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PPB18 - Hands-on Training Course on Programming in Python - Announcement / Reminder
by Pedro L. Fernandes 09 Jul '18

09 Jul '18

Course Announcement / Reminder PPB18 Programming in Python (for Biologists, but not only) with Allegra Via, Vincenza Colonna and David P. Judge Key terms: Programming, Python IMPORTANT DATES for this Course Deadline for applications: July 18th 2018 Latest notification of acceptance: July 19th 2018 Course date: July 23rd - July 27th 2018 The GTPB is proud to announce that the above referenced hands-on training course is open for applications Admission: Candidates with adequate profile will be accepted in the next 72 hours after the application until we reach 20 participants. Course description: Python is a programming language that is ideal for data processing. The course will start from zero knowledge, and will introduce the participants to all the basic concepts of programming such as calculating, repeating things, making choices, reading and writing files, filtering and organising data, program logic and writing larger programs. The examples and practical sessions will mostly focus on managing biological data. In particular the sessions will cover: - parsing common file formats (Uniprot, GenBank, PDB, BLAST) - data retrieval from files and their manipulation - finding motifs in sequences - manipulating tables - plotting data The course will be highly interactive and the participants will continuously put theory into practice while learning. At the end of the course, the participants will have a good understanding of programming basics and will have acquired the skills to manage bioinformatics database record and data files. Basic Unix/Linux skills will be provided at the beginning of the course. Participants are welcome to bring to the course the "typical" text file that they may need to filter, manipulate or analyse such a table, a file in fastq or fasta format, a PDB file, etc. The course is directed to biologists with little or no programming experience and aims at making them capable to use Python to autonomously manage and analyse biological data. More information at the GTPB website, http://gtpb.igc.gulbenkian.pt/bicourses/2018/PPB18// Hoping that this course meets your interests, Pedro Fernandes -- The Gulbenkian Training Programme in Bioinformatics Pedro L. Fernandes, Organiser Instituto Gulbenkian de Ciência Rua da Quinta Grande, 6 2780-156 OEIRAS Portugal -- Pedro L. Fernandes Bioinformatics Training Coordinator Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL http://gtpb.igc.gulbenkian.pt

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ELIXIR-EXCELLERAE TtT, August 20-21, Antwerp
by Mateusz Kuzak 09 Jul '18

09 Jul '18

Dear all, I’m pleased to announce the Train the Trainer (TtT) event organised by ELIXIR-EXCELERATE, ELIXIR-Belgium and ELIXIR-NL. Date: August 20-21, 2018 Venue: Antwerp, Belgium Full details and the application form at: https://www.eventbrite.com/e/elixir-excelerate-train-the-trainer-registrati… The course will be taught by Paula Martinez from VIB and ELIXIR-Belgium and myself. This workshop is a great way to improve teaching skills and learn modern, evidence based pedagogy. Should be of interest for anyone who teaches at various training, gives lectures or designs learning content. COURSE DESCRIPTION: The course is organized around 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. This course is meant to offer guidance, ideas and tips for training/teaching design, development and delivery based on research-driven educational principles. There is no course attendance fee. The participants will need to bear their travel, hotel (if any) and meal costs. Candidates from ELIXIR nodes might apply for an ELIXIR Staff Exchange Programme Travel Grant when they fill their application form. Apologise for cross-posting. Mateusz — Mateusz Kuzak Scientific Community Manager | Dutch Techcentre for Life Sciences e-mail: mateusz.kuzak(a)dtls.nl | tel. +31 643707254 twitter: @matkuzak | github: mkuzak | skype: mkuzak Visting address: DTL | Jaarbeurs Innovation Mile (JIM) | 6th floor Beatrixgebouw Jaarbeursplein 6 | 3521 AL Utrecht

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Fwd: postdoc opportunity
by Patrick Deelen 06 Jul '18

