- BBClist - maillist.psb.ugent.be

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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Vacancy: PhD position on copy number variation detection in experimental evolution
by Ridder, Dick de 19 Apr '16

19 Apr '16

Dear all, We are looking for an enthusiastic bionformatics PhD candidate on a project titled "Exploiting copy number variation for rapid improvement of abiotic stress tolerance in crops", a collaboration with the Laboratory of Genetics at Wageningen University. Our goal is to experimentally evolve plants in the laboratory under severe stress conditions – high salt or zinc exposure – and study the resulting genomic changes, which we expect to mainly be copy number variation. This will help us understand the role of copy number variation in plant genome evolution and allow us to find ways of use it in crop plant breeding, to improve stress tolerance. We are looking for an ambitious PhD candidate with an MSc degree in bioinformatics or computer science (with a demonstrable affinity for biology). We are specifically seeking a candidate with a strong background in algorithm development, preferably in NGS data analysis, and demonstrable skills in mathematics and statistics. You will be based in Wageningen, and work in close cooperation with the other PhD candidate in this project and with researchers at Wageningen University and in industry. Additional information about the position can be found at http://tinyurl.com/h2gfvcx. Interested candidates can apply up to May 21, 2016 through this website. Best regards, prof. Dick de Ridder Bioinformatics Group, Wageningen University, The Netherlands

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Vacancy for ELIXIR Technical Lead (Data and Interoperability)
by Mascha Jansen 18 Apr '16

18 Apr '16

Dear all, The ELIXIR-HUb is recruiting a technical officer to support data and interoperability platforms at the ELIXIR Hub: https://www.elixir-europe.org/about/vacancies/elixir-technical-lead <https://www.elixir-europe.org/about/vacancies/elixir-technical-lead> Could you please help to spread this in your networks? The opening closes on April 25. Thanks! Mascha Jansen Coordination FAIR Data projects Dutch Techcentre for Life Sciences Visiting address: Catharijnesingel 54 | 3511 GC Utrecht Postal address: Postbus 19245 | 3501 DE Utrecht E-mail: mascha.jansen(a)dtls.nl Tel: +31 612119993 Website: <>w <http://www.dtls.nl/> <>ww.dtls.nl <http://www.dtls.nl/>

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BioSB Course: In silico life: constraint-based modelling at genome scale, May 9-11 2016, Amsterdam
by Celia.vanGelder＠radboudumc.nl 15 Apr '16

