Service Oriented Architecture and Heterogeneous Model Sharing Environment

1. Service Oriented Architecture and Heterogeneous Model Sharing Environment Wilfred W. Li, Ph.D. wilfred@sdsc.edu National Biomedical Computation Resource Center for Research in Biological Systems San Diego Supercomputer Center University of California, San Diego

2. Modeling the Heart ventricles multicellular lattice crossbridge filament Modeling Synaptic Activity

3. Transformation Based Backprojection for Volume Reconstruction (TxBR)

4. Tools are Ties to Community of UsersEnabling Biomedical Research • New and hardened software • Continuity: Hundreds of users • SMOL (co-developed) Pkg released 17Jan07 • PMV/Vision/ADT: Hundreds of users • Opal: Reused in many products • GAMA (co-developed) • Single sign-on (co-developed) • Re-deployed as web service • MEME (1000’s of users) • New components in larger packages • Web services from NBCR into GEMSTONE; Continuity; Vision/PMV to call APBS • TxBR (EM tomography) used in NCMIR • Network Analysis Modules part of BiologicalNetworks (300 users) • Mechanisms to facilitate use, enhance science • ADT: Facilities use of AutoDock, most used docking software • iAPBS: Hooks for/from CHARMM, Amber, NAMD • Ties to other Resources Sousa, Fernandes & Ramos (2006)

5. Enabling Biomedical Applications with Grid Technology -- Cyberinfrastructure Cyberinfrastructure: raw resources, middleware and execution environment Virtual Organizations Workflow Management Web Service NBCR Rocks Clusters Vision Virtual Filesystem KEPLER

6. Service Oriented Architecture

7. Web Services: Features • Independent of programming language and OS • Not bound to any single platform or specific protocol • All information required to contact a service is captured by the Web Service Description • Web Services Description encapsulates an interface definition, data types being used, and the protocol information

8. Web Services Architecture Service Registry Lookup Publish Service Requestor Service Provider Interact

9. Web Services: Requirements • Accessible through standard Web protocols • Interoperability is important • Standard description language • Publishable to a registry of services • Discoverable via standard mechanisms

10. WSDL • Web Services Definition Language (WSDL) • Standard to describe the invocation syntax of a Web Service • Authors: IBM, Microsoft and others • WSDL is an XML document that describes • Interface types for each port • Content of messages it receives and sends • Bindings of interfaces to protocols • SOAP is default, others possible • Describes the access points (host/port) for the protocol

11. Towards Services Oriented Architectures (SOA) • Scientific applications wrapped as Web services • Provision of a SOAP API for programmatic access • Clients interact with application Web services, instead of Grid resources • Used in practice in NBCR, CAMERA, GLEON, among many others • PDBj, BioGrid-Japan – QM/MM simulations (Opal-OP) • Continuity, AutoDock, APBS, PMV, GEMSTONE (Opal)

12. Opal: Web Service Wrapper

13. GAMA – Grid Account Management Architecture K. Mueller

14. Rapid Grid Deployment

15. CAMERA Labs: Blast Portlet Interface to GOS Annotation Database (GAD) OPAL + ATOMIC + GAMA + NBCR expertise

16. My WorkSphere Overview

17. Web Service based Workflow Composition S. Krishnan

18. Opal WSRF Operation Provider Opal-OP Toolkit K. Ichikawa

19. Opal Web services in Vision M. Sanner

20. PMV developments • Secure web services (GAMA based authentication)for AutoDock on NBCR cluster

21. Ligand Protein Interaction Using Web Services – GEMSTONE • Baldridge, Greenberg, Amoreira, Kondric • GAMESS Service • More accurate Ligand Information • LigPrep Service • Generation of Conformational Spaces • PDB2PQR Service • Protein preparation • APBS Service • Generation of electrostatic information • QMView Service • Visualization of electrostatic potential file • Applications: • Electrostatics and docking • High-throughput processing of ligand-protein interaction studies • Use of small molecules (ligands) to turn on or off a protein function

22. Workflow Management • Use of Opal WS wrapper for rapid application deployment • Possible to add data type mapping • Leverage semantic web technology for interoperability • Use of Strongly Typed web service for data integrity, and better integration of WS based workflow • Data Integration • XML schema definition for data • Required for database storage, query and interface layer • What other standards to adopt and integrate using different namespaces • The bottom line: • WS enables workflow composition using tools such as KEPLER, TAVERNA, Vision in a visual environment (programming still required) • Reusable services by many other clients • Separation of data access and computation

23. Continuity 6.3 In Action at WHOLE HEART SCALE:MRI and Ventricular Mechanics in Murine Heart Failure Remodeling data High-field MRI Costandi PN, Frank LR, McCulloch AD, Omens JH (2006) Role of diastolic properties in the transition to failure in a mouse model of cardiac dilatation.Am J Physiol Heart Circ Physiol 2006 Dec;291(6):H2971-9. Finite Element Model

