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

ELIXIR/GOBLET/GTN hackathon for Galaxy training material re-use
by Frederik Coppens 21 Mar '17

21 Mar '17

Dear all we are organizing an ELIXIR/GOBLET/GTN hackathon for Galaxy training material re-use, aiming to extend and improve the content of the Galaxy Training material repo (https://github.com/galaxy-project/training-material <https://github.com/bgruening/training-material>). You can find more details here <https://docs.google.com/document/d/1dLCL5-2pkWTvmGTz7GyQkb5LEIZ3FBkPvCBoqUP…>. This workshop will take place in Cambridge, UK from 22nd to 24th of May in the framework of ELIXIR-EXCELERATE. If you have experience and interest in improving, streamlining, sharing of training performed using Galaxy, consider to join ! To ensure the hackathon is relevant for all participants, there is a selection procedure. Details how to apply are here <https://docs.google.com/document/d/1dLCL5-2pkWTvmGTz7GyQkb5LEIZ3FBkPvCBoqUP…>, please do so before March 31st ! We will get back to you asap. cheers the organizing committee Frederik Coppens - Project leader & IT manager Applied Bioinformatics And Biostatistics I.T. Support VIB-UGent Center for Plant Systems Biology Ghent University Technologiepark 927 - 9052 Ghent - Belgium Tel. +32(0)9 331 38 12 www.psb.ugent.be <http://www.psb.ugent.be/>

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Workshop: R2 - Genomics analysis and visualization platform
by r2-support 20 Mar '17

20 Mar '17

Dear Researcher, R2 is a free, publicly accessible web-based genomics analysis and visualization platform (http://r2.amc.nl) allowing biomedical researchers, without bioinformatics training, to integrate clinical and genomics data. To help researchers get started, the department of Oncogenomics is organizing a 1 day introduction workshop with hands-on training on Tuesday May 2nd 2017 (09:30-17:00). The workshop will cover the essentials of working with mRNA data in R2 and will be an excellent opportunity to learn how to use this versatile tool. If you are: Studying a specific pathway in disease Trying to find biomarkers in specific tissue Investigating the function of a specific protein Involved in any kind of molecular biology Then this workshop may be of interest to you. Every participant will receive a printed tutorial book. Coffee / tea and a simple lunch will be provided during the workshop. If you are interested in participating in the workshop then please visit the R2 website for more information and registration (http://hgserver1.amc.nl/cgi-bin/r2/main.cgi?option=about_intro_workshop ). The workshop is provided free of charge, however, we will have to charge 25 euro (for administation, lunch, printing costs) in case of a no show on the workshop. Best regards, R2-support r2-support(a)amc.nl Department of Oncogenomics, M1-132 Academic Medical Center University of Amsterdam Meibergdreef 9 1105 AZ Amsterdam the Netherlands ________________________________ AMC Disclaimer : https://www.amc.nl/disclaimer ________________________________

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GenotypTissue Expression (GTEx) Project Community Meeting. Barcelona April 20-21st. Registration OPEN!
by Alexander Botzki 20 Mar '17

20 Mar '17

Dear all, For your information the GTEx community meeting at CRG, Barcelona: http://www.bdebate.org/ca/debat/genotype-tissue-expression-gtex-project-com… Cheers, Alex

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Vacancy ELIXIR Belgium
by Kim DE RUYCK 20 Mar '17

20 Mar '17

Dear all, Within ELIXIR Belgium, we are looking for a Software Developer . The position is in Gent, all information can be found on the provided link. Kind regards, Kim De Ruyck Kim De Ruyck PhD Coordinator ELIXIR Belgium VIB, Technologiepark 927, 9052 GENT | +32 (0)9 33 13 694 www.elixir-belgium.org @ELIXIRnodeBE Subscribe to our mailing list

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[Gtpb] GTPB Advanced Biostatistics course
by Pedro Fernandes IGC 20 Mar '17

