CLOUD BIOINFORMATICS

BY.A.ARPUTHA SELVARAJ

Bioinformatics is…

The development of computational methods for studying the structure, function, and evolution of genes, proteins, and whole genomes;

The development of methods for the management and analysis of biological information arising from genomics and high-throughput biological experiments.

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Why is there Bioinformatics?

Lots of new sequences being added- Automated sequencers- Genome Projects- Metagenomics- RNA sequencing, microarray studies, proteomics,…

Patterns in datasets that can be analyzed using computers

Huge datasets

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• Gramicidine S (Consden et al., 1947), partial insulin sequence (Sanger and Tuppy, 1951)

• 1961: tRNA fragments

• Francis Crick, Sydney Brenner, and colleagues propose the existence of transfer RNA that uses a three base code and mediates in the synthesis of proteins (Crick et al., 1961) General nature of genetic code for proteins. Nature 192: 1227-1232. In Microbiology: A Centenary Perspective, edited by Wolfgang K. Joklik, ASM Press. 1999, p.384

• First codon assignment UUU/phe (Nirenberg and Matthaei, 1961)

Need for informatics in biology: origins

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• The key to the whole field of nucleic acid-based identification of microorganisms…

…the introduction molecular systematics using proteins and nucleic acids by the American Nobel laureate Linus Pauling.

Zuckerkandl, E., and L. Pauling. "Molecules as Documents of Evolutionary History." 1965. Journal of Theoretical Biology 8:357-366

• Another landmark: Nucleic acid sequencing (Sanger and Coulson, 1975)

Need for informatics in biology: origins

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Need for informatics in biology: origins

• First genomes sequenced: – 3.5 kb RNA bacteriophage MS2 (Fiers et al.,

1976)– 5.4 kb bacteriophage X174 (Sanger et al.,

1977)– 1.83 Mb First complete genome sequence of a free-living

organism: Haemophilus influenzae KW20 (Fleischmann et al., 1995)

– First multicellular organism to be sequenced: C. elegans (C. elegans sequencing consortium, 1998)

• Early databases: Dayhoff, 1972; Erdmann, 1978

• Early programs: restriction enzyme sites, promoters, etc… circa 1978.

• 1978 – 1993: Nucleic Acids Research published supplemental information

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Genbank and associated resources doubles faster than Moore’s Law! (< every 18 months)

http://en.wikipedia.org/wiki/Moore’s_law

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Today: So many genomes…

As of mid-August 2010, according to the GOLD GenomesOnline database….

• Eukaryotic genome projects are in progress?(Genome and ESTs) 1548 (517 - 5 years ago)

• Prokaryote genome projects are in progress?5006 (740 - 5 years ago)

• Metagenome projects are in progress?133 (Zero - 5 years ago)

TOTAL 6687 projects (As of Sept 2011: >10,000)

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The Human Genome

The genome sequence is complete - almost!– approximately 3.5 billion base pairs.

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Work ongoing to locate all genes and regulatory regions and describe their functions… …bioinformatics plays a critical role

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Identifying single nucleotide polymorphisms (SNPs) and other changes between individuals

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Bioinformatics helps with……. Sequence Similarity Searching/Comparison

What is similar to my sequence? Searching gets harder as the databases

get bigger - and quality changes Tools: BLAST and FASTA = early time

saving heuristics (approximate methods) Need better methods for SNP analysis! Statistics + informed judgment of the

biologist

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Bioinformatics helps with…….Structure-Function Relationships

Can we predict the function of protein molecules from their sequence?sequence > structure > function

Prediction of some simple 3-D structures possible (a-helix, b-sheet, membrane spanning, etc.)

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Can we define evolutionary relationships between organisms by comparing DNA sequences?- Lots of methods and software,

what is the best analysis approach?

Bioinformatics helps with…….Phylogenetics

WHAT IS NEXT GENERATION SEQUENCING (NGS)?

Sanger (“dideoxy sequencing or chain termination”) Sequencing

Single stranded DNA from sample* extended by polymerase from primer then randomly terminated by dideoxy nucleotide (ddNTP)

Variable length DNA fragments radiolabelled or fluorescently detected ddNTP

*sample derived from amplified cDNA, genomic clones or whole genome shotgun

Sanger Pro’s & Con’s

• Advantages– Relatively accurate– Relatively long (500 –

1500) bp reads

• Disadvantage– Relatively costly in terms

of reagents and relatively low throughput

Next Generation Sequencing (NGS)

Sequence Assembly

on HPC

Roche 454

Life Tech. Ion Torrent

Illumina HiSeq

Life Tech SOLiD Oxford Nanopore “GridION”

Polonator

HeliScope

Pacific Biosciences

SMRT Cell

(General) NGS Pro’s & Con’s

• Advantages– Very high throughput– Very cheap data

production

• Disadvantages– Relatively short reads– Relatively higher error

rates– Bioinformatics of

assembly is much more challenging

General Workflow

1. Template preparation2. Sequencing & imaging3. Genome alignment/assembly

COPING WITH THE BIOINFORMATICS CHALLENGE

Challenge

Assembling “next generation sequence” (NGS) data requires a great deal of computing power and gigabytes memory

Software often can execute in parallel on all available computer processing unit (CPU) cores.

