- BBClist - maillist.psb.ugent.be

FW: Will you be joining us at VIBes in Biosciences? – 27-29 Sept 2017, Ghent
by Alexander Botzki 29 Aug '17

29 Aug '17

Dear all, On behalf of the organiser of VIBes 2017 Best regards, Alex Subject: Will you be joining us at VIBes in Biosciences? – 27-29 Sept 2017, Ghent Last weeks to register for VIBes in Biosciences – 27-29 Sept 2017 – Gent No Images? Click here<http://email.vibconferences.be/t/r-e-jliyvky-kjiylrdhht-b/> [Last weeks to register for VIBes in Biosciences – 27-29 Sept 2017 – Gent]<http://email.vibconferences.be/t/r-l-jliyvky-kjiylrdhht-r/> Dear colleague The international PhD student symposium VIBes in Biosciences will not only be hosting PhD students from all VIB research centers but we will also be welcoming PhD students from 21 different countries. Why should you also join VIBes? · For its unique training opportunities · To network with speakers and fellow PhD students · To get a bird’s eye view of research in life sciences · To receive first-hand career advice from excellent scientists · To find out how to start a spin-off based on your scientific ideas, · And last but not least, to have lots of fun! Are you feeling the vibes? Discover the full program on www.vibes2017.com<http://email.vibconferences.be/t/r-l-jliyvky-kjiylrdhht-y/> and make sure to register before September 10. Less than 2 weeks to go! Looking forward to seeing you in Ghent! The VIBes organizing committee [Register here] The VIBes organizing committee Nandita Bodra Jolien Bridelance Evi De Keuckelaere Ludger Goeminne Harmonie Etienne Aleksandra Lewandowska Halina Novak Rocco Stirparo Maria Tossounian Marlies Vanden Bempt Jaana van Gastel Marleen Vanstraelen Yannick Vervoort Jessica Vetters Iryna Voytyuk Yessica Wouters [The sponsors of VIBes in Biosciences]<http://email.vibconferences.be/t/r-l-jliyvky-kjiylrdhht-t/> [Upcoming VIB Conferences]<http://email.vibconferences.be/t/r-l-jliyvky-kjiylrdhht-i/> [http://i2.cmail19.com/static/eb/master/13-the-blueprint-3/images/facebook.p…]<http://email.vibconferences.be/t/r-l-jliyvky-kjiylrdhht-d/> [http://i4.cmail19.com/static/eb/master/13-the-blueprint-3/images/twitter.png]<http://email.vibconferences.be/t/r-l-jliyvky-kjiylrdhht-h/> [http://i7.cmail19.com/static/eb/master/13-the-blueprint-3/images/website.png]<http://email.vibconferences.be/t/r-l-jliyvky-kjiylrdhht-k/> [http://i10.cmail19.com/static/eb/master/13-the-blueprint-3/images/tweet-ico…] Tweet <http://email.vibconferences.be/t/r-tw-jliyvky-kjiylrdhht-n/> [http://i2.cmail19.com/static/eb/master/13-the-blueprint-3/images/lishare-ic…] Share <http://email.vibconferences.be/t/r-li-jliyvky-kjiylrdhht-x/>

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Final seats available for: BioSB Course Pattern Recognition (5th edition) - 25-29 September 2017
by Femke Francissen 28 Aug '17