06 Jul '18

---------- Forwarded message ---------- From: Gosia Trynka <gosia(a)sanger.ac.uk> Date: Fri, Jul 6, 2018 at 12:34 PM Subject: postdoc opportunity To: "patrickdeelen(a)gmail.com" <patrickdeelen(a)gmail.com> Zam Iqbal at EBI and myself at Sanger Institute, are recruiting for an ESPOD position. These are prestigious fellowships that give a unique opportunity to work closely with groups at the two Institutes which are located at the Wellcome Genome Campus. We are recruiting for a postdoc to lead on a very exciting project, assessing gene regulation in the MHC region using variation graphs. Zam is one of the leaders in the field of variation graphs algorithms. Whilst my group has strong expertise in gene expression regulation in the context of immune cells and linking these effects with immune disease variants. This is an opportunity to apply algorithms at the forefront of sequence alignment methods to a wide variety of functional genomics data generated in my group and deposited in public resources, to ultimately help interpret the function of immune-disease associated variants. More details about the project can be found in this link: https://www.embl.de/jobs/pdf/ESPOD_Fellowship_project_4.pdf Get in touch if you have any questions. Please apply if this sounds exciting, the deadline is approaching soon, July 20th. Best regards, Gosia

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interested in shaping your trainers' capacities - announcement of train the trainer events this year
by Alexander Botzki 04 Jul '18

04 Jul '18

Hi all, on behalf of colleagues from ELIXIR training, please see below the announcements. Cheers, Alex COURSE ANNOUNCEMENT ELIXIR-EXCELERATE is pleased to announce the following Train the Trainer (TtT) events: - August 20-21, 2018 Venue: Antwerp, Belgium Full details and the application form at: https://www.eventbrite.com/e/elixir-excelerate-train-the-trainer-registrati… - September 27-28, 2018 Venue: Italian National Research Council (CNR), Rome, Italy Full details and the application form at: https://elixir-iib-training.github.io/website/2018/09/27/train-the-trainer-… - October 9-11, 2018 (2 days) Venue: Science for Life Laboratory, Solna, Sweden Full details and the application form at: https://elixir-iib-training.github.io/website/2018/10/09/train-the-trainer-… COURSE DESCRIPTION: The course is organized around 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. This course is meant to offer guidance, ideas and tips for training/teaching design, development and delivery based on research-driven educational principles. There is no course attendance fee. The participants will need to bear their travel, hotel (if any) and meal costs. Candidates from ELIXIR nodes might apply for an ELIXIR Staff Exchange Programme Travel Grant<https://docs.google.com/document/d/1YbbHoH2YYbM6sbPGypOTkIcNToYXo5XPcn99CSV…> when they fill their application form. We apologise for cross-posting. Thank you for your interest, kind regards, Loredana Le Pera. (ELIXIR-IIB Training Coordinator Deputy)

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bioinfo/biostatistician job at the University of Luxembourg
by Aurélien GINOLHAC 02 Jul '18

02 Jul '18

Dear all, The Life Sciences Research Unit of the University of Luxembourg is looking for a bioinfo/biostatistician. Fixed term contract of 3 + 2 years. Enthusiasm and knowledge of R required. All details here: http://emea3.mrted.ly/1vsqq <https://t.co/oSTeBBA0Tn> Best regards, Aurelien Ginolhac -- University of Luxembourg Faculty of Science, Technology and Communication Life Science Research Unit Campus Belval, Biotech II – Office 4.22 6, Avenue du Swing L-4367 Belvaux Phone: (+352) 46 66 44 6560

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PostDoc positions available
by Claesson, Marcus 01 Jul '18

01 Jul '18

Two postdoc positions are now available in my lab: https://www.ucc.ie/en/hr/vacancies/research/full-details-888782-en.html https://www.ucc.ie/en/hr/vacancies/research/full-details-888796-en.html Please circulate to anyone who might be interested. Marcus -- Marcus J. Claesson, PhD Lecturer at School of Microbiology & Principal Investigator at APC Microbiome Ireland University College Cork Western Road, Cork, Ireland Tel: +353-(0)21-4901390 Email: m.claesson(a)ucc.ie<mailto:m.claesson@ucc.ie> http://orcid.org/0000-0002-5712-0623

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OLA'2019 @Thailand
by El-ghazali Talbi 28 Jun '18