20 Mar '17

Announcement / Reminder We are pleased to inform that applications for the ABSTAT17 training course are open. http://gtpb.igc.gulbenkian.pt/bicourses/ABSTAT17 Please note that this time, due to unusual circumstances, the registration process must be completed very quickly. Our apologies for that. Best wishes Pedro Fernandes Bioinformatics Training Coordinator Instituto Gulbenkian de Ciência _______________________________________________ GTPB mailing list GTPB(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

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PhD position: Amsterdam and Delft, The Netherlands
by Lodewyk Wessels 18 Mar '17

18 Mar '17

PhD position: ‘TRANSFER LEARNING FOR PERSONALISED CANCER TREATMENT’ COLLABORATING INSTITUTES Technical University of Delft (TUDelft), Delft VU University Medical Center, VUMC, Amsterdam and The Netherlands Cancer Institute (NKI), Amsterdam. PROJECT DESCRIPTION How can we find better diagnostic markers for early stages of cancer? How can we better predict which therapy is best for which patient? The aim of the ‘COMPUTE CANCER’ project is to develop a novel methodological and computational framework that improves the selection of diagnostic and predictive biomarkers from cancer genomics data. Our strategy is to adapt known prediction methods (e.g. penalized regression, random forests) to allow for the inclusion of ‘co-data’: auxiliary information on the genomic variables derived from other data sources. Examples include p-values from related external studies or genomic and drug response data from cancer cell lines. INTERDISCIPLINARY COLLABORATION The group of Mark van de Wiel (Biostatistics, VUMC) will focus on developing ‘weighted learners’, where the challenge is to determine weights from co-data in an automatic and objective way. The groups of Marco Loog, Marcel Reinders and Lodewyk Wessels (TUDelft and NKI) will develop transfer learning approaches that exploit large cell line response data sets to predict therapy response in tumors. We will focus on response to chemotherapy in neo-adjuvant breast cancer and metastatic colorectal cancer. The project is embedded within broad oncological collaborations within the VUMC as well as the NKI. The successful candidate will be employed at the TUDelft and will spend at least two days per week at the NKI. Regular meetings between project partners and oncologists will be held to generate sufficient cohesion and momentum. CANDIDATE PROFILE We are seeking a highly motivated PhD candidate with: • A degree in bioinformatics, computer science or a related discipline • Experience in statistics, machine learning and/or pattern recognition • Proficiency in bioinformatics programming languages (e.g. R, Python) • Good cross-disciplinary collaborative and communication skills • Experience in analysing high-throughput molecular data is a plus • Experience in cancer biology and clinical applications is a plus INTERESTED? Please send CV and motivation letter to Magali Michaut (m.michaut(a)nki.nl) & Lodewyk Wessels (l.wessels(a)nki.nl) Please include the names and contact information of at least two references. DEADLINE 17 April 2017

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[bioinfo] CFP MLSB17 11th Machine Learning in Systems Biology Workshop
by Alexander Botzki 17 Mar '17

