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

Vacancies: Java and Front-end web developers @ UMCG
by Morris Swertz 17 Nov '16

17 Nov '16

Dear all I am happy to announce we have two new positions in our MOLGENIS software team to create open source software to analyse the terabytes of new NGS and biobank data for 'personalized’ genome diagnostics and research, enjoy use of state-of-the-art techniques and frameworks in coordination with colleagues from the data management and analysis teams, and write a lot of great code. *Senior Java developer with a passion for health research & applications* We seek an experienced Java developer to work on the data backbone of a "google drive” for large-scale research data, analysis backbone for data processing, annotation and interpretation, and data integration backbone based on ontologies. On top of that you will also work on "apps" to for research data publication, for diagnostic interpretation of DNA data, to make European biobank data findable and reusable, and to drive high-performance computing pipelines. see http://ow.ly/XQyt306egxL *Skilled Frontend Web developer for biobanking and genome interpretation* We also seek a skilled front-end developer to design and implement attractive user interfaces, co-develop elegant web services, and help in testing and operations with an eye for quality. You work especially at the frontend of a "google drive” for large-scale research data, analysis frontends for data processing, annotation and interpretation, data integration frontends based on ontologies and 'apps' to visualise research results, aid DNA diagnostic interpretation and make European biobanks findable and reusable. See http://ow.ly/i9md306g3D3 *Work environment* Both positions are at the Genomics Coordination Center (GCC) of the University Medical Centre Groningen, Department of Genetics. Along with 25 IT colleagues we work on smart open-source software to accelerate research and improve health care applications via web applications, high-performance computing analysis pipelines and large-scale e-infrastructure (cluster, storage, cloud). Furthermore, you will work with users of diverse backgrounds: geneticists, epidemiologists, statisticians, IT experts, data modelers and doctors, and you can participate in national and European projects such as BBMRI, ELIXIR, DTL, RD-connect and CORBEL. Please apply using the following links: Senior Java Developer http://ow.ly/XQyt306egxL Frontend Web Developer http://ow.ly/i9md306g3D3 Best wishes Morris -- Dr. Morris A. Swertz Coordinator BBMRI-NL common services for IT Coordinator DTL sector health Coordinator NFU biobank catalogue working group Head Section Systems Genetics & Genomics Coordination Center Associate Professor - Big data in biomedicine Dept. of Genetics, CB50 University Medical Center Groningen P.O. Box 30001 9700 RB GRONINGEN The Netherlands Phone +31 50 3617100 Fax + 31 50 3617230 Email m.a.swertz(a)rug.nl

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Introduction to Python for Biologists 12-16 Dec 2016 Edinburgh - Few places left
by Bert Overduin 14 Nov '16

