- BBClist - maillist.psb.ugent.be

Job opening for an (Associate) Scientist Bioinformatics & Modeling at DSM
by Roubos, Hans 10 Mar '16

10 Mar '16

Job opening for an (Associate) Scientist Bioinformatics & Modeling at DSM Dear friends. Currently we have a job opening for an (Associate) Scientist Bioinformatics & Modeling at the DSM Biotechnology R&D Center located in The Netherlands. https://www.linkedin.com/jobs2/view/107086720?trk=vsrp_jobs_res_name&trkInf…<https://www.linkedin.com/jobs2/view/107086720?trk=vsrp_jobs_res_name&trkInf…> Kind regards, Hans Roubos Hans Roubos | Principal Scientist Bioinformatics & Modeling | DSM Food Specialties B.V. | Alexander Fleminglaan 1 | 2613 AX Delft | Netherlands | T +31 (0)15 2792147 | Trade Register Number 27235314 | Stay connected: [http://static.dsm.com/content/dam/dsm/images/twitter.png] <https://twitter.com/DSM> [http://static.dsm.com/content/dam/dsm/images/linkedin.png] <https://www.linkedin.com/company/3108> [http://static.dsm.com/content/dam/dsm/images/youtube.png] <https://www.youtube.com/user/dsmcompany> [http://static.dsm.com/content/dam/dsm/images/googleplus.png] <https://plus.google.com/117689312065000346895#117689312065000346895/posts> [http://static.dsm.com/content/dam/dsm/images/facebook.png] <https://www.facebook.com/DSMcompany> [http://static.dsm.com/content/dam/dsm/images/DSM_Email_EN.jpg] ________________________________ DISCLAIMER: This e-mail is for the intended recipient only. If you have received it by mistake please let us know by reply and then delete it from your system; access, disclosure, copying, distribution or reliance on any of it by anyone else is prohibited. If you as intended recipient have received this e-mail incorrectly, please notify the sender (via e-mail) immediately.

1 0

Edinburgh Genomics Bioinformatics workshops - GATK, Linux, RNA-seq, MinION, Python
by Bert Overduin 10 Mar '16

10 Mar '16

Dear all, We have currently a large variety of bioinformatics workshops open for registration, ranging from general entry level workshops, like "Linux for Genomics", which is targeted towards those who have never used the command line before, to more specialised and advanced ones, like "Oxford Nanopore MinION Sequencing - Data Handling, Analysis and Applications". Note that we are offering now three(!) different weeklong Python courses, an introductory one, an advanced one, as well as one focused on data manipulation and visualisation. All three are taught by dr Martin Jones, founder of Python for Biologists (http://pythonforbiologists.com) and author of several books on Python ( http://pythonforbiologists.com/index.php/books/) Registration for all workshops can be done through the workshop pages indicated below, on which you can also find much more detailed information about each workshop. I hope to see you at one (or more) of our workshops! With kind regards, Bert Overduin *2-day GATK Best Practices for Variant Discovery* Date: Thu 14 & Fri 15 April 2016 Price: £50 (day 1) / £100 (day 1 + day 2) Registration: first come first serve Deadline: Thu 30 March 2016 noon Details: https://genomics.ed.ac.uk/gatk-best-practices-variant-discovery *1-day Linux for Genomics* Date: Fri 13 May 2016 Price: £155 Registration: first come first serve Deadline: Fri 29 April 2016 noon Details: https://genomics.ed.ac.uk/linux-genomics *2-day Introduction to RNA-seq Data Analysis* Date: Thu 19 & Fri 20 May 2016 Price: £310 Registration: participant selection Deadline: Thu 21 April 2016 noon Details: https://genomics.ed.ac.uk/introduction-rna-seq-data-analysis *1-day Oxford Nanopore MinION Sequencing - Data Handling, Analysis and Applications* Date: Mon 13 June 2016 Price: £155 Registration: participant selection Deadline: Mon 16 May 2016 noon Details: https://genomics.ed.ac.uk/oxford-nanopore-minion-sequencing-data-handling-a… *5-day Introduction to Python for Biologists* Date: Mon 11- Fri 15 July 2016 Price: £500 Registration: first come first serve Deadline: Mon 13 June 2016 noon Details: https://genomics.ed.ac.uk/introduction-python-biologists-july-2016 *5-day Advanced Python for Biologists* Date: Mon 25 - Fri 29 July 2016 Price: £500 Registration: first come first serve Deadline: Mon 27 June 2016 noon Details: https://genomics.ed.ac.uk/advanced-python-biologists-july-2016 *5-day Data Manipulation and Visualisation with Python* Date: Mon 5 - Fri 9 September 2016 Price: £500 Registration: first come first serve Deadline: Mon 8 August 2016 noon Details: https://genomics.ed.ac.uk/data-manipulation-and-visualization-python -- Bert Overduin, PhD TRAINING AND OUTREACH BIOINFORMATICIAN Bert.Overduin(a)ed.ac.uk 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.

