- BBClist - maillist.psb.ugent.be

Two job openings at ELIXIR-Luxembourg Node: 1) Science/Project Manager 2) Software Developer
by Venkata Pardhasaradhi SATAGOPAM 24 Aug '16

24 Aug '16

Dear all ELIXIR-Luxembourg Node offers two job openings at Luxembourg Centre For Systems Biomedicine (LCSB), University of Luxembourg. Please find the more details from the following URLs 1) Science Manager for the Luxembourgish ELIXIR Node: http://emea3.mrted.ly/15vs5 <http://emea3.mrted.ly/15vs5> 2) Software Developer for web-based translational medicine knowledge management and analysis tools: http://emea3.mrted.ly/15vrg <http://emea3.mrted.ly/15vrg> Please circulate these positions in your circles. 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 +352-466-644-6949 venkata.satagopam(a)uni.lu <mailto:venkata.satagopam@uni.lu> http://lcsb.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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Multiple research positions in computational and systems biology
by Francisco Azuaje 23 Aug '16

23 Aug '16

Dear all, Please find attached information on PhD and post-doctoral positions at Jagath Rajapakse's team at Nanyang Technological University (NTU), Singapore. Regards, Francisco. _________________________________ Francisco Azuaje, PhD Principal Investigator NORLUX Neuro-Oncology Laboratory 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 http://www.norlux.lu 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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Job opening - Bioinformatician UMC Utrecht (Dutch)
by Bruggen Martijn van der 22 Aug '16

22 Aug '16

Bio-Informatisch Analist Pathologie Je werkt als bio-informatisch-analist voor een gecertificeerd, modern uitgerust laboratorium dat onder andere GeneScan en Next Gen Sequencing analyses voor DNA en RNA uitvoert. Met als speciale opdracht analyse van somatische mutaties bij tumoren, die essentieel zijn bij de behandeling van deze patiënten. Jouw taak bestaat uit het verwerken van deze ‘next generation sequencing’-resultaten met behulp van specifieke software en vastgelegde procedures op linux-computers en in het centrale computer cluster. Daarnaast bied je ondersteuning aan algemene bio-informatische vraagstukken van de afdeling Pathologie en werk je mee aan onderzoeksprojecten waarbij nieuwe analyses worden uitgewerkt. Je werkt zelfstanding en maakt een goede planning van de werkzaamheden. Het is eveneens jouw taak om afwijkingen in routineresultaten te signaleren en deze samen met collega bio-informatici te beoordelen. Je communiceert met de KMBP en de lab-specialisten over de resultaten. Ook lever je een bijdrage aan het bestaande kwaliteitssysteem van beide afdelingen. Afdeling De Moleculaire Pathologie maakt onderdeel uit van de unit Diagnostiek Laboratoria Pathologie. De afdeling Pathologie valt onder de Divisie Laboratorium en Apotheek (DLA). Je wordt gedetacheerd naar de afdeling Medische Bio-Informatica van de afdeling Genetica. Daar werk je in een team van bio-informatici met als speciale opdracht moleculaire pathologie. Binnen deze samenwerking geldt voor beide afdelingen dat een belangrijk doel is om de recente technologische ontwikkelingen (bijvoorbeeld de nieuwste sequencing-technologie, zoals ‘whole exome’ en ’whole genome sequencing’) effectief toe te passen in de patiëntenzorg. Profiel Je bent een bio-informatisch analist die een relevante HBO opleiding heeft afgerond. Het is een pre als je ervaring hebt met de verwerking en interpretatie van 'next generation sequencing'-data, linux, scripting, SQL-databases en computer-clusters. Ervaring op het gebied van de moleculaire diagnostiek in een diagnostische setting spreekt in je voordeel. Je hebt een enthousiaste, flexibele werkhouding en vindt het leuk om in een team samen te werken. Communicatief ben je uitstekend onderlegd. Het salaris voor deze 100% functie bedraagt maximaal € 2.921,00 bruto per maand op basis van een fulltime dienstverband (werkweek van 36 uur). Het betreft een vaste aanstelling, beginnend met een jaarcontract. Meer informatie Voor meer inhoudelijke informatie over deze vacature, neem contact op met de contactpersoon, mevrouw W.T.M. van Blokland, HA Moleculaire Pathologie, telefoon 088 7574252. Email w.t.m.vanblokland(a)umcutrecht.nl<mailto:w.t.m.vanblokland@umcutrecht.nl>. Acquisitie n.a.v. deze vacature wordt niet op prijs gesteld.

