A Basic Introduction         to Genomics        and OpenHelix                                                    John Ben ...
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• Each organism has 1 unique...
All living things are made of protein                                       The human body has                            ...
What is the relationship between     proteins, RNA and DNA?    For example, imagine that a caris a living organism        ...
DNA is a descriptionof all the parts of the whole car              Copyright OpenHelix. No use or           reproduction w...
RNA reads the description,                    and builds the parts DNA givesinstructions                                 R...
Each unique car partis the same as a unique protein            Copyright OpenHelix. No use or         reproduction without...
When all the car parts are assembled  then you have a complete car                                     When all the protei...
Together, all the parts     make a car                              All the proteins                                      ...
Proteomics: is the study of proteins• Structure: appearance and formation• Interactions: with other proteins or organisms ...
Quick review …                What is Genomics?• Genomics: the study of all the genes in a cell, or  living organism, incl...
The human genome looks like this… It is shaped like a ball                Numerically, it appears like this:              ...
The Project to Map the                             Human Genome• It was a “Race” between  private industry and public  uni...
Speed and Cost of Mapping• First human genome  took 12 yr and $3 billion• Today, it takes 3 days  and costs US $10,000• 20...
Genomic Explosion  Since 2002, over 3,000 completed genomes    have been mapped.  200+ eukaryotes such as puffer    fish, ...
We are enteringa new age of discovery:THE GENOMICS ERA         Copyright OpenHelix. No use or      reproduction without ex...
Genomics will impact almost every field ofstudy, and will change our lives …Health & medicine, Biology & Chemistry,Agricul...
Genomics and   Energy                                 Genomists are studying                                    the fungi ...
Spontaneous Combustion          is often caused by fungiThe specific genes are identified and isolated. And then  manufact...
Apple Computer’s iCloud server site      in North Carolina, USAwill manufacture renewable energy           from bio-gas   ...
Genomics and    Law              Copyright OpenHelix. No use or           reproduction without express written   22       ...
Genomics andHealth Medicine             Copyright OpenHelix. No use or          reproduction without express written   25 ...
Disease Diagnosis• Scanning genes for disease risks• Detecting cancer early            Copyright OpenHelix. No use or     ...
Human gene                                analysis to detectwww.23andme.com                                  disease risk ...
ExampleCopyright OpenHelix. No use orreproduction without express     28written consent
Pharmaco-genomics:      Drug therapies  tailored to individuals• Design drug therapy basedon the individual’s genome• Smal...
The growth in Genomic Resources is huge:                                 4000+ today                                      ...
Zebrafish and human genomeare similar and possess manyhomologues (similar genes)•   Zebrafish are easy to breed•   Easy to...
Chinese and American catfishgenes are used to studyhuman LIVER CANCER  Because a gene in the liver  of catfish and humans ...
Challenge: Finding the right resource• Thousands of resources in dozens of areas     •   Variation and Medical     •   Pro...
4000 Databases are too many for            anyone to search        or even learn effectivelyOpenHelix focuses on the 300 m...
Human Genome Project • The human genome   information was released on   web, available free / Open   Access. • The informa...
UCSC HOMEPAGE          Since 2003, OpenHelix has developed           and continues to support a set of 6                  ...
UCSC HOME PAGE LINK TO TRAINING          MATERIALS       LINK TO        UCSC      TRAINING        PAGE               Copyr...
OpenHelix maintains            the top UCSC Tutorial   Copyright OpenHelix. No use orreproduction without express written ...
OpenHelix’s UCSC UCSC outsources to OpenHelix to                  BROWSER TUTORIAL                provide online training ...
NIH awardedOpenHelix a grant  to develop 100Online Tutorials for  the world’s topgenomic resources   Copyright OpenHelix. ...
NIH uses  OpenHelixOnline Tutorials   Copyright OpenHelix. No use orreproduction without express written   41             ...
SciVerse / Science Direct   Example of OpenHelix ApplicationIn 2011, Elsevier SciVerse / ScienceDirect  choose OpenHelixto...
Worldwide                                 Genomic Databases                                       OpenHelix has           ...
Search for Resources:               www.openhelix.com                                tag AND snpstag AND snps             ...
Search Results: www.openhelix.com         Copyright OpenHelix. No use or reproduction without express written consent   45
Find Resources: www.openhelix.com                                                                                       Re...
Search Results: www.openhelix.com                                                          Go to resource                 ...