1 0

BioSB Course Kick start R (4th edition), April 25, 2016, Amsterdam
by Femke Francissen 10 Mar '16

10 Mar '16

*BioSB Course Kick start R (4th edition) * *Date: April 25, 2016* *Location: Amsterdam* *Course Coordinator: Douwe Molenaar (VU)* *Website*, including course programme: http://biosb.nl/education/course-portfolio/course-kick-start-r/ *Registration: * http://biosb.nl/education/course-portfolio/course-kick-start-r/enrollment-k… On April 25, 2015, BioSB organises the fourth edition of the Kick Start R course in Amsterdam. The goal of this kick-start course is to: 1. Introduce the structure and philosophy behind the R-language. 2. Introduce a number of tools specific to the R-language. This is an introductory course to speed up the study of R. *Target audience* Primarily targeting researchers from academia, but participants from the private sector are also welcome. The course is part of the Education Programme of BioSB, 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. Best regards, ** ** *Femke Francissen* Community manager BioSB BioSB Research School Visiting address: Geert Grooteplein 28, route 260, 6525 GA Nijmegen Postal address: P.O. box 9101, route 260, 6500 HB Nijmegen E-mail: femke.francissen(a)biosb.nl Tel: +31 24 36 19 500 Mobile: +31 6 17 90 4888 Skype: femke.francissen Website: www.biosb.nl LinkedIn link <http://nl.linkedin.com/in/femkefrancissen>

1 0

GATK Best Practices for Variant Discovery workshop 14-15 April 2016 (third announcement)
by Bert Overduin 08 Mar '16

08 Mar '16

Dear all, We still have places available for the first day of our GATK Best Practices for Variant Discovery workshop (the lectures part). This workshop will focus on the core steps involved in calling variants with the Broad Institute’s Genome Analysis Toolkit ( https://www.broadinstitute.org/gatk/) which is one of the most, if not the most, commonly used tool for variant calling. We are very lucky to have this workshop delivered by three members of the GATK team, which means you will receive training by the most expert instructors imaginable. As they have to come all the way from the United States, we cannot promise we will organise this workshop again soon, so if you're interested in variant calling / GATK, this really is an opportunity not to be missed! The workshop will be as interactive as possible, and offer plenty of opportunity for questions and answers. For more information and to register, please visit https://genomics.ed.ac.uk/gatk-best-practices-variant- <https://genomics.ed.ac.uk/gatk-best-practices-variant-discovery>discovery <https://genomics.ed.ac.uk/gatk-best-practices-variant-discovery>. Note that the second day of the workshop (the hands-on part) is currently fully booked, but it is still possible to be placed on the waiting list, in case any places become available closer to the workshop date. Please feel free to forward this mail to anyone else potentially interested and/or to print out the attached flyer for further distribution. Hope to see many of you in April! With kind regards, Bert -- Bert Overduin, PhD TRAINING AND OUTREACH BIOINFORMATICIAN Bert.Overduin(a)ed.ac.uk 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.

1 0

Want to learn how to build your science or high-tech startup? Join the Bootcamp by ACE Venture Lab – May 9-13 in Amsterdam!
by Yulia Bodnar 07 Mar '16

07 Mar '16

*Want to learn how to build your science or high-tech startup? Join the Bootcamp by ACE Venture Lab – May 9-13 in Amsterdam!* <https://podio.com/webforms/3841158/296341> ACE Venture Lab is accepting applications for the Bootcamp! <https://podio.com/webforms/3841158/296341> On May 9-13 ACE Venture Lab organizes a Bootcamp <http://www.ace-venturelab.org/bootcamp/> – an intensive training program for researchers, senior scientists and MSc students that want to convert their science or high-tech ideas into a feasible company. We invite a team of Silicon Valley specialists and startup experts to mentor you on launching your business. The Bootcamp covers all stages of business creation and development, teaching you how to translate your science or tech concept into viable business. During the program you will test your business assumptions, analyze potential challenges and learn how to make your idea an attractive proposition for investors and customers. *Interested to join?* Read more about the program <http://www.ace-venturelab.org/bootcamp/>and apply here! <https://podio.com/webforms/3841158/296341> Time: May 9-13 Location: ACE Venture Lab <http://www.ace-venturelab.org/>, Science Park 402, 1098 XH Amsterdam For questions contact us at yulia(a)ace-vlab.nl. -- *Yulia Bodnar* +31617835493 Program Manager Science Park 402 1098 XH Amsterdam Twitter <https://twitter.com/ACE_Vlab> | LinkedIn <http://www.linkedin.com/groups?gid=3709264> http://ace-venturelab.org