28 Aug '17

*BioSB Course Pattern Recognition (5th edition)* *Date: 25-29 September 2017* *Location: AMC, Amsterdam* *Course Coordinator: Perry Moerland (AMC)* Website: http://biosb.nl/education/course-portfolio/pattern-recognition/ Registration: http://biosb.nl/education/course-portfolio/pattern-recognit ion/enrollment/ Please note that this course is free of charge for PhDs who are or become a member of the BioSB research school <http://biosb.nl/about/members/biosb-membership-information/>. *Description* Many problems in bioinformatics require classification: prediction of the class to which a certain object (i.e. a gene, protein, cell, patient, …) belongs. This calls for algorithms that can assign the most likely label (discrete output) to an object, given one or more measurements on that object. For most interesting problems, the underlying physics are too complex to explicitly design such an algorithm. In such cases, often a machine learning approach is taken: an algorithm is constructed, with parameters that are tuned based on an available dataset of training examples. The algorithm should predict the labels for these examples as well as possible, yet still generalize, i.e. perform well on objects not seen before. Some examples of classification problems in bioinformatics are gene finding (sequence in, gene presence out), diagnostics (gene expression data in, diagnosis out), data integration (measurements in, probability of interaction out), etc. In this course, we will introduce basic techniques from the fields of pattern recognition and machine learning to solve bioinformatics problems in a mixture of theory and lab sessions. After having followed this course, the student has a good understanding of basic pattern recognition techniques and is able to recognize what method is most applicable to data analysis problems (s)he encounters in bioinformatics applications. Topics include parametric and non-parametric classifiers, feature selection, dimensionality reduction, clustering, hidden Markov models, neural networks, and support vector machines. The course is aimed at PhD students with a background in bioinformatics, computer science or a related field, and life sciences. Participants from the private sector are also welcome. A working knowledge of basic statistics and linear algebra is assumed. Preparation material on statistics and linear algebra will be distributed before the course, to be studied by students missing the required background. The structure of the course is as follows: - *Monday *(Introduction; Marcel Reinders): Introduction to pattern recognition: measurements, features, classification. Supervised vs. unsupervised learning, relation to regression. Bayesian framework: risk, cost; evaluation: ROCs, cross-validation. Density estimation: histograms, nearest neighbour, Parzen, Gaussian Bayesian classification. - *Tuesday* (Classification; Perry Moerland): Parametric classifiers: (D)LDA, (D)QDA. Nonparametric classifiers: k-NN, Parzen. Discriminant analysis: LDA, logistic regression. Decision trees and random forests. - *Wednesday* (Feature selection and extraction; Lodewyk Wessels): Feature selection: criteria, search algorithms (forward, backward, branch & bound). Sparse classifiers: Ridge, LASSO. Feature extraction: PCA, Fisher. Embeddings: MDS. - *Thursday* (Clustering and HMMs; Perry Moerland): Hierarchical clustering. Agglomerative clustering. Model-based clustering: mixtures-of-Gaussians, Expectation-Maximization. Hidden Markov models. - *Friday* (Selected advanced topics; Marcel Reinders): Artificial neural networks. Support vector machines. Classifier ensembles. Complexity and regularisation. Deep learning. *Target audience * The course is aimed at PhD students with a background in bioinformatics, computer science or a related field, life sciences. Participants from the private sector are also welcome. A working knowledge of basic statistics and linear algebra is assumed. Preparation material on statistics and linear algebra will be distributed before the course, to be studied by students missing the required background. *Learning objectives* After having followed this course, the student has a good understanding of basic pattern recognition and machine learning techniques and is able to recognize what method is most applicable to data analysis problems (s)he encounters in bioinformatics applications. This course is part of the Education Programme of BioSB <http://biosb.nl/education/course-portfolio-2/>, 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. ** ** *Femke Francissen* Community manager BioSB Research School *NEW V*isiting address (as of 1 July 2017): Jaarbeurs Innovation Mile (JIM) | 6th floor Beatrixgebouw | Jaarbeursplein 6 | 3521 AL Utrecht *NEW **Postal address *(as of 1 July 2017): Postbus 8500 | 3503 RM Utrecht E-mail: femke.francissen(a)biosb.nl Mobile: +31 6 17 90 4888 Skype: femke.francissen Website: www.biosb.nl LinkedIn link <http://nl.linkedin.com/in/femkefrancissen>

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postdoc position on dynamic 3D chromatin structures in plants in response to developmental cues and environmental changes; U-Tubingen
by Tom Ruttink 24 Aug '17

