The aim of the course is to educate users in performing high-level analysis of ready normalized gene expression data, and interpretation of the results. An overview of the whole analysis process as well as planning of the experiment will be covered during the course, but the focus of the course program will be on analysing and interpreting ready preprocessed gene expression data in terms of their annotations using J-Express.

The course will be held completely in a computer lab, aiming for as much hands on analysis as possible, with short introductions and discussions at regular intervals. Computers will have the J-Express software readily installed. You may bring your own laptop if you already are using J-Express regularly, and your laptop has sufficient hardware capabilites (most important memory).

Tentative program available here. We'll start the first day at 09.00 and finish off by 16.00 the last day

The course is free of charge. Participants should organize their transportation and accomodation. Number of participants limited to 20

Any questions can be directed to Kjell Petersen and Anne-Kristin Stavrum by sending an email to registration@bccs.uib.no.

Latest update

The course is now fully booked with 20 participants. Questions about last moment free seats can be adressed to the above listed e-mail adress, and you will be put on a waiting list.

Ensembl Workshop September 2007 in Bergen

The Computational Biology Unit is organizing a 4-days course, which will cover EnsEMBL Browser, API (core and compara), and BioMart. The course will consist of lectures and hands-on practices both for wet-lab biologists and bioinformatics programmers. Participants are encouraged to bring problems/questions about their research to try to tackle these during the workshop using Ensembl. Basic knowledge of programming in Perl is expected for days 2&3 (API), as well as for day 4 (BioMart). See program below. Also, the workshop will focus on chordates, not lower animals none of plants or prokaryotes.

Time: Sep. 3rd - 6th, 2007
Place: Bergen (Building will be announced later)
Operating system: windows (day 1), linux (days 2 to 4)

Preliminary program:

Day 1 (Sep. 3rd): Browser
Bert Overduin (European Bioinformatics Institute)
This 1st-day course offers participants the possibility of gaining lots of hands-on experience in the use of the Ensembl genome browser but also provides them with the necessary background information. The workshop is primarily targeted at wet-lab researchers.

Day 2 (Sep. 4th): Ensembl Core databases and API
Albert J. Vilella (European Bioinformatics Institute)
The set of species-specific Ensembl Core databases stores genome sequences and most of the annotation information. This includes the gene, transcript and protein models annotated by the Ensembl automated genome analysis and annotation pipeline. Ensembl Core databases also store assembly information, cDNA and protein alignments, external references, markers and repeat regions data sets. This is a practical tutorial to show how to programmatically access the data by writing rapid and reliable code using the Ensembl Perl API. With practical examples to work with coordinate systems, slices, features, genes, transcripts, exons, translations, external references, etc.

Day3 (Sep. 5th): Ensembl Compara database and API
Albert J. Vilella (European Bioinformatics Institute)
The Ensembl Compara multi-species database stores the results of genome-wide species comparisons re-calculated for each release. The comparative genomics set includes pair-wise whole genome alignments and synteny regions. The comparative proteomics data set contains ortholog and paralog predictions and protein family clusters. This is a practical tutorial to show how to access the comparative multispecies data using the Ensembl Compara Perl API, with practical examples to work with pair-wise and multiple genomic alignments, synteny, gene families, trees and homologies.

Day4 (Sep. 6th): BioMart
Richard Holland (European Bioinformatics Institute)
BioMart provides data warehousing and query mechanisms for the quick and simple discovery of data within Ensembl and other databases. It forms an integral part of the Ensembl website and can be explored at http://www.ensembl.org/biomart/martview . This one day course of tutorials and practical workshops will cover the use of the BioMart web query interfaces and programming APIs in the first half, and in the second half will teach you how to convert your own data into BioMart format and set up your own web query interface to present this data to your users.

The course is FREE of charge.

Please send an email to contact@bioinfo.no if you have questions.

The MCB research school and CBU are organizing a 5-days course in molecular dynamics simulations. The course will consist of lectures and hands-on practicals and is meant for beginners.

Participants are expected to have basic knowledge of protein and DNA structure. The first day will be devoted to a pre-course meant to provide the necessary background knowledge to understand the lectures and go through the practicals.

