Presentation on theme: "Comb-e-Chem Jeremy Frey Sept 2004 Drug Design & Delivery: The role of e-Science Jeremy Frey School of Chemistry University of Southampton, UK X-ray single."— Presentation transcript:
Comb-e-Chem Jeremy Frey Sept 2004 Drug Design & Delivery: The role of e-Science Jeremy Frey School of Chemistry University of Southampton, UK X-ray single Mol STM Raman Ocean Monolayer
Jeremy G. Frey e-Science e-Science is about global collaboration in key areas of science, and the next generation of infrastructure that will enable it. e-Science will change the dynamic of the way science is undertaken. John Taylor, DG of UK OST [The Grid] intends to make access to computing power, scientific data repositories and experimental facilities as easy as the Web makes access to information. Tony Blair, 2002
Jeremy G. Frey The UK e-Science Challenge £120M over a 3 Year Programme to create the next generation IT infrastructure to support e-Science and Business £120M over a 3 Year Programme to create the next generation IT infrastructure to support e-Science and Business Essential that UK plays a leading role in Global Grid development with the USA and EU Essential that UK plays a leading role in Global Grid development with the USA and EU Phase 1: Started roll out of plan for Grid Research, Development and Support of e-Science Pilot Projects Phase 1: Started roll out of plan for Grid Research, Development and Support of e-Science Pilot Projects
Jeremy G. Frey Cambridge Newcastle Edinburgh Oxford Glasgow Manchester Cardiff Southampton London Belfast DL RAL Hinxton UK e-Science Grid
Jeremy G. Frey National e-Science Centre (NeSC) NeSC is in Edinburgh NeSC is in Edinburgh Provides Courses & Meetings Provides Courses & Meetings Also has some funding for fellowships to visit NeSC Also has some funding for fellowships to visit NeSC
Jeremy G. Frey The Collaboratory Concept In 1989, William Wulf, then with the U.S. National Science Foundation, defined a collaboratory as In 1989, William Wulf, then with the U.S. National Science Foundation, defined a collaboratory as "a center without walls, in which the nation's researchers can perform their research without regard to geographical location, interacting with colleagues, accessing instrumentation, sharing data and computational resources, and accessing information in digital libraries."
Jeremy G. Frey HPC Analysis Storage Analysis Experiment Computing HPC Scientist The Current Client – Server ad hock model
Jeremy G. Frey The Future The Grid Model - Information Utilities MIDLEWAREMIDLEWARE Experiment Computing Storage Analysis Scientist
Jeremy G. Frey Access Grid Full multi-site video conferencing over the IP network Full multi-site video conferencing over the IP network Many sites now in the UK all running the same system Many sites now in the UK all running the same system System originated in the USA so also sites there. System originated in the USA so also sites there.
Jeremy G. Frey The Grid Grid is needed because Grid is needed because – Volume of data (real time data, images, video) – Scale of computation (analysis, simulation) – Complexity of process (automation) – Variable demands on computation – Provenance (audit trials, timestamps, process)
Jeremy G. Frey Bristol Chemistry ECS Stats Chemistry Combi Centre Southampton NCS IUPAC RSC IBM CCDC Pfizer IT Innovation Comb-e-Chem Partners GSK AZ
Jeremy G. Frey CombeChem People & Places IBM GSK Pfizer AZ
Jeremy G. Frey People Chemistry (Southampton & Bristol) – –Mike Hursthouse, Chris Frampton, Jon Essex, Jeremy Frey, Guy Orpen, Stephan Christensen, Thomas Gelbrich, Sam Peppe, Hongchen Fu, Graham Tizard, Suzanna Ward, Lefteris Danos National Crystallography Service (NCS) – –Simon Coles, Mark Light, Ann Bingham Electronics and Computer Science (Southampton) – –Dave De Roure, Luck Moreau, Mike Luck, Hugo Mills, Graham Smith, Simon Miles, Nicky Harding, Gareth Hughes, monica Schraefel, Terry Payne It-Innovation (Southampton) – –Mike Surridge, Ken Meacham, Steve Taylor, Daren Marvin Statistics (Southampton) – –Alan Welsh, Sue Lewis, Ralph Manson, Dave Woods Rutherford Appleton Laboratory
Jeremy G. Frey Synthesis Structure Analysis & Correlation Modelling Dissemination Prediction Design PlanGoal Properties All steps must be Grid Aware I will illustrate the application of e-Science to some of these stages using examples from the Comb-e-Chem Project
Jeremy G. Frey Synthesis Structure Analysis & Correlation Modelling Dissemination Prediction Design PlanGoal Properties All steps must be Grid Aware Salt Selection Smart Lab Crystallography Structural Similarities Non-linear optical effects Simulations Publication@Source Combinatorial Chemistry Semantic Grid Descriptors With examples…….