24 Aug '17

Dear, could you please circulate this job announcement through your e-mail list? thank you in advance, kind regards, Tom Ruttink Senior Scientist Genomics ILVO Instituut voor Landbouw-, Visserij- en Voedingsonderzoek Flanders research institute for Agriculture, Fisheries and Food Eenheid Plant - Groei en Ontwikkeling | Plant Sciences Unit - Growth and Development Caritasstraat 39 9090 Melle (Belgium) T +32 9 272 28 78 tom.ruttink(a)ilvo.vlaanderen.be<mailto:tom.ruttink@ilvo.vlaanderen.be> www.ilvo.vlaanderen.be<http://www.ilvo.vlaanderen.be/> www.ilvogenomics.be<http://www.ilvogenomics.be/> [http://intranet.ilvo/Portals/0/images/Communicatie/Huisstijl/Twitter.jpg]<https://twitter.com/ILVOvlaanderen> [http://intranet.ilvo/Portals/0/images/Communicatie/Huisstijl/FB.jpg?ver=201…] <http://www.facebook.com/instituutvoorlandbouwenvisserijonderzoek> [http://intranet.ilvo/Portals/0/images/Communicatie/Huisstijl/LinkedIn.jpg] <https://www.linkedin.com/company/ilvo> /////////////////////////////////////////////// [http://intranet.ilvo/Portals/0/images/Communicatie/Huisstijl/Leeuw.jpg]

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Vacancy: senior bioinformatics scientist
by Nicola Bonzanni 23 Aug '17

23 Aug '17

Dear All, We are currently looking for a senior bioinformatics scientist to join our team. More information below or at https://www.enpicom.com/careers/. Kind Regards, Nicola Bonzanni, CSO ENPICOM | Science Park 402 | 1098 XH Amsterdam www.enpicom.com<http://www.enpicom.com/> +31 (0)20 895 0964 +31 (0)648 913793 WORKING AT ENPICOM ENPICOM is a young, dynamic and expanding biomedical software development company. We use computational biology to build solutions that truly matter and improve people's lives and health. Originally setup in 2015 to create tailored computational solutions for life science, but since 2017 also on a mission to bring innovative products to the market to support the development, guidance and monitoring of immunotherapies. Our first product under development is a T-cell receptor and B-cell receptor repertoire analysis platform. ENPICOM has a strong focus on developing bleeding edge technology, combined with a passion for the well-being of people. Quality, creativity and self-development are our top priorities. We believe in a good work-life balance. We offer flexible working hours, flexibility in organizing your work and an employee stock ownership plan. WE AIM HIGH You are a best-in-class bioinformatician and considered an expert in your field, have a getting the job done mentality, stand for quality and continuous improvement. You believe your job is never finished and can always be improved. You don't mind a good discussion on the best solution and are continuously looking for the latest technology and features, all in the interest of the best results. You are a true team player and want to share your knowledge and learn from others, yet you are also perfectly capable of working independently. YOUR ROLE As senior bioinformatics scientist in our team, you will have a leading role in coordinating our customer projects and at the same time will be deeply involved in product development. You run the internal validation studies, provide content support to the commercial team, write (white) papers, present at conferences and are involved in customer deployment. YOUR PROFILE Required Qualifications: * A PhD in Bioinformatics or Computational Biology * At least 4 years of hands-on Next-Generation Sequencing data analysis experience * Proficiency in R and/or Python * Working experience with Linux operating system * An excellent scientific track-record, backed by publications and recommendations * Experience in handling multiple projects in parallel * Excellent communication skills * Fluent in English (speaking Dutch is an advantage) Desirable experience: * Experience in TCR/BCR repertoire analysis and/or immunology * Experience in an object-oriented programming language like Java or C++ LOCATION 's-Hertogenbosch, The Netherlands JUST CONTACT US If you need more information about this job opportunity or are already excited to get on board, mail or call Nicola Bonzanni (Chief Scientific Officer) at n.bonzanni(a)enpicom.com. We look forward to hearing from you.

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ELIXIR-EXCELERATE Train the Trainer event - Salerno, Italy - 27-29 September, 2017
by Alexander Botzki 22 Aug '17

