- BBClist - maillist.psb.ugent.be

Software engineer position in the area of clinical and translational medicine domain
by Venkata Pardhasaradhi SATAGOPAM 06 Jun '18

06 Jun '18

Dear all We are looking for a "software engineer for web-based translational medicine knowledge management and analysis tools” at Luxembourg Centre For Systems Biomedicine (LCSB), University of Luxembourg. Please refer the below URL for more details: http://recruitment.uni.lu/en/details.html?id=QMUFK026203F3VBQB7V7VV4S8&nPos… 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 +352-466-644-36421 venkata.satagopam(a)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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AlCoB 2018: call for participation
by IRDTA 04 Jun '18

04 Jun '18

AlCoB 2018: call for participation********************************************************************************** 5th INTERNATIONAL CONFERENCE ON ALGORITHMS FOR COMPUTATIONAL BIOLOGY AlCoB 2018 Hong Kong June 25-26, 2018 Co-organized by: The Hong Kong Polytechnic University Department of Computing Research Group on Mathematical Linguistics (GRLMC) Rovira i Virgili University http://grammars.grlmc.com/AlCoB2018/ ********************************************************************************** PROGRAM Monday, June 25 09:00 - 09:30 Registration 09:30 - 09:40 Opening 09:40 - 10:30 Tatsuya Akutsu. Algorithms for Analysis and Control of Boolean Networks - Invited lecture 10:30 - 11:00 Coffee break 11:00 - 12:15 Ricson Cheng, Matthew Dohlen, Chen Pekker, Gabriel Quiroz, Jincheng Wang, Ran Libeskind-Hadas and Yi-Chieh Wu. Reconciliation Feasibility of Non-binary Gene Trees under a Duplication-Loss-Coalescence Model Andreas Dwi Maryanto Gunawan. Solving the Tree Containment Problem for Reticulation-visible Networks in Linear Time Leo van Iersel, Remie Janssen, Mark Jones, Yukihiro Murakami and Norbert Zeh. Polynomial-time Algorithms for Phylogenetic Inference Problems 12:15 - 13:45 Lunch 13:45 - 14:35 Ben Raphael. Algorithms for Cancer Evolution - Invited lecture 14:35 - 14:50 Break and Group photo 14:50 - 16:05 Alexsandro Alexandrino, Carla Lintzmayer and Zanoni Dias. Approximation Algorithms for Sorting Permutations by Fragmentation-weighted Operations Klairton Brito, Andre Rodrigues Oliveira, Ulisses Dias and Zanoni Dias. Heuristics for the Sorting Signed Permutations by Reversals and Transpositions Problem Guilherme Miranda, Carla Negri Lintzmayer and Zanoni Dias. Sorting Permutations by Limited-size Operations 16:05 - 16:20 Coffee break 16:20 - 17:10 Poster presentations 17:15 - 19:15 Touristic visit --- Tuesday, June 26 09:00 - 09:50 Bin Ma. De Novo Protein Sequencing with Mass Spectrometry and Its Medical Applications - Invited lecture 09:50 - 10:20 Coffee break 10:20 - 11:35 Michael Sadovsky, Sergey Tsarev and Maria Senashova. Fast Algorithm for Vernier Search of Long Repeats in DNA Sequences with Bounded Error Density Eugen Czeizler, Alexandru Popa and Victor Popescu. Fixed Parameter Algorithms and Hardness of Approximation Results for the Structural Target Controllability Problem Chenqi Mou. Symbolic Detection of Steady States of Autonomous Differential Biological Systems by Transformation into Block Triangular Form 11:35 - 11:50 Break 11:50 - 12:40 Jordi Silvestre-Ryan and Ian Holmes. Consensus Decoding of Recurrent Neural Network Basecallers Ezra B. Wijaya, Erwandy Lim, David Agustriawan, Chien-Hung Huang, Jeffrey J.P. Tsai and Ka-Lok Ng. Utilizing Imputation and Meta-analysis to Identify DNA-methylation-mediated MicroRNAs in Ovarian Cancer 12:40 - 12:50 Closing 12:50 - Lunch

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Bioinformatician position at UCL (Brussels)
by Benoît Van den Eynde 04 Jun '18

