Java Adaptive Mathematical Modeling Engine (JAMME) Leeland Artra, Cell Systems Initiative (CSI) Zheng Li, Department of Bioengineering University of Washington,

Slides:

Advertisements

Similar presentations

1 DTI/EPSRC 7 th June 2005 Reacting to HCI Devices: Initial Work Using Resource Ontologies with RAVE Dr. Ian Grimstead Richard Potter BSc(Hons)

Advertisements

An Operational Metadata Framework For Searching, Indexing, and Retrieving Distributed GIServices on the Internet By Ming-Hsiang.

Introduction to Databases

UNDERSTANDING JAVA APIS FOR MOBILE DEVICES v0.01.

1 Richard White Design decisions: architecture 1 July 2005 BiodiversityWorld Grid Workshop NeSC, Edinburgh, 30 June - 1 July 2005 Design decisions: architecture.

1 Introduction to XML. XML eXtensible implies that users define tag content Markup implies it is a coded document Language implies it is a metalanguage.

CIM2564 Introduction to Development Frameworks 1 Overview of a Development Framework Topic 1.

Problem-Solving Environments: The Next Level in Software Integration David W. Walker Cardiff University.

Software Reuse Building software from reusable components Objectives

1 SWE Introduction to Software Engineering Lecture 22 – Architectural Design (Chapter 13)

An framework for model-driven product design and development using Modelica Adrian Pop, Olof Johansson, Peter Fritzson Programming Environments Laboratory.

Software Frameworks for Acquisition and Control European PhD – 2009 Horácio Fernandes.

Architecture & Data Management of XML-Based Digital Video Library System Jacky C.K. Ma Michael R. Lyu.

Workshop on Cyber Infrastructure in Combustion Science April 19-20, 2006 Subrata Bhattacharjee and Christopher Paolini Mechanical.

1212 CHAPTER DATABASES. © 2005 The McGraw-Hill Companies, Inc. All Rights Reserved Competencies Distinguish between the physical and logical view.

ICS (072)Database Systems Background Review 1 Database Systems Background Review Dr. Muhammad Shafique.

Outline Chapter 1 Hardware, Software, Programming, Web surfing, … Chapter Goals –Describe the layers of a computer system –Describe the concept.

The middleware that makes real time integration a reality.

Jun Peng Stanford University – Department of Civil and Environmental Engineering Nov 17, 2000 DISSERTATION PROPOSAL A Software Framework for Collaborative.

Building software from reusable components.

APPLICATION SOFTWARE DEVELOPMENT BASIS Ivanov, Vladimir Software Program Manager ITC Software.

Chapter 3 Software Two major types of software

IPlant Collaborative Tools and Services Workshop iPlant Collaborative Tools and Services Workshop Overview of Atmosphere.

Annual SERC Research Review - Student Presentation, October 5-6, Extending Model Based System Engineering to Utilize 3D Virtual Environments Peter.

LÊ QU Ố C HUY ID: QLU OUTLINE  What is data mining ?  Major issues in data mining 2.

Copyright © 2007 Ramez Elmasri and Shamkant B. Navathe Slide 1- 1 Chapter 1 - Introduction: Databases and Database Users - Outline Types of Databases and.

SCRAM Software Configuration, Release And Management Background SCRAM has been developed to enable large, geographically dispersed and autonomous groups.

MySQL GUI Administration Tools Rob Donahue Manager, Distributed Systems Development May 7th, 2001 Rob Donahue Manager, Distributed Systems Development.

OpenAlea An OpenSource platform for plant modeling C. Pradal, S. Dufour-Kowalski, F. Boudon, C. Fournier, C. Godin.

CSS/417 Introduction to Database Management Systems Workshop 5.

1 CSE 2102 CSE 2102 CSE 2102: Introduction to Software Engineering Ch9: Software Engineering Tools and Environments.

PROJECT NAME: DHS Watch List Integration (WLI) Information Sharing Environment (ISE) MANAGER: Michael Borden PHONE: (703) extension 105.