15 Apr '16

Dear colleague, The BioSB course In silico life: constraint-based modelling at genome scale (first edition), is open for registration. Please spread this message to other researchers in your network that might be interested. Date: May 9-11, 2016 Location: Amsterdam Course Coordinators: Bas Teusink (VU), Brett Olivier (VU), Vrije Universiteit Amsterdam, Celia van Gelder (BioSB) Speakers & tutors: Dr. Filipe Branco dos Santos (UVA), Prof. Frank Bruggeman (VU), Dr. Richard Notebaard (RUMC), Dr. Peter Schaap (WUR), Prof. Bas Teusink (VU), Dr. Katy Wolstencroft (LIACS), Dr. Ahmad Zeidan (Chr. Hansen), Dr. Zheng Zhao (DSM), Jasper Koehorst (WUR), Dr. Brett Olivier (VU) Website: http://biosb.nl/education/course-portfolio-2/course-constraint-based-modell… Registration: http://biosb.nl/education/course-portfolio-2/course-constraint-based-modell… Target audience Constraint-based modelling is a rapidly growing field that is being use in both fundamental and applied research and biotechnology. It sits at the intersection between quantitative metabolic modelling, bioinformatics and cellular physiology and, as such, is an example of systems biology at work. While participants would benefit from some knowledge of either quantitative modelling, bioinformatics or microbial physiology this is not required. This includes, for example, scientists working in a laboratory and wanting to learn more about building or using genome-scale models, as well as, those who have used basic FBA, but want to know how else it can be applied to their research. Course description Constraint-based modelling is a powerful modelling methodology that is being used to model a diverse range of biological phenomena. These include both fundamental and applied questions relevant to biotechnology, microbiology and medicine. Central to constraint-based modelling is the use of a genome-scale reconstructions (GSR’s) that maps out the metabolism of a cell as a biochemical reaction network. In this course you will be introduced to: * techniques for the construction of a working GSR: tools, tricks and pitfalls * the underlying mathematical definition and description of a constraint-based model * methods for interrogating models and interpreting results, such as Flux Balance Analysis and Flux Variability Analysis * software and standards The preliminary course structure will be to divide each day into both lectures and practical sessions so that learned theory can immediately be applied in silico. Full Course Programme Monday (09/05/2016) Tuesday (10/05/2016) Wednesday (11/05/2016) FALW, WN-F654 O2 Building 01W08 O2 Building 01W08 9:30 -11:00 Bas Teusink (VU) b.teusink(a)vu.nl<mailto:b.teusink@vu.nl> Frank Bruggeman (VU) f.j.bruggeman(a)vu.nl<mailto:f.j.bruggeman@vu.nl> Filipe Branco dos Santos (UVA) f.brancodossantos(a)uva.nl<mailto:f.brancodossantos@uva.nl> 11:00 - 11:30 Coffee Coffee Coffee 11:30 - 12:45 Peter Schaap (WUR) peter.schaap(a)wur.nl<mailto:peter.schaap@wur.nl> Bas Teusink (VU) b.teusink(a)vu.nl<mailto:b.teusink@vu.nl> Richard Notebaard (RUMC) Richard.Notebaart(a)radboudumc.nl<mailto:Richard.Notebaart@radboudumc.nl> 12:45 - 13:30 Lunch Lunch Lunch 13:30 - 14:30 Genome annotation Jasper Koehorst (WUR) jasperkoehorst(a)gmail.com<mailto:jasperkoehorst@gmail.com> FAME Brett Olivier b.g.olivier(a)vu.nl<mailto:b.g.olivier@vu.nl> SBML models, tools & databasesL Brett Olivier (VU) b.g.olivier(a)vu.nl<mailto:b.g.olivier@vu.nl> 14:30 - 15:30 FAIR data and models Katy Wolstencroft (LU) k.j.wolstencroft(a)liacs.leidenuniv.nl<mailto:k.j.wolstencroft@liacs.leidenuniv.nl> 15:30 - 16:00 Coffee Coffee Coffee 16:00 - 17:00 Zheng Zhao (DSM) zheng.zhao(a)dsm.com<mailto:zheng.zhao@dsm.com> Ahmad Zeidan (Chr Han) DKAHZE(a)chr-hansen.com<mailto:DKAHZE@chr-hansen.com> Final wrap-up & discussion 17:00 - 17:30 Wrap-up & discussion Wrap-up & discussion 17:30 - Drinks (BioSB) Dinner (self organised) BioSB Education Programme The course is part of the Education Programme of BioSB, the Netherlands Bioinformatics and Systems Biology Research School, which offers training and education for in bioinformatics and systems biology. More information about BioSB can be found at www.biosb.nl<http://www.biosb.nl>. Kind regards, Celia van Gelder, BioSB Dr. Celia W.G. van Gelder Education Manager BioSB Coordinator Education CMBI Programme Manager Learning DTL/ELIXIR-NL tel. +31613375327 e-mail: Celia.vanGelder(a)radboudumc.nl<mailto:Celia.vanGelder@radboudumc.nl> websites: www.nbic.nl<http://www.nbic.nl/>, www.biosb.nl, www.cmbi.ru.nl<http://www.cmbi.ru.nl/>, www.dtls.nl Postal address: CMBI 260 Radboud University Nijmegen-Medical Centre PO Box 9101 6500 HB Nijmegen The Netherlands Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629. The Radboud university medical center is listed in the Commercial Register of the Chamber of Commerce under file number 41055629.

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Machine Learning in Systems Biology, 10th international Workshop
by Dijk, Aalt-Jan van 14 Apr '16