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Still places left on Linux for Genomics workshop Thursday 29 September 2016
by Bert Overduin 22 Aug '16

22 Aug '16

Dear all, We have still places left on our 1-day Linux for Genomics workshop on Thursday 29 September 2016. Note that this workshop is specifically aimed at anyone *without any command-line experience!* *Workshop description:* Genomic studies produce vast amounts of data, usually in the form of very large text files. Linux is particularly suited to working with such files, and is therefore arguably one of the most important tools in a bioinformatician’s toolkit. The Linux command line enables one to view, filter and manipulate large text files that are difficult or impossible to handle with applications like Word or Excel, write pipelines to perform certain tasks and run bioinformatics software for which no web interface is available. In this workshop we will provide a basic introduction to Linux, covering the most used commands, followed by a brief introduction to several popular command-line tools that were especially developed for genomics(e.g. samtools and bedtools). The workshop will be mostly hands-on. In the tutorials genomic data and file formats commonly used in genomics (e.g. BED, FASTA, FASTQ, GFF/GTF, SAM/BAM, VCF) will be used (and explained). *1-day Linux for Genomics* Date: Thursday 29 September 2016 Price: £155 (includes coffee/tea and lunch) Registration: first come first serve Deadline: Thursday 15 September 2016 noon Details: http://genomics.ed.ac.uk/services/linux-genomics <https://genomics.ed.ac.uk/services/linux-genomics> Cheers, Bert -- Bert Overduin, PhD TRAINING AND OUTREACH BIOINFORMATICIAN Bert.Overduin(a)ed.ac.uk orcid.org/0000-0002-5281-8838 EDINBURGH GENOMICS The University of Edinburgh Ashworth Laboratories The King's Buildings Charlotte Auerbach Road Edinburgh EH9 3FL Scotland, United Kingdom tel. +44(0)1316507403 http://genomics.ed.ac.uk The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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bioinformatic analist university medical center Utrecht, dept pathology
by Nijman, I.J. 22 Aug '16

22 Aug '16

HI, Wij zoeken een bioinformatica analist in het UMCU, afdeling pathologie, die naast routine diagnostiek ook interessante research projecten bioinformatisch kan ondersteunen. Link naar de vacature: http://www.werkenbijumcutrecht.nl/vacatures/Paginas/bio-informatisch-analis… Mvg, Ies nijman ******************************************************************************* I.J. Nijman, PhD [Beschrijving: Beschrijving: Beschrijving: cid:image005.jpg@01CE605D.A1F9A2C0] Utrecht Medical Center, Department of Genetics Visiting adres: Universiteitsweg 100 | 3584 CG | Utrecht | The Netherlands | Mailing address: STR.1.305 PO Box 85060 | 3508 AB Utrecht | The Netherlands | phone +31 (0) 887568204 / (+31) (0)6 29080780 ******************************************************************************* ------------------------------------------------------------------------------ De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. Denk s.v.p aan het milieu voor u deze e-mail afdrukt. ------------------------------------------------------------------------------ This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197. Please consider the environment before printing this e-mail.

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Data Manipulation and Visualisation with Python, Edinburgh, 5-9 Sep 2016 - Few days left to register!
by Bert Overduin 22 Aug '16

