- BBClist - maillist.psb.ugent.be

EuBIC 2018 developer’s meeting - Extended project submission deadline
by EuBIC developer's meeting 16 Sep '17

16 Sep '17

*— EuBIC 2018 developer’s meeting —* *Project proposal submission deadline extended!* Project submission proposal is now open until *September 24, 2017*. EuBIC members will be present at the HUPO conference in Dublin this week. Find us there at the bioinformatics hub to get more information about the developer’s meeting and discuss your project proposal. To submit a project proposal please follow the instructions provided here: http://uahost.uantwerpen.be/eubic18/submission.html *EuBIC 2018 developer’s meeting* Date: January 9-12, 2018 Venue: Hotel Monasterium PoortAckere, Oude Houtlei 56, 9000 Gent, Belgium For more details on the program, please check the website: http://uahost.uantwerpen.be/eubic18/ *Key dates* *September 24, 2017: Extended project proposal submission deadline* October 2, 2017: Announcement of selected projects October 2, 2017: Conference registration opens January 9-12, 2018: EuBIC 2018 developer's meeting in Ghent *Topics* Hackathon projects can cover all topics in proteomics bioinformatics, including, but not limited to: - Tools - Extension of existing bioinformatics tools under the guidance of their original authors - Development of novel bioinformatics tools to solve open problems - Benchmarking - Compilation of gold-truth datasets - Collection of reference algorithmic implementations - Specification of benchmarking criteria - Workflows - Definition of formal protocols - Development of tutorials for bioinformatics software usage - Data analysis - (Re)analysis of publicly available proteomics datasets *More information* - website: http://uahost.uantwerpen.be/eubic18/ - social media hashtag: #EuBIC18 - conference email: eubic18(a)gmail.com *Sponsorship *inquiries are welcome at eubic18(a)gmail.com We look forward to welcoming you in Ghent! On behalf of the organizing committee, Wout Bittremieux

1 0

Registration open for: BioSB RNA-seq data analysis course (7th edition) on 6-8 November 2017
by Femke Francissen 13 Sep '17

13 Sep '17

BioSB RNA-seq data analysis course (7th edition) Date: 6-8 November 2017 Location: Leiden University Medical Center, the Netherlands Course coordinators: Peter-Bram ‘t Hoen (LUMC), Leon Mei (LUMC), Jan Oosting (LUMC), Szymon Kielbasa (LUMC) Course website: http://biosb.nl/education/course-portfolio/rna-seq/ . Registration: http://biosb.nl/education/course-portfolio/rna-seq/ enrollment-rna-seq-2017/ Course description The BioSB research school and partner LUMC are organizing a 3-day course on RNA-seq data analysis. This is an advanced course for people with experience in NGS. The course will consist of lectures, Galaxy and R practicals and will cover the analysis pipelines for differential transcript expression and variant calling. Examples will be taken from human and mouse studies. The course does not cover prokaryotic RNA profiling nor plant- and metagenomics aspects. Course topics - RNA-seq experimental approaches and study design - Quality control and alignment - Statistics for differential gene expression - eQTL analysis and allele specific expression - Single cell RNA sequencing - Fusion transcript detection - Small RNA profiling - Software for RNA-seq data analysis Target audience Participants for the RNA-seq course should preferably have participated in the general NGS course or otherwise have demonstrated hands-on experience with NGS data analysis. The course is aimed at PhD students and post-docs, but scientific programmers and data analysts with a background in biology and bioinformatics may also attend. NB: The practicals are mostly in R. We require that participants have at least basic knowledge of R and experience in running R scripts. Participants must bring own laptops capable of running RStudio. Please download and install RStudio before the course. For Galaxy tutorial, please install firefox or google chrome web browser. Registrations will be handled on a first-come-first-served basis but experience and motivation will be reviewed.Registrations will be handled on a first-come-first-served basis but experience and motivation will be reviewed. Seats have been reserved for participants in the FP7-funded projects RD-Connect <http://rd-connect.eu/> and BBMRI-NL <https://www.bbmri.nl/>. 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>

1 0

Registration open for BioSB course: Protein Structures (4th edition) - 31 Oct-3 Nov 2017
by Femke Francissen 13 Sep '17

