genomics and openhelix - basic intro 12apr09

A Basic Introduction to Genomics

and OpenHelix

John Ben [email protected]

April 2012

Copyright OpenHelix. No use or reproduction without express written consent1

Copyright OpenHelix. No use or reproduction without express written consent

2

What is Genomics?

Genomics: the study of all the genes in a cell, or living organism, including: DNA, RNA, and Protein

a GENOME is the entire DNA sequence

(chain) and the gene information for that organism

Copyright OpenHelix. No use or reproduction without express written

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• Each organism has 1 unique DNA • DNA orchestrates the manufacture of genes,

protein, and all the life systems of an organism• The human genome has 25,000 genes inside• Like a finger print or eye retina are unique, the

genome for each person is unique.


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All living things are made of protein

There are 10,000,000 different proteins building the

world’s organisms

The human body has 100,000 proteins


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What is the relationship between proteins, RNA and DNA?

For example, imagine that a car is a living organism


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DNA is a description of all the parts of the whole car


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RNA reads the description, and builds the parts

DNA gives instructions

RNA builds each part


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Each unique car part is the same as a unique protein


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When all the proteins are combined you

have a living organism

When all the car parts are assembled then you have a complete car


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Together, all the parts make a car All the proteins

make an organism


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Proteomics: is the study of proteins

• Structure: appearance and formation• Interactions: with other proteins or organisms


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• Bioinformatics: the use of math and computer science to study biology and especially genomics and proteomics

Quick review … What is Genomics?• Genomics: the study of all the genes in a cell, or

living organism, including:1. DNA (genotype)2. RNA (transcriptome)3. Protein (proteome)

• Proteomics: the study of proteins– Structure: appearance and formation– Interactions: with other proteins or organisms


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The human genome looks like this…

It is shaped like a ball Numerically, it appears like this:

This is BIOINFORMATICS: using numbers and charts to represent 3D (real) life


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The Project to Map the Human Genome

• It was a “Race” between private industry and public universities

• The project cost $3 billion, and took 12 yrs

• Finished in 2002. • Was called “the Golden Path”• Public universities “won” and

the human genome information was released on web, available free / Open Access.

Speed and Cost of Mapping• First human genome

took 12 yr and $3 billion• Today, it takes 3 days

and costs US $10,000• 2013 will cost $1,000

and take 4 hours


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Genomic Explosion

Since 2002, over 3,000 completed genomes have been mapped.

200+ eukaryotes such as puffer fish, chicken, dog, fruit fly, mouse, rat, bee, chimpanzee, cow, flatworm, sheep, pig, sea urchin

Corn, rice, grapes, nutsBacteria, virusesHundreds more are

being completed every year.


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We are entering a new age of discovery:

THE GENOMICS ERA


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Genomics will impact almost every field of study, and will change our lives …

Health & medicine, Biology & Chemistry, Agriculture, Energy, Defense, Law, Engineering, Archaeology & Anthropology, Public Administration & Business,

And new areas of science that wedo not even know about yet!


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Genomics and Energy

Genomists are studying the fungi genome

to understand which proteins speed up,

or slow down combustion (fire)


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The specific genes are identified and isolated. And then manufactured and sold to biological-fuel energy generation companies

Spontaneous Combustion is often caused by fungi


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Apple Computer’s iCloud server sitein North Carolina, USA

will manufacture renewable energy from bio-gas


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Crime committed in

1962 finally solved

in 2012, thanks to

DNA analysis.

14 PATENT TRIALS EVERY YEAR; MONSANTO FIGHTS TO CONTROL THE USE OF ITS GENETICALLY ENGINEERED CORN SEEDS

Genomics and Law


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Genomics and Health Medicine


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Disease Diagnosis

• Scanning genes for disease risks• Detecting cancer early


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Human gene analysis to detect

disease riskwww.23andme.com


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Example


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Pharmaco-genomics: Drug therapies

tailored to individuals

• Design drug therapy basedon the individual’s genome• Small differences in each person’s genome

causes different response to drugs• Protect people who will suffer harmful side

effects from particular drugs• Future will be custom-designed drugs for each

person, based on their genome map.


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The growth in Genomic Resources is huge: 4000+ today

Sequence in data repositories (in mega bps)

Number of Databases & Resources in NAR


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Zebrafish and human genome

are similar and possess many homologues (similar genes) • Zebrafish are easy to breed• Easy to change Zebrafish genes and test quickly• Safe way to simulate human genome testing• Important in cancer research• Univ of Utah, Huntsman Cancer Inst received

the Nobel Prize in 2002 for colon cancer research done via Zebrafish.


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Chinese and American catfish genes are used to study human LIVER CANCER

Because a gene in the liver of catfish and humans are similar: homologues.

Challenge: Finding the right resource

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• Thousands of resources in dozens of areas

• Variation and Medical• Protein• Pathways• Nucleotides• Literature• Genome Databases (prokaryotes and viruses)• Genome Databases (Eukaryotes• Expression• Analysis and Algorithms


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4000 Databases are too many for anyone to search or even learn effectively

OpenHelix focuses on the 300 most important resources and tools.


