BWE2007 2014-2015

Introduction slides for BWE2007 at Maastricht University.

Transcript

1. Bioinformatics & Systems Biology trajectory Egon Willighagen 1 BWE2007
2. What is Bioinformatics? 2 Computer Sciences, Statistics Biology Bioinformatics
3. Bioinformatics is important for modern research 3 The goal of Bioinformatics is to increase understanding of biological systems using computationally intensive techniques and large databases with biological information.
4. Bioinformatics in BWE 4
5. Why is bioinformatics important to YOU?!? • Online-available biological information: o To better understand biological processes (learning) o To expand knowledge on biological systems (learning) o To formulate research hypothesis (research) o To design experiments (research) o NOT: Maintaining and developing biological databases (-> Bioinformatician) • Analyzing (large-scale) biological data o Having an overview of available tools & methods o Knowing when you should use which tool or method o Understanding how to use the (basic) tools & methods o Interpret your results o Understand findings in published research papers o NOT: Design/develop your own tools & methods and advanced data analysis (-> Bioinformatician) 5 The goal of Bioinformatics is to increase understanding of biological systems using computationally intensive techniques and large databases with biological information.
6. Schedule Block 2.4 • Biological Databases • Genetic Regulation • Gene Expression • Pathway Analysis • Network Analysis • Metabolomics Block 2.5 • Genetic Variation • Protein Structure • Sequence Alignment and BLAST • Modelling (Matlab) • Systems Biology 6
7. Head of the Bioinformatics-BiGCaT department Prof. Dr. Ir. Chris Evelo COORDINATORS (all BiGCaT) • BGK - Dr. Susan Coort • BWE – Dr. Egon Willighagen • MLW - Dr. Drs Lars Eijssen Organisation - coordination Chris Susan Lars Egon
8. OTHER INSTRUCTORS • Dr. Rachel Cavill (TGX / DKE) • Dr. Martina Kutmon (BiGCaT) • Anwesha Dutta, MSc (BiGCaT) • Jonathan Melius, MSc (BiGCaT) • Rianne Fijten, MSc (Toxicology) • Christian Oertlin, BSc (BiGCaT) - SA Organisation - instructors 8 Rachel Christian Rianne Jonathan Nuno Bart Anwesha Tina Elisa • Bart Smeets, MSc (BiGCaT) • Elisa Cirillo, MSc (BiGCaT) • Nuno Nunes, MSc (BiGCaT) • Linda Rieswijk, MSc (BiGCaT / TGX) Linda
9. • The Bioinformatics trajectory (BWE2007) in year 2 runs in periods 4 and 5.  In period 5 further topics will be covered  Background on all topics is given in the Course Book • Lectures will mostly be in Dutch Slides and practical exercises are in English The case has to be submitted in English • The Bioinformatics exam will be at the end of block 2.5. • This exam is separate from the block exam • The exam is an open book computer exam • Active participation in all practical sessions will be signed off Practical Information 9
10. • There will be two cases related to the practical sessions  You have to do the cases individually  Submit within ~ nine days after the practical (deadline is indicated)  Submit your results using SafeAssign  We will grade the case with either ‘0’ (insufficient) or ’1’ (sufficient)  You will receive some individual feedback, but no extensive corrections  After the submission deadline, the correct answers are discussed and thereafter made available Cases 10
11. Catch up possibilities** • Practical not signed off • Case not submitted • Insufficient case * The replacement assignments and replacement cases are made available at Eleum ** 75% rule!  Submit replacement assignment within 7 days after practical  Submit replacement case within 7 days after original submission deadline  Resubmit case within 7 days after feedback 11 * *
12. Blackboard • The slides of the lecture are available at the start of the lecture • Per practical session/case literature references may be provided • The exercises are available before the start of each practical session • The answers to the questions are available after the practical session • The case results are available after the debriefing BOOKS (available at the “studielandschap”) • Understanding bioinformatics M Zvelebil and J.O. Baum • Bioinformatics: Sequence and genome analysis David W. Mount • Bioinformatics and Functional Genomics J. Pevsner FURTHER LITERATURE is indicated per topic in the course book Course Material 12
13. Eleum (2014-400-BWE2007) 13