- BBClist - maillist.psb.ugent.be

Workshop: Functional Plant Bioinformatics, 14-15 Sept, Ghent BE
by Klaas Vandepoele 13 Jul '17

13 Jul '17

*Workshop FUNCTIONAL PLANT BIOINFORMATICS* Organised by ELIXIR Belgium and the VIB Bioinformatics Core Date: 14-15 September 2017 Location: Ghent, Belgium *Goals* This workshop will introduce the basic concepts of comparative and functional -omics data analysis in plants through lectures and practical hands-on sessions. Both plant biologists and geneticists with an interest in bioinformatics, data analysis, and comparative & regulatory genomics should attend this training. After this workshop, you will have a good understanding of the organization and evolution of plant gene families and know how to extract relevant biological information from -omics gene sets. *Summary* DAY 1 Introduction plant comparative genomics (genes, gene families, synteny analysis) + introduction PLAZA platform Functional characterization of plant genes (Families, GO, InterPro) DAY 2 Gene set analysis for different plant -omics data sets: - functional interpretation of RNA-Seq and ChIP-Seq genes using the PLAZA Workbench - co-expression and Transcription Factor analysis *Prerequisites* basic knowledge of genes, genomes, transcript profiling, BLAST, homology, Gene Ontology (no programming skills are required). More info and registration: click here <http://www.vib.be/en/training/research-training/courses/Pages/Functional-Pl…> -- Prof. Dr. Klaas Vandepoele Tel. 32 (0)9 33 13822 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, Belgium --------------------------------------------------------- Lab website: http://bioinformatics.psb.ugent.be/cig/ BIG N2N: http://www.bign2n.ugent.be/ Twitter: http://twitter.com/plaza_genomics ---------------------------------------------------------

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[Gtpb] Large-scale bioinformatics for Immuno-Oncology - Course announcement for Sept 2018
by Pedro L. Fernandes 10 Jul '17

10 Jul '17

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

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[Gtpb] Introductory BIOSTSTISTICS for Biologists - course announcement for Sept 2018
by Pedro L. Fernandes 10 Jul '17

10 Jul '17

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

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Registration open: BioSB Course Pattern Recognition (5th edition) - 25-29 September 2017
by Femke Francissen 06 Jul '17

06 Jul '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-recognition/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 such problems. We will introduce the pattern recognition pipeline: measuring, feature extraction and selection, classification and evaluation. The course is a mixture of theory sessions and lab courses. During the lab courses Matlab will be used and a brief introduction to Matlab will be provided. The course has to be completed afterwards with a 5-10 page report describing the analysis of a biological dataset using some of the methods taught in the course. 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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looking for Phd student for computational design of a receptor protein.
by Arnout Voet 05 Jul '17

05 Jul '17

Dear All, At the laboratory for biomolecular modelling and design we are currently looking for a PhD student (or non-eu postdoc) for a project dealing with the computational design of a novel protein receptor as a building block for synthetic biology. This projects deals with the biomolecular modelling methods, structural bioinformatics, and combines both computer aided drug design methods with computer aided protein design methods. For more information please consult the job offer at : https://icts.kuleuven.be/apps/jobsite/vacatures/54249555?lang=en or contact me Kindest Regards, Arnout Voet Assistant-Professor Laboratory of biomolecular modelling and design Celestijnenlaan 200G 3001 Heverlee Belgium Tel: +3216324496 https://www.chem.kuleuven.be/lbmd/index.html

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vacancy bioinformatician
by Demeyere Mieke 04 Jul '17

04 Jul '17

Dear all Here<https://www.howest.be/documenten/vacatures/2017093%20Praktijk%20Lector%20on…> you can find a vacancy for a bioinformatician. Thank you for sending to who's interested! Enjoy the holidays! With kind regards Mieke Demeyere Opleidingscoördinator Biomedische Laboratoriumtechnologie [http://innovatiebeurs.be/assets/files/made/assets/files/partners/howest.be_…] Howest University of Applied Sciences Campus Rijselstraat Rijselstraat 5 - 8200 Brugge Tel.: +32 50 38 12 77 Fax: +32 50 38 11 71 www.howest.be/blt<http://www.howest.be/blt> Denk aan het milieu vooraleer je dit bericht of de bijlagen uitprint!