04 Jun '18

Dear All, The de Duve Institute at the Université catholique de Louvain (Brussels) is looking for a highly motivated post-doctoral bioinformatician with hybrid-expertise, able to integrate bioinformatics/computational biology/systems biology/biostatistics, and data from different omics-approaches in the context of biological questions. The suitable candidate would be working within the context of the ‘DECODE’ consortium, whose research aims are at the interface of the immunobiology of cell death processes and cancer immunotherapy. For more details, please refer to the attached job offer. Do not hesitate to forward this email to anyone who might be interested. Best regards, Auriane Sibille Assistant to Professor Benoît Van den Eynde Ludwig Institute for Cancer Research Ltd de Duve Institute, Université catholique de Louvain Av. Hippocrate, 75 Bte B1.74.03 B - 1200 Brussels BELGIUM Phone: +32 2 764 75 80 Fax: +32 2 764 75 90 E-mail: auriane.sibille(a)bru.licr.org<mailto:auriane.sibille@bru.licr.org>

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[Gtpb] MSc level scholarship available
by GTPB Administration 02 Jun '18

02 Jun '18

Dear All A nice opportunity for someone wanting to have a fresh start at Bioinformatics Training provision. Biodata-PT, the Portuguese national infrastructure for biomedical data, is selecting a Training Assistant to scale-up from the GTPB training model, and lay-out the plans to reproduce training at the country level. International connections, substantial learning in Bioinformatics and practice in training provision. Training Assistant for Biodata.pt (recruiting) http://www.eracareers.pt/opportunities/index.aspx?task=global&jobId=100246 Please help us to find the right person. Open for applications from June 4th to June 15th Thank you 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 _______________________________________________ GTPB mailing list GTPB(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb Click here to unsubscribe: https://lists.igc.gulbenkian.pt/mailman/options/gtpb/bbclist%40psb.vib-ugen…

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Course Data management and computational workflows, 25 June 2018, Amsterdam
by Celia van Gelder 02 Jun '18

02 Jun '18

Dear all Please find below the information about the course Data Management and Computational Workflows that will take place June 25 in Amsterdam. Registration is free of charge. There are ca. 20 places. First come, first serve. It is a course from the regular SURFsara portfolio but for this edition there is a focus on life sciences examples. The weblink for the course is here: https://www.surf.nl/en/agenda/2018/06/course-data-management-and-computatio… Please spread this announcement in your organization as you see fit. Best Celia SURFsara, ELIXIR-nl and ELIXIR introduce how data management based on iRODS can be incorporated into computational workflows. Date: 25 Jun 2018 Time: 09:30-16:30 Location: <https://www.surf.nl/en/about-surf/contact/directions-to-surfsara/index.html> SURFsara Science Park 140 VK1/2 Prior knowledge needed? No Description With the advance of new technologies, data volumes and numbers of files are constantly increasing. Good datamanagement is therefore an essential part of data-driven research. In response to the need of researchers and new regulations (e.g. GDPR) for better data management tools, we are currently developing a data management platform at SURFsara on the basis of iRODS. For whom? Bioinformaticians, computational biologists, data stewards in the field Life Sciences. Training objectives Learn about the concept of iRODS’s resource abstraction Gain hands on experience with managing data with iRODS Steer data flows across different iRODS administrative domains Work with metadata attached to data managed by iRODS and how to query for data using this metadata. After an introduction the training will purely be hands-on and will be taught in the style of software and data carpentry, i.e. live-coding sessions with exercises. Topics in this course will include: Data Life Cycle and FAIR principles * iRODS concepts * Metadata and searching for data in iRODS * Building a computational pipeline that draws on data managed in iRODS Requirements (or pair up with someone familiar with): Bash commands and basic python You need to be able to connect with ssh, bring your own client

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Summer School on Rare Disease and Orphan Drug Registries including BYOD - Sep 10-14 2018 - Rome, Italy
by Celia van Gelder 02 Jun '18

