July 2017 - BBClist - maillist.psb.ugent.be

Bioinformatics position available at the Erasmus MC Cancer Computational Biology Center
by Harmen van de Werken 04 Oct '19

04 Oct '19

A bioinformatics position is currently available at the Erasmus MC Cancer Computational Biology Center. http://www.erasmusmc.nl/vacature/?num=21578 Please apply, if you are enthusiastic and eager to improve our knowledge on cancer biology. Harmen van de Werken

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Introduction to Python for Biologists 11-15 September 2017
by Bert Overduin 27 Jul '17

27 Jul '17

Dear all, In September we are again offering one of our most popular workshops, i.e. the 5-day Introduction to Python for Biologists. As this workshop starts completely from scratch it is especially suited to those with little or no previous programming experience. The workshop is taught by Martin Jones, founder of Python for Biologists ( https://pythonforbiologists.com/introduction/) Martin is a very experienced Python instructor and author of several books on Python ( https://pythonforbiologists.com/python-books/) More details on the workshop can be found below. With kind regards, Bert ************************ INTRODUCTION TO PYTHON FOR BIOLOGISTS DATE: Monday 11 – Friday 15 September 2017 VENUE: The King's Buildings, The University of Edinburgh, Edinburgh, Scotland, UK REGISTRATION DEADLINE: Monday 28 August 2017 noon CANCELLATION DEADLINE: Monday 4 September 2017 noon PLACES: 20 (first come, first served) REGISTRATION FEE: £525 (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-pyt hon-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 Overduin an 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. During the workshop students will use their own laptops. Instructions for any software to be installed will be sent out prior to the course. 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. Final day The schedule for the final day will be set based on the progress of the course and the interests of the students. We will have time set aside for attendees to finish exercises, work on their own data, or get one-on-one help with real-world problems arising from their research. We may also use some of the time to cover more advanced topics of interest to the attendees, including BioPython, data visualisation, packaging and distributing code, and using alternative interfaces such as iPython. -- 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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eScience Academy Essential Skills Workshops Utrecht September 2017
by Celia van Gelder 26 Jul '17

26 Jul '17

The Netherlands eScience Center is organising a series of eScience Academy Essential Skills Workshops to teach essential computing skills for scientific research. Those are single-day, focused workshops based on Software Carpentry lessons. Three events coming in September are: • Version Control with Git and Collaboration with GitHub https://escience-academy.github.io/2017-09-06-git-github/ • Unix Shell and Task Automation https://escience-academy.github.io/2017-09-07-shell-automation/ • Introduction to Scientific Data Analysis in Python https://escience-academy.github.io/2017-09-08-python-intro/ More information about the events: • The Eventbrite pages can be found here: <https://www.eventbrite.nl/o/netherlands-escience-center-8536296706> https://www.eventbrite.nl/o/netherlands-escience-center-8536296706 • In case you or potential participants have questions, please send an e-mail to <mailto:training@esciencecenter.nl> training(a)esciencecenter.nl • eScience Center LinkedIn page: <https://www.linkedin.com/feed/update/urn:li:activity:6295911502721482752> https://www.linkedin.com/feed/update/urn:li:activity:6295911502721482752 please spread the word about it. best regards, Mateusz Kuzak NLeSc m.kuzak(a)esciencecenter.nl

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postdoc position available
by Pedro Ballester 26 Jul '17

26 Jul '17

Dear all, I am searching for a postdoc to work on a project involving applied machine learning and modelling pharmacogenomics data. These are the details: http://ballester.marseille.inserm.fr/Postdoc-Computational-Drug-Design.pdf I will be grateful if you could circulate this opening in your own centres too. Best regards, Pedro

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PhD position available in Computational Biology/Oncology - Brussels
by Vincent Detours 25 Jul '17

25 Jul '17

Hello, A PhD position is available in the Computational Biology Group of IRIBHM, Universite Libre de Bruxelles. The appointment is full time for two years, then renewable for another two years. The work will focus on RNA editing in cancer—a major but mostly unexplored source of transcriptional variation in human cancers—using both whole tumor and single cell transcriptome sequencing. For an introduction to the contribution of our group to the topic see http://www.cell.com/cell-reports/abstract/S2211-1247(15)01043-8. The research will focus on the functional consequences of RNA editing and on its connection with innate immunity. IRIBHM is among the top biology lab in Belgium. It hosts ~130 researchers with interdisciplinary background and diverse research interests, including cancer biology, stem cells, brain and thyroid development. The research of the Computational Biology Group is independent (not service-oriented), but strongly connected with experimental and clinical collaborators. The applicant must hold a master degree in mathematics, computer science, engeneering or physics and have a strong interest in biology and medicine. Individual with a master in the life sciences and leaning on the geeky side of biological science with proven programming skills are also encouraged to apply. CV with grades, letter of motivation and two references should be e-mailed to vdetours(a)ulb.ac.be with title 'PhD opening 2017’ by August 28th 2017. Please, forward this announcement to whoever might be interested. All the best, Vincent Detours, Ph. D. http://homepages.ulb.ac.be/~vdetours/ IRIBHM - Université Libre de Bruxelles Bldg C, room C.4.116 ULB, Campus Erasme, CP602 808 route de Lennik B-1070 Brussels Belgium Phone: +32-2-555 4220 Fax: +32-2-555 4655 Skype: vdetours E-mail: vdetours at ulb.ac.be

