- BBClist - maillist.psb.ugent.be

Workshop: R2 - Genomics analysis and visualization platform
by r2-support 01 Feb '18

01 Feb '18

Dear Researcher, R2 is a free, publicly accessible web-based genomics analysis and visualization platform (http://r2.amc.nl<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 Monday April 23rd 2018 (09:30-17:00). The workshop will cover the essentials of working with genomics 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 for the workshop. Best regards, R2-support r2-support(a)amc.nl r2.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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PostDoc in Systems Biology (Luxembourg)
by Thomas SAUTER 31 Jan '18

31 Jan '18

The University of Luxembourg invites applications for the following vacancy in the Life Sciences Research Unit of its Faculty of Sciences, Technology and Communication (FSTC) in the Systems Biology Lab. Post doc (Assistant chercheur) in Systems Biology (M/F) * Ref: F1-080013 * 2-year fixed-term contract * Full-time (40 hours/week) * Starting date: As soon as possible Application via: http://emea3.mrted.ly/1ptrm Research area: The research focus is molecular systems biology. In particular, we are interested in the * Development and testing of fast algorithms for modelling signaling networks, within the Probabilistic Boolean modelling framework * Computational analysis of cancer specific signaling networks * Analysis and integration of experimental data in collaboration with biological partners Your Role * The successful candidate will perform research related to the topics of the Systems Biology Laboratory; possible collaborations e.g. with the Luxembourg Centre of Systems Biomedicine and industrial partners. * Participation in teaching activities: Bachelor in Life Sciences / in Integrated Systems Biology / Doctoral School of Molecular and Systems Biomedicine. * Submission of grant proposals and (co-)supervision of Master and PhD students will be encouraged. Your Profile * PhD degree in Bioinformatics or Computational Systems Biology (or equivalent) * Solid background in Bioinformatics and Systems Biology documented by peer-reviewed publications. * Background in the biology of signal transduction is an asset. * Proficient knowledge in English is mandatory. Knowledge of German and/or French is an advantage. We offer * Young team of highly motivated researchers * Modern and well-equipped laboratory * Multidisciplinary international environment Further Information Applications should contain the following documents: * Motivation letter * Curriculum vitae * List of publications * Copies of diplomas * Names of potential references Please apply online by 15/02/2018.: http://emea3.mrted.ly/1ptrm The University of Luxembourg is an equal opportunity employer -- Prof. Dr. Thomas Sauter Professor of Systems Biology Life Sciences Research Unit Université du Luxembourg 6, avenue du Swing L-4367 Belvaux Campus Belval Building Biotech 2 (BT2), Room 4.05 Tél.: +352-46 66 44 6296 Fax: +352-46 66 44 6435 e-mail: thomas.sauter(a)uni.lu<mailto:thomas.sauter@uni.lu> http://bio.uni.lu/research_areas/systems_biology http://misb.uni.lu<http://misb.uni.lu/> http://www.melplex.eu<http://www.melplex.eu/>

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Galaxy User Conference in Freiburg March 15-16
by Frederik Coppens 30 Jan '18

30 Jan '18

Dear all The Freiburg Galaxy team is organizing a Galaxy User Conference 15th to 16th of March 2018. The focus is on gathering interesting talks from the Galaxy community about their applications and use cases of Galaxy, and learn from each other. We also want to take this opportunity to kickstart the ELIXIR <https://www.elixir-europe.org/> Galaxy Community. We started a Galaxy Working group <https://www.elixir-europe.org/about/groups/galaxy-wg> a few years ago, which has now matured into an ELIXIR Community. If you are using Galaxy, do consider attending this meeting. Registration is free. You can find more information and the link to register here : https://usegalaxy-eu.github.io/galaxy-freiburg/events/2018-03-15-ELIXIR-Gal… cheers Frederik 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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[Gtpb] CPANG18 - Computational PANgenomics - Course Announcement
by GTPB Administration 30 Jan '18

