS FOR BIOLOGISTS Oliver Hooker PR Statistics -- Oliver Hooker PR statistics 3/1 128 Brunswick Street Glasgow G1 1TF +44 (0) 7966500340 www.prstatistics.com www.prstatistics.com/organiser/oliver-hooker/

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COURSE - Bioinformatics using LINUX
by Oliver Hooker 28 Apr '16

28 Apr '16

Course: Introduction to bioinformatics using LINUX Instructor: Dr. Martin Jones This course will run from 15th – 19th August 2016 at SCENE (the Scottish Centre for Ecology and the Natural Environment), Loch Lomond National Park, Glasgow. Course overview: Most high-throughput bioinformatics work these days takes place on the Linux command line. The programs which do the majority of the computational heavy lifting — genome assemblers, read mappers, and annotation tools — are designed to work best when used with a command-line interface. Because the command line can be an intimidating environment, many biologists learn the bare minimum needed to get their analysis tools working. This means that they miss out on the power of Linux to customize their environment and automate many parts of the bioinformatics workflow. This course will introduce the Linux command line environment from scratch and teach students how to make the most of its tools to achieve a high level of productivity when working with biological data. Availability: 15 places total. Course programme Monday 15th – Classes from 09:00 to 17:00 (approximately) ● Session 1 - The design of Linux In the first session we briefly cover the design of Linux: how is it different from Windows/OSX and how is it best used? We'll then jump straight onto the command line and learn about the layout of the Linux filesystem and how to navigate it. We'll describe Linux's file permission system (which often trips up beginners), how paths work, and how we actually run programs on the command line. We'll learn a few tricks for using the command line more efficiently, and how to deal with programs that are misbehaving. We'll finish this session by looking at the built in help system and how to read and interpret manual pages. ● Session 2 - System management We'll first look at a few command line tools for monitoring the status of the system and keeping track of what's happening to processor power, memory, and disk space. We'll go over the process of installing new software from the built in repositories (which is easy) and from source code downloads (which is trickier). We'll also introduce some tools for benchmarking software (measuring the time/memory requirements of processing large datasets). Tuesday 16th - Classes from 09:00 to 17:00 (approximately) ● Session 3 - Manipulating tabular data Many data types we want to work with in bioinformatics are stored as tabular plain text files, and here we learn all about manipulating tabular data on the command line. We'll start with simple things like extracting columns, filtering and sorting, searching for text before moving on to more complex tasks like searching for duplicated values, summarizing large files, and combining simple tools into long commands. ● Session 4 - Constructing pipelines In this session we will look at the various tools Linux has for constructing pipelines out of individual commands. Aliases, shell redirection, pipes, and shell scripting will all be introduced here. We'll also look at a couple of specific tools to help with running tools on multiple processors, and for monitoring the progress of long running tasks. Wednesday 17th - Classes from 09:00 to 17:00 (approximately) ● Session 5 – EMBOSS EMBOSS is a suite of bioinformatics command-line tools explicitly designed to work in the Linux paradigm. We'll get an overview of the different sequence data formats that we might expect to work with, and put what we learned about shell scripting to biological use by building a pipeline to compare codon usage across two collections of DNA sequences. ● Session 6 – Using a Linux server Often in bioinformatics we'll be working on a Linux server rather than our own computer— typically because we need access to more computing power, or to specialized tools and datasets. In this session we'll learn how to connect to a Linux server and how to manage sessions. We'll also consider the various ways of moving data to and from a server from your own computer, and finish with a discussion of the considerations we have to make when working on a shared computer. Thursday 18th - Classes from 09:00 to 17:00 (approximately) ● Session 7 – Combining methods In the next two sessions — i.e. one full day — we'll put everything we have learned together and implement a workflow for next-gen sequence analysis. In this first session we'll carry out quality control on some paired-end Illumina data and map these reads to a reference genome. We'll then look at various approaches to automating this pipeline, allowing us to quickly do the same for a second dataset. ● Session 8 – Combining methods The second part of the next-gen workflow is to call variants to identify SNPs between our two samples and the reference genome. We'll look at the VCF file format and figure out how to filter SNPs for read coverage and quality. By counting the number of SNPs between each sample and the reference we will try to figure out something about the biology of the two samples. We'll attempt to automate this analysis in various ways so that we could easily repeat the pipeline for additional samples. Friday 19th - Classes from 09:00 to 16:00 (approximately) ● Session 9 – Customization Part of the Linux design is that everything can be customised. This can be intimidating at first but, given that bioinformatics work is often fairly repetitive, can be used to good effect. Here we'll learn about environment variables, custom prompts, soft links, and ssh configuration — a collection of tools with modest capabilities, but which together can make life on the command line much more pleasant. In this last session there will also be time to continue working on the next-gen sequencing pipeline. The afternoon of Friday 19th is reserved for finishing off the next-gen workflow exercise, working on your own datasets, or leaving early for travel. The cost is £530 (+VAT) including lunches and course materials. An all-inclusive option is also available at £660 (+VAT); this includes breakfast, lunch, dinner, refreshments, accommodation and course materials. Participants will need a laptop with a recent version of LINUX installed. Please send inquiries to oliverhooker(a)prstatistics.com or visit the website www.prstatistics.com Please feel free to distribute this information anywhere you think suitable. Other related courses - email for details oliverhooker(a)prstatistics.com INTRODUCTION TO PYTHON FOR BIOLOGISTS (May) ADVANCES IN DNA TAXONOMY USING R (August) GENETIC DATA ANALYSIS USING R (August) PHYLOGENETIC DATA ANALYSIS USING R (October) LANDSCAPE (POPULATION) GENETIC DATA ANALYSIS USING R (October) Upcoming courses - email for details oliverhooker(a)prstatistics.com ADVANCING IN STATISTICAL MODELLING USING R (May) TIMES SERIES DATA ANALYSIS FOR ECOLOGISTS AND CLIMATOLOGISTS (May) ADVANCES IN SPATIAL ANALYSIS OF MULTIVARIATE ECOLOGICAL DATA: THEORY AND PRACTICE (July) INTRODUCTION TO BAYESIAN HIERARCHICAL MODELLING (August) MODEL BASED MULTIVARIATE ANALYSIS OF ECOLOGICAL DATA USING R (October) APPLIED BAYESIAN MODELLING FOR ECOLOGISTS AND EPIDEMIOLOGISTS (October) SPATIAL ANALYSIS OF ECOLOGIC AL DATA USING R (November) Dates still to be confirmed - email for details oliverhooker(a)prstatistics.com STABLE ISOTOPE MIXING MODELS USING SIAR, SIBER AND MIXSIAR USING R INTRODUCTION TO R AND STATISTICS FOR BIOLOGISTS BIOINFORMATICS FOR GENETICISTS AND BIOLOGISTS Oliver Hooker PR~Statistics 3/1 128 Brunswick Street Glasgow G1 1TF +44 (0) 7966500340 www.prstatistics.com www.prstatistics.com/organiser/oliver-hooker/

