Download - 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
consent3
• 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.
Copyright OpenHelix. No use or reproduction without express written consent
4
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
Copyright OpenHelix. No use or reproduction without express written consent
5
What is the relationship between proteins, RNA and DNA?
For example, imagine that a car is a living organism
Copyright OpenHelix. No use or reproduction without express written consent
6
DNA is a description of all the parts of the whole car
Copyright OpenHelix. No use or reproduction without express written consent
7
RNA reads the description, and builds the parts
DNA gives instructions
RNA builds each part
Copyright OpenHelix. No use or reproduction without express written consent
8
Each unique car part is the same as a unique protein
Copyright OpenHelix. No use or reproduction without express written consent
9
When all the proteins are combined you
have a living organism
When all the car parts are assembled then you have a complete car
Copyright OpenHelix. No use or reproduction without express written consent
10
Together, all the parts make a car All the proteins
make an organism
Copyright OpenHelix. No use or reproduction without express written consent
11
Proteomics: is the study of proteins
• Structure: appearance and formation• Interactions: with other proteins or organisms
Copyright OpenHelix. No use or reproduction without express written consent
12
• 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
Copyright OpenHelix. No use or reproduction without express written consent
13
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
Copyright OpenHelix. No use or reproduction without express written
consent14
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
Copyright OpenHelix. No use or reproduction without express written
consent15
Copyright OpenHelix. No use or reproduction without express written
consent16
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.
Copyright OpenHelix. No use or reproduction without express written consent
17
We are entering a new age of discovery:
THE GENOMICS ERA
Copyright OpenHelix. No use or reproduction without express written consent
18
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!
Copyright OpenHelix. No use or reproduction without express written consent
19
Genomics and Energy
Genomists are studying the fungi genome
to understand which proteins speed up,
or slow down combustion (fire)
Copyright OpenHelix. No use or reproduction without express written consent
20
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
Copyright OpenHelix. No use or reproduction without express written consent
21
Apple Computer’s iCloud server sitein North Carolina, USA
will manufacture renewable energy from bio-gas
Copyright OpenHelix. No use or reproduction without express written consent
22
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
Copyright OpenHelix. No use or reproduction without express written consent
25
Genomics and Health Medicine
Copyright OpenHelix. No use or reproduction without express written consent
26
Disease Diagnosis
• Scanning genes for disease risks• Detecting cancer early
Copyright OpenHelix. No use or reproduction without express written consent
27
Human gene analysis to detect
disease riskwww.23andme.com
Copyright OpenHelix. No use or reproduction without express written
consent28
Example
Copyright OpenHelix. No use or reproduction without express written consent
29
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.
Copyright OpenHelix. No use or reproduction without express written
consent30
The growth in Genomic Resources is huge: 4000+ today
Sequence in data repositories (in mega bps)
Number of Databases & Resources in NAR
Copyright OpenHelix. No use or reproduction without express written consent
31
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.
Copyright OpenHelix. No use or reproduction without express written consent
32
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
00
• 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
Copyright OpenHelix. No use or reproduction without express written consent
34
4000 Databases are too many for anyone to search or even learn effectively
OpenHelix focuses on the 300 most important resources and tools.
Copyright OpenHelix. No use or reproduction without express written
consent35
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
Copyright OpenHelix. No use or reproduction without express written consent
36
UCSC HOMEPAGE
Since 2003, OpenHelix has developed and continues to support a set of 6
tutorials for UCSC.
Copyright OpenHelix. No use or reproduction without express written consent
37
UCSC HOME PAGE LINK TO TRAINING MATERIALS
LINK TO UCSC
TRAINING PAGE
Copyright OpenHelix. No use or reproduction without express written consent
38
OpenHelix maintains the top UCSC Tutorial
Copyright OpenHelix. No use or reproduction without express written consent
39
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
Copyright OpenHelix. No use or reproduction without express written consent
40
NIH awarded OpenHelix a grant
to develop 100 Online Tutorials
for the world’s top genomic resources
Copyright OpenHelix. No use or reproduction without express written consent
41
NIH uses OpenHelix
Online Tutorials
Copyright OpenHelix. No use or reproduction without express written consent
42
SciVerse / Science DirectExample of OpenHelix Application
In 2011, Elsevier SciVerse / ScienceDirect choose OpenHelix to custom design a
collection of applications for genomics & bioinformatics
Copyright OpenHelix. No use or reproduction without express written
consent43
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
Copyright OpenHelix. No use or reproduction without express written consent 45
Search Results: www.openhelix.com
Copyright OpenHelix. No use or reproduction without express written consent 46
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
Copyright OpenHelix. No use or reproduction without express written consent 49
Training Materials: Tutorial
Tutorial
Copyright OpenHelix. No use or reproduction without express written consent 50
Training Materials: Slides
Slides
Copyright OpenHelix. No use or reproduction without express written consent 51
Exercises Training Materials: Exercises
Copyright OpenHelix. No use or reproduction without express written consent 52
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
Copyright OpenHelix. No use or reproduction without express written consent 53
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
Copyright OpenHelix. No use or reproduction without express written consent 54
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
55
OpenHelix Customers
Copyright OpenHelix. No use or reproduction without express written
consent56
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
Subscription benefits
• Onsite training limits who can attend• View anywhere, anytime• Available “at your fingertips” when
researching articles in BioMed Central and Elsevier SciDirect
Subscription benefits
• Online learning has proven to be as good as onsite training
• Significant lower cost
Subscription benefits
• 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
Subscription benefits
• 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
<>
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.
Copyright OpenHelix. No use or reproduction without express written
consent66
WorldwideGenomic Resource
Training and Support