Zhonghua Qu and Ovidiu Daescu December 24, 2009 University of Texas at Dallas.

CIS 375—Web App Dev II Microsoft’s.NET. 2 Introduction to.NET Steve Ballmer (January 2000): Steve Ballmer "Delivering an Internet-based platform of Next.

IPlant Collaborative Tools and Services Workshop iPlant Collaborative Tools and Services Workshop Overview of Atmosphere.

FALL 2005CSI 4118 – UNIVERSITY OF OTTAWA1 Part 4 Other Topics RPC & Middleware.

SOFTWARE DESIGN AND ARCHITECTURE LECTURE 07. Review Architectural Representation – Using UML – Using ADL.

WordFreak A Language Independent, Extensible Annotation Tool.

Test Driven Development in the.Net Framework Sam Lee Mayur Mehta Jaymeen Shah McCoy College of Business Administration Texas State University-San Marcos.

XML & Mediators Thitima Sirikangwalkul Wai Sum Mong April 10, 2003.

Contents 1.Introduction, architecture 2.Live demonstration 3.Extensibility.

XML Registries Source: Java TM API for XML Registries Specification.

Design of a Search Engine for Metadata Search Based on Metalogy Ing-Xiang Chen, Che-Min Chen,and Cheng-Zen Yang Dept. of Computer Engineering and Science.

Ocean Observatories Initiative Data Management (DM) Subsystem Overview Michael Meisinger September 29, 2009.

SIMO SIMulation and Optimization ”New generation forest planning system” Antti Mäkinen Dept. of Forest Resource Management / University of Helsinki.

Model Checking and Model-Based Design Bruce H. Krogh Carnegie Mellon University.

NA-MIC National Alliance for Medical Image Computing UCSD: Engineering Core 2 Portal and Grid Infrastructure.

Presented by Scientific Annotation Middleware Software infrastructure to support rich scientific records and the processes that produce them Jens Schwidder.

Building a Topic Map Repository Xia Lin Drexel University Philadelphia, PA Jian Qin Syracuse University Syracuse, NY * Presented at Knowledge Technologies.

March 2004 At A Glance NASA’s GSFC GMSEC architecture provides a scalable, extensible ground and flight system approach for future missions. Benefits Simplifies.

S. Shumilov – Zürich Analytical Visualization Framework - a visual data processing and knowledge discovery system Ivan Denisovich, Serge Shumilov Department.

Cole David Ronnie Julio. Introduction Globus is A community of users and developers who collaborate on the use and development of open source software,

Visualization in Problem Solving Environments Amit Goel Department of Computer Science Virginia Tech June 14, 1999.

© FPT SOFTWARE – TRAINING MATERIAL – Internal use 04e-BM/NS/HDCV/FSOFT v2/3 JSP Application Models.

August 2003 At A Glance The IRC is a platform independent, extensible, and adaptive framework that provides robust, interactive, and distributed control.

Model Design using Hierarchical Web-Based Libraries F. Bernardi Pr. J.F. Santucci {bernardi, University of Corsica SPE Laboratory.

1 Chapter 38 RPC and Middleware. 2 Middleware  Tools to help programmers  Makes client-server programming  Easier  Faster  Makes resulting software.

Data Manipulation with Globus Toolkit Ivan Ivanovski TU München,

SMI 7 May 2008B. Franek SMI++ Framework Knowledge Exchange seminar 1 SMI++ Object-Oriented Framework for Designing and Implementing Distributed Control.

Singleton Academy, Pune. Course syllabus Singleton Academy Pune – Course Syllabus1.

March 2004 At A Glance The AutoFDS provides a web- based interface to acquire, generate, and distribute products, using the GMSEC Reference Architecture.

Integrated Modeling Environment System Engineering Seminar Johnny Medina / Code 531 Chris Stone / Code 531 / Constellation Software Engineering.

IPlant Collaborative Tools and Services Workshop iPlant Collaborative Tools and Services Workshop Overview of Atmosphere.