17 Mar '17

From: Chloe-Agathe Azencott [mailto:chloe-agathe.azencott@mines-paristech.fr] Sent: 17 March 2017 11:12 To: bioinfo(a)sfbi.fr Subject: [bioinfo] CFP MLSB17 11th Machine Learning in Systems Biology Workshop ********************************************************************** CALL FOR ABSTRACTS -- MLSB 2017 The 11th International Workshop on Machine Learning in Systems Biology http://www.mlsb.cc Organized as a Special Session at ISMB/ECCB 2017 July 25, 2017 Prague, Czech Republic *Abstract submission deadline: May 18, 2017* ********************************************************************** Biology is rapidly turning into an information science, thanks to enormous advances in the ability to observe the molecular properties of cells, organs and individuals. This wealth of data allows us to model molecular systems at an unprecedented level of detail and to start to understand the underlying biological mechanisms. This field of systems biology creates a huge need for methods from machine learning, which find statistical dependencies and patterns in these large-scale datasets and that use them to establish models of complex molecular systems. MLSB is a scientific forum for the exchange between researchers from Systems Biology and Machine Learning, to promote the exchange of ideas, interactions and collaborations between these communities. The aim of MLSB is to contribute to the cross-fertilization between the research in machine learning methods and their applications to systems biology (i.e., complex biological and medical questions) by bringing together method developers and experimentalists. KEY DATES Submission deadline: May 18, 2017 Author notification: June 8, 2017 Early bird registration deadline ISMB/ECCB 2017: June 15, 2017 MLSB 2017: July 25, 2017 SUBMISSIONS We encourage submissions presenting novel methods for discovering complex structures (e.g. interaction networks, molecular structures), statistical machine learning methods for analysis of various high-throughput -omics data, and methods supporting systems-level data analysis. We are calling for 1-4 page abstracts describing either: - Original work on machine learning in systems biology. These should describe method development and application, and we encourage authors to submit recent ideas for discussion. - Highlights describing computational aspects of work that has recently been published or accepted for publication in a peer-reviewed journal or at the main conference. Abstracts will be considered for a talk or a poster presentation. The abstract must be in PDF format (file extension .pdf) and can be up to 4 pages long, including all figures and references. If you only wish to be considered for a poster, then a one page abstract is sufficient. A non-exhaustive list of topics suitable for this workshop are: - Active learning/experimental design - Bayesian methods - Biomarker identification - Clustering/biclustering - Data integration/fusion/multi-view learning - Deep learning - Epigenetics - Feature/subspace selection - Genome-wide association studies - Graph inference/completion - Kernel methods - Machine learning algorithms - Metabolic modeling and reconstruction - Metabolomics - Multitask/structured output prediction - Precision medicine - Probabilistic inference - Protein function and structure prediction - Protein-protein interaction networks - Rational drug design - Regulatory genomics - Semi-supervised learning - Sequence annotation - Signaling networks - Synthetic biology - Systems identification - Time-series analysis - Transcriptomics CHAIRS Chloé-Agathe Azencott (MINES ParisTech, France) Magnus Rattray (University of Manchester, UK) -- Chloe-Agathe Azencott CBIO Mines ParisTech - Institut Curie - INSERM U900 http://cazencott.info

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CFP MLSB17 11th Machine Learning in Systems Biology Workshop
by Ridder, Dick de 17 Mar '17

17 Mar '17

********************************************************************** CALL FOR ABSTRACTS -- MLSB 2017 The 11th International Workshop on Machine Learning in Systems Biology http://www.mlsb.cc Organized as a Special Session at ISMB/ECCB 2017 July 25, 2017 Prague, Czech Republic *Abstract submission deadline: May 18, 2017* ********************************************************************** Biology is rapidly turning into an information science, thanks to enormous advances in the ability to observe the molecular properties of cells, organs and individuals. This wealth of data allows us to model molecular systems at an unprecedented level of detail and to start to understand the underlying biological mechanisms. This field of systems biology creates a huge need for methods from machine learning, which find statistical dependencies and patterns in these large-scale datasets and that use them to establish models of complex molecular systems. MLSB is a scientific forum for the exchange between researchers from Systems Biology and Machine Learning, to promote the exchange of ideas, interactions and collaborations between these communities. The aim of MLSB is to contribute to the cross-fertilization between the research in machine learning methods and their applications to systems biology (i.e., complex biological and medical questions) by bringing together method developers and experimentalists. KEY DATES Submission deadline: May 18, 2017 Author notification: June 8, 2017 Early bird registration deadline ISMB/ECCB 2017: June 15, 2017 MLSB 2017: July 25, 2017 SUBMISSIONS We encourage submissions presenting novel methods for discovering complex structures (e.g. interaction networks, molecular structures), statistical machine learning methods for analysis of various high-throughput -omics data, and methods supporting systems-level data analysis. We are calling for 1-4 page abstracts describing either: - Original work on machine learning in systems biology. These should describe method development and application, and we encourage authors to submit recent ideas for discussion. - Highlights describing computational aspects of work that has recently been published or accepted for publication in a peer-reviewed journal or at the main conference. Abstracts will be considered for a talk or a poster presentation. The abstract must be in PDF format (file extension .pdf) and can be up to 4 pages long, including all figures and references. If you only wish to be considered for a poster, then a one page abstract is sufficient. A non-exhaustive list of topics suitable for this workshop are: - Active learning/experimental design - Bayesian methods - Biomarker identification - Clustering/biclustering - Data integration/fusion/multi-view learning - Deep learning - Epigenetics - Feature/subspace selection - Genome-wide association studies - Graph inference/completion - Kernel methods - Machine learning algorithms - Metabolic modeling and reconstruction - Metabolomics - Multitask/structured output prediction - Precision medicine - Probabilistic inference - Protein function and structure prediction - Protein-protein interaction networks - Rational drug design - Regulatory genomics - Semi-supervised learning - Sequence annotation - Signaling networks - Synthetic biology - Systems identification - Time-series analysis - Transcriptomics CHAIRS Chloé-Agathe Azencott (MINES ParisTech, France) Magnus Rattray (University of Manchester, UK)