22 Aug '16

Dear all, There only a few days left to register for our brand new "Data Manipulation and Visualisation with Python" workshop, that will be given from 5-9 September 2016 in Edinburgh. *Workshop description:* This workshop focuses on a number of Python packages for manipulating, plotting and visualising scientific data, i.e. pandas, matplotlib, seaborn and processing. The workshop will be taught by Martin Jones of Python for Biologists ( http://pythonforbiologists.com/index.php/introduction-to-python-for-biologi…) who also teaches our very successful Introductory and Advanced Python workshops. A few examples of figures you will learn to make during the workshop can be found on the Python for Biologists Twitter feed: https://twitter.com/pythonforbiolog. Note that we encourage participants to bring their own data, as there will be time to work on them during the workshop. *Requirements:* For this workshop a background in biology and a basic knowledge of Python is required. *More information:* More information can be found here: https://genomics.ed.ac.uk/services/data-manipulation-and-visualisation-pyth… . Please don't hesitate to mail me (bert.overduin(a)ed.ac.uk) or Martin Jones ( martin(a)pythonforbiologists.com) in case you have any questions regarding the workshop. With kind regards, Bert -- Bert Overduin, PhD TRAINING AND OUTREACH BIOINFORMATICIAN Bert.Overduin(a)ed.ac.uk orcid.org/0000-0002-5281-8838 EDINBURGH GENOMICS The University of Edinburgh Ashworth Laboratories The King's Buildings Charlotte Auerbach Road Edinburgh EH9 3FL Scotland, United Kingdom tel. +44(0)1316507403 http://genomics.ed.ac.uk The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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[Gtpb] GTPB Bioinformatics Training course REMINDER - Precision Medicine - PM16
by Pedro L. Fernandes 22 Aug '16

22 Aug '16

The Gulbenkian Training Programme in Bioinformatics Applications for the bioinformatics training course PM16 - Precision Medicine with Fatima Al-Shahrour, Javier Perales and Elena Piñero are open. IMPORTANT DATES for this Course Deadline for applications: Sept 12th 2016 <======================= Course dates: Sept 27th - Sept 30th 2016 Please refer to the course website http://gtpb.igc.gulbenkian.pt/bicourses/PM16 for details. Course Description The implementation of cancer genomics into the clinic is becoming a reality. Personalised medicine or Precision medicine as other authors refers, uses molecular data of a specific patient to guide clinical decisions such as prevention, diagnosis and treatment. This will revolutionize healthcare and will play a dominant role in the future of cancer therapy. Bioinformatics analyses are essential to identify patients who will benefit from treatment based on their molecular profile, and to tailor chemotherapeutic regimens accordingly. The aim of the course is to present a complete computational pipeline for the analysis and interpretation of Next-Generation Sequencing (NGS) data such as exome sequencing or targeted panels that are commonly used in the clinic. We will address the implementation of large-scale genomic sequencing in clinical practice and the recently developed computational strategies for the analysis of NGS data with a particular emphasis on the interpretation of the results, selection of biomarkers of drug response and afford opportunities to match therapies with the characteristics of the individual patient's tumour. Exercises and case studies focused on cancer will be used to illustrate the principles of how genetics influence led to refining diagnoses and personalized treatment of cancer disease. Best regards Pedro Fernandes -- Pedro Fernandes GTPB Coordinator Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL Tel +351 21 4407912 http://gtpb.igc.gulbenkian.pt -- Pedro Fernandes Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL Tel +351 21 4407912 http://gtpb.igc.gulbenkian.pt Upcoming courses: PM16 - Precision Medicine, Sep 27 3DAROC16 - 3C-based data analysis and 3D reconstruction of chromatin folding, Oct 10 AAIRR16 - Analysis of Adaptive Immune Receptor Repertoires, Nov 2 AET16 - Applied Evolutionary Theory, Nov 7 _______________________________________________ GTPB mailing list GTPB(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

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Post-doctoral Researcher on Machine learning based Diagnostic Algorithms on human clinical and cohort data
by Venkata Pardhasaradhi SATAGOPAM 19 Aug '16

19 Aug '16

Dear all “Post-doctoral Researcher position on Machine learning based Diagnostic Algorithms on human clinical and cohort data" is available at LCSB, University of Luxembourg. Please refer the following URL for more details: http://recruitment.uni.lu/en/details.html?nPostingId=6564&nPostingTargetId=… <http://recruitment.uni.lu/en/details.html?nPostingId=6564&nPostingTargetId=…> 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 +352-466-644-6949 venkata.satagopam(a)uni.lu <mailto:venkata.satagopam@uni.lu> http://lcsb.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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[Gtpb] GTPB Bioinformatics Training course REMINDER - AET16 - Applied Evolutionary Theory
by Pedro Fernandes 16 Aug '16