Redmond Protocols Plugfest 2016 Jinghui Zhang Office Interoperability Test Tools (Test Suites and Open Source Projects) Software Engineer Microsoft Corporation.

Introduction: AstroGrid increases scientific research possibilities by enabling access to distributed astronomical data and information resources. AstroGrid.

Tools and Services Workshop Overview of Atmosphere

DOE 2000 PI Retreat Breakout C-1

Module 01 ETICS Overview ETICS Online Tutorials

Software Engineering with Reusable Components

Criteria for rapid prototyping

Presentation transcript:

Java Adaptive Mathematical Modeling Engine (JAMME) Leeland Artra, Cell Systems Initiative (CSI) Zheng Li, Department of Bioengineering University of Washington, Seattle

CSI JAMME Proposal for NIGMS Program Introduction of JAMME Proposed collaborative project between NSR (National Simulation Resource for Circulatory Mass Transport and Exchange NIH/NCRR) and CSI to provide a complete software & database environment for real time biological modeling. Integration of NSR’s JSIM model simulation environment with CSI’s Moulage System framework, Metagraph data representation model, and a new object database management system.

CSI JAMME Proposal for NIGMS Program Background (available software at NSR and CSI) JSIM is an integrative model simulation environment being developed at NSR. Moulage is a real time data sharing & analysis system framework. Metagraph is a code name for a data and process representation language used to describe structures and methods that capture a computerized abstraction of the scientific process. The new object database management system being developed at CSI. Its primary goal is to provide a dynamic data engine that can handle complex hyper-graph / XML / Metagraph queries directly.

CSI JAMME Proposal for NIGMS Program JSIM Design Goals Easy-to-use end-user interface. Low barriers to entry of math modelling for biologically-inclined users. Facilitate collaborative model development (integration) –Integration at mathematical level. –Integration at component level. (“Plug-and-play”). Connectivity to heterogeneous data sources. Facilitate collaborative software development. Facilitate distributed-computing. Flexibility and Extensibility at all levels –math model classes and representations –hierarchical component libraries –numeric libraries

CSI JAMME Proposal for NIGMS Program JSIM Architecture

CSI JAMME Proposal for NIGMS Program Items Needed By JSIM Persistence Engine Intelligent Distributed Analysis Engine Visual Programming Ability Ability to Import Various Modeling Data Ability to Directly Interface With Experiment Data

CSI JAMME Proposal for NIGMS Program Moulage Design Goals Create a development framework that automatically can provide: Transparent access Ability to accept multiple data sources Easy sharing of data Data in form usable by object-oriented databases Multiple tools for analysis Dynamic version distribution

CSI JAMME Proposal for NIGMS Program Moulage Base Components Inspector: analysis, application DataObject: data IOController: IO operations DataObjectManager: database Translator: file to/from object textual data binary data remote data Translator DataObject DataObjectManager IOController Analysis / Application (Inspector)

CSI JAMME Proposal for NIGMS Program JAMME Approach 100% Core Java –Any needed classes built directly from on the 1.2 core –Carefully engineered to work within the Java Virtual Machine constraints –Allow operation as Stand alone application Command line utility (batch processing) Applet (Web and integration)

CSI JAMME Proposal for NIGMS Program Integration Overview Start with JSIM JSIM

CSI JAMME Proposal for NIGMS Program Integration Overview - Moulage Enhance by adapting to Moulage JSIM Analysis MML Data IO

CSI JAMME Proposal for NIGMS Program Integration Overview - Metagraph Enhance by creating Metagraph Data Structures JSIM Analysis MML Data IO

CSI JAMME Proposal for NIGMS Program Integration Overview - ODB Enhance by adding new object database JSIM Analysis IO

CSI JAMME Proposal for NIGMS Program Integration Overview - ODBMS Enhance by allowing distributed database processing of analysis JSIM Analysis IO Analysis ODBMS

CSI JAMME Proposal for NIGMS Program Integration Overview - Result Resulting in a set of reusable components Analysis IO Analysis ODBMS JAMME T-Cell Modeling Query Engine ‘X’