13 Sep '17

BioSB course Protein Structures: production, prowess, power, promises, and problems (4th edition) Date: 31 October - 3 November 2017 Location: CMBI, Radboudumc, Nijmegen, the Netherlands Course coordinator: Gert Vriend (CMBI, Radboudumc) Lecturers: Daniel Hoffmann (University Duisburg/Essen (TBC)), Hanka Venselaar (CMBI), Wouter Touw (CMBI) *Website*: course website <http://biosb.nl/education/course-portfolio/protein-structures-production-pr…> *Registration:* registration form <http://biosb.nl/education/course-portfolio/protein-structures-production-pr…> Target audience The course is suitable for both PhD students working in structural bioinformatics as well as for PhD students in the life sciences who want to learn more about using structural informatioin in their research. The course schedule accommodates both groups, parallel sessions for both groups will be scheduled when necessary. Course Description In the right hands, protein structures are a ‘power’ful tool to answer bio-molecular questions. Knowledge of the structure is a pre-requisite for rational drug design, for biotechnology, for chemical biology, and for answering a whole series of biomedical questions. In this course we will discuss the ‘production’ of protein structures by NMR, X-ray, and homology modelling. These methods all have their pro’s and cons so a certain ‘prowess’ is needed to follow all ‘promises’ and start attacking bio-medical ‘problems’ using protein structures. The course will be split in three parts: - Part 1) Looking and seeing things in protein structures, learning to operate the software, understanding some of the algorithms. - Part 2) Protein structure determination (prediction) with NMR, X-ray, and homology modelling, and the possibilities and problems that come with each of these three techniques. - Part 3) Applying all that was learned in real-life example studies. Course topics Day 1: Homology modelling seminar Day 2: Protein structure comparison seminars Day 3: Electrostatics and molecular dynamics seminars Day 4: Protein structure determination and validation seminars Day 5: Own project executed with help from CMBI staff Examples of questions you will be able to answer after follwing the course: - Why is a person with this mutation sick? Or in other words, how does the molecular phenotype cause a disease state? - This enzyme converts mannose. Can I make is specificity broader? - This enzyme doesn’t function in my in vitro assay. Should I add some ions? - I want to add a tag to my enzyme, should I put it on the N-terminus, the C-terminus, or is something different needed? - This receptor binds a ligand, but if I look at the structure, that ligand doesn’t fit at all. Can I predict motions that take place upon ligand binding? 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>

1 0

post-doc offer
by Eric Bonnet 11 Sep '17

11 Sep '17

Post-doctorate in omics data integration and network science “Proteogenomic analysis of patient-specific network perturbations caused by genetic alterations in cancer” Context The diagnostic of cancer in a patient begins with a clinical examination followed by a blood test, medical imaging and often ends with the histopathological analysis of a tumor biopsy in order to establish the cancer type and the therapeutic strategy. One of the objectives of the France Genomic Medicine 2025 plan is to improve diagnostic and treatment selection by also taking into account genomic profiling obtained from NGS sequencing. However, recent research from the NCI Clinical Proteomic Tumor Analysis Consortium (CPTAC) demonstrated that the integration of proteomic profiles with genomic information, now referred to as "proteogenomics," reveals subtypes of cancers that are inaccessible by NGS. Our project is a transverse initiative (https://proteogenomics.wordpress.com/) between three CEA french research centers CNRGH-LBI (National Human Genome Research Center – Bioinformatics lab), BIG-EDyP (Biosciences and Biotechnology Institute of Grenoble – Proteomics lab), LIST-LADIS (Laboratory of Embedded Systems and Technology – Big data analysis lab) and BIFI-COSNET lab (Institute for Biocomputation and Physics of Complex Systems – Complex systems and networks lab) from the University of Zaragoza to contribute to the emergence of proteogenomics in precision medicine. Our final goal is to implement a "patient-centered" software solution capable of structuring, integrating and interrogating genomic and proteomic profiles from the same tumor in order to improve diagnostic and therapy. We will develop methods that capture and model the deregulations of molecular networks at stake in cancer, to identify patient-specific network perturbations and exploit them to provide better diagnostic. We already achieved significant progress on two in silico developments (not yet published) which can be considered as building blocks to our project: - We designed and implemented a graph-based database to structure and interrogate multi-omic tumoral data. This database was constructed using the triple-store technology to allow writing complex queries and to facilitate aggregation of public biological data repositories. - We developed a proteogenomic workflow to analyse proteomic data using a priori information extracted from transcriptome profiling. This approach, evaluated on a cancer cell line, allowed us to identify genetic alterations translated at the proteome level. Objectives The post-doctorate will develop a methodology to explore patient-specific perturbations on molecular networks and particularly on signaling pathways caused by genetic alterations (single nucleotide variants, aberrant transcript splicing) identified from proteogenomic profiling of tumor biopsies. He will leverage complexity of these multi-omic data to assess the impact of genetic variants on multiple regulatory dimensions, from transcriptional to post-translational levels. To reach this goal, the applicant will first analyse onco-proteogenomic data to infer patient-specific genetic alterations affecting its genome, transcriptome, proteome or phosphoproteome. Then, he/she will work on (i) the structuring of data obtained from each patient to define relationships between multi-omic measurements and (ii) the development of complex queries to reveal multidimensional perturbations. These investigations will be carried out using the multilayer network formalism and algorithms. This rapidly expanding research field was already successfully applied to multi-omic data to extract biological subnetworks, to identify genes with maximum influence on the process of perturbation spreading and to classify patients into cancer subtypes. Resources This methodology will be developed using large-scale omics data made publicly available by several international research consortia (GTEX, CPTAC, NIH Epigenomics Roadmap) and tested on proteogenomic profiles in-house produced from cancer cell lines. Moreover, data storage and computational needs required by this large-scale project will be available at the CEA HPC infrastructure. Host laboratories The recruited young researcher will be hosted by the BIG-EDyP laboratory in Grenoble and will evolve within a multidisciplinary research team. He/she will also spend research periods in collaborating laboratories to optimize progression of the research project. Expected competences The applicant should have a PhD in computational biology or related domains. He/she should be experienced in omics fields with at least one of these fields of expertise: bioinformatics, data integration or network science, and strong interest for all of them. Moreover, programming experience is required. Research contract Funding for a one-year post-doctoral contract is already available with gross annual salary range from about €41,000 to €58,000 depending on experience. We are looking for a candidate motivated to apply for additional funding at the CEA Enhanced Eurotalents Programme (http://eurotalents.cea.fr/) Contact If you are interested by this opportunity please send your CV, a motivation letter and names of referees to christophe.battail(a)cea.fr.