16 Aug '16

The Gulbenkian Training Programme in Bioinformatics Applications for the bioinformatics training course AET16 - Applied Evolutionary Theory with Claudia Bank, Rafael Guerrero and Stephan Peischl are open. Please refer to the course website http://gtpb.igc.gulbenkian.pt/bicourses/AET16 for details. IMPORTANT DATES for this Course Deadline for applications: Oct 25th 2016 Course dates: Nov 7th - Nov 11th 2016 Course Description For many of its history, our knowledge of evolution has been based heavily on theoretical models and hypotheses. In the age of novel experimental and technological approaches, we are now increasingly able to evaluate this theory; however, the basics of how and why to develop and analyse a simple model are often forgotten in the process of NGS analysis. This course aims at training evolutionary biologists in classical modelling and teach them ways to approach their own research questions through evolutionary theory. Primarily through interactive hands-on sessions, complemented by an introduction to the cornerstones of modelling and its application to data analysis, this course will familiarize the participants with ways of approaching a research question with a simple model, and different strategies at gaining insight from the model. In groups of two, course participants will develop and analyse their own toy model in the course and present their findings to the group on the last day. Topics that will be covered in the course include the following: Why and how are models useful? How to write down/develop a model How simple/complicated should a model be? Which modelling approach/programming language should I use for my question? How to nail down a question with a model Extracting results from an equation/simulation How to evaluate a model using empirical data Participants can use their preferred programming language during the hands-on sessions, and free access to Wolfram Mathematica will be provided. The instructors have modelling experience using Mathematica, R, Python, and C++. Best regards Pedro Fernandes -- Pedro Fernandes GTPB Coordinator Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL Tel +351 21 4407912 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] GTPB Bioinformatics Training course REMINDER - 3DAROC16 - 3C-based data analysis and 3D reconstruction of chromatin folding
by Pedro Fernandes 16 Aug '16

16 Aug '16

The Gulbenkian Training Programme in Bioinformatics Applications for the bioinformatics training course 3DAROC16 3C-based data analysis and 3D reconstruction of chromatin folding are open. with Marc Marti-Renom, François Serra and Davide Baù IMPORTANT DATES for this Course Deadline for applications: September 30th 2016 Notification of acceptance within 72 hours of application (working days count) Course date: Oct 10th to Oct 14th 2016 Please refer to the course website http://gtpb.igc.gulbenkian.pt/bicourses/3DAROC16 for details. Course Description 3C-based methods, such as Hi-C, produce a huge amount of raw data as pairs of DNA reads that are in close spatial proximity in the cell nucleus. Overall, those interaction matrices have been used to study how the genome folds within the nucleus, which is one of the most fascinating problems in modern biology. The rigorous analysis of those paired-reads using computational tools has been essential to fully exploit the experimental technique, and to study how the genome is folded in the space. Currently, there is a clear expansion on the wealth of data on genome structure with the availability of many datasets of Hi-C experiments down to 1Kb resolution (see for example: http://hic.umassmed.edu/welcome/welcome.php ; http://promoter.bx.psu.edu/hi-c/view.php or http://www.aidenlab.org/data.html ). In this course, participants will learn to use TADbit, a software designed and developed to manage all dimensionalities of the Hi-C data: 1D - Map paired-end sequences to generate Hi-C interaction matrices 2D - Normalize matrices and identify constitutive domains (TADs, compartments) 3D - Generate populations of structures which satisfy the Hi-C interaction matrices 4D - Analyze and compare different samples. Participants can bring- specific biological questions and/or their own 3C-based data to analyse during the course. At the end of the course, participants will be familiar with the TADbit software and will be able to fully analyse Hi-C data. Note: Although the TADbit software is central in this course, alternative software will be discussed for each part of the analysis. Best regards Pedro Fernandes -- Pedro Fernandes GTPB Coordinator Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL Tel +351 21 4407912 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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