22 Aug '17

On behalf of Allegra and for those you wish to get or extend trainer skills Dear Training Coordinators, Three weeks ago, we announced the 9th ELIXIR-EXCELERATE TtT course, which will take place in Salerno, IT, 27-29 September. Could you please make aware the community of trainers in your node of this opportunity? Thank you, Allegra COURSE ANNOUNCEMENT Please circulate this email to those who might be interested. ELIXIR-IIB, in cooperation with the ELIXIR-EXCELERATE Train-The-Trainer programme, is pleased to announce a Train the Trainer (TtT) event in connection with a training course on “Best Practices for RNA-Seq analysis<https://elixir-iib-training.github.io/website/2017/09/27/RNA-seq-Salerno.ht…>”. IMPORTANT DATES: Course date: 27-29 September 2017 VENUE: University of Salerno, Fisciano (SA), Italy. We will accept a maximum of 15 participants. Priority will be given to candidates from ELIXIR nodes. Notifications of acceptance will be sent shortly after the application, which will remain open until we reach 15 participants. Full details and the application form at: https://elixir-iib-training.github.io/website/2017/09/27/train-the-trainer-… COURSE DESCRIPTION: The course is made up of four sessions, covering: · Learning principles and how they apply to training and teaching · Teaching techniques that can be used to enhance learner engagement and participation · Assessment and feedback in training and teaching · Lesson, course, and materials design Examples and discussions will also focus on the challenges presented by academic teaching. Who may be interested in this course? Whoever wants to become a teacher or a better one. If you have questions like the following ones, this course may be very helpful to you. · How learning works? · How can I use learning principles to improve my teaching? · How can I make my teaching more engaging and effective? · How should I adjust my teaching to different types of learners? · How can I help slow learners? · How can I assess whether my students are actually understanding my lessons? Are they actually learning? · What is the best balance between theory and practice? · How can I best assess whether learning is occurring and/or has occurred? · What works in a classroom and what doesn’t? · Etc. Should you have any question about organisational issues, do not hesitate to contact the ELIXIR-IIB Training Team (elixir.ita.training(a)gmail.com<mailto:elixir.ita.training@gmail.com>) or the local organiser Anna Marabotti (amarabotti(a)unisa.itamarabotti<mailto:amarabotti@unisa.itamarabotti>@unisa.it<http://unisa.it/>). If you have questions regarding the course goals and content, you may contact the trainers: Allegra Via (allegra.via(a)gmail.com<mailto:allegra.via@gmail.com>) and Pedro Fernandes (pfern(a)igc.gulbenkian.pt<mailto:pfern@igc.gulbenkian.pt>). Thank you for your interest, The Organisers and the ELIXIR-IIB Training Team

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[Gtpb] MSc level Scholarship in Portugal (technical support and consulting in Bioinformatics)
by Pedro L. Fernandes 11 Aug '17

11 Aug '17

MSc level Scholarship in Portugal (technical support and consulting in Bioinformatics) The activities proposed for this position have the purpose of contributing to the development of the IGC Bioinformatics suport facility in the context of the Biodata.pt infrastructure. The candidate will perform technical support and consulting regarding the analysis of biological data using existing computational approaches. She/He also contribute to the development of a computational infrastructure suitable for the execution of bioinformatics analysis. He/She will promote the use of computational methods in the analysis of biological data through the production and delivery of training materials and computational resources. Finally, he/she will contribute to the creation of a wider network of bioinformatics support units at the national level. http://www.eracareers.pt/opportunities/index.aspx?task=global&jobId=92103 -- 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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Hellenic Bioinformatics Conference - Heraklion, Greece, September 6-9
by Yves Moreau 03 Aug '17