30 Jan '18

ANNOUNCEMENT CPANG18 Computational PANgenomics with Tobias Marschall and Erik Garrison 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: February 23rd 2018 Course date: March 6th - March 9th 2018 Candidates with adequate profile will be accepted in the next 72 hours after the application until we reach 20 participants. Course Description Reference genomes have become central to bioinformatics approaches, and form the core of standard analyses using contemporary sequencing data. However, the use of linear reference genomes, which provide the sequence of one representative genome for a species, is increasingly becoming a limitation as the number of sequenced genomes grows. In particular, they tend to bias us away from the observation of variation in the genomes we study. A general solution to this problem is to use a pangenome that incorporates both sequence and variation from many individuals as our reference system. This pangenome is naturally modeled as a graph with annotations, and can provide all the functionality traditionally provided by linear reference genomes. Unlike linear reference genomes, a pangenome readily incorporates both small and large variation, allowing bias-free genotyping at known alleles. In this course we will explore the use of modern bioinformatic tools that allow researchers to use pangenomes as their reference system when engaging in studies of organisms of all types. Such techniques will aid any researcher working on organisms of high genetic diversity or on organisms lacking a high-quality reference genome. This course targets all researchers interested in learning about an exciting paradigm shift in computational genomics. Objectives Participants first will learn about limitations of linear reference-based methods and work through a brief refresher or introduction to standard approaches for processing sequencing data, including read alignment and variant calling. Provided these motivating examples, we will use data from a variety of relevant sources to develop an intuition about pangenomic methods and a practical familiarity with applicable tools. More information, and access to the application process here: http://gtpb.igc.gulbenkian.pt/bicourses/2018/PANG18 Ref: Computational pan-genomics: status, promises and challenges The Computational Pan-Genomics Consortium Author Notes Briefings in Bioinformatics, Volume 19, Issue 1, 1 January 2018, Pages 118135, https://doi.org/10.1093/bib/bbw089 (OPEN ACCESS) 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 Tel +351 21 4407912 http://gtpb.igc.gulbenkian.pt -- The Gulbenkian Training Programme in Bioinformatics General Office 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

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PostDoc in Bioinformatics / Biostatistics (Luxembourg)
by Enrico Glaab 29 Jan '18

29 Jan '18

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Two PhD positions in Australia
by Kim DE RUYCK 25 Jan '18

25 Jan '18

Below are 2 PhD positions in Sydney, Australia. Kind regards, Kim De Ruyck Dear colleagues, I will really appreciate if you could advertise these two PhD positions and/ or pass on this information to anyone who is interested. Both positions are available for domestic and international students. 1. Metagenomics and bioremediation [ https://www.westernsydney.edu.au/graduate_research_school/grs/scholarships/… | https://www.westernsydney.edu.au/graduate_research_school/grs/scholarships/… ] 2. Plant-microbial interaction [ https://www.westernsydney.edu.au/graduate_research_school/grs/scholarships/… | https://www.westernsydney.edu.au/graduate_research_school/grs/scholarships/… ] Many thanks for you help. Kind regards Braj Prof Brajesh Singh Director | Global Centre for Land-Based Innovation Professor | Hawkesbury Institute for the Environment Western Sydney University Locked Bag 1797, Penrith, NSW 2751, Australia Ph: +61 2 4570 1329 | Fax: +61 2 4570 1314 Mob: +61 404187962 | Email: [ mailto:b.singh@westernsydney.edu.au | b.singh(a)westernsydney.edu.au ] [ http://www.westernsydney.edu.au/gclbi | http://www.westernsydney.edu.au/gclbi ] [ http://www.westernsydney.edu.au/hie | http://www.westernsydney.edu.au/hie ] Twitter account: @Prof_Braj_Singh

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Solvay workshop on "Dynamics on Biological systems: Modelling genetic, signalling and microbial networks"
by Karoline Faust 24 Jan '18

24 Jan '18

Dear colleagues, We are happy to announce the Solvay workshop on "Dynamics on Biological systems: Modelling genetic, signalling and microbial networks", which will take place in Brussels from 2-4 May 2018. Registration is free of charge but required (limited number of places). We also encourage attendees to present a poster. More information can be found here: http://www.solvayinstitutes.be/event/workshop/dynamics_2018/dynamics_2018.h… Please do not hesitate to diffuse this announcement. We look forward to welcoming you in Brussels in May 2018. Best regards, The Organising Committee: Geneviève Dupont (ULB, Brussels, Belgium) Karoline Faust (KU Leuven, Belgium) Claude Gérard (UCL, Louvain, Belgium) Didier Gonze (ULB, Brussels, Belgium) Jean-Christophe Leloup (ULB, Brussels, Belgium)

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RV: to post a message - Course MIAGE 2018
by Laura Galisteo Garzon 23 Jan '18

