Applied Bioinformatics

Transcription

1 Applied Bioinformatics Course Overview & Introduction to Linux Bing Zhang Department of Biomedical Informatics Vanderbilt University

2 What is bioinformatics Bio Bioinformatics informatics Hypotheses Questions Samples Experiments Storage/retrieval Visualization Computational methods Statistical methods Data DNA RNA Protein Metabolite Phenotype Sequence Expression Structure Interaction 2

3 Genomic sequences Completely Sequenced Genomes September 2012 First bacterial (H. influenzae) First eukaryote (yeast) First metazoan (C. elegans) Human genome project ( ) 3

4 4 Genome sequencing costs plunge

5 The Cancer Genome Atlas (TCGA) Mission (Bio) To accelerate the understanding of the molecular basis of cancer through the application of genome analysis technologies target (Data) 25 tumor types x 500 cases each Exome/whole genome sequencing Copy number variation Promoter methylation mrna expression mirna expression 5

6 Why now? Bio Hypotheses Questions Samples Experiments informatics Data informatics Storage/retrieval Visualization Computational methods Statistical methods DNA RNA Protein Metabolite Phenotype Sequence Expression Structure Interaction 6

7 Roles for different investigators in bioinformatics Algorithm developer Statisticians Mathematicians Computer scientists Tool developer Bioinformaticians Data provider/consumer Biologists Graph courtesy of 7

8 Comprehensive resource list 01/ /

9 Sequence and structure databases Genbank: Annotated collection of all publicly available DNA sequences 126,551,501,141 bases in 135,440,924 sequence as of April 2011 UniProt: Comprehensive resource for protein sequences and functional information 534,242 reviewed entries as of January 2012 PDB: 3D structures of large biological molecules, including proteins and nucleic acids 79,180 structures as of February 2012 Pfam: Collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs) 13,672 families as of November

10 Genome browsers UCSC genome browser Ensembl genome browser 10

11 Gene-centric databases Entrez Gene NCBI/NIH All completely sequenced genomes One gene per page Ensembl BioMart EMBL-EBI and Sanger Institute Vertebrates and other selected eukaryotic species Batch information retrieval 11

12 Gene expression data Gene Expression Omnibus (GEO) ArrayExpress 12

13 Pathway and network resources Gene Ontology (GO): Pathway databases KEGG: Reactome: WikiPathways: Protein-protein interaction databases DIP: MINT: BioGRID: HPRD: Protein-DNA interaction database Transfac: 13

14 Course content and grades Team members: William Bush, Ph.D., Qi Liu, Ph.D., Zhongming Zhao, Ph.D. Date Room Subject Instructor Homework (HW) / Project 2/ PRB Course overview & Introduction to Linux Zhang 2/ A-C LH Pairwise sequence alignment Zhao 2/ A-C LH Multiple sequence alignment Zhao 2/ PRB Inferring phylogenetic relationships Zhao HW I distribution (20 pts) 2/ A-C LH Gene prediction Bush 2/ A-C LH Gene regulatory elements and conservation Bush HW I due 2/ LH In silico and In clinico characterization of genetic variations Bush HW II distribution (20 pts) 3/3 407 A-C LH Supervised analysis of gene expression data Zhang 3/5 407 A-C LH Unsupervised analysis of gene expression data Zhang HW II due 3/7 206 PRB Functional interpretation of gene lists Zhang 3/ A-C LH Next-Generation Sequencing data analysis Liu HW III distribution (20 pts) 3/ A-C LH Data Analysis Project Zhang & Liu 3/ LH HW III due 3/ A-C LH 3/ A-C LH Project presentation Project presentation (40 pts) 3/ PRB HW assignments will be graded by each instructor for their respective sections. Final Grade = sum of the three hw scores and the project presentation score (100 pts in total). A: ; B: 75-84; C: 65-74; D: 55-64; F:

15 Course materials and assignments Lecture slides available at Homework assignments available at the same URL on the distribution date (2/21, 2/28, 3/10) Homework assignments are due on paper at the beginning of class on the due date (2/26, 3/5, 3/14). There will be a 10% per day deduction for late reports. Start thinking about forming project teams (~5 person per team) Instructor contact information Dr. Bing Zhang: bing.zhang@vanderbilt.edu Dr. Zhongming Zhao: zhongming.zhao@vanderbilt.edu Dr. William Bush: william.s.bush@vanderbilt.edu Dr. Qi Liu: qi.liu@vanderbilt.edu 15

16 ACCRE Advanced Computing Center for Research & Education The compute cluster currently consists of more than 500 Linux systems with quad or hex core processors Linux system An operating system (OS) like Windows or Mac Portable, multi-tasking, multi-user OS High performance and free, making it idea for high performance computing clusters 16

17 Get an ACCRE account Registration form Name, VUNetID, Department (VU), School (VU), , Phone, Position Group: IGP300b_ab (igp300b_ab) Primary research area: bioinformatics Primary application: Existing Application Primary application name: R Primary application type: Serial Expected typical number of processors: NA Expected typical number of concurrent running jobs: 1 Linux experience: Expected compilers/languages: C, C++, R, perl, python Expected external libraries: NA BlueArc User: No Other useful information: NA 17

18 Logging onto the cluster and change password Windows Mac Application: SSH ( Two steps: add profile -> edit profile Host name: vmplogin.accre.vanderbilt.edu Username: your_user_name Spotlight to find the application: Terminal Command: ssh Change password Exit rsh vmpsched passwd exit 18

19 19 Logging onto the cluster and change password (using SSH in Windows)

20 Logging onto the cluster and change password (using Terminal in Mac) You won t see any response while typing password, which is fine. 20

21 Hierarchical File system / /home bin etc usr tmp home scratch chmod /home/igptest cp date bin lib annie igptest cody grep mv rm vi diff find gcc id make perl ssh libc.so libgpfs.so libjpeg.so libstdc++.so bin docs src myprog.sh prog1.c dothis.pl prog2.f77 dothat.py prog3.cpp /home/igptest/src/prog3.cpp 21

22 Working with directories pwd (prints your present working directory) ls (lists directory contents) mkdir (makes a directory) cd (changes directories).. (parent directory). (current directory) ~ or no parameter (home directory) rmdir (removes an empty directory) 22

23 Working with files more (displays the contents of a file) space bar to show next page q to exist cp (copies files) mv (renames/moves files) rm (removes files) 23

24 Getting help man (display manual pages for a command) man ls (display manual for the ls command) space bar to show next page q to exist Alternatives of ls ls -a (do not ignore entries starting with.) ls -l (use a long listing format) ls -al (use a long listing format and do not ignore entries starting with.) 24

25 Editing files with nano cd (change to home directory) nano.bashrc (use nano to edit file.bashrc, which includes commands that are executed when starting the system). Add setpkgs a R to the end of the file (this will allow you to use the R environment which has been installed in the ACCRE system for statistical computing). 25

26 Copying files to/from a local computer Windows Mac Application: SSH ( Application: Fugu ( Connect to: vmplogin.accre.vanderbilt.edu Username: your_user_name Don t change other items 26

27 27 Copying files to/from a local computer (using SSH in Windows)

28 28 Copying files to/from a local computer (using Fugu in Mac)

29 Homework Get an ACCRE account Log onto the cluster and change password Get familiar with the Linux commands introduced today Copy the file sample_file.txt under directory /home/igptest to your home directory Add setpkgs a R to the end of your.bashrc file 29