1 0

SMRTLeiden Scientific Events – June 6 – 8, LUMC: Registration is now open!
by S.Y.Anvar＠lumc.nl 04 Mar '16

04 Mar '16

Dear colleagues, Register<http://programs.pacificbiosciences.com/e/1652/SMRTLeiden--register/3kbp6p/4…> now for the SMRTLeiden<http://www.lgtc.nl/SMRTLeiden> Scientific events - SMRT Scientific Conference: Changing the World, One Molecule at a Time! and the SMRT Informatics Developers Conference. These events will cover topics from microbes to human health! You can view the preliminary program<http://programs.pacificbiosciences.com/e/1652/SMRTLeiden--speakers/3kbp6r/4…>. SMRT Scientific Conference: Changing the World, One Molecule at a Time! is a two-day symposium featuring key experts and opinion leaders sharing scientific discoveries and novel analytical achievements using PacBio® Sequencing platforms. June 6 and 7, 2016 Leiden, Netherlands Leiden University Medical Center Keynote speakers: * Evan Eichler, Ph.D., University of Washington, USA * Hagen Tilgner, Ph.D., Stanford University, USA * Steven GE Marsh Ph.D., Anthony Nolan Research Institute, UK * Shinichi Morishita, Ph.D., University of Tokyo, Japan * Gene Myers, Ph.D., Max Planck Institute, Germany SMRT Informatics Developers Conference is a collaborative event to develop and improve data analysis tools for SMRT® Sequencing technology June 8, 2016 Leiden, Netherlands Leiden University Medical Center The goal of the conference is to advance development of analytical tools for PacBio data by enabling in-person brainstorming and idea exchange among software developers and the bioinformatics community. Through facilitation of open discussion and collaboration, the event will nurture development of new and existing open source tools for de novo assembly, genome phasing, structural variations, epigenetics and full-length mRNA sequencing data analysis. Featured speakers: * Gene Myers, Ph.D., Max Planck Institute, Germany * Jason Chin, Ph.D., PacBio, USA * Shinichi Morishita, Ph.D., University of Tokyo, Japan * Yahya Anvar, Ph.D., Leiden University Medical Center, Netherlands * Elizabeth Tseng, Ph.D., PacBio, USA * Lance Hepler, Ph.D., PacBio, USA These events are free and open to all members of the scientific community. Discount codes for your hotel accommodations will be provided in your registration confirmation email. Best regards, Yahya Anvar, PhD Department of Human Genetics | Leiden University Medical Center --------------------------------------------------------------------------------------------------------------------------------------------------------- Office: R05-022 | Phone: +31 71 526 8559 | email: s.y.anvar(a)lumc.nl<mailto:s.y.anvar@lumc.nl> Address: Postzone: S-04-P, Postbus 9600, 2300 RC Leiden | Visiting Address: Einthovenweg 20, 2333 ZC Leiden ---------------------------------------------------------------------------------------------------------------------------------------------------------

1 0

Proteomics Informatics Workshop series
by Katrijn Vannerum 04 Mar '16

04 Mar '16

Dear all, A series of three one-day workshops for PhD students and post-docs working in the field of proteomics using mass spectrometry is organized by the Belgian Proteomics Association (BePA). Please see: http://www.ugent.be/doctoralschools/en/doctoraltraining/courses/specialistc… Kind regards, Katrijn Vannerum PhD Project manager BIG N2N (Bioinformatics Institute Ghent From Nucleotides to Networks) Ghent University http://www.bign2n.ugent.be/ twitter: @N2N_UGent Katrijn.Vannerum(a)UGent.be<mailto:Katrijn.Vannerum@UGent.be> Technologiepark 927 9052 Gent, Belgium +32 (0)9 331 36 85 [logo_BIG N2N_signature]

1 0

[Gtpb] NDARC16 - NGS Data Analysis RNAseq and ChIPseq - Announcement
by Pedro Fernandes 02 Mar '16