23 Jan '18

De: Laura Galisteo Garzon Enviado el: martes, 23 de enero de 2018 9:28 Para: 'bbclist(a)psb.ugent.be.' Asunto: to post a message - Course MIAGE 2018 Appreciate if you can post this announcement to your network: MIAGE 2018 Course in Multi-omic Integrative Analysis of Gene Expression 5-9 March 2018 Centro de Investigación Príncipe Felipe, Valencia, Spain http://bioinfo.cipf.es/aconesawp/?page_id=1560<https://cipf.us17.list-manage.com/track/click?u=4756961f40c63b8d4b0c95d76&i…> The Genomics of Gene Expression lab presents the second edition of this course that aims to teach the students how to perform an integrative analysis of different omic data types in order to model the regulation of gene expression. To this end, we will first study in depth the pre-processing and statistical analysis of the different omic data types with a special focus on Next Generation Sequencing technologies such as RNA-seq, ChIP-seq, ATAC-seq, DNA-seq and Methyl-seq, but also metabolomics or proteomics. Next, we will study several integration examples to cover different integration strategies. All these lectures will be complemented with hands-on sessions. R programming language will be mostly used. Finally, we will also have a longer practical session to recapitulate all the learned lessons by solving a real integration problem. During this last session, the students can analyze either their own data or the data provided by the organizers. The course is targeted to students and researchers with some experience in bioinformatics analysis and R programming language that wish to learn more about the integration of different omic data types. The course is restricted to a maximum of 25 participants. The official language of the course will be English. The students must bring their own computers. The organizers will provide information about the software or R libraries to be installed before the course, as well as the files or data needed for the course. Pre-registration deadline: 9th of February, 2018 If you wish to pre-register to this course, you must send the following documentation to Sonia Tarazona (starazona(a)cipf.es<mailto:starazona@cipf.es>) before the 9th of February, 2018 wiht your CV and the enrollment form, which can downloaded from here<https://cipf.us17.list-manage.com/track/click?u=4756961f40c63b8d4b0c95d76&i…>. Payment deadline: 20th of February, 2018 - Price: 500 €. The price includes meals and coffees, as well as the gala dinner. Further information at: http://bioinfo.cipf.es/aconesawp/?page_id=1560<https://cipf.us17.list-manage.com/track/click?u=4756961f40c63b8d4b0c95d76&i…>

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[Gtpb] ELB18F Entry Level Bioinformatics - REMINDER
by GTPB Administration 22 Jan '18

22 Jan '18

REMINDER ELB18F Entry Level Bioinformatics (First course in 2018) our entry level course with a soft introduction to NGS data analysis with David P. Judge, Pedro L. Fernandes and Daniel Sobral The GTPB is proud to announce that the above referenced hands-on training course is open for applications Important dates IMPORTANT DATES for this Course Deadline for applications: February 8th 2018 Course dates: February 19th - February 23rd 2018 Candidates with adequate profile will be accepted in the next 72 hours after the application until we reach 20 participants. This is an entry level course aimed that those with a reasonable biological background but no significant experience with bioinformatics. The course is broadly based around a series of exercises in which a combination of simple analytical tools and reference to publicly available databases is applied to the investigation of a single human gene. The training manual for the course is comprised of detailed instructions for the tasks undertaken. Included are, questions (with answers) and discussion of and the interpretation of the results achieved. Participants are asked to imagine an interest in the disease aniridia. Course exercises then provide extremely detailed instruction leading participants to discover the gene primarily associated with this disease and all that is interesting about that gene and its protein products. This course will also provide a soft introduction to Next Generation Sequencing (NGS) data analysis. This part of the course aims at providing basic skills that are needed when one needs to process NGS data, such as evaluating data quality, trimming sequences, changing data formats, visualising data, etc. Then, participants will learn how to address a simple transcriptomics problem, stepwise, using open source bioinformatics tools. http://gtpb.igc.gulbenkian.pt/bicourses/2018/ELB18F 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 Tel +351 21 4407912 http://gtpb.igc.gulbenkian.pt -- The Gulbenkian Training Programme in Bioinformatics General Office 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

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Upcoming Edinburgh Genomics Courses
by MEDD Nathan 22 Jan '18

22 Jan '18

Dear All Edinburgh Genomics is pleased to offer a selection of excellent bioinformatics workshops this spring/summer. We offer a range of courses covering both basic and more advanced bioinformatics skills. Please follow the links below for more information on course content and how to register. Monday 9 - Friday 13 April - Data Manipulation and Visualisation with Python (https://genomics.ed.ac.uk/services/data-manipulation-and-visualisation-pyth…) Monday 14 - Friday 18 May - Introduction to Linux and Workflows for Biologists (https://genomics.ed.ac.uk/services/introduction-linux-and-workflows-biologi…) Monday 11 - Friday 15 June - Introduction to Python for Biologists (https://genomics.ed.ac.uk/about-us/introduction-python-biologists-june-2018) Monday 9 - Friday 13 July - Advanced Python for Biologists (https://genomics.ed.ac.uk/services/advanced-python-biologists) These workshops are first come, first served, so register now to avoid disappointment! All the above courses are taught by Dr Martin Jones (Founder, Python for Biologists, https://pythonforbiologists.com) and are held at the Kings Buildings Campus, University of Edinburgh. Check out the Edinburgh Genomics training page, https://genomics.ed.ac.uk/services/training , for more upcoming courses. Kind Regards Nathan Medd Edinburgh Genomics - Training Assistant -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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