Operating system: linux
Number of participants: 20 max.
Place: HiB, Thormohlensgt 55, Bergen

Preliminary program:

May 21: pre-course, lectures and hands-on
Knut Teigen (IBMB, UiB) & Nathalie Reuter (CBU, UiB)
basic linux commands, molecular modeling, force fields, protein data bank, visualization with VMD

May 22-23: Amber simulation package
Ross Walker (San Diego Super Computing Center & University of California San Diego)
General overview of Amber and its programs, running and analyzing a simulation, visualization of the trajectories, introduction to MD algorithms, implicit solvent, non-standard residues

May 24: membrane proteins (to be confirmed)

May 25: getting started with MD simulations on your own system (to be confirmed)

The aim of the course is to educate users already familiar with the basic workflow of microarray analysis, on the more advanced topics of:

• experimental design, multiple testing statistics, statitics for integrating genomic data, gene set based analysis, analysis using linear models and analysis of Illumina data

• efficient use of J-Express and to cover the more advanced features of this analysis tool.

• Dr Rainer Breitling, Groningen Bioinformatics Centre (GBiC), University of Groningen, Netherland
• Dr Arnoldo Frigessi, Dept of Biostatistics, University of Oslo, Norway
• Dr Natalie Thorne, Dept of Applied Mathematics and Theoretical Physics (DAMTP), University of Cambridge, United Kingdom

The course have been divided into two modules:

• Mocule 1: Analysis using J-Express Dec 4th - 5th (starts 10.00 first day, ends 16.00 last day)
• Module 2: Experimental design and advanced analysis Dec 6th - 8th (starts 10.00 first day, ends 12.00 last day)

Select the dates and modules you will be attending in the registration form. Also remember to notify in the form if you are bringing your own laptop, highly recommended at least for module 1.

Register here.

Programme available here

Course free of charge. Participants should organize their transportation and accomodation. Number of participants limited to 20

The aim of the course is to introduce basic resources available through the internet, and to teach basic and more advanced sequence analysis methods.

The students will acquire a basic understanding of how the methods work, what assumptions they are based on, their relative strengths, weaknesses, and limitations. The course will cover the major biological databases, and analysis of both protein and nucleotide sequences. Basic sequence analysis methods that will be covered include: 1) pairwise sequence comparisons and comparisons to databases, 2) multiple sequence alignments, and 3) patterns and profiles. In addition, the protein sequence analysis part will include the use of domain and motif prediction resources. The nucleotide sequence analysis part will cover topics such as gene regulation and comparative genomics. The course will consist of lectures and exercises.

The sequence analysis course is targeted primarily to biologists that have little or no previous bioinformatics experience.

Lecturers will be Cedric Notredame (Structural and Genetic Information, C.N.R.S, Marseille), and Boris Lenhard, Rein Aasland and Pål Puntervoll (CBU).

Registration deadline has passed. (Inquiries for late registration: contact@bioinfo.no.)

Programme.

Course web page.

The aim is to introduce R as a powerful tool for analyzing any type of data.

The course will consist of lectures together with practicals and exercices.

The lecturer will be Frederic Guyon, invited from the Denis-Diderot University in Paris. The practical sessions will be jointly organized by Frederic Guyon and staff at CBU (Trond Bø, David Fredman, Eric Hajjar) and NTNU (Endre Anderssen).

Program and practical information available here

Please, take advantage of the early announcement to contact us (contact@bioinfo.no) if you have questions/suggestions regarding the course.

Registration deadline has passed. (Inquiries for late registration: contact@bioinfo.no.)

CBU is giving an introductory course in the use of Web Services within bioinformatics (19-21 of April). The course will be given by Jan Christian Bryne (CBU) and will consist of lectures and exercises. Use of selected bioinformatic Web Services will be demonstrated and attendants will learn how to set up their own Web Services. A basic knowledge of XML and programming is required. Although the methodology is language-independent, Java will be used as the main programming language for the course.

The course is free of charge but participants must arrange for transportation and accommodation. The number of participants is limited to 25.

Registration deadline has passed. (Inquiries for late registration: contact@bioinfo.no.)

Course website

4-days Structure Prediction Course Sept 19-22, 2005

The course will consist of lectures and exercices, including a tutorial on the Modeller program www.salilab.org/modeller.

Lecturers:
  Darrell Conklin (Dpt of Computing, City University, London)
  William R. Taylor & Jose Saldanha (National Institute for Medical Research, London)
  M.S. Madhusudhan & Eswar Narayanan (Dpt of Biopharmaceutical Sciences, Andrej Sali Lab, Univ. California San Francisco).

Program and practical information available here

Course free of charge.
Participants should organize their transportation and accomodation. See here
Number of participants limited to 25.
Registration is closed. Participants accepted to the course will receive an email this week.

