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NB: the course overview will not be updated as of January 1, 2014. A new overview is being set up at the BioSB website. You can find the updated course overview here.

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Course Portfolio

The NBIC PhD School offers a comprehensive programme of advanced courses on a variety of topics and technologies and allows the creation of a personalised education programme that specifically fits your research and interests. Our courses have been developed since 2009 in close collaboration with the bioinformatics community in the Netherlands and are taught by leading experts in the field. Each course is a combination of lectures and hands-on activities.

The programme is accessible for you when your expertise is in bioinformatics or life science and when you are:

  • a PhD student
  • a researcher, clinician, working in academia, the hospital or industry
  • a teacher (please read our how to get involved section)
  • a programmer, lab technician or research assistant or any other interested in learning bioinformatics.

The courses that we offer can be combined to fit your own interest. In order to make appropriate choices on your personal education programme, the courses are categorised in: 

Technology - principles, theoretical background and application of technologies

Application - emphasis on the application of bioinformatics technologies

Life Sciences - applications of bioinformatics in (NGS) Life Sciences

Each course in the T or A track is worth 3 EC and consists of one week of lectures and hands-on sessions. Courses also contain preparatory literature and a final assignment at the end. Life Sciences (LS) courses adhere to a less strict format, ranging from one day to several days and are always co-organised with other parties.

Technology

Managing and Integrating Information in the Life Sciences

Frequency is once per two years
Course Coordinators: Dr. Marco Roos (UvA), Dr. Katy Wolstencroft (VU), Celia van Gelder (NBIC)
Keywords: Knowledge-based information management, Database workhorses, Web services for collaboration and data integration, Semantic data integration
Last occasion: June 17 - 21st, 2013 in Leiden, the Netherlands (2013 programme)

Optimisation Techniques in bioinformatics and systems biology

Frequency is once per two year: expected 2013 (pre-register)
Course Coordinators:  Dr. Jaap Kaandorp (UvA), Celia van Gelder (NBIC)
Keywords: Local optimalisation methods, Global Optimalisation (e.g. Monte-Carlo sampling, Basin hopping technique), Global Stochastic Optimalisation (simulated annealing, evolutiony algorithms), Dynamic Programming
Last occasion: May 2010 (2010 programme)

Pattern recognition

Frequency is once per two year: expected early 2015 (pre-register)
Course Coordinators: dr. ir. P.D. Moerland (UVA), dr. ir. Dick de Ridder (TUDelft), dr. L.F.A. Wessels (NKI), Celia van Gelder (NBIC)
Keywords: Pattern recognition
Last occasion: January 21 - 25th, Amsterdam, the Netherlands (2013 programme)

Application

Algorithms for Biological Networks

Frequency is once per two year: expected January 2014 (pre-register)
Course Coordinators: Prof. dr. Marcel Reinders (TUD), Dr. Dick de Ridder (TUDelft), Prof. Dr. Jaap Heringa (VU), Celia van Gelder (NBIC)
Keywords: Properties of biological networks, Network inference, Alternative network models, Integrative bioinformatics, Network algorithms
Last occasion: January 2012 (link to 2012 programme)

Comparative genomics: from evolution to function

Frequency: once per two years: expected 2013 (pre-register)
Course Coordinators: Dr. Berend Snel (UU), Prof. Dr. Martijn Huynen (RU), Prof. Dr. Jaap Heringa (VU), Celia van Gelder (NBIC)
Keywords: Sequence analysis, protein-protein interaction, pathways prediction, genomics
Last Occasion: June 2011 in Utrecht (2011 programme)

Protein structures: production, prowess, power, promises, and problems

(full course description)
Frequency:
 once per two year:
Next occasion: 4-8 November 2013
Course Coordinators: prof. dr. Gert Vriend (RU), Celia van Gelder (NBIC)
Keywords: Protein structure visualisation, analysis and scientific application

Life Sciences

Next Generation Sequencing (NGS) data analysis

Frequency is once to twice per year. (pre-register)
Course Coordinators: Jeroen Laros (LUMC), Wilfred van IJcken (EMC), Judith Boer (LUMC), Johan den Dunnen (LUMC)
Keywords: Next-generation sequencing data analysis
Last Occasion: August 2013, Utrecht
Next occasion: 8th edition expected Winter 2014, Groningen (The Netherlands) (programme 2013 edition)