02 Jun '18

COURSE ANNOUNCEMENT Please circulate this email to those who might be interested. The National Centre for Rare Diseases, Istituto Superiore di Sanità (Rome, Italy), in collaboration with ELIXIR-IIB, ELIXIR-NL, RD-Connect, EURORDIS, Orphanet, EuRRECa, European Reference Networks, EPIRARE and ICORD, is pleased to announce the "6th International Summer School on Rare Disease and Orphan Drug Registries", including Bring Your Own Data Registries. COURSE DESCRIPTION: Registries are key resources in order to increase timely and accurate diagnosis, improve patients management, tailor treatments, facilitate clinical trials, support healthcare planning and speed up research. The course will provide participants with useful tools and methodologies for establish a registry, the quality of the data collected and how a registry is turned into a FAIR resource. It intends: i) to promote the establishment of Findable, Accessible, Interoperable, Reusable (FAIR) registries in compliance with IRDiRC and EU Recommendations; ii) to support cooperation among different registry stakeholders and coordination with registries that are developed within European Reference Networks and National Plans in the EU. The course is organized in two training modules with the following objectives: * the first one (“Rare Disease Registries”, September 10-12, 2018) will provide participants with useful tools and methodologies to plan, establish and manage the registry activities. * the second one (“Bring Your Own Data - BYOD”, September 13-14, 2018) will be a hands-on experience (Bring Your Own Data), where the attendees work with FAIR data experts to make their data FAIR and linked to other data that has been made FAIR before. The "6th International Summer School on Rare Disease and Orphan Drug Registries" is open to health professionals, researchers, medical specialists, registry curators, database managers and representatives of patients’ associations involved in or intend to establish a rare disease registry, including ERN registries. Registration is possible for: - the first training module (Rare Disease Registries, Sept. 10-12, 2018) - the second training module (Bring Your Own Data- BYOD, Sept. 13-14, 2018) - or both (Rare Disease Registries and BYOD, Sept. 10-14, 2018). FEE: Registration is free of charge. Please, note that travel, subsistence and other costs incurred by the participants to attend the event are not covered by the organisers. VENUE: Aula Rossi, Istituto Superiore di Sanità, Via Giano della Bella, 34 - Rome, Italy. IMPORTANT DATES: Deadline for applications: 16 June 2018 Course date: 10-14 September 2018 Full details at: <http://old.iss.it/cnmr/?lang=1&id=2795&tipo=3> http://old.iss.it/cnmr/?lang=1&id=2795&tipo=3 Should you have any question, do not hesitate to contact the Organisers at <mailto:rareregistries-school@iss.it> rareregistries-school(a)iss.it We apologise for cross-posting. Please, email us back with the word REMOVE as the subject line, if you don't want to receive messages from ELIXIR-IIB Training anymore. Kind regards, the Organisers. -- ELIXIR-IIB Training https://elixir-iib-training.github.io/website/ <https://docs.google.com/uc?export=download&id=0B0c7_C2GRNsQTEpVMXRDeDBiQnM&…> _______________________________________________ Training-coordinators mailing list Training-coordinators(a)elixir-europe.org <mailto:Training-coordinators@elixir-europe.org>

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Register now for BioSB course: Algorithms for Biological Networks - June 25-29, Wageningen
by Femke Francissen 31 May '18

31 May '18

BioSB Course: Algorithms for Biological Networks (5th edition)Course coordinators: dr. Maria Suarez Diez (WUR), prof. dr. Dick de Ridder (WUR), dr. Jeroen de Ridder (UMCU) *Date:* June 25-29, 2018 *Location:* Wageningen University & Research *Website:* link to course page <https://www.biosb.nl/education/course-portfolio/course-algorithms-for-biolo…> *Registration:* link to registration form <https://www.biosb.nl/education/course-portfolio/course-algorithms-for-biolo…> Course description Molecular biology is concerned with the study of the presence of and interactions between molecules, at the cellular and sub-cellular level. In bioinformatics and systems biology, algorithms and tools are developed to model these interactions, with various goals: predicting yet unobserved interactions, assigning functions to yet unknown molecules through their relations with known molecules; predicting certain phenotypes such as diseases; or just to build up biological knowledge in a structured way. Such interaction models are often best modelled as networks or graphs, which opens up the possibility of using a large number of readily available algorithms for inferring networks, performing simulations of biology, optimising paths or flows through networks, graph-based data integration and graph mining. Many of these algorithms can be applied (sometimes with slight alterations) to solve a particular biological problem, such as modeling transcriptional regulation or predicting protein interaction/complex formation, but also to derive systems behaviour by breaking down networks into modules or motifs with certain characteristics. In this course, we will first give a brief overview of molecular biology, the advent of high-throughput measurement techniques and large databases containing biological knowledge, and the importance of networks to model all this. We will highlight a number of peculiar features of biological networks. Next, a number of basic network models (linear, Boolean, Bayesian) will be discussed, as well as methods of inferring these from observed measurement data. A number of alternative network models more suited for high-level simulation of cellular behaviour will also be introduced. Building on the network inference methods, a number of ways of integrating various data sources and databases to refine biological networks will be discussed, with specific attention to the use of sequence information to refine interaction and transcription regulation networks. Finally, we will give some examples of algorithms exploiting the networks found to learn about biology, specifically for inspecting protein interaction networks. Course programme The tentative course programme and course materials can be found here <http://www.bioinformatics.nl/courses/BioSB-AfBN/>. Target audience The course is aimed at PhD students with a background in bioinformatics, computer science or a related field; a working knowledge of basic statistics and linear algebra is assumed. The BioSB course “Pattern recognition” <https://www.biosb.nl/education/course-portfolio/pattern-recognition/> and the ASCI course “Advanced pattern recognition” (a1) discuss many of the tools used in this course, but it is not required to have followed these. Prior knowledge of molecular biology is a bonus, but also not strictly required. BioSB research school 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.

