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BioUML - extensible workbench for systems biology

Laboratory of Bioinformatics,

Novosibirsk, Russia.

www.itcsoftware.com

2004 -2010 ITC Software All rights reserved.

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Schedule

9.30 – 9.40 Introduction

9.40 – 10.00 Visual modeling, graphical notations

10.00 – 10.20 BioUML main concepts and architecture overview

10.20 – 11.00 Demonstration of BioUML workbench from the customer view point.

11.00 – 11.15 Coffee break

11.15 – 11.30 Simulations with BioUML.MATLAB plug-in, Java plug-in.

11.30 – 11.45 Usage of BioUML in real life projects – Cyclonet and Biopath (codename) projects

11.45 – 12.15 Current work and further development

12.15 – 12.30 Discussion

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The challenge

"We now have unprecedented ability to collect data about nature but there is now a crisis developing in biology, in that completely unstructured information does not enhance understanding. We need a framework to put all of this knowledge and data into — that is going to be the problem in biology. We've reached the stage where we can't talk to each other — we've all become highly specialized. We need a framework, a framework where people can come back to us and say, 'Yes, I understand.' Driving toward that framework is really the big challenge.“

Sydney Brenner

Sydney Brenner, 2002 Nobel Prize winner

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Main BioUML concepts and ideas

• Visual modeling• Plug-in based architecture (Eclipse platform runtime from

IBM).• Meta model – problem domain neutral level of

abstraction that describes system as compartmentalized graph. It is also common contract for all parties (software developers, problem domains specialists, annotators, mathematicians).

• Diagram type concept – formally defines graphical notation and provides its incorporation into BioUML workbench.

• Module concept - allows developer to incorporate databases on biological pathways into BioUML framework taking into account database peculiarities.

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Visual Modeling

The problem of modeling and simulating of complex systems can be significantly simplified for customers by using computer systems providing visual modeling.

These visual depictions offer alternative syntax to completely and formally specify models.

A number of visual syntaxes were developed and implemented in computer systems for electrical engineering and computer science. The most known graphical language for computer science is UML – Unified Modeling Language.

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The OMG specification states:

"The Unified Modeling Language (UML) is a graphical language for visualizing,specifying, constructing, and documenting the artifacts of a software-intensive system.

The UML offers a standard way to write a system's blueprints, including conceptualthings such as business processes and system functions as well as concrete things suchas programming language statements, database schemas, and reusable softwarecomponents."

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UML diagrams

• use case diagram• class diagram• behavior diagrams:

– statechart diagram– activity diagram– interaction diagrams:

• sequence diagram• collaboration diagram

• implementation diagrams:– component diagram– deployment diagram

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UML use case diagram

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UML class diagram

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UML state chart diagram

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UML activity diagram

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UML sequence diagram

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UML collaboration diagram

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If we will consider UML architecture from developer view point then we will note:

1) UML was really designed for modeling software systems and are hardly suitable for other problem domains.

2) UML has complicated structure that is quite hard for implementation. OMG specification is more the 700 pages.

3) UML was not designed for visual modeling and simulation of dynamics of complex systems.

That is why we need new language for modeling biological systems and we called this language BioUML.

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Graphical notations for biological pathways

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Some graphical notations for biological pathways

Kohn K.W. (1999). Molecular Interaction Map of the Mammalian Cell Cycle Control and DNA Repair Systems. Mol. Biol.Cell. 10, 2703-2734.Kitano H. (2003). A graphical notation for biochemical networks. BIOSILICO Vol. 1. No. 5.R. Maimon and S. Browning (2001). Diagrammatic Notation and Computational Grammar for Gene Networks. Proceedings of the International Conference on Systems Biology. 2001.Cook D.L. et al. (2001). A basis for a visual language for describing, archiving and analyzing functional models of complex biological systems. Genome Biol. 2. RESEARCH 0012.Database specific notations:- KEGG/Metabolic pathways; GeneNet system;

TRANSPATH …

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Kohn K.W. (1999). Molecular Interaction Map of the Mammalian Cell Cycle Control and DNA Repair Systems. Mol. Biol.Cell. 10, 2703-2734.