14 Nov '16

We still have a few places left on the following course: INTRODUCTION TO PYTHON FOR BIOLOGISTS DATE: Monday 12 – Friday 16 December 2016 VENUE: The King's Buildings, The University of Edinburgh, Edinburgh, Scotland, UK REGISTRATION DEADLINE: Monday 28 November 2016 noon CANCELLATION DEADLINE: Monday 5 December 2016 noon PLACES: 20 (first come, first served) REGISTRATION FEE: £500 (includes coffee/tea, but no lunch) INFORMATION: Bert Overduin (bert.overduin(a)ed.ac.uk) Martin Jones ( martin(a)pythonforbiologists.com) TO REGISTER: http://genomics.ed.ac.uk/services/introduction- python-biologists 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. The workshop is structured so that the parts of the language most useful for bioinformatics are introduced as early as possible, and that students can start writing plausibly-useful programs after the first few sessions. After completing the workshop, students should be in a position to (1) apply the skills they have learned to tackling problems in their own research and (2) continue their Python education in a self-directed way. "Great learning from someone with a biology background rather than computer science - meant we were on the same wavelength." (February 2016) "Brilliantly well-run. From the book; to the USB stick with all the files we need; to the topics covered; to the system of helping us one-on-one, I cannot fault this course." (February 2016) INSTRUCTORS Dr. Martin Jones (Founder, Python for Biologists) Dr. Bert Overduin (Training and Outreach Bioinformatician, Edinburgh Genomics) WORKSHOP FORMAT The workshop is delivered over ten half-day sessions. Each session consists of roughly a one hour lecture followed by two hours of practical exercises, with breaks at the organiser’s discretion. Each session uses examples and exercises that build on material from the previous one, so it’s important that students attend all sessions. A description of the sessions can be found at the bottom of this page. WHO SHOULD ATTEND This workshop is aimed at 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. If in doubt, take a look at the detailed session content below or drop Martin Jones or Bert Overduinan email. REQUIREMENTS Students should have enough biological/bioinformatics background to appreciate the examples and exercise problems (i.e. they should know what a protein accession number, BLAST report, and FASTA sequence is). No previous programming experience or computer skills (beyond the ability to use a text editor) are necessary. SESSION CONTENT 1. Introduction In this session I introduce the students to Python and explain what we expect them to get out of it and how learning to program can benefit their research. I explain the format of the course and take care of any housekeeping details (like coffee breaks and catering arrangements). I outline the edit-run-fix cycle of software development and talk about how to avoid common text editing errors. In this session, we also check that the computing infrastructure for the rest of the course is in place (e.g. making sure that everybody has an appropriate version of Python installed). Core concepts introduced: source code, text editors, whitespace, syntax and syntax errors, Python versions 2. Manipulating text In this session students learn to write very simple programs that produce output to the terminal, and in doing so become comfortable with editing and running Python code. This session also introduces many of the technical terms that we’ll rely on in future sessions. I run through some examples of tools for working with text and show how they work in the context of biological sequence manipulation. We also cover different types of errors and error messages, and learn how to go about fixing them methodically. Core concepts introduced: terminals, standard output, variables and naming, strings and characters, special characters, output formatting, statements, functions, methods, arguments, comments. 3. Working with files I introduce this session by talking about the importance of files in bioinformatics pipelines and workflows, and we then explore the Python interfaces for reading from and writing to files. This involves introducing the idea of types and objects, and a bit of discussion about how Python interacts with the operating system. The practical session is spent combining the techniques from session 2 with the file IO tools to create basic file- processing scripts. Core concepts introduced: objects and classes, paths and folders, relationships between variables and values, text and binary files, newlines. 4. Lists and loops A discussion of the limitations of the techniques learned in session 3 quickly reveals that flow control is required to write more sophisticated file-processing programs, and I introduce the concept of loops. We look at the way in which Python loops work, and how they can be used in a variety of contexts. We explore the use of loops and lists together to tackle some more difficult problems. Core concepts introduced: lists and arrays, blocks and indentation, variable scoping, iteration and the iteration interface, ranges. 5. Conditions I use the idea of decision-making as a way to introduce conditional tests, and outline the different building-blocks of conditions before showing how conditions can be combined in an expressive way. We look at the different ways that we can use conditions to control program flow, and how we can structure conditions to keep programs readable. Core concepts introduced: Truth and falsehood, Boolean logic, identity and equality, evaluation of statements, branching. 6. Writing functions We discuss functions that we’d like to see in Python before considering how we can add to our computational toolbox by creating our own. We examine the nuts and bolts of writing functions before looking at best-practice ways of making them usable. We also look at a couple of advanced features of Python - named arguments and defaults. Core concepts introduced: argument passing, encapsulation, data flow through a program. 7. Regular expressions I show how a range of common problems in bioinformatics can be described in terms of pattern matching, and give an overview of Pythons regex tools. We look at the building blocks of regular expressions themselves, and learn how they are a general solution to the problem of describing patterns in strings, before practising writing some specific examples of regular expressions. Core concepts introduced: domain-specific languages, modules and namespaces. 8. Dictionaries We discuss a few examples of key-value data and see how the problem of storing them is a common one across bioinformatics and programming in general. We learn about the syntax for dictionary creation and manipulation before talking about the situations in which dictionaries are a better fit that the data structures we have learned about thus far. Core concepts introduced: paired data types, hashing, key uniqueness, argument unpacking and tuples. 9. Working with the filesystem We discuss the role of Python in the context of a bioinformatics workflow, and how it is often used as a language to “glue” various other components together. We then look at the Python tools for carrying out file and directory manipulation, and for running external programs - two tasks that are often necessary in order to integrate our own programs with existing ones. Core concepts introduced: processes and subprocesses, the shell and shell utilities, program return values. 10. BioPython I discuss the benefits of having frequently-used code packaged into a library and give a quick overview of the BioPython project. We look at how BioPython can be used for sequence manipulation, and contrast the resulting code with our examples from previous sessions, showing the benefits of each. We see how we can use BioPython to do a job - GenBank file parsing - that would require a huge amount of coding if we were to write a program from scratch. Students carry out some exercises involving sequence object manipulation and explore the parts of the BioPython hierarchy relevant to their interests. Core concepts introduced: object hierarchies, packages. -- Bert Overduin, PhD TRAINING AND OUTREACH BIOINFORMATICIAN Bert.Overduin(a)ed.ac.uk orcid.org/0000-0002-5281-8838 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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Fwd: Still some seats available for BioSB Course Comparative Genomics: from evolution to function - November 21-25, 2016 in Nijmegen
by Celia van Gelder 14 Nov '16