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COURSE - INTRODUCTION TO PYTHON FOR BIOLOGISTS
by Oliver Hooker 20 Apr '16

20 Apr '16

INTRODUCTION TO PYTHON FOR BIOLOGISTS This course is being delivered by Dr Martin Jones, an expert in Python and author of two text books, Python for Biologists [http://www.amazon.com/Python-Biologists-complete-programming-beginners/dp/1…] Advanced Python for Biologists [http://www.amazon.com/Advanced-Python-Biologists-Martin-Jones/dp/1495244377/] This course will run from 23rd - 27th May 2016 at SCENE (the Scottish Centre for Ecology and the Natural Environment), Loch Lomond National Park, Glasgow. Course overview: Python is a dynamic, readable language that is a popular platform for all types of bioinformatics work, from simple one-off scripts to large, complex software projects. This workshop is aimed at complete beginners and assumes no prior programming experience. It gives an overview of the language with an emphasis on practical problem-solving, using examples and exercises drawn from various aspects of bioinformatics work. After completing the workshop, students should be in a position to (1) apply the skills they have learned to tackle problems in their own research and (2) continue their Python education in a self-directed way. Curriculum: Day 1: Module 1 - Introduction Module 2 - Output and text manipulation Day 2: Module 3 - File IO and user interfaces Module 4 - Flow control 1: loops Day 3: Module 5 - Flow control 2: conditionals Module 6 - Organizing and structuring code Day 4: Module 7 – Regular expressions Module 8 - Dictionaries Day 5: Module 9 – Interaction with the file system Module 10 - Optional free afternoon to cover previous modules and discuss data more details at http://prstatistics.com/course/introduction-to-python-for-biologists-ipyb/ Intended audience: This workshop is aimed at all researchers and technical workers with a background in biology who want to learn programming. The syllabus has been planned with complete beginners in mind; people with previous programming experience are welcome to attend as a refresher but may find the pace a bit slow. Teaching format: The workshop is delivered over ten half-day sessions (see the detailed curriculum below). Each session consists of roughly a one hour lecture followed by two hours of practical exercises, with breaks at the organizer’s discretion. There will also be plenty of time for students to discuss their own problems and data. Assumed background: Students should have enough biological background to appreciate the examples and exercise problems (i.e. they should know about DNA and protein sequences, what translation is, and what introns and exons are). No previous programming experience or computer skills (beyond the ability to use a text editor) are necessary, but you'll need to have a laptop with Python installed. The cost is £530 (+VAT) including lunches and course materials. An all-inclusive option is also available at £660 (+VAT); this includes breakfast, lunch, dinner, refreshments, accommodation and course materials. Participants will need a laptop with a recent version of Python installed. Please send inquiries to oliverhooker(a)prstatistics.co.uk or visit the website www.prstatistics.com Please fee free to distribute this information anywhere you think suitable Other upcoming courses - TIME SERIES MODELS FOR ECOLOGISTS AND CLIMATOLOGISTS; GENETIC DATA ANALYSIS USING SIAR; ; APPLIED BAYESIAN MODELLING FOR ECOLOGISTS AND EPIDEMIOLOGISTS; SPATIAL ANALYSIS OF ECOLOGICAL DATA USING R; ADVANCING IN STATISTICAL MODELLING USING R; INTRODUCTION TO STATISTICS AND R FOR BIOLOGISTS; DNA TAXONOMY; ; BIOINFORMATICS FOR GENETICISTS AND BIOLOGISTS; MULTIVARIATE ANALYSIS OF SPATIAL DATA; ADVANCES IN DNA TAXONOMY USING R; Oliver Hooker PR statistics 3/1 128 Brunswick Street Glasgow G1 1TF +44 (0) 7966500340 www.prstatistics.com www.prstatistics.com/organiser/oliver-hooker/ -- Oliver Hooker PR statistics 3/1 128 Brunswick Street Glasgow G1 1TF +44 (0) 7966500340 www.prstatistics.com www.prstatistics.com/organiser/oliver-hooker/