28 Jun '18

Apologies for cross-posting. Appreciate if you can distribute this CFP to your network. **************************************************************************************** OLA'2019 International Conference on Optimization and Learning: Challenges and Applications 29-31 Jan 2019 Bangkok Thailand http://ola2019.sciencesconf.org/ **************************************************************************************** OLA is a conference focusing on the future challenges of optimization and learning methods and their applications. The conference OLA'2019 will provide an opportunity to the international research community in optimization and learning to discuss recent research results and to develop new ideas and collaborations in a friendly and relaxed atmosphere. OLA'2019 welcomes presentations that cover any aspects of optimization and learning research such as optimization for learning, learning for optimization, optimization and learning under uncertainty, new high-impact applications, parameter tuning, 4th industrial revolution, hybridization issues, optimization-simulation, meta-modeling, high-performance computing, parallel and distributed optimization and learning, surrogate modeling, multi-objective optimization ... Submission papers: We will accept submissions in two different formats: - S1: Extended abstracts of work-in-progress and position papers of a maximum of 3 pages - S2: Original research contributions of a maximum of 10 pages Important dates: =============== Submission deadline Oct 19 2018 Notification of acceptance Nov 9, 2018 Proceedings: Accepted papers in categories S1 and S2 will be published in the proceedings that will be available at the conference. In addition, a post-conference indexed Springer book and special issue of Journal (ITOR International Transaction on Operational Research) is planned to be published. Participants will be invited to submit extended versions of their work for consideration. -- ******************************************** OLA'2019 Int. Conference on Optimization and Learning 29-31 Jan 2019, Bangkok, Thailand http://ola2019.sciencesconf.org ******************************************** Prof. El-ghazali TALBI Polytech'Lille, University Lille - INRIA - CNRS

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PhD and Postdoc positions
by Patrick Deelen 26 Jun '18

26 Jun '18

Application Deadline: Open Until Filled Job Description The *Radboud Institute of Molecular Life Sciences – department of Internal Medicine* – (https://www.radboudumc.nl) investigates the molecular mechanisms of human immune and infectious diseases. By integrating fundamental and clinical research, we obtain multifaceted knowledge of (patho) physiological processes. The Research Group of Vinod Kumar ( https://www.radboudumc.nl/en/people/vinod-kumar-magadi-gopalaiah) invites talented and highly motivated candidates to apply for a *PhD and Post-Doctoral Researchers (m/f) (Immuno-genetics, bioinformatics, Systems Biology)* starting on 1st of September 2018. The postdoctoral position will be for two years initially with a possibility of extension. The successful candidates will work in the domain of bioinformatics related to infectious diseases. Our group uses a multidisciplinary approach, including genetic/immunologic/transcriptomic/proteomic data integration and network biology, and GWAS to develop novel therapeutic treatments for infectious diseases. The successful postdoc candidate is expected to lead bioinformatics projects related mainly to human genetic and omic data analysis and develop bioinformatics pipelines for predicting genetic risk as well as to understand infectious processes. The successful candidate is expected to interact closely with clinicians and wet-lab scientists for discovering new genetic mechanisms using big data from both patient and population-based cohorts, followed by data analysis and data integration to determine correlations between molecular layers and genetics, and ends with the formulation of hypotheses that will be verified in functional experiments. *Your profile: *A strong interest in conducting collaborative research on the topic outlined above is paramount. Candidates are expected to be interested in working at the boundaries of several research domains. • PhD degree in Systems Biology, Computational Biology, Bioinformatics, Biophysics, Computer Science or a related discipline • Documented knowledge and experience in the analysis of biological high-throughput data is a requirement • Knowledge in statistical methods in the context of biological systems • Strong experience with programming (Python, Perl, C++, R) • Well-developed collaborative skills *For further information:* Please contact Dr. Vinod Kumar Email: v.kumar(a)umcg.nl *Applications:* Complete applications in English should include a CV, certificates, transcripts, a brief statement of research experiences and interests and the contact details of at least two possible referees.