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PhD opportunity in Bioinformatics or Computational Biology
by Francisco Azuaje 04 Jul '17

04 Jul '17

Dear colleagues, We are seeking candidates for a PhD research position at LIH: https://www.lih.lu/jobs/detail/phd-student-in-the-area-of-bioinformatics-or…. Please share this information with potential candidates. Francisco. _________________________________ Francisco Azuaje, PhD Principal Investigator Proteome and Genome Research Unit Department of Oncology Luxembourg Institute of Health 1A-B, rue Thomas Edison, L-1445 Strassen Luxembourg Tel: +352 26970-875 Fax: +352 26970-719 Email: francisco.azuaje(a)lih.lu<mailto:francisco.azuaje@lih.lu> Website: https://www.lih.lu/ [http://files.lih.lu/outlookSignature/lih.jpg] Join us on Facebook and follow our activities on Twitter: https://www.facebook.com/Luxembourg.Institute.of.Health http://twitter.com/LIH_Luxembourg This message (including any attachments) is intended for the addressee only and may contain confidential and/or privileged information and/or information protected by intellectual property rights. If you have received this message by mistake, please notify the sender by return e-mail and delete this message from your system. You should not use, alter, copy or distribute this message or disclose its contents to anyone. E-mail transmission can not be guaranteed to be secure or error free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. Luxembourg Institute of Health shall not be responsible nor liable for the proper and complete transmission of the information contained in this communication nor for any delay in its receipt or damage to your system.

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FW: Announcement of the 2nd Annual European Core Community Workshop on 18th September 2017
by Alexander Botzki 04 Jul '17

04 Jul '17

FYI ---- Dear colleagues, We are happy to announce the 2nd Annual European Bioinformatics Core Community (ÄBC2) Workshop taking place * on September 18, 2017 in Tübingen, Germany * as an independently organized satellite workshop of the German Conference on Bioinformatics (GCB) 2017 This workshop is a joint second installment of the similar workshops at ECCB and GCB 2016. Keynotes: Nicola Aceto (Basel) is going to talk about parallel exome and transcriptome analysis in circulating tumor cells. Camille Stephan-Otto Attolini (Barcelona) will present her lessons learned with charging clients for services and Johannes Köster (Amsterdam, Harvard, Essen) shares his experience with tools and workflow management. We are looking forward to your participation. For more information on registration and presentation submission please refer to: http://www.aebc2.eu/ For general information about travel and accommodation in Tübingen please visit the GCB website<http://gcb2017.de>: http://gcb2017.de/ Please forward this e-mail to your colleagues, co-workers and other interested people that may be interested in this event. Best regards, Sven Nahnsen & Dieter Beule Quantitative Biology Center (QBiC) Berlin Institute of Health (BIH) University of Tübingen Sven Rahmann & Daniel Stekhoven University Hospital Essen, ETH Zurich University of Duisburg-Essen, UA Ruhr

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Overview of courses and workshop in BE and NL
by Alexander Botzki 02 Jul '17

02 Jul '17

Dear all, I would like to share with you a link to the ELIXIR TeSS platform where you can find a daily updated list of bioinformatics training courses and events taken place in e.g. Belgium and the Netherlands. https://tess.elixir-europe.org/events?country%5B%5D=Belgium&country%5B%5D=N… Many colleagues from the ELIXIR training platform and their partner organisations work hard to feed the overview. We hope that it is a useful resource for many of you. Please forward the link to colleagues who might not be aware of the aggregated event list and training material list. If you are a content provider organising courses in bioinformatics, please contact me to evaluate how your events could be aggregated and uploaded to TeSS, too. Best regards, Alexander Alexander Botzki - Head of VIB Bioinformatics Core | Training Coordinator ELIXIR-BE VIB Bioinformatics Core Rijvisschestraat 126, 9052 GENT, Belgium | +32 9 248 16 00 www.bits.vib.be<http://www.bits.vib.be/> | @vibbioinfocore | https://corefacilities.vib.be<https://corefacilities.vib.be/> [E-mail-signature] [signatureFooter (002)]

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Vacancy DevOps Engineer / Systems Administrator in Maastricht
by Coonen Maarten (FACBURFHML) 29 Jun '17

29 Jun '17

Dear BBC-list, The Maastricht UMC+ DataHub team is looking for a talented DevOps engineer / systems administrator. DataHub develops and manages an institutional repository for research data and enables researchers to store and retrieve scientific data in a sustainable way. You will work in close collaboration with central IT-services and our own DataHub development team. Besides (Linux) system and software administration, the position will also challenge you in configuration and automated deployment of both proven and experimental technologies. Additionally, you will build and manage our continuous testing framework and you'll get familiar with data management standards and interoperability. More information about the position and department can be found here in English<https://datahub.mumc.maastrichtuniversity.nl/devops-engineer-systems-admini…> and hier in het Nederlands<https://www.werkenbijmumc.nl/vacature/10605-02s0000wnp>. Deadline is 28 July 2017 Feel free to distribute this e-mail amongst your network. Best regards, Maarten Coonen Data Architect DataHub Maastricht E m.coonen(a)maastrichtuniversity.nl<mailto:m.coonen@maastrichtuniversity.nl> | maarten.coonen(a)mumc.nl<mailto:maarten.coonen@mumc.nl> I https://datahub.mumc.maastrichtuniversity.nl<https://datahub.mumc.maastrichtuniversity.nl/> English https://datahub.mumc.maastrichtuniversity.nl/devops-engineer-systems-admini… Nederlands https://www.werkenbijmumc.nl/vacature/10605-02s0000wnp

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