- BBClist - maillist.psb.ugent.be

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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[Gtpb] Introductory Bioinformatics IB16 . course announcement
by Pedro L. Fernandes 31 Oct '16

31 Oct '16

The Gulbenkian Training Programme in Bioinformatics Applications for the bioinformatics training course IB16S Introductory Bioinformatics (Second course in 2016) - our entry level course with a soft introduction to NGS data analysis with David P. Judge, Pedro Fernandes and Daniel Sobral IMPORTANT DATES for this Course Deadline for applications: November 30th 2016 Course date: December 12th - December 16th 2016 Candidates with adequate profile will be accepted in the next 72 hours after the application until we reach 20 participants. Overview This is an entry level course aimed that those with a reasonable biological background but no significant experience with bioinformatics. The course is broadly based around a series of exercises in which a combination of simple analytical tools and reference to publicly available databases is applied to the investigation of a single human gene. The training manual for the course is comprised of detailed instructions for the tasks undertaken. Included are, questions (with answers) and discussion of and the interpretation of the results achieved. Participants are asked to imagine an interest in the disease aniridia. Course exercises then provide extremely detailed instruction leading participants to discover the gene primarily associated with this disease and all that is interesting about that gene and its protein products. This course will also provide a soft introduction to Next Generation Sequencing (NGS) data analysis. This part of the course aims at providing basic skills that are needed when one needs to process NGS data, such as evaluating data quality, trimming sequences, changing data formats, visualising data, etc. Then, participants will learn how to address a simple transcriptomics problem, stepwise, using open source bioinformatics tools. Objectives The operation of the various programs used in the exercises will be explained, but only to the extent that allows a user to select parameters intelligently and to interpret results. The course will provide participants with an awareness of a wide range of bioinformatics tools and sufficient experience to use those tools in basic investigations with a relatively high degree of user independence. In the training course design, this is intentionally built-in, to allow us to show a wide range of analytical techniques while providing enough experience to break the ice in all of them. Target Audience This course is intended for those wishing to investigate how they might begin to exploit the ever expanding abundance of computing and data resources for researchers seeking help in using them. Best, Pedro Fernandes -- Pedro Fernandes Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL Tel +351 21 4407912 http://gtpb.igc.gulbenkian.pt Upcoming courses: AAIRR16 - Analysis of Adaptive Immune Receptor Repertoires, Nov 2 AET16 - Applied Evolutionary Theory, Nov 7 IBSTAT16 - Introductory Biostatistics for Biologists, Nov 14 IB16S - Introductory Bioinformatics, Dec 12 _______________________________________________ GTPB mailing list GTPB(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

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CORBEL: Data Visualisation for Biology
by Alexander Botzki 28 Oct '16

28 Oct '16

Data Visualisation for Biology: a practical workshop on design, techniques and tools 30th Jan - 3rd Feb 2017, EMBL-EBI Application deadline: Friday, 11th November 2016 http://www.ebi.ac.uk/training/events/2017/data-visualisation-biology-practi… As biological datasets increase in size and complexity, we are moving more and more from an hypothesis-driven research paradigm to a data-driven one. As a result, exploration of that data has become even more crucial than in the past. In this 5-day workshop, we will dive into the topic of biological data visualization and how it can be used to gain insight in and get a "feel" for a dataset, so that targeted analyses can be defined. We will start by covering theoretical questions like: What is data visualization? How do we perceive images? How can we visualise data in the best possible way? As the workshop continues, it will become more and more hands-on and interactive; a large part will be committed to creating visualisations using the P5 javascript library, based on biological data. In the workshop, we will focus on omics (e.g. genomics, transcriptomics) data rather than e.g. imaging data. This course is in association with CORBEL and KU Leuven Kind regards Vera -- Vera Matser PhD Training Liaison Officer, EMBL-EBI ORCID: 0000-0002-2010-6844 Tel: +44 (0)1223 49 4149 Skype: vera_matser e-mail: matser(a)ebi.ac.uk Twitter: @VeraMatser URL: www.ebi.ac.uk/training Find us in on-course®: www.on-course.eu European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Genome Campus Hinxton Cambridge CB10 1SD UK

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