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Still some places left on 1-day Linux for Genomics workshop, Friday 13 May 2016
by Bert Overduin 20 Apr '16

20 Apr '16

Dear all, We have still some places left on our 1-day Linux for Genomics workshop on Friday 13 May 2016. Note that this workshop is specifically aimed at anyone *without any command-line experience*. Workshop description: Genomic studies produce vast amounts of data, usually in the form of very large text files. Linux is particularly suited to working with such files, and is therefore arguably one of the most important tools in a bioinformatician’s toolkit. The Linux command line enables one to view, filter and manipulate large text files that are difficult or impossible to handle with applications like Word or Excel, write pipelines to perform certain tasks and run bioinformatics software for which no web interface is available. In this workshop we will provide a basic introduction to Linux, covering the most used commands, followed by a brief introduction to several popular command-line tools that were especially developed for genomics (e.g. samtools and bedtools). The workshop will be mostly hands-on. In the tutorials genomic data and file formats commonly used in genomics (e.g. BED, FASTA, FASTQ, GFF/GTF, SAM/BAM, VCF) will be used (and explained). *1-day Linux for Genomics* Date: Fri 13 May 2016 Price: £155 Registration: first come first serve Deadline: Fri 29 April 2016 noon Details: https://genomics.ed.ac.uk/linux-genomics Cheers, Bert -- Bert Overduin, PhD TRAINING AND OUTREACH BIOINFORMATICIAN Bert.Overduin(a)ed.ac.uk EDINBURGH GENOMICS The University of Edinburgh Ashworth Laboratories The King's Buildings Charlotte Auerbach Road Edinburgh EH9 3FL Scotland, United Kingdom tel. +44(0)1316507403 http://genomics.ed.ac.uk The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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SCS2016 Orlando: Abstract submission deadline THIS friday
by Bart Cuypers 19 Apr '16

19 Apr '16

Dear Colleague, We would like to invite you to the twelfth edition of the ISCB Student Council Symposium on Friday 8th July 2016 during ISMB in Orlando, Florida, US. SCS is a yearly recurrent interdisciplinary symposium, linked to ISMB. Its main goal is to bring together students and young researchers from computational biology, bioinformatics, systems biology, and related fields. This symposium includes an ice-breaking event, internationally renowned keynote speakers, oral presentations, flash presentations, a poster session and the famous social event in the evening. Therefore, it provides you with the opportunity to present your research to an international audience, learn about state-of-the art research and build a worldwide scientific network. We are excited to announce our two Keynotes John Quackenbush and Janet Thornton. These experts in the fields of cancer systems biology and structural bioinformatics, respectively, will be talking about their research and experiences as leaders at the forefront of science. You can learn more about them here: http://symposium.iscbsc.org/node/187 Abstract Submission is currently open, but the deadline is this Friday 22th of April. You can submit an abstract via on http://symposium.iscbsc.org/ . You can also apply for one of our travel fellowships at the same link. Registration is possible via the main conference website: https://www.iscb.org/ismb2016-registration Please help us spread the word by sharing our flyer (please find it attached), and using the hashtag #SCSOrlando2016 on social media. We look forward to seeing you in Orlando, Florida this summer! Bart Cuypers and Ben Siranosian SCS2016 Chair and Co-chair P Please consider the environment before printing this e-mail Disclaimer: Http://www.itg.be/disclaimer Directions to our location(s): http://g.co/maps/ua89b

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