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BioSB 2017 - Conference update - Detailed programme online!
by Femke Francissen 17 Mar '17

17 Mar '17

*BioSB 2017 conference update* *4-5 April 2017* Congrescentrum De Werelt, Lunteren, NL Conference website: http://www.aanmelder.nl/biosb2017 Register here <https://www.aanmelder.nl/biosb2017/wiki/218454/registration> BioSB 2017 is the 3rd edition of the Dutch Bioinformatics & Systems Biology conference. The conference discusses the latest developments in bioinformatics, systems and computational biology and interrelated disciplines, and their wide-ranging applications in life sciences & health, agriculture, food & nutrition. This year's conference will be co-organised by the BioSB research school <http://www.biosb.nl/>, UMC Groningen <https://www.umcg.nl/>, University of Groningen <http://www.rug.nl/> and ELIXIR-NL <http://www.dtls.nl/elixir-nl/elixir-nl-2/>. *** Detailed programme online* ------------------------------------------------------------ The programme of the conference is now online, including the topical sessions. View the full programme here <https://www.aanmelder.nl/biosb2017/part_program> You can still submit abstracts for a poster presentation. Submit here <https://www.aanmelder.nl/biosb2017/wiki/218444/abstract%20submission> *** Winner of the BioSB Young Investigator Award 2017: Ahmed Mahfouz* ------------------------------------------------------------ The selection committee selected a winner for this year's BioSB Young Investigator Award: Ahmed Mahfouz, LUMC. The award will be presented to Ahmed on *April 4* after which he will give an honorary lecture. The award is sponsored by the BioSB research school. Read more <https://www.aanmelder.nl/biosb2017/wiki/218447/biosb%20young%20investigator…> *** Industry meeting (BIUP): Entrepreneurship in Bioinformatics* ------------------------------------------------------------ On *April 5 *(13:15 - 14:30) the Bioinformatics Industrial Platform <https://www.dtls.nl/community/interest-groups/bioinformatics-industrial-use…> organises an inspiring industry session at the BioSB 2017 conference. This year's topic will be 'Entrepreneurship in Bioinformatics'. Three managers of successful bioinformatics companies are invited as speakers: - The Hyve - Harry van Haaften - Euretos - Arie Baak - Edgeleap - Marijana Radonjic These three companies started as bioinformatics start-ups and have grown into successful companies. We will learn about the do's and dont's of how to become a successful start-up in bioinformatics. Read more <https://www.aanmelder.nl/biosb2017/wiki/218404/industry%20/%20biup%20meeting> *** Repositive workshop: **Finding & Accessing Human Genome Data or Research* ------------------------------------------------------------ *April 4* (15:45 - 16:15) - Researchers rely on acquiring external data to validate, benchmark and supplement research findings. Funders require researchers to make their datasets accessible for further reuse. The goal of this workshop is to make researchers in genetics/genomics aware of the existing challenges with genomic data access and reuse and to present a number of tools and resources that researchers can use directly for simplifying their data access workflows. Repositive is a sponsor of the conference. Read more <https://www.aanmelder.nl/biosb2017/wiki/249981/repositive%20workshop> *** BioSB PhD retreat - April 3* ------------------------------------------------------------ - The Young Computational Biologistst <http://www.youngcb.nl/> are organising a PhD retreat on *April 3*, the day preceding the BioSB 2017 conference. The retreat will feature: - Keynote: Dr. Amrapali Zaveri, Stanford University - Keynote: Dr. Erik Schultes, FAIR Data Scientific Project Leader at DTL - Workshop organised by Amrapali Zaveri: 'How to use SPARQL Endpoints to query various biological data resources' - PhD flash talks - Dinner in Lunteren followed by social activity Abstracts for the flash talks should be submitted before March 20! Read more <https://www.aanmelder.nl/biosb2017/wiki/218435/biosb%20phd%20retreat> *** Contact & more information* ------------------------------------------------------------ You can find the latest conference updates at the conference website <http://www.aanmelder.nl/biosb2017>. Regular updates will also be sent via the BioSB mailing list. If you have any questions about the conference, please contact Femke Francissen, via femke.francissen(a)biosb.nl - On Twitter we will use the hashtag: #BioSB17 - Follow us on Twitter via @BioSB_nl - Like us on Facebook <https://www.facebook.com/BIOSB-122337454509903/?ref=hl>

