Genomics and OpenHelix - Basic Intro 12apr09
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Genomics and OpenHelix - Basic Intro 12apr09

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As the world enters the Genomics Era, training is essential. A laymen's intro to genomics. and an intro OpenHelix many services.

As the world enters the Genomics Era, training is essential. A laymen's intro to genomics. and an intro OpenHelix many services.

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  • The keyword cloud is known as a Wordle.
  • Since there are 7 billion people in the world today, there are 7 billion different human genomes.
  • As of 2007, we have identified 1m< unique proteins from about 100 organisms
  • You may want to tell the audience, A car has 30,000 parts
  • Each part of a car is like each protein of a human bodyRNA makes each part and assembles them into a car.
  • The definition of BIOINFORMATICS is rigged to enter slowly. Make sure to wait for it.
  • The shape is real, but colors are added for effect.The numerical sequence on the right is only a small portion of an entire genome
  • NEW MACHINE $50,000WILL BECOME A COMMON TOOL TO ANALYZE GENOME, EVERYONE CAN DO IT.IT WILL BE AVAILABLE ALL AROUND THE WORLD
  • Most commonly studied fungi are shelf mushrooms Thermophilic (cause combustion) and thermotolerant (inhibit combustion)
  • Hay stacks burning in USA
  • This server storage site is opening in 2012Renewable energy means the energy does not come from fossil fuels like coal or oil.Increasingly, more and more energy will be created from burning animal waste or recycling garbage and turning it into “bio-gas”.Genome research is playing a crucial role in the development of bio-fuels.
  • Already there are hundreds of criminal and patent legal battles where a genome is critical evidence. In 2013 when the cost of mapping and identifying a genome drops to $1,000 the number of cases will probably increase 1000%
  • $100
  • A homologue is when the gene of two different species is almost the same.
  • UCSC: University of California at Santa CruzThis is the UCSC Genome and Bioinformatics home pageThe UCSC Browser is the most popular and commonly used resource to study genomics in the world. It is free.[march 2012]
  • US National Institute of Health Library
  • US National Institute of Health Library
  • Elsevier’s SciVerse / ScienceDirect uses OpenHelix