14 Apr '16

Call for Papers & Highlight track abstracts: 10th International Workshop Machine Learning in Systems Biology (MLSB-2016) Organized as a ECCB pre-conference workshop, September 3-4, 2016, World Forum, The Hague, Netherlands SUMMARY Biology is rapidly turning into an information science, thanks to enormous advances in the ability to observe the molecular properties of cells, organs and individuals. This wealth of data allows us to model molecular systems at an unprecedented level of detail and to start to understand the underlying biological mechanisms. This field of systems biology creates a huge need for methods from machine learning, which find statistical dependencies and patterns in these large-scale datasets and that use them to establish models of complex molecular systems. MLSB is a scientific forum for the exchange between researchers from Systems Biology and Machine Learning, to promote the exchange of ideas, interactions and collaborations between these communities. TARGET AUDIENCE The aim of this workshop is to contribute to the cross-fertilization between the research in machine learning methods and their applications to systems biology (i.e., complex biological and medical questions) by bringing together method developers and experimentalists. WORKSHOP TOPICS (NON EXHAUSTIVE) Methods: Active learning/Experimental design, Bayesian Methods, Clustering/Biclustering, Data integration/fusion/multi-view learning, Feature/subspace selection, Graph inference/completion, Kernel Methods, Machine Learning Algorithms, Multitask/Structured output prediction, Probabilistic inference, Semi-supervised learning, Systems identification, Time-series analysis Applications: Biomarker identification, Epigenetics, Genome-wide association studies, Metabolic modeling and reconstruction, Metabolomics, Protein function and structure prediction, Protein-protein interaction networks, Rational drug design methods, Regulatory genomics, Sequence Annotation, Signaling networks, Synthetic biology IMPORTANT DATES May 30, 2016: Full length manuscript submission May 30, 2016: Highlight track abstract submission June 30, 2016: Decision notifications for manuscripts and abstracts July 20, 2016: Final camera-ready manuscript submission August 19, 2016: Registration deadline September 3-4, 2016: Workshop INVITED SPEAKERS Prof. Ziv Bar-Joseph, School of Computer Science Carnegie-Mellon University, USA Prof. Jukka Corander, Department of Mathematics and Statistics, University of Helsinki, Finland Prof. Lodewyk Wessels, The Delft Bioinformatics Lab, Delft University of Technology, The Netherlands Prof. Yvan Saeys, VIB Inflammation Research Center, Ghent University, Belgium SUBMISSIONS We encourage submissions bringing forward methods for discovering complex structures (e.g. interaction networks, molecule structures), statistical machine learning methods for analysis of various high-throughput omics data, and methods supporting systems-level data analysis. The submissions are organized into the following two tracks: 1. Manuscripts (preferentially up to 5000 words) describing original work on machine learning in systems biology. These should describe method development and applications broadly in the topics listed above (see Workshop topics). Accepted proceedings track papers will be published in BMC Bioinformatics. The publications need to match the standards of the journal; please prepare your submissions using the BMC instructions (http://www.bioinformatics.nl/MLSB2016/BMC_guidelines.pdf) The publication is subject to open access fee (special reduced price negotiated by MLSB). 2. Highlights Track abstracts (1-2 pages) describing computational aspects of work that has been recently published in a journal (or are “in press”) as well as unpublished/on-going work. Submissions will be evaluated by at least three reviewers from an international programme committee of experts in the field. The most relevant and most original submissions will be accepted as full oral presentations and/or as poster presentations at the workshop. Submission is through the Easychair system: https://easychair.org/conferences/?conf=mlsb2016 REGISTRATION Registration via the general ECCB2016 registration system http://www.eccb2016.org/registration/ PROGRAMME COMMITTEE Antti Airola Chloé-Agathe Azencott Alexis Battle Michael A. Beer Andreas Beyer Karsten Borgwardt Céline Brouard Gal Chechik Chao Cheng Manfred Claassen Florence D’Alché-buc Dick de Ridder Saso Dzeroski Pierre Geurts Markus Heinonen James Hensman Lars Kaderali David Knowles Stefan Kramer Anshul Kundaje Harri Lähdesmäki François Laviolette Christina Leslie Hiroshi Mamitsuka Martin Renqiang Min Yves Moreau Alan Moses Sara Mostafavi Bernard Ng Mahesan Niranjan William Noble Uwe Ohler Tapio Pahikkala Nico Pfeifer Gerald Quon Magnus Rattray Juho Rousu Yvan Saeys Guido Sanguinetti Li Shen Motoki Shiga Oliver Stegle Koji Tsuda Giorgio Valentini Aalt-Jan van Dijk Jinbo Xu

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bytemal Aachen conference
by Cirillo Elisa (BIGCAT) 14 Apr '16

14 Apr '16

Dear all, We are excited to announce that after the great start of the conference series byteMAL in Maastricht, the next conference is coming up in Aachen on 17th June 2016. byteMAL - Bioinformatics for Young inTernational researchers Expo - is a conference series that is directed especially at young researchers in the fields of bioinformatics and computational biology and aims to provide a new networking platform for the exchange of knowledge and expertise across borders. We are very happy that Prof. Dr. Ben MacArthur from University of Southampton, Prof. Dr. Ines Thiele from University of Luxembourg and Prof. Dr. Olaf Wolkenhauer from University of Rostock will give the keynote presentations. Furthermore, participants will have the chance to present their projects during the poster session or their newly developed tools during the application showcase session. Online registration is possible until 20th May 2016. For more information about the event, please visit our website (http://projects.bigcat.unimaas.nl/bytemal/aachen/) or take a look at the flyer attached. You can also find us on Facebook (www.facebook.com/bytemal<http://www.facebook.com/bytemal>) or Twitter (https://twitter.com/byteMAL_Aachen) We are looking forward to seeing you there! Thank you and best wishes On behalf of the Organisational Team Lisa Turnhoff Doctoral Candidate AICES Graduate School Joint Research Center for Computational Biomedicine (JRC-COMBINE) RWTH Aachen University Augustinerbach 2a 52062 Aachen Germany Phone: +49 241 80 99210 Web: http://www.combine.rwth-aachen.de<http://www.combine.rwth-aachen.de/>? ?

