Metamodeling and Modeling language for Systems Biology SB-UML Magali ROUX-ROUQUIE CNRS, Paris.

Slides:

Advertisements

Similar presentations

Major Influences on the Design of ODM Dan Chang (IBM) Elisa Kendall (Sandpiper) MDSW 2004.

Advertisements

Andrea Maurino Web Service Design Methodology Batini, De Paoli, Maurino, Grega, Comerio WP2-WP3 Roma 24/11/2005.

Issue 134 Metamodel for OWL 2 Peter Haase, Elisa Kendall, Boris Motik, Evan Wallace.

Language Specification using Metamodelling Joachim Fischer Humboldt University Berlin LAB Workshop Geneva

Visual Model-based Software Development EUD-Net Workshop, Pisa, Italy September 23 rd, 2002 University of Paderborn Gregor Engels, Stefan Sauer University.

Profiles Construction Eclipse ECESIS Project Construction of Complex UML Profiles UPM ETSI Telecomunicación Ciudad Universitaria s/n Madrid 28040,

1 UML ++ Mohamed T IBRAHIM University of Greenwich -UK.

Using UML, Patterns, and Java Object-Oriented Software Engineering Chapter 2, Modeling with UML, Part 4 UML 2 Metamodel.

7M701 1 Information Systems Modelling and Design with.

Unified Modeling Language

Model-Based Programming: Executable UML with Sequence Diagrams By Ruben Campos Cal State L.A. Computer Science Thesis Work Spring 2007.

Amit, Keyur, Sabhay and Saleh Model Driven Architecture in the Enterprise.

1 UML – an overview What is UML? UML stands for Unified Modelling Language. ”The Unified Modelling Language is a visual language for specifying, constructing.

Use of Ontologies in the Life Sciences: BioPax Graciela Gonzalez, PhD (some slides adapted from presentations available at

UML CASE Tool. ABSTRACT Domain analysis enables identifying families of applications and capturing their terminology in order to assist and guide system.

Ontologies Reasoning Components Agents Simulations An Overview of Model-Driven Engineering and Architecture Jacques Robin.

1 Conceptual Modeling of Topic Maps with ORM Versus UML Are D. Gulbrandsen The XML group, Center for Information Technology Services, University of Oslo,

Data Analysis (and User Interaction) GEOG 463 5/7/04.

Systems Engineering Foundations of Software Systems Integration Peter Denno, Allison Barnard Feeney Manufacturing Engineering Laboratory National Institute.

Mining Metamodels From Instance Models: The MARS System Faizan Javed Department of Computer & Information Sciences, University of Alabama at Birmingham.

Using UML Models for the Performance Analysis of Network Systems Nico de Wet and Pieter Kritzinger Department of Computer Science University of Cape Town.

Basic Concepts The Unified Modeling Language (UML) SYSC System Analysis and Design.

Workshop on Integrated Application of Formal Languages, Geneva J.Fischer Mappings, Use of MOF for Language Families Joachim Fischer Workshop on.

Slide 1 Wolfram Höpken RMSIG Reference Model Special Interest Group Second RMSIG Workshop Methodology and Process Wolfram Höpken.

Metadata Tools and Methods Chris Nelson Metanet Conference 2 April 2001.

TC Methodology Massimo Cossentino (Italian National Research Council) Radovan Cervenka (Whitestein Technologies)

MDE Model Driven Engineering Xavier Blanc Université Pierre et Marie Curie

Introduction to MDA (Model Driven Architecture) CYT.

SOFTWARE DESIGN AND ARCHITECTURE LECTURE 18. Review User interface Design principles Design Guidelines.

Assessing the Suitability of UML for Modeling Software Architectures Nenad Medvidovic Computer Science Department University of Southern California Los.

Tools for Diagrammatic Specifications Stian Skjerveggen Supervisors: Yngve Lamo, Adrian Rutle, Uwe Egbert Wolter.

1 MFI-5: Metamodel for Process models registration HE Keqing, WANG Chong State Key Lab. Of Software Engineering, Wuhan University

METACASE. WHAT THIS PRESENTATION IS ABOUT  What’s META MODELING?  What’s METACASE?  METAEDIT+ 5.1 EVALUTION PROGRAM  Diagram and its kinds.

SaveUML System design. System overview Possible...

Modeling Component-based Software Systems with UML 2.0 George T. Edwards Jaiganesh Balasubramanian Arvind S. Krishna Vanderbilt University Nashville, TN.

1 © 1999 Microsoft Corp.. Microsoft Repository Phil Bernstein Microsoft Corp.

Verification of behavioural elements of UML models using B Truong, Ninh-Thuan and Souquieres, Jeanine In Proceedings of the 2005 ACM Symposium on.

Automata Based Method for Domain Specific Languages Definition Ulyana Tikhonova PhD student at St. Petersburg State Politechnical University, supervised.

The Unified Modeling Language (UML)

Mining the Biomedical Research Literature Ken Baclawski.