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[Gtpb] Large-scale bioinformatics for Immuno-Oncology - REMINDER
by Pedro L. Fernandes 20 Jul '17

20 Jul '17

REMINDER IO17 Large-scale bioinformatics for Immuno-Oncology with Francesca Finotello and Federica Eduati IMPORTANT DATES for this Course Deadline for applications: Aug 30th 2017 Course dates: Sept 20th - Sept 22nd 2017 Candidates with adequate profile will be accepted in the next 72 hours after the application, until we reach 20 participants. Course description: The immuno-oncology approach leverages on the unique capability of the immune system to recognize and kill tumour cells. This action is hampered by escape mechanisms put in place by tumour cells like, for instance, the engagement immune checkpoints, i.e. inhibitory molecules that modulate the amplitude and duration of immune responses. Immunotherapies that block checkpoint molecules are amongst the most promising approaches in immuno-oncology for the enhancement of antitumour immunity. Thanks to high-throughput technologies, such as next-generation sequencing (NGS) and proteomics, we have now access to large-scale tumour data that can be used to investigate the interplay between tumour and immune cells and the role of the immune system in tumour progression and response to therapy. In this course, you will learn to use bioinformatics tools and mathematical modelling techniques operating on high-throughput tumour data, in order to extract features that can be used to characterise this complex tumour-immune cell interface, such as: - tumour antigens recognized by T cells - tumour-infiltrating immune cells - deregulated signalling pathways in cancer and immune cells A fully practical, hands-on approach will ensure that the newly acquire skills can be used with a great deal of autonomy. Additional details here: http://gtpb.igc.gulbenkian.pt/bicourses/IO17/ We hope that this training course will meet your interests, Pedro Fernandes -- Pedro L. Fernandes Bioinformatics Training Coordinator Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL http://gtpb.igc.gulbenkian.pt _______________________________________________ GTPB mailing list GTPB(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

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[Gtpb] Introductory BIOSTSTISTICS for Biologists - REMINDER
by Pedro L. Fernandes 20 Jul '17

20 Jul '17

REMINDER IBSTATB17 Introductory Biostatistics for Biologists with Ana Luisa Papoila and Fernanda Diamantino. The above referenced hands-on training course is open for applications IMPORTANT DATES for this Course Deadline for applications: Aug 30th 2017 Course dates: Sept 11th - Sept 15th 2017 Candidates with adequate profile will be accepted in the next 72 hours after the application, until we reach 20 participants. Course Description: This is one of our "Foundations" type courses, providing a systematic and detailed review of fundamental concepts and techniques in Biostatistics. Participants can expect to go through a set of exercises that are based on biomedical problems. These exercises are preceded by short lectures that are simple to follow. The lectures are designed to provide the conceptual framework that is needed to release the training power of the exercises, not to flood the participants with formality, which will be kept to a minimum. We will make use of a highly interactive methodology, taking advantage of our well equipped Bioinformatics training room. With this approach, we expect to bring the participants to a high degree of usage independence in using the methods that we cover. Main topics: Descriptive Statistics; Probability; Statistical Inference; Design of Experiments. Detailed description here: http://gtpb.igc.gulbenkian.pt/bicourses/IBSTATB17/ Hoping that this course meets your interests, Pedro Fernandes -- Pedro L. Fernandes Bioinformatics Training Coordinator Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL http://gtpb.igc.gulbenkian.pt _______________________________________________ Research mailing list Research(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/research ----- End forwarded message ----- _______________________________________________ GTPB mailing list GTPB(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

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FW: [Training-coordinators] 2nd international de.NBI symposium
by Alexander Botzki 20 Jul '17

20 Jul '17

On behalf of the organiser: Dear all, We would like to cordially invite you to attend the 2nd international de.NBI symposium “The Future Development of Bioinformatics Germany and Europe”. The symposium will be held on October 23-25, 2017 at the Center for Interdisciplinary Research (ZiF) in Bielefeld. This 2nd international symposium is leading on a series of annual international conferences on bioinformatics by the German Network for Bioinformatics Infrastructure http://www.denbi.de/ (de.NBI) and covers a diversity of different topics concerned with bioinformatics and life sciences, such as - Mining the Proteome and the Metabolome - Cloud Computing for Life Sciences - Microbial Bioinformatics - Plant Bioinformatics - Human Bioinformatics - Data Resources and Data Management - RNA Bioinformatics and Galaxy Please refer to the attached poster and the symposium homepage http://www.denbi.de/symposium2017 for more information. - Registration deadline until September 15, 2017 - Abstract submission until September 23, 2017 With best regards on behalf of the organizing committee Daniel Wibberg de.NBI training coordinator / ELIXIR Germany training coordinator (deputy)