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BioVis at ISMB 2016 Call for Participation
by Jan Aerts 14 Apr '16

14 Apr '16

The BioVis Interest Group (http://www.biovis.net) is organizing a meeting at ISMB in 2016. This meeting brings together researchers from the visualization, bioinformatics, and biology communities with the purpose of educating, inspiring, and engaging visualization researchers in problems in biological data visualization, as well as bioinformatics and biology researchers in state-of-the-art visualization research. BioVis@ISMB 2016 is co-located with ISMB 2016 <http://www.iscb.org/ismb2016> and will be taking place on July 8in Orlando, Florida at the Disney World Resort Swan and Dolphin hotel <http://www.iscb.org/ismb2016-accommodation>. The main ISMB 2016 conference will run from July 8 through July 12. There are three possible ways to participate in BioVis@ISMB: [1] New Research: Participants are invited to submit an abstract describing high-quality original research. Abstracts will be reviewed by the program committee and all accepted abstracts will be included in the poster session. The authors of selected abstracts will be asked to give a brief oral presentation during the SIG meeting. [2] Highlights: Participants may submit an abstract describing work published in the previous year as well as additional work undertaken since publication. The program committee will review these abstracts. Additionally, the BioVis SIG program committee may also invite authors of outstanding publications from other venues. The authors of selected abstracts will give an oral presentation during the SIG meeting. [3] Posters: We seek work in progress and preliminary results; previously published work from other venues; visualization challenges. Key Dates for BioVis@ISMB: - May 3, 2016 - Submission deadline for the Highlights Track and New Research Track - May 17, 2016 - Submission deadline for Poster Track - May 20, 2016 - Notifications for Highlights, New Research, and Posters For more info on BioVis@ISMB see: http://biovis.net/2016/ismb/ BioVis is also holding a meeting at IEEE VisWeek in 2016. For more info on BioVis@VIS see:http://biovis.net/2016/ieeevis/ General chairs - G. Elisabeta Marai, University of Illinois at Chicago, USA - Jan Aerts, KU Leuven, Belgium Paper chairs - Daniel Weiskopf, University of Stuttgart, Germany - Marc Streit, Johannes Kepler University Linz, Austria Poster chairs - Michel Westenberg, Eindhoven University of Technology, The Netherlands - William Ray, The Ohio State University, USA Publication chairs - Alexander Lex, University of Utah, USA - Florin Chelaru, MIT, USA Primer & challenges chair - Eamonn Maguire, CERN, Switzerland Highlights chair - Julian Heinrich, CSIRO, Australia Data contest chairs - Raghu Machiraju, The Ohio State University, USA - Cagatay Turkay, City University, London, UK Design contest chairs - Ryo Sakai, KU Leuven, Belgium - Francis Rowland, EBI, UK Industry and fundraising chair - Hector Corrado Bravo, University of Maryland, USA Website chairs - Tuan Dang, University of Illinois at Chicago, USA - Anamaria Crisan, University of British Columbia, Canada Publicity chairs - Jillian Aurisano, University of Illinois at Chicago, USA Steering Committee - Kay Nieselt, University of Tuebingen, Germany - Nils Gehlenborg, Harvard Medical School, USA - Jessie Kennedy, Edinburgh Napier University, UK - Jos Roerdink, University of Groningen, The Netherlands - Raghu Machiraju, The Ohio State University, USA (Chair) ================================================ Prof Jan Aerts * Visual Data Analysis Lab (vda-lab.be) * Data Visualization Lab (datavislab.org) * Bioinformatics - ESAT/STADIUS, Faculty of Engineering ( www.kuleuven.be/bioinformatics) * iMinds Medical IT Department (www.iminds.be) KU Leuven - University of Leuven Kasteelpark Arenberg 10 bus 2446 3001 Leuven-Heverlee ORCID: http://orcid.org/0000-0002-6416-2717 Tel: +32 16 321053 Fax: +32 16 321970 VAT BE 0419 052173

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