02 Mar '16

REMINDER Dear all, The Applications for the bioinformatics training course NDARC16 - NGS Data Analysis RNAseq and ChIPseq, are now OPEN. IMPORTANT DATES for this Course Deadline for applications: March 20th 2016 Course dates: March 29th - April 1st 2016 Details are available here: http://gtpb.igc.gulbenkian.pt/bicourses/NDARC16 Overview High-throughput technologies such as next generation sequencing (NGS) can routinely produce massive amounts of data. These technologies allow us to describe all variants in a genome or to detect the whole set of transcripts that are present in a cell or tissue. However, such datasets pose new challenges in the way the data have to be analyzed, annotated and interpreted which are not trivial and are daunting to the wet-lab biologist. This course covers state-of-the-art and best-practice tools for NGS RNA-seq and ChIP-seq data analysis, which are of major relevance in today's genomic and gene expression studies. Methods The course is comprised of practical exercises preceded by short lectures. Exercises will be conducted primarily in the R programming language. Target Audiences Enthusiastic and motivated wet-lab biologists who want to gain more of an understanding of NGS data and eventually progress to analysing their own data. Pre-requisites There is a lot of material to cover in the course, so we will assume that you are familiar with a few basics before you come. The tool that will we do most of the analysis in is R. There will be a short recap of the key concepts at the beginning of the course; however it will be beneficial if you are already familiar with how to read data into R, perform basic subset operations and produce simple plots. Some introductory statistics, such as summary statistics for continuous data (mean, variance etc) and interpreting the results of a t-test, will be also be assumed. See "Statistics at Square One"" Chapters 1, 2, 3 and 7 (Statistics at Square One - BMJ) for a good overview. Basic unix skills, such as being able to list the contents of a directory and copy files, would also be an advantage. See "Session 1" of the Software Carpentry training for a Unix introduction (Shell-novice material from the Software Carpentry Foundation). Best wishes Pedro Fernandes GTPB Coordinator -- Pedro Fernandes 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

1 0

SCS2016 Friday 8th July 2016, Orlando, Florida - Abstract Call Open
by SCS2016 02 Mar '16

02 Mar '16

Dear Colleague, We would like to invite you to the twelfth edition of the ISCB Student Council Symposium on *Friday 8th July 2016 *during ISMB in *Orlando*, Florida, US. SCS is a yearly recurrent interdisciplinary symposium, linked to ISMB. Its main goal is to bring together students and young researchers from computational biology, bioinformatics, systems biology, and related fields. This symposium includes an ice-breaking event, internationally renowned keynote speakers, oral presentations, flash presentations, a poster session and the famous social event in the evening. Therefore, it provides you with the opportunity to present your research to an international audience, learn about state-of-the art research and build a worldwide scientific network. We are excited to announce our two Keynotes *John Quackenbush* and *Janet Thornton*. These experts in the fields of cancer systems biology and structural bioinformatics, respectively, will be talking about their research and experiences as leaders at the forefront of science. You can learn more about them here: http://symposium.iscbsc.org/node/187 *Abstract Submission* is currently *open* on http://symposium.iscbsc.org/ . You can also apply for one of our *travel fellowships* at the same link. Registration will open later trough the main conference website: https://www.iscb.org/ismb2016-registration Please help us spread the word by sharing our flyer (please find it attached), and using the hashtag #SCSOrlando2016 on social media. We look forward to seeing you in Orlando, Florida this summer! Bart Cuypers and Ben Siranosian SCS2016 Chair and Co-chair

1 0

[Gtpb] PDA16 - Proteomics Data Analysis - Announcement
by Pedro Fernandes 01 Mar '16

01 Mar '16

Dear all, The Applications for the bioinformatics training course PDA16 - Proteomics Data Analysis, are now OPEN. IMPORTANT DATES for this Course Deadline for applications: April 2nd 2016 Course dates: April 11th - April 15th 2016 Details are available here: http://gtpb.igc.gulbenkian.pt/bicourses/PDA16 Course description Mass spectrometry based proteomic experiments generate ever larger datasets and, as a consequence, complex data interpretation challenges. In this course, the concepts and methods required to tackle these challenges will be introduced, covering both protein identification and quantification. The course will rely exclusively on free and user friendly software, all of which can be directly applied in your lab upon your return from the course. An introduction to the available online resources and repositories will also be given. Here you will see how to link the results from proteomic experiments with external data to conduct pathway, gene ontology and interaction analyses. In the course, you will also learn how to submit data to the ProteomeXchange online repositories, and how to browse and reprocess publicly available data from these repositories. The course will provide a solid basis for beginners, but also new perspectives to those already familiar with standard data interpretation procedures in proteomics. Best wishes Pedro Fernandes GTPB Coordinator -- Pedro Fernandes 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

1 0