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ELIXIR Innovation and SME Forum "Data-Driven Innovation in Food, Nutrition and Microbiome"
by Kim De Ruyck 19 Jul '17

19 Jul '17

Dear, I would like to inform you on a meeting that is being organized by ELIXIR. Please find information below. You are welcome to spread information to interested parties. [ https://www.elixir-europe.org/events/elixir-innovation-and-sme-forum-data-d… | ELIXIR Innovation and SME Forum ] on " Data-Driven Innovation in Food, Nutrition and Microbiome”, Brussels, 9-10 October 2017 . This Innovation and SME Forum brings together companies active in the probiotics, food and health sectors to stimulate interaction between companies and academic partners. The event is organized as a series of interactive sessions on "Data Sources", "Tools and Analysis" and "Integration Challenges" enabling microbiome research and innovation. It will showcase a selection of free data resources and services available through ELIXIR as well as examples of innovative companies already using public data in their business. Participants will also learn about the training opportunities on food, nutrition and microbiome resources available through ELIXIR. Companies and SMEs will have the opportunity to present their activities and explore possible collaborations through a dedicated flash-talk session. Confirmed speakers include Wim Haentjens (European Commission, DG Research & Innovation – Agri-food unit), Peer Bork (Group Leader, European Molecular Biology Laboratory) and Silvia Miret Catalan (Director Nutrition & Health Discover at Unilever). More information on the event can be found here: [ https://www.elixir-belgium.org/events/SMEforum_91017 | events page ] – [ https://drive.google.com/file/d/0B8in1NtGRloYTi1VVGgxWF92NFk/view | program ] - [ https://www.eventbrite.co.uk/e/data-driven-innovation-in-food-nutrition-and… | registration ] . Contacts: Kim De Ruyck (ELIXIR Belgium Coordinator, kim.deruyck(a)elixir-belgium.org) and Pablo-Roman Garcia (ELIXIR Industry Officer, pablo.roman(a)elixir-europe.org) This ELIXIR event runs back-to-back with the international workshop on " [ http://www.ewi-vlaanderen.be/evenementen/personalised-nutrition-better-heal… | Personalised nutrition for better health - targeting the microbiome ] " which is organized by OECD and the Department of Economy, Science and Innovation (EWI) of the Flemish government and takes place on 10-11 October 2017 . This workshop will address policy needs to develop this area. Contact: Kathleen D'Hondt (Policy Analyst, kathleen.dhondt(a)ewi.vlaanderen.be) Kind regards, Kim De Ruyck -- Kim De Ruyck PhD Coordinator ELIXIR Belgium VIB, Technologiepark 927, 9052 Gent | +32 (0)9 33 13 694 [ http://www.elixir-belgium.org/ | www.elixir-belgium.org ] [ https://twitter.com/ELIXIRnodeBE | @ELIXIRnodeBE ] [ http://eepurl.com/cl-xOX | Subscribe to our mailing list ] [ https://www.elixir-belgium.org/events/SMEforum_91017 ]

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Training Course on Best practices for RNA-Seq data analysis Salerno Italy
by Celia van Gelder 19 Jul '17

19 Jul '17

COURSE ANNOUNCEMENT Please circulate this email to those who might be interested (apologies if you have already received this announcement) ELIXIR-IIB, in collaboration with University of Salerno, Italy, is pleased to announce the upcoming training course on "Best practices for RNA-Seq data analysis". IMPORTANT DATES: Course date: 27-29 September 2017 Deadline for applications: 11 September 2017 Selection will start on July 20th and those with an adequate profile will be accepted immediately, until we reach 25 participants. VENUE: Campus di Fisciano, University of Salerno, Via Giovanni Paolo II n. 132, 84084 Fisciano (SA), Italy. Full details at: https://elixir-iib-training.github.io/website/2017/09/27/RNA-seq-Salerno.ht… COURSE DESCRIPTION: The aim of this course is to get a deeper understanding of RNA-Seq experiments, providing a theoretical introduction to the data processing steps, together with practical sessions illustrating the use of the most popular data analysis tools. Starting from the raw sequenced data coming from different phenotypical samples (e.g disease vs healthy control samples), genes which are differentially expressed between the two conditions are determine. COURSE OBJECTIVES Students will gain an understanding of: - experimental design - quality control - theoretical principles of RNA-Seq data analysis process - how to identify differentially regulated genes - how to identify alternative splicing events - how to identify gene fusion events - multiple testing correction - biological interpretation of RNA-seq data Should you have any question, do not hesitate to contact the ELIXIR-IIB Training Team (elixir.ita.training(a)gmail.com <mailto:elixir.ita.training@gmail.com> ) and/or the local organiser Dr. Anna Marabotti (amarabotti(a)unisa.it <mailto:amarabotti@unisa.it> ). Thank you for your interest, the Organisers and the ELIXIR Training Team Anna Marabotti (ELIXIR Training Team and University of Salerno, Italy) Loredana Le Pera (ELIXIR Training Team and IIT, Italy) Allegra Via (ELIXIR Training Coordinator, CNR-IBPM, Italy)

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