Bioinformatics for Cell Biologists

Transcription

1 Bioinformatics for Cell Biologists Rickard Sandberg Karolinska Institutet May 2013

2 OUTLINE INTRODUCTION Introduce yourselves HISTORY MODERN What is bioinformatics today? COURSE ONLINE LEARNING OPPORTUNITIES

3 INTRODUCE YOURSELVES 1-minute summary Project (1 sentence summary) Bioinformatics resources you are currently using Expectations of the course

4 THE ORIGIN Bioinformatics as a subject was born when we obtained methods to read DNA and protein sequences When the number of protein and DNA sequences made manual sequence comparisons and alignments impractical

5 MARGARET DAYHOFF Margaret Dayhoff, Started the Atlas of Protein Sequence and Structure (1969) Started the Protein Identification Resource (1972) to search for related sequences (homology) to infer evolutionary relationships (phylogeny) substition matrix, 1-letter amino acid code, point-accepted-mutations (PAM)

6 MILESTONES IN ALGORITHMIC DEVELOPMENT Algorithmic development in sequence comparisons Needleman-Wunch algorithm (1970) Smith-Waterman algorithm for alignment (1981) FASTP algorithm by Lipman and Pearson (1985) FASTA algorithm by Pearson, Lipman (1988) BLAST program implemented (Altshul et al.) (1990) BLAT program by Jim Kent (2000s)

7 DATABASES Institutes and centers for bioinformatics National Center for Biotechnological Information, NCBI (1988) European Bioinformatics Institute, EBI (1992) Famous databases established Swiss-Prot database created by University of Geneva and EMBL (1986) PRINTS database of protein motifs (Attwood and Beck) 1994 GenBank by NCBI (1982), EMBL-Bank (1980)

8 GENBANK (NCBI) SEQUENCE GROWTH

9 DATABASES CONTAINING INFORMATION OF HUMAN SEQUENCE VARIATION

10 COMPARATIVE GENOMICS

11 METAGENOMICS

12 COMMON PATTERN TO ALL THESE DATA

13 DEFINITION Computational methods for the anaylses of biological processes

14 IMPORTANT ASPECTS OF BIOINFORMATICS Tools that drive new biological discoveries Extends experiments one single genes - allows for generalization Have changed how we make experiments Storage, indexing, retrieval, comparison and visualization of biological data

15 BIOINFORMATICS-BASED DISCOVERIES Comparative genomics was imperative in identifying the microrna:rna interaction rules

16 GENOME-WIDE MINDSET Genomics are changing the way we ask questions in biology

17 When graduate students approach me these days about what is an interesting area to go into if you want to make a major contribution to biomedical research, the first thing out of my mouth is bioinformatics we are woefully short in terms of having a critical mass of people who understand both biology and computational approaches Francis Collins, director of the National Human Genome Research Institute

18 In the future, use of biological information collected in repositories, will play an ever increasingly important role in biology. European Molecular Biology Organization, EMBO, is considering information biology as one of the cornerstones of modern/future biology!

19 PROGRAM Bioinformatics for Cell Biologists May 2013 Mon 13th Tue 14th Wed 15th Thu 16th Fri 17th 9 am Introduction Alignments Gene expression analyses Genome-wide methods to Preparation time for :15 Rickard S. Åsa B. Rickard S. study translational regulation individual presentations :30 Ola Larsson, CCK :45 10 am Introduction Protein bioinformatics Network analyses of gene Statistics for Genomic Examination :15 Rickard S. Åsa B. expression data Studies presentations :30 Erik Fredlund, MTC Rickard S. (7+3 min per person) :45 Rickard, Åsa och Daniel 11 am Bioinformatics Phylogeny Next-gen bioinformatics ChIP-Seq data analyses Examination :15 Overview Lars Arvestad, SciLife Rickard S. Mikael Huss, SciLife presentations :30 Rickard S. (7+3 min per person) :45 Rickard, Åsa och Daniel 12 PM :15 L U N C H L U N C H L U N C H L U N C H L U N C H :30 :45 1 PM Computer lab 1. Computer lab 2. Computer lab 3. Computer lab 4. Examination :15 Genomic resources Alignments, Protein Gene expression with ChIP-Seq analyses in Galaxy presentations :30 bioinformatics microarrays and RNA-Seq How to use public (7+3 min per person) :45 repositories Rickard, Åsa och Daniel 2 PM Examination :15 Rickard Åsa och Daniel Rickard och Daniel Rickard och Daniel presentations :30 (7+3 min per person) :45 Rickard, Åsa och Daniel 3 PM :15 :30 :45 4 PM :15 :30 :45 5 PM Room A216, CMB, Berzelius väg 35 Enter, Computer lab, Utopia, Berzelius (close to Restaurant Jöns Jacob and KI library)

20 PRACTICALS All lectures will be in room A216 Code to enter the doors: 2000 All computer labs in Utopia Examination in A216 (powerpoint or white board)

21 EXAMINATION Methods workshop Recieve a Nature Biotechnology methods primer Task: present the method for the rest of the class 10 min (7+3) individual presentations Examiners: Me, Asa and Daniel Friday

22 TYPES OF BIOINFORMATIC ANALYSES Use bioinformatics resources online (tools and db) Use bioinformatics software environments (e.g. R) Develop new tools to address new questions (e.g. python, perl)

23 ONLINE COURSES OVERVIEW

24 I NTRODUCTION COURSERA H ISTORY M ODERN C OURSE O NLINE L EARNING O PPORTUNITIES

25 GALAXY

26 ROSALIND

27 SOFTWARE CARPENTRY

28 COFFEE Questions?