24. Virtual Cell Virtual Cell – Continuity Integration Plans Objective: Develop utilities and computing infrastructure to join the model authoring environment of Virtual Cell with the parallel computing capabilities of Continuity Cell models for Continuity Continuity • Proposed development activities: • Create VCell utilities to export Continuity-ready cell model and geometry descriptions • Deploy Continuity as a grid-based parallel solving engine accessible by VCell • Graphical, intuitive model authoring • Database of existing cell models • Dynamic compilation of cell model descriptions • Highly accessible parallel solvers Access to parallel solvers for VCell A. McCulloch

25. Subcellular Level Modeling: Integrating Image Analysis, Mesh Generation, and Simulation • Pipeline Image Pre-processing Feature Extraction Geometric Modeling Physical Modeling Simulation Z. Yu

26. Receptor xtal struct Ligands N/A available Explicit MD Org. synth ZINC NCI ACD • - Different methods of structure generation • Reduction of snapshots Snapshot 10 ps Ligand PDBs Receptor ensemble Translational Medicine Research: Relaxed Complex Method and Virtual Screening AutoDock Post-processing ranking schemes Set of docked complexes, BEs R. Amaro

27. BiologicalNetworks 300+ users, Java Webstart application, several modules, tested on Windows and Mac

28. 3D Myocyte Integrative Project – Dealing with Models Ontology Services ontologies Image Repository Services (Annot.) Image Repository Annotation Services Modeling Software Confocal Images EM Images Image Segments Geometry, Mesh & Transform Repository Model Repository Services (Annot.) Model Repository SBML Models cellML Models Other Models External data sets e.g., parameters A. Gupta

29. Selected References • I. Foster, "Service-oriented science," Science, vol. 308, pp. 814-7, 2005. • P. J. Hunter, W. W. Li, A. D. McCulloch, and D. Noble, "Multi-scale Modeling Standards, Tools, Databases for the Physiome Project," Computer, vol. 39, pp. 48-54, 2006. • S. Krishnan, B. Stearn, K. Bhatia, K. K. Baldridge, W. W. Li, and P. W. Arzberger, "Opal: Simple Web Services Wrapers for Scientific Applications," presented at International Conference of Web Services, Chicago, USA, 2006. • K. Ichikawa, S. Date, S. Krishnan, W. W. Li, K. Nakata, Y. Yonezawa, H. Nakamura, and S. Shimojo, "OPAL OP: An Extensible Grid-Enabling Wrapping Tool For Legacy Applications," presented at 3rd International Workshop on Grid Computing & Applications (GCA2007), Singapore, 2007. • W. W. Li, N. A. Baker, K. Baldridge, J. A. McCammon, M. H. Ellisman, A. Gupta, M. J. Holst, A. D. McCulloch, A. Michailova, P. Papadopoulos, A. Olson, M. Sanner, and P. W. Arzberger, "National Biomedical Computation Resource (NBCR): Devloping End-to-End Cyberinfrastructure for Multiscale Modeling in Biomedical Research " CTWatch Quarterly, vol. 2, pp. 6-17, 2006. • NSF Cyberinfrastructure Vision for 21st Century http://www.nsf.gov/pubs/2007/nsf0728/index.jsp

30. Summary • Opal enables rapidly exposing legacy applications as Web services • Provides features like Job management, Scheduling, Security, and Persistence • More information, downloads, documentation: • http://nbcr.net/services/ • NBCR Tools: http://nbcr.net/tools.php. • NBCR Summer Institute 2007, Calit2, UCSD: July 30 – Aug 3, 2007 http://nbcr.net/si/2007.

31. Before we get started • Should have Java (1.5.x) and Apache Ant (1.7.0) installed • Install Apache Ant from: http://ant.apache.org/ • Set environment variables: • JAVA_HOME to point to the JDK installation • ANT_HOME to point to the Ant installation • Make sure that these can be accessed from the command prompt • Add $JAVA_HOME/bin and $ANT_HOME/bin to PATH • Run the commands “java” and “ant” to ensure that all variables are set correctly

32. Download Software Prerequisites • Might want to create a new folder called “Tutorial” on your Desktop • Download and Extract Axis • http://nbcr.net/services/downloads/tutorial/axis-1_2_1.zip • Extract inside Tutorial directory • Download and Extract Tomcat • http://nbcr.net/services/downloads/tutorial/jakarta-tomcat-5_0_30.zip • Extract inside Tutorial directory • Set the environment variable CATALINA_HOME • Control Panel -> System -> Advanced

33. Download Opal • Download and Extract Opal • http://nbcr.net/services/downloads/tutorial/opal-ws-1.0RC1.zip • Extract inside Tutorial directory • Compile the sources • On the command prompt, cd to the above location • Type “ant -f build-opal.xml compile” • Watch for error messages, if any