14 Nov '16

*BioSB Course Comparative Genomics: from evolution to function (3rd edition) * *Date:* November 21-25, 2016 *Location*: CMBI, Radboudumc, Nijmegen, the Netherlands *Course coordinators:* Berend Snel (UU), Martijn Huynen (Radboudumc), Jaap Heringa (VU), Celia van Gelder (BioSB) *Course website*: http://biosb.nl/education/course-portfolio/ course-comparative-genomics/ *Registration:* http://biosb.nl/education/course-portfolio/ enrollment-comparative-genomics-from-evolution-to-function-course-2016/ *More information*: education(a)biosb.nl *Course description* Comparative genomics between species and between types of data facilitates the understanding of what these data really reflect about the underlying biological processes. Comparative genomics therewith relies on a solid understanding of basic elements of Bioinformatics like homology and orthology. Moreover it is important to know the assumptions and heuristics of bioinformatic methods for comparative genomics and hence we aim to let participants develop an understanding of why these methods sometimes fail (or misdetect) as a consequence of a variety of biological /evolutionary causes, and in which situations which method is most appropriate. The first two days of the course provide a basis for the course with the aim to move “beyond blast” in terms of the most sensitive homology searches, domain level analysis of protein evolution as well as more fine grained definitions of relatedness as can be obtained from the proper interpretation of gene trees (i.e. various levels of orthology). This foundation is used to discuss in the three following days in more detail three topics: (1) the study of functional and evolutionary consequence of (genome) duplications, (2) the evolution of interactions and complexes and (3) the prediction and evolution of genomic regulatory elements and of RNA structures *Target audience* The course is intended for PhD students and master students in bioinformatics or geneticists and experimental biologists with a strong interest in evolution of the eukaryotes. It is especially relevant to students who want to compare various types of genomics data between species. Participants are expected to have some hands on experience with tools like blast, constructing multiple sequence alignments and phylogenetic trees, and in addition to have some familiarity with concepts such as orthology, synteny and protein domains. *Programme* *Monday November 21: Distant homology and protein domains (lecturer Jaap Heringa)* Topics & Tools: Divergent and convergent evolution, (multiple) sequence alignment, psiblast, jackhmmer, hhsearch, pfam, homology and function, undetected orthology from failure to detect homology, paralogs and function specificity prediction *Tuesday Nov 22: Small scale orthology and large scale databases (lecturers Martijn Huynen, Berend Snel)*Topics & Tools: tree reconciliation, relation between homology and orthology, ensembl compara, COGs, inparalogs vs outparalogs, fusion and fission *Wednesday Nov 23: Comparative Interactomics (lecturers Jaap Heringa, Martijn Huynen/John van Dam)* Topics & Tools: network alignment, phylogenetic profiles, biogrid, cytoscape, Bayesian data integration, neofunctionalization vs subfunctionalization *Thursday Nov 24 : Genome duplications (lecturer Berend Snel)* Topics & Tools: yeast gene order browser, synteny, consequences of genome duplications, timing of duplications, ensembl biomart *Friday Nov 25: Finding functional elements in DNA and RNA sequences, Biased gene conversion (lecturer Martijn Huynen)* Topics & Tools: phylogenetic footprinting, (phylogeny aware) gibbs sampling, RNA secondary structure prediction based on sequences and on experimental data, biased gene conversion & positive selection. *BioSB Education Programme* This 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. *More information* For more information about the course you can contact Celia van Gelder at *education(a)biosb.nl <education(a)biosb.nl>*. -- Dr. Celia W.G. van Gelder Programme Manager Learning DTL/ELIXIR-NL Training Education Manager BioSB tel. +31613375327 e-mail: celia.van.gelder(a)dtls.nl websites: www.dtls.nl, www.biosb.nl skype: celia.van.gelder Postal address: DTL PO Box 19245 3501 DE Utrecht