CIM LAB MEETING Presentation on UML Rakesh Mopidevi Kwangyeol Ryu.

11 th NASA/ESA Workshop on Product Data Exchange 2009 Allison Barnard Feeney, NIST David Price, Eurostep.

Chapter 5 System Modeling. What is System modeling? System modeling is the process of developing abstract models of a system, with each model presenting.

An Unstructured Semantic Mesh Definition Suitable for Finite Element Method Marek Gayer, Hannu Niemistö and Tommi Karhela

UML Profile BY RAEF MOUSHEIMISH. Background Model is a description of system or part of a system using well- defined language. Model is a description.

Yu, et al.’s “A Model-Driven Development Framework for Enterprise Web Services” In proceedings of the 10 th IEEE Intl Enterprise Distributed Object Computing.

Using UML, Patterns, and Java Object-Oriented Software Engineering Chapter 2, Modeling with UML: UML 2 Metamodel Note to Instructor: The material in this.

Rational Rose For System Design What is Rational Rose? Rational Rose is the visual modeling software solution that lets you create, analyze, design,

Ontologies Reasoning Components Agents Simulations An Overview of Model-Driven Engineering and Architecture Jacques Robin.

Object Oriented Programming and Data Abstraction Earl Huff Rowan University.

Object Oriented Analysis & Design By Rashid Mahmood.

International Workshop 28 Jan – 2 Feb 2011 Phoenix, AZ, USA Modeling Standards Activity Team Model-based Systems Engineering (MBSE) Initiative Roger Burkhart.

OMG Architecture Ecosystem SIG Enterprise Data World 2011.

SysML 2.0 Requirements for Visualization

SysML v2 Formalism: Requirements & Benefits

State Digrams in UML: A Formal Senmatics using Graph Transformations

Web Ontology Language for Service (OWL-S)

Software Architecture & Design Pattern

Seminar 1 Design of Informatics Systems

SysML 2.0 Concept and Needs for Visualization

Chapter 2, Modeling with UML, Part 4 UML 2 Metamodel

Object Oriented Analysis and Design

Modelling Clinical Information Using UML

Introduction to UML.

Piotr Kaminski University of Victoria September 24th, 2002

Software Design Lecture : 14.

OOPSLA Workshop on Domain-Specific Modeling Tools Workgroup

PASSI (Process for Agent Societies Specification and Implementation)

Software Architecture & Design

Presentation transcript:

Metamodeling and Modeling language for Systems Biology SB-UML Magali ROUX-ROUQUIE CNRS, Paris

What is Systems Biology ? T. Ideker, T. Galitski, L. Hood. A new approach to decoding life: Systems biology. Annu. Rev. Genomics Hum Genet 2 (2001)

DATA level 1 DATA MODEL level 2 Virtual Cell Relational Model Object Model SBML (XML) file Ontology

DATA level 1 DATA MODEL level 2 METAMODEL level 3 META METAMODEL level 4 Virtual Data Relational Model Object Model SBML (XML) file Ontology Language

METAMODELlevel MODEL level BIND database model Action ontology model ? Metamodel for Systems Biology

Looking for a Conceptual Metamodel … Static Dynamic

Mapping between State Description and Process Description M. Roux-Rouquie and JL Le Moigne. The systemic paradigm and its relevance for modeling biological functions (2002) CR Biol. 325:

Looking for a modeling language: The Unified Modeling Language (1) UML is a language originally developed for software engineering. This is a language for visualizing, specifying, constructing and documenting any kind of systems. It decouples the model from the platform. It describes: –concepts and their relationships (abstract syntax and semantics) –constraint language (OCL) –diagrams and notation for concepts –interchange format (XMI)

Major Advantages A standard language maintained by OMG and used by thousands of people over the world, Both, the formalism and the knowledge can be represented in UML Different formalisms can be expressed in the same standardized language Looking for a modeling language: The Unified Modeling Language (2)

The Unified Modeling Language (UML) State diagramInteraction diagram UML State diagram and Interaction Diagram

Extensions for RT systems with UML 2.0 (IBM Rational) Passive classActive class

A SB profile with UML 2.0 (CNRS proposal against RPF14) OMGOMG Life SciencesLife Sciences Research DTFResearch DTF MeetingMeeting Boston, September 9th 2003

SB-UML: FormOccurrence © CNRS

Example: TR_Photo-Isomerization Definition: Modifications of the molecular geometry after the absorption of a photon.

Molecular State vs population

Modeling Simulation

CellML vs SB-UML

Modeling States of cyclin-dependent Cdk2 kinase

Individual cell vs population Signal (molecule concentration) per cell In a imited population (less than 10 cells) In a large population

Conclusion (1) Model-driven approach Metamodel for systems biology in UML UML models in a variety of formalisms Semantic integration (before 2010, as announced by Alex Polonsky !)

Conclusion (2) Model transformation