Transcript

  • 1. A Basic Introduction to Genomics and OpenHelix John Ben DeVette johnben@devettepublishing.com April 2012 1Copyright 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 Copyright OpenHelix. No use or reproduction without express written 2 consent
  • 3. a GENOME is the entire DNA sequence (chain) and the gene information for that organism• 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, theCopyright OpenHelix. No use or genome for each person is unique.reproduction without expresswritten consent 3
  • 4. All living things are made of protein The human body has 100,000 proteins There are10,000,000 differentproteins building the world’s organisms Copyright OpenHelix. No use or reproduction without express written 4 consent
  • 5. What is the relationship between proteins, RNA and DNA? For example, imagine that a caris a living organism Copyright OpenHelix. No use or reproduction without express written 5 consent
  • 6. DNA is a descriptionof all the parts of the whole car Copyright OpenHelix. No use or reproduction without express written 6 consent
  • 7. RNA reads the description, and builds the parts DNA givesinstructions RNA builds each part Copyright OpenHelix. No use or reproduction without express written 7 consent
  • 8. Each unique car partis the same as a unique protein Copyright OpenHelix. No use or reproduction without express written 8 consent
  • 9. When all the car parts are assembled then you have a complete car When all the proteins are combined you have a living organism Copyright OpenHelix. No use or reproduction without express written 9 consent
  • 10. Together, all the parts make a car All the proteins make an organism Copyright OpenHelix. No use or reproduction without express written 10 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 11 consent
  • 12. 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• Bioinformatics: the use of math and computer science to study biology and especially genomics and proteomics Copyright OpenHelix. No use or reproduction without express written 12 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 13 consent
  • 14. 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. Copyright OpenHelix. No use or reproduction without express 14 written consent
  • 15. 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 15 written consent
  • 16. 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, flatwor m, sheep, pig, sea urchin Corn, rice, grapes, nuts Bacteria, viruses Hundreds more are being completed every year.Copyright OpenHelix. No use orreproduction without express 16written consent
  • 17. We are enteringa new age of discovery:THE GENOMICS ERA Copyright OpenHelix. No use or reproduction without express written 17 consent
  • 18. Genomics will impact almost every field ofstudy, 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 we do not even know about yet! Copyright OpenHelix. No use or reproduction without express written 18 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 19 consent
  • 20. Spontaneous Combustion is often caused by fungiThe specific genes are identified and isolated. And then manufactured and sold to biological-fuel energy generation companies Copyright OpenHelix. No use or reproduction without express written 20 consent
  • 21. Apple Computer’s iCloud server site in North Carolina, USAwill manufacture renewable energy from bio-gas Copyright OpenHelix. No use or reproduction without express written 21 consent
  • 22. Genomics and Law Copyright OpenHelix. No use or reproduction without express written 22 consent
  • 23. Genomics andHealth Medicine Copyright OpenHelix. No use or reproduction without express written 25 consent
  • 24. Disease Diagnosis• Scanning genes for disease risks• Detecting cancer early Copyright OpenHelix. No use or reproduction without express written 26 consent
  • 25. Human gene analysis to detectwww.23andme.com disease risk Copyright OpenHelix. No use or reproduction without express written 27 consent
  • 26. ExampleCopyright OpenHelix. No use orreproduction without express 28written consent
  • 27. 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 29 consent
  • 28. The growth in Genomic Resources is huge: 4000+ today Sequence in data repositories (in mega bps) Number of Databases & Resources in NARCopyright OpenHelix. No use orreproduction without express 30written consent
  • 29. Zebrafish and human genomeare similar and possess manyhomologues (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 31 consent
  • 30. Chinese and American catfishgenes are used to studyhuman LIVER CANCER Because a gene in the liver of catfish and humans are similar: homologues. Copyright OpenHelix. No use or reproduction without express written 32 consent
  • 31. Challenge: Finding the right resource• Thousands of resources in dozens of areas • Variation and Medical • Protein 00 • Pathways • Nucleotides • Literature • Genome Databases (prokaryotes and viruses) • Genome Databases (Eukaryotes • Expression • Analysis and Algorithms
  • 32. 4000 Databases are too many for anyone to search or even learn effectivelyOpenHelix focuses on the 300 most important resources and tools. Copyright OpenHelix. No use or reproduction without express written 34 consent
  • 33. 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 seminarsCopyright OpenHelix. No use orreproduction without express 35written consent
  • 34. 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 36 consent
  • 35. UCSC HOME PAGE LINK TO TRAINING MATERIALS LINK TO UCSC TRAINING PAGE Copyright OpenHelix. No use or reproduction without express written 37 consent
  • 36. OpenHelix maintains the top UCSC Tutorial Copyright OpenHelix. No use orreproduction without express written 38 consent
  • 37. OpenHelix’s UCSC UCSC outsources to OpenHelix to BROWSER TUTORIAL provide online training for the UCSC Landing page Browser Genome 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 39 consent
  • 38. NIH awardedOpenHelix a grant to develop 100Online Tutorials for the world’s topgenomic resources Copyright OpenHelix. No use orreproduction without express written 40 consent
  • 39. NIH uses OpenHelixOnline Tutorials Copyright OpenHelix. No use orreproduction without express written 41 consent
  • 40. SciVerse / Science Direct Example of OpenHelix ApplicationIn 2011, Elsevier SciVerse / ScienceDirect choose OpenHelixto custom design a collection of applications for genomics & bioinformatics Copyright OpenHelix. No use or reproduction without express written 42 consent
  • 41. Worldwide Genomic Databases OpenHelix has 107 tutorials for the top 90 resourcesCopyright OpenHelix. No use orreproduction without express 43written consent
  • 42. Search for Resources: www.openhelix.com tag AND snpstag AND snps Search Copyright OpenHelix. No use or reproduction without express written consent 44
  • 43. Search Results: www.openhelix.com Copyright OpenHelix. No use or reproduction without express written consent 45
  • 44. Find Resources: www.openhelix.com Resources that match query Available tutorials Copyright OpenHelix. No use or reproduction without express written consent 46
  • 45. Search Results: www.openhelix.com Go to resource Query matchView movie in OH training Training Materials materials Query match in OH Blog Query match on resource website Copyright OpenHelix. No use or reproduction without express written consent 47
  • 46. 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
  • 47. Training Materials: Tutorial Tutorial Copyright OpenHelix. No use or reproduction without express written consent 49
  • 48. Training Materials: Slides Slides Copyright OpenHelix. No use or reproduction without express written consent 50
  • 49. Training Materials: Exercises Exercises Copyright OpenHelix. No use or reproduction without express written consent 51
  • 50. Subscribed Tutorials: www.openhelix.com/subscriptions.sht• ml Tutorials and Training Materials on nearly 100 resources including: – dbSNP – NCBI Entrez – dbGaP – STRING Tutorials – Ensembl – GHR – GIBBS Motif Sampler – miRBase – PFAM & many more… Copyright OpenHelix. No use or reproduction without express written consent 52
  • 51. Sponsored Tutorials: www.openhelix.com/cgi/freeTutorials.• cgi Sponsored Resource Tutorials – PDB – UCSC Genome – UCSC Table Browser – UCSC Additional Tools Sponsored Tutorials – SBKB – ENCODE – NIEHS SNPs – World Tour – And more… Copyright OpenHelix. No use or reproduction without express written consent 53
  • 52. 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… Copyright OpenHelix. No use or reproduction without express written consent 54
  • 53. 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. Nouse or reproduction without 55express written consent
  • 54. OpenHelix Customers Copyright OpenHelix. No use or reproduction without express written 56 consent
  • 55. 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
  • 56. Subscription benefits• Onsite training limits who can attend• View anywhere, anytime• Available “at your fingertips” when researching articles in BioMed Central and Elsevier SciDirect
  • 57. Subscription benefits• Online learning has proven to be as good as onsite training• Significant lower cost
  • 58. 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
  • 59. 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
  • 60. 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
  • 61. 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.
  • 62. Worldwide Genomic Resource Training and SupportCopyright OpenHelix. No use orreproduction without express 66written consent