1 0

BBC2017, Leuven 13th-14th December - Registration open
by Daniele Parisi 09 Sep '17

09 Sep '17

Dear Mr/Mrs, we are happy to announce that the registration for the 13th edition of the BENELUX BIOINFORMATICS CONFERENCE is officially opened. The BBC is the key annual event that brings together researchers working at the intersection of a broad range of disciplines including computer science, biology, and medicine in Belgium, the Netherlands and Luxembourg. Don't miss the chance to use the power of our network, join the conference by filling in the REGISTRATION FORM available on this link https://goo.gl/forms/psc1ADA9Ag4o53Z23 The event will take place on WEDNESDAY 13TH AND THURDAY 14TH OF DECEMBER IN LEUVEN. The draft of the program, the list of keynotes and other useful information will be soon uploaded on the WEBSITE https://bbc2017blog.wordpress.com/ We are looking forward to meet you and discover your research at the conference. Kind regards The organization committee -- DANIELE PARISI PhD student at ESAT - STADIUS, Yves Moreau's group President of RSG Belgium Board member of PhD Leuven society Kasteelpark Arenberg 10 - box 2446 3001 Leuven, Belgium Tel: +32488794394

1 0

Fwd: ISCB Belgium RSG and IB2 Bioinformatics STUDENT DAY
by Daniele Parisi 08 Sep '17

08 Sep '17

SPECIAL BIOINFORMATICS EVENT: second edition of ISCB BELGIUM RSG and IB2 Bioinformatics STUDENT DAY FRIDAY, THE 13TH OF OCTOBER 2017 Plenary Room, U-Residence Building, ULB-VUB La Plaine-Etterbeek campus, Brussels REGISTRATION (DEADLINE 6TH OF OCTOBER) Registration is free. Please register before the 1st of October with the following link: https://goo.gl/forms/nJ2ZNCqt13URjsk03 [1] ABSTRACT CALL (DEADLINE 1ST OF OCTOBER) You can submit an abstract for oral/poster presentation. Nine PhDs-Postdoc abstracts will be selected for oral presentations. Please send your abstract to this address ib2rgs(a)gmail.com For the Full program and abstract call information, PLEASE SEE THE ATTACHED PDF On Behalf of RSG Belgium and IB2, Guillaume, Andrea and Daniele -- DANIELE PARISI PhD student at ESAT - STADIUS, Yves Moreau's group President of RSG Belgium Board member of PhD Leuven society Kasteelpark Arenberg 10 - box 2446 3001 Leuven, Belgium Tel: +32488794394 Links: ------ [1] https://goo.gl/forms/nJ2ZNCqt13URjsk03