1-day Ensemble Course May 4, 2005

1-day course with hands-on training. Ensembl is a joint project between EMBL-EBI ad the Sanger Institute to develop a software system which produces and maintain automatic annotation on metazoan genomes. Available at www.ensembl.org.

Lecturers: scientists from the Ensembl help-desk.

Date: May, 4th 2005 (morning + afternoon)

Registration deadline: April 15th.

Bioinformatics for Proteomics - 11-14 April 2005

The course will be arranged by CBU and PROBE (Proteomics unit in Bergen) www.probe.uib.no.

The course gives an introduction to proteomics and MS-instruments used for proteomics. Programs for protein identification and characterization are described, as well as programs for analysing data from proteomic instruments. The algorithms and statistical significance behind programs are described.
:
The course is aimed at people (biologists, informaticians, others) who
- want to know what proteomics is
- want to know the basic principles behind MS-instruments
- want to know central bioinformatics problems related to proteomics, and programs for solving them

The participants should have some knowledge in protein chemistry. There is also a wish that they should have some (minimum) algorithmic and statistical background.

The course is limited to 20 participants, and will be given at PROBE, located at Building for Basic Biology Science, www.uib.no/bbb.

Registration is closed. For late registration please contact Ingvar Eidhammer (ingvar at ii.uib.no).

More info and programs at www.ii.uib.no/~ingvar/kurs/Plan.html

Microarray Data Analysis Course February 28- March 4, 2005.

New: Tentative programme.

In collaboration with the Norwegian Microarray Consortium (NMC), CBU arranges a five-days course on analysis of microarray gene expression data. The course will consist of lectures and hands-on practicals and will cover pre-processing of microarray data (filtering, normalisation etc) and un-supervised and supervised analysis. The course is intended both for biological and meidcal students and researchers as well as informaticians and statisticians. The practicals will give participants experience with using J-Express, BASE, SciCraft, PubGene, and eGOn. The course will be given by staff CBU and NMC staff (including Endre Anderssen, Vidar Beisvåg, Trond Bø, Bjarte Dysvik, Eivind Hovig, Inge Jonassen, Kjell Petersen, Laila Stordrange) and invited lecturers Carsteen Friis (CBS, Denmark) and Patrick Kemmeren (Utrecht). The course is limited to 25 participants and will be given at the High Technology Centre in Bergen.

Registration closed. Contact Inge Jonassen (inge.jonassen at bccs.uib.no) for late registration.

Lecturer: Marit Holden, Norwegian Computing Center

The course will consist in 12 lessons, 6 lessons each day. More details about the program will be available soon.

Topics: advanced measures of uncertainty, hypothesis testing, multivariate data, regression, clustering, experimental design, stochastic simulation, bayesian inference.

Place: Computational Biology Unit, HiB, Datablokk, 5th floor. Thormøhlensgt. 55, Bergen

To sign up for the course, register at:
http://www.bioinfo.no/training/courses/registration
(registration deadline: Nov. 20th, 2004)

The course will introduce basic concepts (including quantitatively) in population genetics/genomics to an audience already familiar with basic concepts in molecular biology. There will be both lectures on theory and basic problem sets on the material covered. The lecturer for the first two days will be Professor Carlos Bustamante (Cornell University, USA). The last day, with a lecture by Bjørn Høyheim (Norwegian National Veterinary School, Oslo), will apply basic principles to the Atlantic salmon as a model, an organism of particular interest to the Norwegian community...

Program:

* October 11-12: Carlos Bustamante (Cornell University, USA)
* October 13 Bjørn Høyheim (Norwegian National Veterinary School, Oslo)

To sign up for the course, register at:
http://www.bioinfo.no/training/courses/registration
(registration deadline: Sept. 15th, 2004)

The course is annouced early, to give participants the opportunity to acquire programming skills, if needed. An excellent starting point for aquiring basic programming skills, and to get aquainted with Python is the course "Introduction to Programming using Python" [PDF] by Katja Schuerer et al., which is made for biologists. All programming examples are biological in nature, and the course is suitable for self study. Potential participants are also encouraged use the bioinfo.no discussion forum for discussing Python programming, and an informal crash course in programming may be organised during the spring if this is of interest.

The course will be an intensive 5-day workshop.

Interesting link: http://www.dalkescientific.com/writings/NBN/

A 'follow-up' page for the participants to the course.