Solution: OpenHelix Training• 100 Online Tutorial Suites  – Self-run narrated tutorial     • Introduction on how to use th...
Training Materials: Tutorial     Tutorial       Copyright OpenHelix. No use or reproduction without express written consen...
Training Materials: Slides                           Slides     Copyright OpenHelix. No use or reproduction without expres...
Training Materials: Exercises                                          Exercises       Copyright OpenHelix. No use or repr...
Subscribed Tutorials:     www.openhelix.com/subscriptions.sht•                           ml    Tutorials and Training Mate...
Sponsored Tutorials:     www.openhelix.com/cgi/freeTutorials.•                            cgi    Sponsored Resource Tutori...
OpenHelix Blog: blog.openhelix.com• Daily news and information  about genomics  data, research and resources• Weekly video...
Additional Progrms• BioMed Central      – Articles are searched for resources      – We show the resources that we have tu...
OpenHelix Customers      Copyright OpenHelix. No use or    reproduction without express written   56                  cons...
Subscription benefits• Researchers use tutorials to learn new  genomics databases and resources• Professors save time in c...
Subscription benefits• Onsite training limits who can attend• View anywhere, anytime• Available “at your fingertips” when ...
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 sub...
Subscription benefits• Been training on bioinformatics resources  since 2003• Extensive relationships with resource  provi...
Current resource providers• UCSC Genome Browser  – University of California, Santa Cruz  – Funded by National Human Genome...
End Users (Subscribers)• Government Agencies   – National Institutes of Health• Research Centers   – MD Anderson Cancer Ce...
Worldwide                              Genomic Resource                             Training and SupportCopyright OpenHeli...
Genomics and OpenHelix - Basic Intro 12apr09
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.

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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
  • Genomics and OpenHelix - Basic Intro 12apr09

    1. 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. 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. 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. 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. 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. 6. DNA is a descriptionof all the parts of the whole car Copyright OpenHelix. No use or reproduction without express written 6 consent
    7. 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. 8. Each unique car partis the same as a unique protein Copyright OpenHelix. No use or reproduction without express written 8 consent
    9. 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. 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. 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. 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. 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. 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. 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. 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. 17. We are enteringa new age of discovery:THE GENOMICS ERA Copyright OpenHelix. No use or reproduction without express written 17 consent
    18. 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. 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. 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. 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. 22. Genomics and Law Copyright OpenHelix. No use or reproduction without express written 22 consent
    23. 23. Genomics andHealth Medicine Copyright OpenHelix. No use or reproduction without express written 25 consent
    24. 24. Disease Diagnosis• Scanning genes for disease risks• Detecting cancer early Copyright OpenHelix. No use or reproduction without express written 26 consent
    25. 25. Human gene analysis to detectwww.23andme.com disease risk Copyright OpenHelix. No use or reproduction without express written 27 consent
    26. 26. ExampleCopyright OpenHelix. No use orreproduction without express 28written consent
    27. 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. 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. 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. 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. 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. 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. 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. 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. 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. 36. OpenHelix maintains the top UCSC Tutorial Copyright OpenHelix. No use orreproduction without express written 38 consent
    37. 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. 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. 39. NIH uses OpenHelixOnline Tutorials Copyright OpenHelix. No use orreproduction without express written 41 consent
    40. 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. 41. Worldwide Genomic Databases OpenHelix has 107 tutorials for the top 90 resourcesCopyright OpenHelix. No use orreproduction without express 43written consent
    42. 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. 43. Search Results: www.openhelix.com Copyright OpenHelix. No use or reproduction without express written consent 45
    44. 44. Find Resources: www.openhelix.com Resources that match query Available tutorials Copyright OpenHelix. No use or reproduction without express written consent 46
    45. 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. 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. 47. Training Materials: Tutorial Tutorial Copyright OpenHelix. No use or reproduction without express written consent 49
    48. 48. Training Materials: Slides Slides Copyright OpenHelix. No use or reproduction without express written consent 50
    49. 49. Training Materials: Exercises Exercises Copyright OpenHelix. No use or reproduction without express written consent 51
    50. 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. 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. 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. 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. 54. OpenHelix Customers Copyright OpenHelix. No use or reproduction without express written 56 consent
    55. 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. 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. 57. Subscription benefits• Online learning has proven to be as good as onsite training• Significant lower cost
    58. 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. 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. 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. 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. 62. Worldwide Genomic Resource Training and SupportCopyright OpenHelix. No use orreproduction without express 66written consent
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