Many functional annotation processes (e.g. database searching, gene expression statistical analyses) also demand a lot of computing power

“High Performance Computing” and “Cloud

Computing”

Computer Nodes

Network Storage

Your local workstation/

laptop

What is Cloud Computing? Pooled resources: shared with many

users (remotely accessed) Virtualization: high utilization of

hardware resources (no idling) Elasticity: dynamic scaling without

capital expenditure and time delay Automation: build, deploy, configure,

provision, and move without manual intervention

Metered billing: “pay-as-you-go, only for what you use

Cloud Computing

Cloud Bioinformatics Module

Raw Data/Results/

Snapshots

Task-Specialized

Server

Input Job Message Queue

Output Job Message Queue

Job StatusNotification

CustomizedMachine

Image

Start-up(w/parameters)

A More Complete Picture…

Raw Data + Results

WebPortal

ProjectRelationalDatabase

DatabaseLoader

Case Study in Bioinformatics on the Cloud

Used Amazon Web Serviceshttp://aws.amazon.com

Assembled ~99 raw NGS transcriptome sequence datasets from 83 species, on 16 Amazon EC2 instances with 8 CPU cores, 68 GB of RAM, ~200 hours of computer time, total run in less than one working day.

Each single machine of the required size would likely have cost at least ~$10,000 (and time) to purchase, and incur significant operating costs overhead (machine room space, power supplies, networking, air conditioning, staff salaries, etc.)

The above run could be started up in a few minutes and cost ~ $500 to complete. Once done, no machines left idling and unused…

Software for (NGS) Bioinformatics

Bundled with sequencing machines:e.g. Newbler assembler with Roche 454

3rd party commercial:DNA Star (www.dnastar.com)Geneious (http://www.geneious.com/)GeneWiz (http://www.genewiz.com)And others…

Open Source:Lots (selected examples to be covered in this

workshop)

What do I need to run bioinformatics software locally?

Some common bioinformatics software is platform independent, hence will run equally under Windows and UNIX (Linux, OSX)

Most other software targets Unix systems. If you are running Microsoft Windows and want to run such software locally, the easiest way to do this(?) is to install some version of Linux (suggest “Ubuntu”) as a dual boot or (less intrusively) as a guest operating system in a virtual machine, e.g.http://www.vmware.com/products/player/

But, what are *we* going to use here?

WestGrid @ SFU / IRMACSWestGrid is a consortium member of “Computer

Canada”https://computecanada.org/

“bugaboo” cluster: 4328 cores total: 1280 cores, 8 cores/node, 16 GB/node, x86_64, IB. Plus 3048 cores, 12 cores/node, 24GB/node, x86_64, IB. capability cluster, 40 Core Years

Access to other Westgrid resources through LAN and WAN

More details from Brian Corrie tomorrow…

Galaxy Genomics Workbench

http://galaxy.psu.edu/(also http://main.g2.bx.psu.edu/)

THE ROADMAP

What is Bioinformatics?

Road Map

AnnotationSequences(Formats)

Visualization of Sequence & Annotation

Search &Alignments

NGS

SequenceDatabases

Sequence Assembly

Specific Applications

Sequence Assembly of Transcriptomes Sequence Assembly of Whole Genomes Annotation of de novo Assembled Sequences Identification and Analysis of Sequence Variation Comparative Genomic Analysis and Visualization Meta-Analysis of Annotated Sequence Data

Survey: Workshop Expectations I How to find significance in the huge amount of

data that Next Gen sequencing, but also microarrays etc. generate.

A basic understanding of how to analyse next generation sequencing data.

Learn some hands-on computer experience learning to use software for analysing sequence

data; what can be done and how to do it. genome assembly + meta-analysis

Survey: Workshop Expectations II The basics of alignment and SNP calling with next-gen

sequencing, and what kind of programs are out there to do these tasks and then analyze the large datasets (I've been trying to figure this out on my own through reading the literature and it's quite time consuming so any info provided through the workshop would be very helpful - thanks)

The main workflow for processing sequence data from the beginning to the more specific paths of analyses. Also the concepts, significance of the adjustable parameters behind the various algorithms used in the workflow.

Survey: Workshop Expectations III I expect to learn the basic bioinformatics tools. Learn different sequence alignment

software/technologies (i.e. BWA, Abyss, etc.). Learn more about the complexities of NGS sequencing

Next generation sequencing, data analysis etc. Parameters regulating assembly of contigs. How to take

raw data to an assembly, control the main parameters for assembly, mass analyze data for annotation and SNPs

How to compare expression profiles using RNA transcriptomes.

Want to learn new things

Survey: Operating System Being Used

Microsoft Windows on Intel/AMD – 14 (86.7%) Most running Windows 7 (some XP & Vista) One uses Linux through Westgrid and the IRMACS

clusterSome of you also thinking of running Linux

Apple OS X – 2 (13.3%) Snow Leopard Release Apple Lion, running Windows 7 using Parallels

Linux on Intel - 2 (13.3%)

Looking Ahead…What will you need for this workshop?

Mainly, just a laptop running a web browser(Optional) access to Linux/Unix locally (VM Player)

Reading list:Will give review citations for future lecturesFor next week, suggest that you surf to

http://www.ncbi.nlm.nih.gov/

Thank You