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GIGA (ULg) - Unit of Animal Genomics - Immediately available PhD and postdoctoral positions
by Sandra Lopez - GIGA ULg 11 Nov '16

11 Nov '16

Dear all, The Unit of Animal Genomics (GIGA - University of Liège) is seeking applicants for two immediately available PhD positions in the area of genomic selection of livestock and a postdoctoral position in the area of population and evolutionary genomics. Please find attached the job descriptions. Regards, Sandra Lopez and Sandrina Evrard. GIGA - Coordination Université de Liège Quartier Hôpital Avenue de l'Hôpital 11 - B34 B-4000 LIEGE Tél + 32 4 366 98 03 or 43 94 Fax + 32 4 366 41 98 www.giga.ulg.ac.be

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Postdoc (Research Associate) in Biomedical Data Visualization at LCSB, University of Luxembourg
by Venkata Pardhasaradhi SATAGOPAM 11 Nov '16

11 Nov '16

Dear all, The Luxembourg Centre of Systems Biomedicine (LCSB), University of Luxembourg has the following vacancy. Postdoc (Research Associate) in Biomedical Data Visualization (m/f) * Ref. S-STR-4002-00-B * Fixed-term contract for 2 years with possibility of renewal for up to 5 years, 40h/week * Employee status (start date: as soon as possible) Area: Visualization and visual exploration of complex biomedical knowledge. The research will focus on development and implementation of new approaches to visualize molecular interaction networks. In particular, the successful candidate will propose new methods to combine different sources of data, including bioinformatics databases and high-throughput omics, on diagrams of molecular mechanisms. Problems to address will, among others, concern combined visualization of graph representations and protein structures. Please refer the following URL for more details http://emea3.mrted.ly/18rye Best regards, Venkata -- Venkata P. Satagopam Bioinformatics Core Luxembourg Centre For Systems Biomedicine (LCSB) University of Luxembourg Campus Belval, House of Biomedicine II 6, avenue du Swing L-4367 Belvaux T +352-466-644-6421 F +352-466-644-6949 venkata.satagopam(a)uni.lu<mailto:venkata.satagopam@uni.lu> http://lcsb.uni.lu ----- This message is confidential and may contain privileged information. It is intended for the named recipient only. If you receive it in error please notify me and permanently delete the original message and any copies. -----

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Positions available - GIGA - ULg - BIO3 group
by Sandra Lopez - GIGA ULg 10 Nov '16

10 Nov '16

Dear all, The BIO3 (Biostatistics, Biomedicine, Bioinformatics) group at the GIGA-R Medical Genomics Unit of the University of Liège (Belgium) is offering - a post-doctoral position within a newly obtained TÉLÉVIE project entitled “Drivers and Markers in Pancreatic Cancer”. The aim of the project is to identify molecular drivers and markers of initiation, progression and dissemination of pancreatic ductal adenocarcinoma (PDAC). - a position for a scientist programmer within the WELBIO project “DESTinCT”. The latter aims to develop an analytic pipeline and software tools in the research area of large-scale omics integrated gene-gene interaction analyses. Please find attached the job descriptions. Sandra Lopez and Sandrina Evrard GIGA - Coordination Université de Liège Quartier Hôpital Avenue de l'Hôpital 11 - B34 B-4000 LIEGE Tél + 32 4 366 98 03 or 43 94 Fax + 32 4 366 41 98 www.giga.ulg.ac.be