Jeremy G. Frey The Comb- e -Chem Project The exponential world of Combinatorial Synthesis and High throughput analysis meets the exponentially growing power of computing Funding EPSRC, IBM, GSK, AZ, Southampton
Jeremy G. Frey The Comb-e- Chem Vision Structures DB Properties DB Structure + PropertiesKnowledge + Prediction Automation & Remote interaction Co-Laboratory Interaction between users & Dark Labs Simulation and calculation
Jeremy G. Frey Design Automation Analysis Structures Models Properties Experiment
Jeremy G. Frey All about Automation Experiments Information & Knowledge Design Design Synthesis Synthesis Measurement Measurement Analysis Analysis Databases Databases Agents Agents
Jeremy G. Frey Plan & COSHH Digital Model Information Integration Report Knowledge Goal Literature Synthesis Smart Laboratory Analysis
Jeremy G. Frey Plan & COSHH Digital Model Information Integration Report Knowledge Goal Literature Synthesis not just one laboratory but many co-laboratories working together Analysis Smart Laboratory
Jeremy G. Frey Making best use of the Plan COSHH
Jeremy G. Frey Laboratory Context COSHHPlanRecord Annotation Guide Experimenters Digital Context
Jeremy G. Frey Chemistry Starts in the Lab Lab NCS Structure Raw data DatabasePublication
Jeremy G. Frey Chemistry Starts in the Lab Lab NCS Structure Raw data DatabasePublication URI
Jeremy G. Frey Semantic Grid Project Inference based on the semantics Importance of Ontology But problem of contradictions even within a domain This is not an avoidable issue
Jeremy G. Frey XML Gaussian ab initio program Gaussian ab initio program XML wrapper Simulation program XML wrapper Interface Personal Agent But need more general descriptions for services RDF – resource description framework DAML-S (for describing services)
Jeremy G. Frey Databases Database will become the key method of handling all data Database will become the key method of handling all data Metadata must be generated at inception and added as data traverses the workflow Metadata must be generated at inception and added as data traverses the workflow Version control, audit and backup handled at the database level. Version control, audit and backup handled at the database level.
Jeremy G. Frey Talk The UK e-Science Programme The Comb-e-Chem Project Smart Lab NCS Grid Service Structure Analysis Services Dissemination & Publication
Jeremy G. Frey Users ExperimentExpert Data & control links Access Grid links Experiment Remote (Dark) Laboratory Centralised remote equipment, multiple users, few experts Model for National crystallographic Service NCSModel for National crystallographic Service NCS
Jeremy G. Frey Expert Manufacturer Support Service Users Experiment Users Experiment Users Experiment Local link External link Access grid & control links Expert is the central resource in short supply Model for Combinatorial Raman ProjectModel for Combinatorial Raman Project
Jeremy G. Frey Sample Raw images Processed diffraction pattern Structure CIF Database Validation Journal Synthesis Smart LabsNCSArchive CCDC metadata Automated structure determination
Jeremy G. Frey Archiving of Data RAW DATA: Automatic archiving and retrieval with Atlas Datastore (RAL) Development of schema for retrieval of crystallographic metadata from relational databases (ISIS Data analysis group) Storage Resource Broker (SRB): Uniform access interface to different types of storage devices RESULTS DATA: Automatic deposition of CIF data with CCDC GRID- enabled pre-deposition database
Jeremy G. Frey Data Trail Drill down through the analysis path Drill down through the analysis path Look at increasingly raw data Look at increasingly raw data Often large expansion in quantity and variety at each stage Often large expansion in quantity and variety at each stage
Jeremy G. Frey Publication@Source Must be able to track back to the original data Must be able to track back to the original data Primary reason is to allow new analysis in the future by other researchers. Primary reason is to allow new analysis in the future by other researchers. In a university environment this may be viewed as a public responsibility in business environment ensuring maximum value from investment. In a university environment this may be viewed as a public responsibility in business environment ensuring maximum value from investment. Does have implications for provenance and even fraud! Does have implications for provenance and even fraud!
Jeremy G. Frey Journals: Publication @ source Journal MaterialsDatabaseMultimediaLaboratory DataPaper Full record
Jeremy G. Frey Context Most important provenance provides context Most important provenance provides context Needed to provide the Semantics Needed to provide the Semantics Allows other programs to understand the information (i.e. not just informed human) Allows other programs to understand the information (i.e. not just informed human) Allows inference Allows inference Also useful in synthetic laboratory Also useful in synthetic laboratory
Jeremy G. Frey Publication Chain Institution Laboratory Student Journal Bibliography Professional Body Archive
Jeremy G. Frey e-Bank Project Link comb-e-chem and other semantic grid science projects to the e-print system at Southampton Link comb-e-chem and other semantic grid science projects to the e-print system at Southampton Provide dissemination and provenance Provide dissemination and provenance
Jeremy G. Frey Changing the way we work Data Provenance Quantum Mechanical Analysis Properties Prediction Data Mining, QSAR, etc Design of Experiment E-Lab: Combinatorial Synthesis E-Lab: Properties Measurement E-Lab: X-Ray Crystallography Laboratory Processes Laboratory Processes Structures DB Properties DB Data Streaming Authorship/ Submission Visualisation Agent Assistant Laboratory Processes Samples
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