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Representation of multimolecular complexes: stimulatory and inhibitory complexes of E2F1, DP1, and pRb. (a) E2F1:DP1 dimer; (b) E2F1:DP1:pRb trimer; (c) E2F1:DP1 bound to promoter element E2 (transcriptional activation shown); (d) E2F1:DP1:pRb bound to E2 (transcriptional inhibition shown). Note that the promoter element can be occupied either by E2F1:DP1 or by E2F1:DP1:pRb (alternative binding represented by interaction lines joined at an acute angle).

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Kitano H. (2003). A graphical notation for biochemical networks. BIOSILICO Vol. 1. No. 5.

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R. Maimon and S. Browning.

Diagrammatic Notation and Computational Grammar for Gene Networks. Proceedings of the International Conference on Systems Biology. 2001.

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Formal description and modeling of biological systems require coordinated efforts of different group of researchers:

• programmers - they should provide computer tools for this task.

• problem domain experts - they should specify what and how should be described.

• experimenters and annotators - they should describe corresponding data following to these rules.

• mathematicians - they should provide methods for models analysis and simulations.

BioUML architecture separates these tasks so they can be effectively solved by corresponding group of researchers and provides simple contract how these groups and corresponding software parts should communicate.

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p53, The gatekeeper of death:

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Cook D.L. et al. (2001). A basis for a visual language for describing, archiving and analyzing functional models of complex biological systems. Genome Biol. 2. RESEARCH 0012.

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KEGG - metabolic pathways

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KEGG - signaling pathways

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GeneNet system

B1+..+BM

A1+...+AN C1+...+CK

A chemical formalism was employed as a basis for describing the events occurring in biological pathways

2 types of relationships between entities:reaction - the interaction between the entities that leads to the appearance of new entityregulatory event - the effect of an entity on a certain reaction

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GeneNet – antiviral responce

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TRANSPATH database

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TRANSPATH – p53 pathway

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BioUML architecture

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Plug-in based architecture

Plug-in- plugin.xml- Java jar

files

A plug-in is the smallest unit of BioUML workbench function that can be developed and delivered separately into BioUML workbench. A plug-in is described in an XML manifest file, called plugin.xml. The parsed contents of plug-in manifest files are made available programmatically through a plug-in registry API provided by Eclipse runtime. - extension points are well-defined function points in the system where other plug-ins can contribute functionality. - extension is a specific contribution to an extension point. Plug-ins can define their own extension points, so that other plug-ins can integrate tightly with them.

Plug-in - plugin.xml

- Java jar filesPlug-in

- plugin.xml- etc.

Eclipse platform runtime

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Meta model

Executable model

Graph structure

Standard module

Database

Database adapter

Java objects

Gene Protein …

Diagram types- Semantic map- Pathway- Pathway simulation

Eclipse platform runtime Workbench UI

Diagram editor

Analysistools

Simulation tools

Other tools

Views, editors

Menus, toolbars, etc.

GeneNet module

KEGG/pathwaysmodule

TRANSPATHmodule

SBML module

Perspectives

Diagram view part

Diagram editor part

DiagramType-semantic controller-diagram view builder-diagram filter

ModuleType-diagram types-data categories-query engine

Query engine

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<?xml version="1.0" encoding="UTF-8"?><plugin id="ru.biosoft.plugins.javascript“ version="0.7.4"> <requires> <import plugin="org.apache.log4j"/> <import plugin="ru.biosoft.access"/> <import plugin="ru.biosoft.workbench"/> <import plugin="biouml.workbench"/> </requires>

<runtime> <library name="jsplugin.jar“/> </runtime>

<extension-point name="function" id="function"/> <extension-point name="function" id="hostObject"/>

Plugin.xml example (1)

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<extension-point name="function" id="function"/> <extension-point name="function" id="hostObject"/>

<extension id="help" point="ru.biosoft.plugins.javascript.function"> <function name="help" class="ru.biosoft.plugins.javascript.Global" method="help" varargs="true"> <doc description="%help.descr"> <argument name="obj" type="Object" obligatory="true“ description="%help.arg_1"/> <example code="%help.ex_1c" description="%help.ex_1d"/> <example code="%help.ex_2c" description="%help.ex_2d"/> <example code="%help.ex_3c" description="%help.ex_3d"/> </doc> </function> </extension>

Plugin.xml example (2)

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help.descr = Returns description for the specified JavaScript function \ or host object.\nThis description should be loaded using \ 'biouml.pligins.javascript.function' or \\n'biouml.pligins.javascript.hostObject' extension point.

help.arg_1 = JavaScript object of function name.

help.ex_1c = help()

help.ex_1d = will print description of 'help' function itself.

help.ex_2c = help(print)

help.ex_2d = will print description of 'print' function.

help.ex_3c = help(sbw)

help.ex_3d = will print description of sbw host object.

