Physics Colloquium, University of Chicago May 2008

1. Computation and Knowledge Ian Foster Computation Institute Argonne National Lab & University of Chicago

4. Knowledge Generation in Astronomy ~1600 30 years ? years 10 years 6 years 2 years

5. Astronomy, from 1600 to 2000 Automation 10 -1  10 8 Hz data capture Community 10 0  10 4 astronomers (10 6 amateur) Computation Data 10 6  10 15 B aggregate 10 -1  10 15 Hz peak Literature 10 1  10 5 pages/year

6. Astronomy, from 1600 to 2000 Automation 10 -1  10 8 Hz data capture Community 10 0  10 4 astronomers (10 6 amateur) Computation Data 10 6  10 15 B aggregate 10 -1  10 15 Hz peak Literature 10 1  10 5 pages/year Text mining Federation/ collaboration Data analysis Complex system modeling Hypothesis generation Experiment design

7. FLASH Turbulence Simulation (R.Fisher, D.Lamb, et al.) LLNL BG/L External users access processed dataset 74 million files 154 TB 1 week, 65K CPUs 11M CPU hours Largest compressible homogeneous isotropic turbulence simulation 23 TB 3 weeks @ 20 MB/sec (GridFTP) Globus

10. Send 1 GB partitioned into equi-sized files over 60 ms RTT, 1 Gbit/s WAN Megabit/sec File size (Kbyte) (16MB TCP buffer) Number of files John Bresnahan et al., Argonne Globus

12. Lag Plot for Data Transfers to Caltech Credit: Kevin Flasch, LIGO

15. Cancer Biology Globus

18. Discovery (1): Registries Duke OSU NCI NCI Globus

19. Discovery (2): Standardized Vocabularies Core Services Grid Service Uses Terminology Described In Cancer Data Standards Repository Enterprise Vocabulary Services References Objects Defined in Service Metadata Publishes Subscribes to and Aggregates Queries Service Metadata Aggregated In Registers To Discovery Client API Index Service Globus

21. Text Mining

23. GeneWays Online Journals Pathways GeneWays Andrey Rzhetsky et al. Screening 250,000 journal articles 2.5M reasoning chains 4M statements

24. Image: Andrey Rzhetsky

26. Image: Andrey Rzhetsky

27. Image: Andrey Rzhetsky

28. Image: Andrey Rzhetsky

29. Evidence Integration: Genetics & Disease Susceptibility Identify Genes Phenotype 1 Phenotype 2 Phenotype 3 Phenotype 4 Predictive Disease Susceptibility Physiology Metabolism Endocrine Proteome Immune Transcriptome Biomarker Signatures Morphometrics Pharmacokinetics Ethnicity Environment Age Gender Source: Terry Magnuson

31. The Data Deluge

32. Images courtesy Mark Ellisman, UCSD

33. Images courtesy Mark Ellisman, UCSD

34. Images courtesy Mark Ellisman, UCSD

35. Images courtesy Mark Ellisman, UCSD A human brain @ 1 micron voxel = 3.5 peta (10 15 )bytes

39. Tagging & Social Networking GLOSS : Generalized Labels Over Scientific data Sources (Foster, Nestorov)

40. High-Performance Data Analytics Functional MRI Ben Clifford, Mihael Hatigan, Mike Wilde, Yong Zhao Globus

41. Many Tasks: Identifying Potential Drug Targets 2M+ ligands Protein x target(s) (Mike Kubal, Benoit Roux, and others)

42. start report DOCK6 Receptor (1 per protein: defines pocket to bind to) ZINC 3-D structures ligands complexes NAB script parameters (defines flexible residues, #MDsteps) Amber Score: 1. AmberizeLigand 3. AmberizeComplex 5. RunNABScript end BuildNABScript NAB Script NAB Script Template Amber prep: 2. AmberizeReceptor 4. perl: gen nabscript FRED Receptor (1 per protein: defines pocket to bind to) Manually prep DOCK6 rec file Manually prep FRED rec file 1 protein (1MB) PDB protein descriptions 4 million tasks 500K cpu-hrs (Mike Kubal, Benoit Roux, and others) 6 GB 2M structures (6 GB) DOCK6 FRED ~4M x 60s x 1 cpu ~60K cpu-hrs Amber ~10K x 20m x 1 cpu ~3K cpu-hrs Select best ~500 ~500 x 10hr x 100 cpu ~500K cpu-hrs GCMC Select best ~5K Select best ~5K

44. An NSF MRI Proposal: PADS: Petascale Active Data Store 500 TB reliable storage (data & metadata) 180 TB, 180 GB/s 17 Top/s analysis Data ingest Dynamic provisioning Parallel analysis Remote access Offload to remote data centers P A D S Diverse users Diverse data sources 1000 TB tape backup

45. Using Computation to Accelerate Science Complex modeling Experiment automation Data analysis Collaboration & federation Hypothesis generation

46. Integrated View of Simulation, Experiment, & Informatics *Simulation Information Management System + Laboratory Information Management System Database Analysis Tools Experiment SIMS* Problem Specification Simulation Browsing & Visualization LIMS + Experimental Design Browsing & Visualization

47. Robot Scientist (University of Wales)