03 Aug '17

Dear colleagues, We are organizing the 10th conference of the Hellenic Bioinformatics society in Heraklion, Crete, on September 6-9, 2017, on genomics & bioinformatics and the future of the field in Greece You can find more information about our conference at https://hscbio.wordpress.com/conferences-when/2017-2/ <https://hscbio.wordpress.com/conferences-when/2017-2/>. We have been able to secure a great panel of invited speakers: * Alfonso Valencia, Spanish National Cancer Research Centre, Spain: Networks based approaches in epigenomics, evolution and biomedicine. * John Ioannidis, Stanford University, USA: Credibility and utility of big data * Peter Karp, SRI, USA: The Omics Dashboard for Interactive Exploration of High-Throughput Data * Lars Jensen, Univ. Copenhagen, Denmark: One tagger, many uses: Simple text-mining strategies for biomedicine * Yves Moreau, University of Leuven, Belgium: Bayesian matrix factorization with side information and application to drug-target activity prediction * Hector-Garcia Martin, Joint Bioenergy Institute, USA: Mathematical modeling of -omics data for biofuel production through synthetic biology * Maria Pilar Francino, CSISP, Spain: Microbiota development in the gut of infants, children and adolescents * Periklis Papadopoulos, San Jose State Univ, USA: Space Technology and Space Biology * Rob Finn, EBI, UK: Expanding the reproducibility of analysis in EBI metagenomics * Carolin Frank, UC Merced, USA: Nitrogen fixation by the foliar conifer microbiome * Daniele Daffonchio, KAUST, SA: Soil development and rhizosphere effect in a High Arctic desert chronoseque-nce. * Folker Meyer, Argonne National Laboratory, USA Title: A novel pipeline for high quality amplicon analysis integrated into MG-RAST * Ewa Szczurek, University of Warsaw, Poland: Statistical and mathematical models in computational oncology * Evangelia Petsalaki, EBI, UK: Integrative study of the role of RhoGAP/GEFs in the Rho protein signaling network * Lynn Schriml, Univ of Maryland, USA: GSC metadata standards in action: MetaSUB and ISD. * Yiota Poirazi, IMBB, Greece: Modelling dendritic and neuronal contributions to cognitive functions * Daniel Lundin, SciLifeLab, Sweden: The evolution of ribonucleotide reduction * David Ussery, University of Arkansas, USA: What is Life? Conserved Functional Domains in a Hundred Thousand Bacterial Genomes * Eleftheria Zeggini, Sanger Center, UK: Progress in understanding the genomic aetiology of osteoarthritis * Panos Roussos, Mount Sinai, NY, USA: Big Data Analysis and Genetic Liability to Common Neuropsychiatric Traits We hope you will be able to support our efforts to promote the development of the field in Greece and will make it to the meeting. Best regards, Dr. IOANNIS ILIOPOULOS UNIVERSITY OF CRETE SCHOOL OF HEALTH SCIENCES

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EuBIC 2018 developer's meeting – Save the date & call for project proposals
by EuBIC developer's meeting 02 Aug '17

02 Aug '17

*— EuBIC 2018 developer’s meeting – Save the date & call for project proposals —* We are pleased to announce that the upcoming EuBIC 2018 developer’s meeting will be held in Ghent, Belgium, on January 9-12, 2018. The EuBIC 2018 developer's meeting will bring together scientists active in the field of bioinformatics and computational proteomics. Date: January 9-12, 2018 Venue: Hotel Monasterium PoortAckere, Oude Houtlei 56, 9000 Gent, Belgium Website: http://uahost.uantwerpen.be/eubic18/ *Key dates* September 17, 2017: Project proposal submission deadline October 2, 2017: Announcement of selected projects October 2, 2017: Conference registration opens January 9-12, 2018: EuBIC 2018 developer's meeting in Ghent *Call for project proposals* The call for topics for the hackathon sessions during the EuBIC 2018 developer's meeting is now open! During the EuBIC 2018 developer’s meeting the participants will engage in a hackathon where they will develop bioinformatics tools and resources. The participants will break up into small groups to work together on these topics in an open, constructive, and productive atmosphere. You can now submit project proposals for inclusion into the EuBIC 2018 developer’s meeting program. Submit your project proposal before 17 September through the meeting website: http://uahost.uantwerpen.be/eubic18/submission.html *Topics* Hackathon projects can cover all topics in proteomics bioinformatics, including, but not limited to: - Tools - Extension of existing bioinformatics tools under the guidance of their original authors - Development of novel bioinformatics tools to solve open problems - Benchmarking - Compilation of gold-truth datasets - Collection of reference algorithmic implementations - Specification of benchmarking criteria - Workflows - Definition of formal protocols - Development of tutorials for bioinformatics software usage - Data analysis - (Re)analysis of publicly available proteomics datasets *More information* - Website: http://uahost.uantwerpen.be/eubic18/ - Social media hashtag: #EuBIC18 - Conference email: *eubic18(a)gmail.com <eubic18(a)gmail.com>* *Sponsorship* inquiries are welcome at *eubic18(a)gmail.com <eubic18(a)gmail.com>* We look forward to welcoming you in Ghent! On behalf of the organizing committee, Wout Bittremieux

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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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