2 1

Utrecht Bioinformatics Center symposium October 2nd
by Patrick Kemmeren 07 Sep '17

07 Sep '17

Dear all, For those of you who are interested, October 2nd we are organizing our yearly Utrecht Bioinformatics Center symposium. During this symposium we usually have two local speakers as well as two external speakers heavily relying on Systems Biology or Bioinformatics in their research. This year we have Eileen Furlong, head of the Genome Biology Unit at EMBL Heidelberg, Lude Franke from UMC Groningen, Vincent Robert from the Westerdijke fungal biodiversity insitute and Guido van den Ackervecken from Utrecht University. The program has a number of interesting and diverse topics including genome regulation and developmental transitions in Drosophila, reconstructing regulatory networks using single cell eQTLs, identifying virulence genes and monitoring emerging isolates in plants and biodiversity informatics using the largest fungal collection. Details of the program and registration (free of charge) can be found here: https://ubc2017.eventbrite.nl -- Patrick Kemmeren, PhD Principal Investigator T +31 (0)88 972 55 05 | M +31 (0)6 53 11 25 53 Princess Maxima Center * * *Princess Máxima Center for Pediatric Oncology* *Location Hubrecht institute*| Uppsalalaan 8 | 3584 CT Utrecht | T +31 (0)88 972 90 00 |***> Website* <http://prinsesmaximacentrum.com/>

1 0

Postdoc position within Janssen-VIB collaboration (oncology)
by Joke Reumers 04 Sep '17

04 Sep '17

Dear all, Within Janssen R&D, there is an open position for a postdoc in oncology, with a strong focus on omics data interpretation and bioinformatics: https://jobs.jnj.com/jobs/1700192601W/Postdoctoral+Scientist+in+Oncology?la… <https://jobs.jnj.com/jobs/1700192601W/Postdoctoral+Scientist+in+Oncology?la…> This postdoc position fits within an existing collaboration with the Aerts Lab of Computational Biology <http://gbiomed.kuleuven.be/english/research/50000622/lcb>. Please feel free to forward to potential other interested candidates, Kind regards, Joke ———————————————————————————— Joke Reumers, PhD Computational Biology @ Discovery Sciences Janssen Pharmaceutical Companies of Johnson & Johnson Turnhoutseweg 32, 2340 Beerse, Belgium jreumers(a)its.jnj.com +32 14 60 3324

1 0

Variant effect prediction course, 31th October - 3th November
by Sari van Heel - Vauhkala 04 Sep '17

04 Sep '17

Dear Members of BBClist, We would like to remind you about an upcoming international course that the Research Group Analysis Techniques in Life Science will organize in Breda (the Netherlands) in October-November 2017: Name course: Variant effect prediction Course date: 31 October – 3 November 2017 Registration fee: €900,- Website: http://www.alsavans.nl/uk%20site/Courses/avans-training-2542.html The digital registration form is available on our website. Should you have any questions, please do not hesitate to contact us by email at: si.vanheel-vauhkala(a)avans.nl<mailto:si.vanheel-vauhkala@avans.nl> Kind regards, Ms. Sari van Heel-Vauhkala Secretary Research Group Analysis Techniques in Life Science Disclaimer ( http://www.avans.nl/over-avans/e-mail-disclaimer )

1 0

ELIXIR Belgium: Python for Data Processing course - 5-6 October 2017 in Leuven
by Alexander Botzki 04 Sep '17

04 Sep '17

Dear all, We would like to announce the following ELIXIR Belgium course which is organised together with Geert Jan Bex from KU Leuven/UHasselt. If you are interesting in intermediate Python programming please do not hesitate to register for this course at http://www.vib.be/en/training/research-training/courses/Pages/Python-for-Da… Python for Data Processing Use Python to solve real data transformation problems. Topics include regular expressions, parsing, data transformation, interaction with databases and external programs using libraries for scientific programming such as numpy, scipy, matplotlib, pandas, and biopython. Prerequisites Aimed for people with programming skills and basic knowledge of Python. If you have no knowledge of Python you should follow an introductory Python course first. Date: 5 and 6 October 2017 Location: ICTS Education Center KULeuven Trainer: Geert Jan Bex (KULeuven/UHasselt) More info and registration: http://www.vib.be/en/training/research-training/courses/Pages/Python-for-Da… Best regards, Alex 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/>

1 0