Advanced NGS course: RNA-seq data analysis

Frequency is once per year or when enough participants have pre-registered.
Course Coordinators: Peter-Bram 't Hoen (LUMC), Celia van Gelder (NBIC)
Keywords: Next-generation sequencing, NGS, data analysis, RNA-seq, transcriptome.
Last edition: October 15-17th, 2012 in Amsterdam (2nd edition) 
Next Occasion: Oct 30 - Nov 1, 2013 in Leiden (Full course description)

Advanced NGS course: de novo Assembly from NGS data

Frequency is once per year or when enough participants have pre-registered.
Course Coordinators: Gabino Sanchez-Perez (WUR), Jan van Haarst (WUR), Hendrik-Jan Megens (WUR), Johan den Dunnen (LUMC), Patrick Koks (NBIC)
Keywords: NGS, next-generation sequencing, Assembly, de novo assembly, reference genome, assembler, k-mer, de Bruijn graphs
Last editionJanuary 8th - 9th, 2013 in Wageningen (2013 programme); Next Occasion: early 2014

Advanced NGS course: Metagenomics approaches and data analysis

Frequency is once per year or when enough participants have pre-registered.
Course Coordinators: Sacha van Hijum (Radboudumc, NIZO food), Bas Dutilh (Radboudumc), Celia van Gelder (NBIC)
Keywords: metagenomes, environmental sequencing, functional profiling, next-generation sequencing, NGS, comparative metagenomics, bacterial genomics, microbial ecology, taxonomy
Last edition: February 6th - 8th, 2013 in Leiden (2013 programme);

Next Occasion: March 31st - April 2nd, 2014 in Nijmegen (2014 programme)

Advanced NGS course: Genomics Resequencing; Variant Detection and Interpretation in a Diagnostic Context

(full course description | information on the 2013 edition)
Course Coordinators: Christian Gilissen (UMC St Radboud), Johan den Dunnen (LUMC), Terry Vrijenhoek (CGD & UMC Utrecht), Jasper Saris (Erasmus MC), Patrick Koks (NBIC) 
Keywords: Read Mapping, Variant Calling, Annotation of Variants, Computational Predictions, Evaluation and Reporting of results, Clinical Interpretation, Clinical Relevance
Next Occasion: 2014

The Power of RNA-seq

(information on the 2013 edition)
Course Coordinators: Gabino Sanchez-Peres, Harm Nijveen, Edouard Severing (EPS, WUR), Patrick Koks (NBIC, WUR) 
Keywords: RNA-seq, transcriptome, experimental design, statistics, data analysis, mapping, quantification, differential expression, interpretation, pathways
Next Occasion: December 16th - 18th, 2013, Wageningen University

Additional courses

Apart from the regularly organised courses in the NBIC PhD School, NBIC BioWise is involved in organising additional courses with other parties:

NBIC / SIB Winterschool

Winterschool: At the intersection of bioinformatics and medicine
Course Coordinators: Patricia Palagi (SIB), Jaap Heringa (NBIC), Celia van Gelder (NBIC)
Keywords: genomics, drug discovery, clinical diagnostics, data integration, data mining, clinical expert systems, variant databases, protein domain knowledge, cancer genomics and treatments, GWAS studies, analysis of medical records and ontologies, drug testing and design
Last occasion: 10-15th March 2013 (2013 programme)

EBI Roadshow

EBI Roadshow part 1: Databases, Alignment, Ensembl, ArrayExpress
Date: April 9 - 10th, 2013 AMC, Amsterdam
Course Coordinators: Antoine van Kampen (AMC), Aldo Jongejans (AMC), Tom Hanckocks (EB), Johanna Langrish (EBI), Celia van Gelder (NBIC) 
Topics: introduction to databases at the EBI, Sequence Searching and Alignment, Ensembl for new users, ArrayExpress and Gene Expression Atlas

EBI Roadshow part 2: Small molecules, gene products and their interaction
Date: July 1st - 5th, 2013, Maastricht University, Maastricht (register)
Course Coordinators: Celia van Gelder (NBIC), Chris Evelo (Maastricht University), Egon Willighagen (Maastricht University), Tom Hancocks (EBI), Vera Matser (EBI) 
Topics: EBI Core resources for advanced analysis around: genes and genomes, proteins, small molecules, interactions, pathways

ICDD2013

International Chemical Discovery and Design course 2013 (ICDD2013)
Date: July 1st - 12th, 2013, Nijmegen University
Course Coordinators: CDD group, Dr. Tina Ritschel
Topics: Protein Modelling, Computational Medicinal Chemistry, Sequence Retrieval, Analysis and Alignment Techniques, Molecular Descriptors & Library Design, Virtual Screening, Scaffold Hopping, QSAR, COMFA