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CALL FOR ABSTRACTS: Summer School on Machine Learning in Drug Design, August 20-22, 2018, Leuven, Belgium - DEADLINE: JULY 15, 2018
by Yves Moreau 25 Jun '18

25 Jun '18

Dear Colleague, The Summer School on Machine Learning in Drug Design will take place on August 20-22, 2018 in Leuven, Belgium. This Summer School will bring together the machine learning, chemoinformatics, and bioinformatics communities from academia and industry to tackle the challenges of complex data integration in drug design and discovery. The format of the event will combine multiple keynote presentations, oral contributions selected from submitted abstracts, and extensive poster sessions with ample time for discussion. We invite you to submit your abstract for oral presentation or poster by July 15, 2018 at http://mldd.esat.kuleuven.be. More information is available below and at http://mldd.esat.kuleuven.be, or by email at mldd(a)esat.kuleuven.be. Registration will open shortly. Best regards, Prof. Yves Moreau, University of Leuven Prof. Sepp Hochreiter, Johannes Kepler University of Linz Prof. Samuel Kaski, Aalto University SCOPE The data sets amenable to mining for drug design are rapidly expanding. This holds not only for the volume of conventional annotation of chemicals (i.e., representations of their chemical structure and their activities in a growing set of validated assays). It also goes for less conventional data sources, such as cellular microscopy or gene expression profiles of chemicals acquired at high throughput. Powerful novel machine learning methods unleashed on these massive volumes of heterogeneous and rich, but noisy and biased data, hold the promise of better and safer drugs to address unmet medical needs. To deliver on that promise, the Summer School calls on the machine learning, big data analytics, cheminformatics and bioinformatics communities to join forces and strengthen collaborative work at the interface of their disciplines. The Summer School will bring together contributors from both academia and industry to foster interdisciplinary exchange in this area where the need for expertise is growing rapidly. Contributions will cover recent advances in chemogenomics, strategies for data fusion, and machine learning. INVITED SPEAKERS Djork-Arné Clevert (Bayer) Daniel Reker (MIT) Gerard van Westen (Leiden University) Florian Nigsch (Novartis) Thomas Blaschke (AstraZeneca) Tim Becker (Harvard University) Gilles Marcou (University of Strasbourg) Val Gillet (University of Sheffield, TBC) INTENDED AUDIENCE AND FORMAT The summer school is intended for academic and industry researchers in machine learning, chemoinformatics, or bioinformatics who are either currently working at the interface between these fields or want to expand their skills to link these three areas. The summer school is also intended as a bridge between academia and industry. The format of the event will combine comprehensive invited presentations, oral contributions selected from submitted abstracts, and extensive poster sessions with ample time for discussion. ABSTRACT SUBMISSION Participants are invited to submit abstracts for oral contributions and posters by July 15, 2018. Abstracts can submitted for consideration for oral presentation (up to 1,000 words) or for consideration as poster only (up to 250 words). Abstracts selected for oral presentation will be notified by July 22, 2018. Abstracts will be available as a book of abstracts and online, but there will be no full proceedings. REGISTRATION AND FEE Early registration fee (before July 20, 2018): €150 (+ 21% VAT) = €181.5 Late registration fee (before August 13, 2018): €250 (+ 21% VAT) = €302.5 The fee covers participation to the meeting and includes coffee breaks and lunch (sandwich lunch). Registration will open shortly. VENUE The Summer School will be held at the Irish College, a beautifully restored historical building in the center of Leuven, Belgium.

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++ Submission deadline extension - ESCS 2018, Athens +++
by Daniele Parisi 25 Jun '18

25 Jun '18

Dear all, In case you hadn't submit your project yet, the executive team of the European Society of Computational Biology and Bioinformatics is glad to announce the extension of the submission to deadline to FRIDAY 13TH JULY 2018 (see flyer attached). Do not miss the chance to apply for a place at the poster session, at the student talk session or to request a travel fellowship. Among the other initiatives, we are also organizing a round table on ethics and bioinformatics, with speakers like prof. Yves Moreau and Dr. Masha Shabani, a unique opportunity for professional and personal growth. Register, submit and read more on our website http://escs2018.iscbsc.org/ -- DANIELE PARISI PhD student at ESAT - STADIUS, Yves Moreau's group President of RSG Belgium Chair of ESCS 2018 Kasteelpark Arenberg 10 - box 01.34 3001 Leuven, Belgium Tel: +32488794394

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