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eScience: A Transformed Scientific Method

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Duncan Hull
Duncan Hull

Presentation by Jim Gray on eScience

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eScience -- A Transformed Scientific Method Jim Gray , eScience Group, Microsoft Research http://research.microsoft.com/~Gray in collaboration with Alex Szalay Dept. Physics & Astronomy Johns Hopkins University http:// www.sdss.jhu.edu/~szalay /
Talk Goals ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
eScience: What is it? ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Science Paradigms ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
X-Info ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],The Generic Problems Experiments & Instruments Simulations facts facts answers questions Literature Other Archives facts facts ?
Experiment Budgets ¼… ½ Software ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Experiment Budgets ¼… ½ Software ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Action item Foster Tools and Foster Tool Support
Project Pyramids In most disciplines there are a few “giga” projects, several “mega” consortia and then many small labs. Often some instrument creates need for giga-or mega-project Polar station Accelerator Telescope Remote sensor Genome sequencer Supercomputer Tier 1, 2, 3 facilities to use instrument + data International Multi-Campus Single Lab
Pyramid Funding ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Action item Invest in tools at all levels
Need Lab Info Management Systems (LIMSs) ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Need Lab Info Management Systems (LIMSs) ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Action item Foster generic LIMS
Science Needs Info Management ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Data Analysis ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Analysis and Databases ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Data Delivery: Hitting a Wall ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],FTP and GREP are not adequate
Accessing Data ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],active databases!
Analysis and Databases ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Action item Foster Data Management Data Analysis Data Visualization Algorithms &Tools
Let 100 Flowers Bloom ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Talk Goals ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
All Scientific Data Online ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Literature Derived and Re-combined data Raw Data
Unlocking Peer-Reviewed Literature ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
How Does the New Library Work? ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Pub Med Central International ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Overlay Journals ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Data Archives articles Data Sets
Overlay Journals ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Journal Management System Data Archives articles title page Data Sets
Overlay Journals ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Journal Management System Journal Collaboration System Data Archives articles title page comments Data Sets
Overlay Journals ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Journal Management System Journal Collaboration System Data Archives Action item Do for other sciences what NLM has done for BIO Genbank-PubMedCentral… articles title page comments Data Sets
Better Authoring Tools ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Conference Management Tool ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Publishing Peer Review ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Why Not a Wiki? ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Why Not a Wiki? ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Action item Foster new document authoring and publication models and tools
So… What about Publishing Data? ,[object Object],[object Object],[object Object],[object Object],[object Object]
Thought Experiment ,[object Object],[object Object],[object Object],[object Object],[object Object]
Objectifying Knowledge ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Objectifying Knowledge ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Warning! Painful discussions ahead: The “O” word: Ontology The “S” word: Schema The “CV” words: Controlled Vocabulary Domain experts do not agree
The Best Example: Entrez-GenBank http:// www.ncbi.nlm.nih.gov / ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Nucleotide sequences Protein sequences Taxon Phylogeny MMDB 3 -D Structure PubMed abstracts Complete Genomes PubMed Entrez Genomes Publishers Genome Centers
Publishing Data ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Roles Authors Publishers Curators Consumers Traditional Scientists Journals Libraries Scientists Emerging Collaborations Project www site Bigger Archives Scientists
Data Pyramid ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Data Sharing/Publishing ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
The Best Example: Entrez-GenBank http:// www.ncbi.nlm.nih.gov / ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Action item Foster Digital Data Libraries (not metadata, real data) and integration with literature Nucleotide sequences Protein sequences Taxon Phylogeny MMDB 3 -D Structure PubMed abstracts Complete Genomes PubMed Entrez Genomes Publishers Genome Centers
Talk Goals ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
backup
Astronomy ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
World Wide Telescope Virtual Observatory http://www.us-vo.org/ http://www.ivoa.net/ ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Why Astronomy Data? ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],IRAS 100  ROSAT ~keV DSS Optical 2MASS 2  IRAS 25  NVSS 20cm WENSS 92cm GB 6cm
Time and Spectral Dimensions The Multiwavelength Crab Nebulae X-ray, optical, infrared, and radio views of the nearby Crab Nebula, which is now in a state of chaotic expansion after a supernova explosion first sighted in 1054 A.D. by Chinese Astronomers. Slide courtesy of Robert Brunner @ CalTech. Crab star 1053 AD
SkyServer.SDSS.org ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
SkyServer SkyServer.SDSS.org ,[object Object],[object Object],[object Object],[object Object]
Demo of SkyServer ,[object Object],[object Object],[object Object],[object Object],[object Object]
SkyQuery ( http://skyquery.net/ ) ,[object Object],[object Object],[object Object],[object Object],[object Object],SELECT o.objId, o.r, o.type, t.objId FROM SDSS:PhotoPrimary o, TWOMASS:PhotoPrimary t WHERE XMATCH(o,t)<3.5 AND AREA(181.3,-0.76,6.5) AND o.type=3 and (o.I - t.m_j)>2
SkyQuery Structure ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],2MASS INT SDSS FIRST SkyQuery Portal Image Cutout
Schema (aka metadata) ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
SkyServer/SkyQuery Evolution MyDB and Batch Jobs ,[object Object],[object Object],[object Object],[object Object]
Ecosystem Sensor Net LifeUnderYourFeet.Org ,[object Object],[object Object],[object Object],[object Object],[object Object],
RNA Structural Genomics ,[object Object],[object Object],[object Object],[object Object]
VHA Health Informatics ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
HDR Vitals Based Body Mass Index Calculation on VHA FY04 Population Source: VHA Corporate Data Warehouse Total Patients 23,876 (0.7%) 701,089 (21.6%) 1,177,093 (36.2%) 1,347,098 (41.5%) 3,249,156 (100%)

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eScience: A Transformed Scientific Method

  • 1. eScience -- A Transformed Scientific Method Jim Gray , eScience Group, Microsoft Research http://research.microsoft.com/~Gray in collaboration with Alex Szalay Dept. Physics & Astronomy Johns Hopkins University http:// www.sdss.jhu.edu/~szalay /
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  • 8. Project Pyramids In most disciplines there are a few “giga” projects, several “mega” consortia and then many small labs. Often some instrument creates need for giga-or mega-project Polar station Accelerator Telescope Remote sensor Genome sequencer Supercomputer Tier 1, 2, 3 facilities to use instrument + data International Multi-Campus Single Lab
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  • 10. Action item Invest in tools at all levels
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  • 48. Time and Spectral Dimensions The Multiwavelength Crab Nebulae X-ray, optical, infrared, and radio views of the nearby Crab Nebula, which is now in a state of chaotic expansion after a supernova explosion first sighted in 1054 A.D. by Chinese Astronomers. Slide courtesy of Robert Brunner @ CalTech. Crab star 1053 AD
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  • 59. HDR Vitals Based Body Mass Index Calculation on VHA FY04 Population Source: VHA Corporate Data Warehouse Total Patients 23,876 (0.7%) 701,089 (21.6%) 1,177,093 (36.2%) 1,347,098 (41.5%) 3,249,156 (100%)