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Human Genome Project

• The human genome information was released on web, available free / Open Access.

• The information is hosted at UC Santa Cruz

• Now known as the UCSC Genome Browser

• Since 2003 UCSC has been outsourcing to OpenHelix to do their online training and seminars


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UCSC HOMEPAGE

Since 2003, OpenHelix has developed and continues to support a set of 6

tutorials for UCSC.


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UCSC HOME PAGE LINK TO TRAINING MATERIALS

LINK TO UCSC

TRAINING PAGE


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OpenHelix maintains the top UCSC Tutorial


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OpenHelix’s UCSC BROWSER TUTORIAL Landing page

UCSC outsources to OpenHelix to provide online training for the UCSC

Genome Browser

Click on this link to launch the actual tutorial in a new window:

UCSC Genome Browser: An Introduction

http://www.openhelix.com/cgi/tutorialInfo.cgi?id=27


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NIH awarded OpenHelix a grant

to develop 100 Online Tutorials

for the world’s top genomic resources


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NIH uses OpenHelix

Online Tutorials


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SciVerse / Science DirectExample of OpenHelix Application

In 2011, Elsevier SciVerse / ScienceDirect choose OpenHelix to custom design a

collection of applications for genomics & bioinformatics


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WorldwideGenomic Databases

OpenHelix has 107 tutorials

for the top 90 resources

Copyright OpenHelix. No use or reproduction without express written consent 44

Search for Resources: www.openhelix.com

tag AND snps Search

tag AND snps


Search Results: www.openhelix.com


Find Resources: www.openhelix.com

Availabletutorials

Resourcesthat match

query

Search Results: www.openhelix.com

Query matchin OH training

materials

Go to resource

View movieTraining Materials

Query matchin OH Blog

Query matchon resource

websiteCopyright OpenHelix. No use or reproduction without express written consent 47

Solution: OpenHelix Training

• 100 Online Tutorial Suites– Self-run narrated tutorial

• Introduction on how to use the resource• Chapters for easy navigation• Use from beginning to end or as reference

– Training Materials• PowerPoint Slides with suggested script• Slide Handouts• Exercises

– Consistent interface and high quality– One place to learn


Training Materials: Tutorial

Tutorial


Training Materials: Slides

Slides


Exercises Training Materials: Exercises


Subscribed Tutorials: www.openhelix.com/subscriptions.shtml

• Tutorials and Training Materials on nearly 100 resources including:– dbSNP– NCBI Entrez– dbGaP– STRING– Ensembl– GHR– GIBBS Motif Sampler– miRBase– PFAM & many more…

Tutorials


Sponsored Tutorials: www.openhelix.com/cgi/freeTutorials.cgi

• Sponsored Resource Tutorials– PDB– UCSC Genome– UCSC Table Browser– UCSC Additional

Tools– SBKB– ENCODE– NIEHS SNPs– World Tour– And more…

Sponsored Tutorials


OpenHelix Blog: blog.openhelix.com• Daily news and information

about genomics data, research and resources

• Weekly video tips on how to use database and tool features

• Weekly “What’s the Answer” thread of biological resource questions and answers from BioStar

• More…

Additional Progrms

• BioMed Central– Articles are searched for resources– We show the resources that we have tutorials on– User can click on resource name to go to the tutorial

• Elsevier’s ScienceDirect– Same as BMC, except as part of the Elsevier third party

application program– Users choose to add the plug-in to their ScienceDirect

platform• SciVee (www.scivee.tv)

– OpenHelix “channel” to watch tip of the weeksCopyright OpenHelix. No use or

reproduction without express written consent

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http://www.scivee.tv/

OpenHelix Customers


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Subscription benefits

• Researchers use tutorials to learn new genomics databases and resources

• Professors save time in creating classroom content

• All use tutorials to keep abreast of new resources


• Onsite training limits who can attend• View anywhere, anytime• Available “at your fingertips” when

researching articles in BioMed Central and Elsevier SciDirect


• Online learning has proven to be as good as onsite training

• Significant lower cost


• Some companies and institutions have dedicated bioinformatics' employees or “cores”

• OpenHelix subscriptions give them the time to focus on more critical tasks—leave introductory training to us

• 10,000s of hours creating and updating tutorial suites– Not cost effective to reproduce


• Been training on bioinformatics resources since 2003

• Extensive relationships with resource providers

• Relied on by many resource providers to create their training programs

Current resource providers• UCSC Genome Browser

– University of California, Santa Cruz– Funded by National Human Genome Research

Institute• ENCODE

– University of California, Santa Cruz• Protein Data Bank

– Rutgers and University of California, San Diego– Multiple funders

• Structural Biology Knowledge Base

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End Users (Subscribers)• Government Agencies

– National Institutes of Health• Research Centers

– MD Anderson Cancer Center– Children’s Mercy Hospital

• Medical Colleges– Mt. Sinai School of Medicine

• Universities– Vanderbilt– Washington University

• Biotech/Pharma– SRC Inc.


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WorldwideGenomic Resource

Training and Support

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