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[Gtpb] GTPB Bioinformatics Training course announcement - QPB16 - Quantitative Proteomics using Bioinformatics
by Pedro L. Fernandes 28 Aug '16

28 Aug '16

The Gulbenkian Training Programme in Bioinformatics Applications for the bioinformatics training course QPB16 - Quantitative Proteomics using Bioinformatics with Mikhail Savitski (EMBL), Roman Zubarev (Karolinska) and Bo Zhang (Karolinska) IMPORTANT DATES for this Course Deadline for applications: Sep 24th 2016 Course dates: Oct 17th - Oct 19th 2016 http://gtpb.igc.gulbenkian.pt/bicourses/QPB16/ Course Description Recent years have seen rapid development in biological mass spectrometry and proteomics. In particular, the quantitative performance has taken a huge leap forward, both as a label-free (LF) approach and as multiplexed quantitative mass spectrometry. This development has enabled new technologies for unbiased characterization of drug molecules with protein targets, which is one of the major challenges in drug development. Here we will explain the basic principle of protein quantification by mass spectrometry. A pragmatic description of strengths and weaknesses of both label-free as well as the multiplexed methodology will be presented. A novel technology, thermal proteome profiling (TPP), will be explained that detects protein drug interactions in living cells. A practical session will take the students through the analysis and interpretation of quantitative mass spectrometry data stemming from the TPP experiment using an R package. In the LF part of the course, we will explain the basics of the identification software DeMix that performs deconvolution of the naturally multiplexed tandem mass spectra, thus significantly improving the identification aspects. An extension to quantification, DeMix Q, introduces the false discovery rate (FDR) for peptide identity transfer between the LC-MS runs, and greatly improves the quantification performance. Both DeMix and DeMix Q are realized based on Open MS package. The participants will learn how to use these programs and process their data. Note: this course is organised on the same week of PathProt, The International forum on Pathway Analysis in Proteomics, that meets annually at the IGC since 2008. Please contact me (pfern(a)igc.gulbenkian.pt) if you wish to submit an abstract. Website at http://gtpb.igc.gulbenkian.pt/PathProt At the moment, GTPB has 5 training courses OPEN for applications. 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 Upcoming courses: PM16 - Precision Medicine, Sep 27 3DAROC16 - 3C-based data analysis and 3D reconstruction of chromatin folding, Oct 10 QPB16 - Quantitative Proteomics using Bioinformatics, Oct 17 AAIRR16 - Analysis of Adaptive Immune Receptor Repertoires, Nov 2 AET16 - Applied Evolutionary Theory, Nov 7 IBSTAT16 - Introductory Biostatistics for Biologists, Nov 14 IB16S - Introductory Bioinformatics, Dec 12 _______________________________________________ GTPB mailing list GTPB(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

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Call for Participation: Computing a Tissue - 1st International Workshop on Modelling Multicellular Systems
by Sara Montagna 24 Aug '16

24 Aug '16

[Apologies for cross-postings. Please send to interested colleagues and students.] ********************************************************************************************************* CALL FOR PARTICIPATION COMPUTING A TISSUE 1st International Workshop on Modelling Multicellular Systems September 4, 2016 To be held in conjunction with the 15th European Conference on Computational Biology (ECCB 2016) The Hague, Netherlands; September 3-7, 2016 --- http://www.eccb2016.org<http://saso2012.univ-lyon1.fr/> ********************************************************************************************************* ---------------- Aims and Scope ---------------- Computational modeling and simulation are emerging as important tools to answer the age-old question in biology: How do cells form tissues? While modern microscopy and bio-image informatics are generating quantitative data on tissue formation at unprecedented rates, computational models are increasingly necessary to interpret these data, test biological hypotheses and ultimately provide a mechanistic understanding of the molecular and cellular mechanisms that drive the morpho-dynamics of multicellular systems. In recent years, computational models of multicellular systemshave been successfully applied in a wide range of fields including animal and plant morphogenesis, stem cell biology, regeneration, vascular development and tissue engineering. Despite notable differences in the application and validation of models, a common set of approaches has emerged to elucidate the logic of the biochemical and biomechanical interactions between cells. The workshop “Computing a tissue” present the state-of-the-art in computational modeling of multicellular systems. It highlights landmark studies of multicellular modeling across a range of biological fields, discusses the strengths and challenges of various modeling approaches and examines the current and upcoming computational methods and tools. All students and researchers interested in the computational modeling of multicellular systems are welcome. ------------------ Topics of Interest ------------------ * Applications of computational modeling to * animal and plant development * regeneration * organ physiology * skin homeostasis * tissue engineering * organoids * Innovative methods concerning * quantitative image analysis * image-based modeling * cell-based models * multi-scale modeling ------------------- Important Deadlines ------------------- Online registration: September 2, 2016 (extended) ---------------- Co - Organisers ---------------- Walter de Back, TU Dresden, Germany Roland Merks, CWI Amsterdam & Uni Leiden, the Netherlands Sara Montagna, Università di Bologna, Italy ————————— Speakers ————————— * Nadine Peyriéras<http://walter.deback.net/ECCB2016/speakers/#peyrieras> (CRNS, France) * Christophe Godin<http://walter.deback.net/ECCB2016/speakers/#godin> (INRIA, France) * Niels Grabe<http://walter.deback.net/ECCB2016/speakers/#grabe> (Uni Heidelberg, Germany) * Jörg Galle<http://walter.deback.net/ECCB2016/speakers/#galle> (Uni Leipzig, Germany) * Natalia Melnikova<http://walter.deback.net/ECCB2016/speakers/#melnikova> (ITMO Uni, Russia) * Stefan Hoehme<http://walter.deback.net/ECCB2016/speakers/#hoehme> (Uni Leipzig, Germany) * Mark Alber<http://walter.deback.net/ECCB2016/speakers/#alber> (Uni Notre Dame, USA) ————————— More Info at http://walter.deback.net/ECCB2016/ —————————