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Fwd: Tenure track in Amsterdam on Multiscale Scientific Computing
by Sanne Abeln 30 May '18

30 May '18

See the link below for a tenure track position in Amsterdam, the closing date is 30 June. http://www.uva.nl/en/content/vacancies/2018/05/18-294-assistant-professor-m… -- Computational Science <http://uva.computationalscience.nl> Lab <http://uva.computationalscience.nl> Master Programme Computational Science <http://www.uva.nl/en/shared-content/subsites/graduate-school-of-sciences/en…> -- -- Sanne Abeln Assistant Professor Bioinformatics - VU University Amsterdam s.abeln(a)vu.nl +31 20 59 87816 www.few.vu.nl/~abeln <http://www.few.vu.nl/%7Eabeln> -- -- Sanne Abeln Assistant Professor Bioinformatics - VU University Amsterdam s.abeln(a)vu.nl +31 20 59 87816 www.few.vu.nl/~abeln <http://www.few.vu.nl/%7Eabeln>

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Upcoming training workshops at Edinburgh Genomics: Linux for Genomics and Intro to RNAseq Analysis
by DUNBAR Donald 29 May '18

29 May '18

Hello all, we have some new dates for our popular Edinburgh Genomics training workshops<https://genomics.ed.ac.uk/services/training>. We now offer registration, on a first come first served basis, to our Linux for Genomics and Introduction to RNAseq Data Analysis workshops developed and taught by our Edinburgh Genomics Bioinformaticians. 1. Introduction to RNAseq Data Analysis, Tuesday 19th to Wednesday 20th June 2018 REGISTER NOW<https://www.surveymonkey.co.uk/r/6QQVF7D> 2. Introduction to RNAseq Data Analysis, Thursday 21st to Friday 22nd June 2018 REGISTER NOW<https://www.surveymonkey.co.uk/r/ZKG5F8N> 3. Linux for Genomics, Monday 25th June 2018 REGISTER NOW<https://www.surveymonkey.co.uk/r/Z8RYF8T> 4. Linux for Genomics, Tuesday 26th June 2018 REGISTER NOW<https://www.surveymonkey.co.uk/r/Z86GFSH> Please use the links provided above to register for a place. These workshops are very popular and have limited places, so please do register as early as you can. We also have a few remaining places on our Advanced Python for Biologists workshop, taught by Dr Martin Jones, founder of Python for Biologists<https://pythonforbiologists.com/>. 1. Advanced Python for Biologists, Monday 9th to Friday 13th July 2018 REGISTER NOW<https://www.surveymonkey.co.uk/r/NDSGYHL> * https://genomics.ed.ac.uk/services/training * https://genomics.ed.ac.uk/services/introduction-rna-seq-data-analysis * https://genomics.ed.ac.uk/services/linux-genomics * https://genomics.ed.ac.uk/services/advanced-python-biologists Please let me know if you have any questions or comments. Feel free to share with colleagues and contacts. With best wishes and we look forward to welcoming you to Edinburgh Genomics. Donald --- Dr Donald Dunbar Bioinformatics Operations Manager Edinburgh Genomics, Genome Science Ashworth Labs, The King's Buildings The University of Edinburgh donald.dunbar(a)ed.ac.uk The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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Job vacancy Cluster Leader Applied Bioinformatics
by Warris, Sven 24 May '18

24 May '18

Dear reader, Our cluster Applied Bioinformatics of Wageningen University and Research is looking for a new cluster leader. For more information about the job vacancy and on how to apply, please visit: https://www.wur.nl/en/Jobs/Vacancies/Show/Cluster-leader-Applied-Bioinforma… Kind regards, Sven Warris

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