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[bioinfo] NETTAB 2017
by Alexander Botzki 16 Mar '17

16 Mar '17

--------------------------------------------------------------------------------- NETTAB 2017 Methods, tools & platforms for Personalized Medicine in the Big Data Era 16-18 October 2017, Palermo, Italy http://www.igst.it/nettab/2017/ CALL FOR ABSTRACTS FOR ORAL COMMUNICATIONS AND POSTERS Keynote Speakers (confirmed only) - Winston Hide, Professor of Computational Biology, University of Sheffield, UK. - Anita Grigoriadis, Lecturer in Cancer Bioinformatics, King's College, London, UK. - Further Keynote speakers will be announced soon. TOPICS The special topic is "Methods, tools & platforms for Personalized Medicine in the Big Data Era", which includes: Data management: Biomedical Big Data Management, Standards for Clinical and Genetic Data, Data Privacy and Security, Omics Data Integration, Biobanks Data analysis: Omics Data analysis, Genetic Mutation Analysis, Biomarkers Discovery, NGS Data Analysis, Patient Information Analytics Tools and Services: Clinical Genomics Services, Models for Clinic and Genetic Data, Mobile tools and applications, Interoperability of Clinical and omic tools, Communication Technologies for Health-Care. Platforms: Integrated Data Warehouses, Integration of Applications and Data Services, Clinical Decision Support Systems, Healthcare Systems Traditional NETTAB topics also apply (see full list in the web site). DEADLINES Abstracts for oral communications: May 26, 2017 Abstracts for posters, software demo and late posters: TBA INSTRUCTIONS Submissions are sought for oral communications, posters and software demos. Abstracts must be submitted at http://www.easychair.org/conferences/?conf=nettab2017 See full instructions: http://www.igst.it/nettab/2017/submissions/instructions-for-authors/ CHAIRS Paolo Romano & Alfonso Urso & Alfonso Valencia CONTACTS Email: nettab.workshops(a)gmail.com Twitter: @NETTABWorkshops Announce list: https://groups.google.com/d/forum/nettab-announce LinkedIn: https://www.linkedin.com/groups/3209661 Paolo Romano IRCCS AOU San Martino IST Genova, Italy Skype: p.romano Email: paolo.romano(a)hsanmartino.it - paolo.dm.romano(a)gmail.com

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