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Join the ECCB 2016 workshop What you need to know about data stewardship and future european research funding
by Celia van Gelder 24 Aug '16

24 Aug '16

*On Saturday 3 September 2016, Erik Schultes (DTL), Marco Roos (LUMC), Mark Thompson (LUMC), Mark Wilkinson (UPM), and Luiz Bonino (DTL, VU) will organise a workshop about FAIR Data stewardship. The workshop is part of the pre-programme of the 15th European Conference on Computational Biology (ECCB 2016 <http://www.eccb2016.org/>), 3-7 September in the Hague. * A broad community of stakeholders recently described a set of guiding principles to ensure that scientific data be Findable, Accessible, Interoperable, and Reusable (FAIR) <http://www.nature.com/articles/sdata201618>. This workshop will provide an introduction to FAIR Data Stewardship in the context of the European research initiatives <http://ec.europa.eu/research/openscience/index.cfm?pg=open-science-cloud>. The morning session will provide a brief introduction to the key issues and ample time for discussion. The afternoon session will be devoted to a practical introduction to data ‘FAIRification’ using real-life datasets. Depending on workshop attendance, the practical session may include hands-on coding activity guided by the workshop organizers. More information: http://www.eccb2016.org/programme/workshops/w6/ You can still register for this ECCB pre-meeting via: http://www.eccb2016.org/registration We look forward to seeing you September 3rd! -- Dr. Celia W.G. van Gelder Programme Manager Learning DTL/ELIXIR-NL Training Education Manager BioSB tel. +31613375327 e-mail: celia.van.gelder(a)dtls.nl websites: www.dtls.nl, www.biosb.nl skype: celia.van.gelder Postal address: DTL PO Box 19245 3501 DE Utrecht

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Join the ECCB 2016 workshop What you need to know about data stewardship and future european research funding
by Celia.vanGelder＠radboudumc.nl 24 Aug '16

24 Aug '16

On Saturday 3 September 2016, Erik Schultes (DTL), Marco Roos (LUMC), Mark Thompson (LUMC), Mark Wilkinson (UPM), and Luiz Bonino (DTL, VU) will organise a workshop about FAIR Data stewardship. The workshop is part of the pre-programme of the 15th European Conference on Computational Biology (ECCB 2016<http://www.eccb2016.org/>), 3-7 September in the Hague. A broad community of stakeholders recently described a set of guiding principles to ensure that scientific data be Findable, Accessible, Interoperable, and Reusable (FAIR)<http://www.nature.com/articles/sdata201618>. This workshop will provide an introduction to FAIR Data Stewardship in the context of the European research initiatives<http://ec.europa.eu/research/openscience/index.cfm?pg=open-science-cloud>. The morning session will provide a brief introduction to the key issues and ample time for discussion. The afternoon session will be devoted to a practical introduction to data ‘FAIRification’ using real-life datasets. Depending on workshop attendance, the practical session may include hands-on coding activity guided by the workshop organizers. More information: http://www.eccb2016.org/programme/workshops/w6/ You can still register for this ECCB pre-meeting via: http://www.eccb2016.org/registration We look forward to seeing you September 3rd! -- Dr. Celia W.G. van Gelder Programme Manager Learning DTL/ELIXIR-NL Training Education Manager BioSB tel. +31613375327 e-mail: celia.van.gelder(a)dtls.nl<mailto:celia.van.gelder@dtls.nl> websites: www.dtls.nl<http://www.dtls.nl/>, www.biosb.nl<http://www.biosb.nl/> skype: celia.van.gelder Postal address: DTL PO Box 19245 3501 DE Utrecht Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629. The Radboud university medical center is listed in the Commercial Register of the Chamber of Commerce under file number 41055629.

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Two job openings at ELIXIR-Luxembourg Node: 1) Science/Project Manager 2) Software Developer
by Venkata Pardhasaradhi SATAGOPAM 23 Aug '16

23 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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