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SWAT4LS 2016 Amsterdam, 5-8th December 2016 - Early bird registration closes tonight!
by Femke Francissen 08 Nov '16

08 Nov '16

** SWAT4LS 2016, Amsterdam, 5-8th December 2016 ** The next SWAT4LS <http://www.swat4ls.org/> will be held in Amsterdam, NL, 5-8th December 2016 and will be a full conference for the second time. The 2016 SWAT4LS conference is the ninth meeting in the series and will provide the same open, vibrant and well-organised environment that has previously brought together researchers, developers, and users, from many fields to discuss goals, current limits and real experiences in the use of Semantic Web technologies in health care and the life sciences. SWAT4LS 2016 will comprise a *tutorials day (5th), main conference (6th and 7th), and a Hackathon day (8th)*. All events will be held in the Netherlands Cancer Institute in Amsterdam. Confirmed keynote speakers for the main conference: - Amos Bairoch - Dietrich Rebholz-Schuhmann - Martin Hofmann-Apitius Registration is open! *NB: Early Bird registration extended to 23:30 CET Tuesday November 8!* *A discount of 20% on the registration fee applies to partners of the Dutch Techcentre for Life Sciences <http://www.dtls.nl> (DTL) and participicants of the upcoming CIViC Hackathon and Curation Jamboree <https://itcr.nci.nih.gov/about-itcr/news/civic-hackathon-and-curation-jambo…>. Read more <http://www.swat4ls.org/workshops/amsterdam2016/registration/>* Read more about the programme & register via the conference website: http://www.swat4ls.org/ For more information, contact: info(a)swat4ls.org

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PostDoc & PhD student positions at BIH (Berlin, Germany)
by Martin Kircher 04 Nov '16

04 Nov '16

Dear colleagues, I will start a computational research group at the Berlin Institute of Health (BIH) in Germany in March 2017. My research will be in the areas of sequence analysis, data mining and functional genomics. One focus will be non-coding sequence variation, specifically analysis of data from Massively Parallel Reporter Assays (MPRA) for promoter and enhancer variants as well computational approaches for identifying functionally relevant genetic changes. At this point, I am trying to fill one fully funded PostDoc position and one PhD student position. Starting date is March 1st, 2017 or later and the application deadline for the PostDoc position is Dec 1st, 2016. I hope you can help me distributing the attached job posts to interested students and researchers. Please do not hesitate to contact me with questions regarding these posts (mkircher(a)uw.edu) Thank you so much! Martin Kircher -- Dr Martin Kircher Senior Fellow Shendure lab University of Washington, Department of Genome Sciences Foege Building S-203B, Box 355065 3720 15th Ave NE, Seattle WA 98195-5065

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PhD student / Postdoc position in Molecular Epidemiology of Osteoarthritis, Leiden, The Netherlands.
by I.Meulenbelt＠lumc.nl 01 Nov '16

01 Nov '16

Dear BeNeLux bioinformatics members, The section Molecular Epidemiology embedded in the department of Medical Statistics and Bioinformatics at Leiden University Medical Center, The Netherlands is looking for either a PhD student or a Postdoc to work on a VICI project aimed at identifying high dimensional molecular profiles in joint tissues marking diverse osteoarthritis subtypes. The second phase of the project will involve applying integrated data analyses of identified molecular profiles with circulating molecular biomarkers. Ultimately, in this precision medicine approach the therapeutic modes of action needed for different OA patients is identified. For further information and submitting applications, please visit: https://www.lumc.nl/over-het-lumc/werken-bij/vacatures-solliciteren/researc… Best wishes, Ingrid Meulenbelt -------------------------------------------------- Ingrid Meulenbelt, PhD Associate Professor Dept. Medical Statistiscs and Bioinformatics Section Molecular Epidemiology Leiden University Medical Center Postzone S05-P Einthovenweg 20 2333 ZC Leiden The Netherlands Tel: +31 71 5269734 -------------------------------------------------

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