Plugin.properties example

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BioUML meta model

The core of BioUML workbench is meta model.

Unlike UML meta mode BioUML meta model is problem domain neutral and provides an abstract layer for comprehensive formal description of wide range of biological and other complex systems.

Content of databases on biological pathways or SBML models are expressed in terms of meta model and then can be used by other workbench plug-ins.

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A Beq1 eq2

R1C

eq3 eq4

R2

1eqdt

dA

32 eqeqdt

dB

4eqdt

dC

Соответствующая ему математическая модель

Пример двух последовательных химических реакций

100 0 0

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A B

-k1[A] k1[A]

R1 C

-k2[B] K2[B]

R2

100 0 0

System structure is described as a graph

Mathematical model of the system

Description of system

components in the database

ID ACC .....//

ID R1A->B

...//

ID BCC .....//

ID R2B->C

...//

ID CCC .....//

A B-k1[A] k1[A]

R1C

-k2[B] K2[B]

R2100 0 0

Example of formalized description of System from two chemical reactions

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Main BioUML meta-model classes to describe system structure as compartmentalized graph

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Diagram type concept

Diagram type defines:• what system components can be shown

in the diagram;• diagram view builder - it is used to

generate view for each diagram element taking into account problem domain peculiarities;

• semantic controller - provides semantic integrity of the diagram during its editing;

• filters – hide or highlight diagram elements according to some selection criteria.

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Module Concept

• The module concept allows to developer define new diagram types and incorporate other databases on biological pathways into BioUML framework.

• The module defines mapping of database content into diagram elements and diagram types that can be used with the database.

• Module also provides query engine that can be used by BioUML workbench to find interactiong components of the system.

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Modules

• standard BioUML module for biological pathways;

• module for models in SBML format;• module for models in CellML format

(only biochemical models);• GeneNet database module;• module for KEGG/Pathways datbase (draft);• module for TRANSPATH database (draft);• GeneOntology (under development).

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Standard BioUML module for biological pathways

The module defines most common biological data types (gene, protein, RNA, substance, reaction, etc.), they mapping into simple text database and three diagram types for description of biological pathways on several semantic levels:

1. Semantic network (ontology) - this diagram type is used to describe semantic relationships between system components, system states, and related problem domain concepts.

2.  Pathway diagram type is used for formalized description of biological pathway structure. This diagram type uses GeneNet graphical notation.

3. Pathway simulation diagram type is extension of pathway structure diagram, where variables are associated with graph nodes and differential equations with graph edges. This allows to BioUML workbench automatically generate mathematical model of the system and simulate its dynamics.

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• Suggested approach can be applied for modeling biological systems using:– Systems of ordinary differential equations– Systems of algebra-differential equations– State and transition diagrams– Hybrid models– Boolean and logical networks– Petri nets– Markov chains– Stochastic models– …

• Limitations– Spatial models– PDE– …

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Meta model

Executable model

Graph structure

Standard module

Database

Database adapter

Java objects

Gene Protein …

Diagram types- Semantic map- Pathway- Pathway simulation

Eclipse platform runtime Workbench UI

Diagram editor

Analysistools

Simulation tools

Other tools

Views, editors

Menus, toolbars, etc.

GeneNet module

KEGG/pathwaysmodule

TRANSPATHmodule

SBML module

Perspectives

Diagram view part

Diagram editor part

DiagramType-semantic controller-diagram view builder-diagram filter

ModuleType-diagram types-data categories-query engine

Query engine

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Formal description and modeling of biological systems require coordinated efforts of different group of researchers:

• programmers - they should provide computer tools for this task.

• problem domain experts - they should specify what and how should be described.

• experimenters and annotators - they should describe corresponding data following to these rules.

• mathematicians - they should provide methods for models analysis and simulations.

BioUML architecture separates these tasks so they can be effectively solved by corresponding group of researchers and provides simple contract how these groups and corresponding software parts should communicate.

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BioUML live demonstration

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Biological databases

Data search and retrieving

Visual modeling

Automated code generation for model simulation of model behavior

Formal description of structure of biological system

MATLAB code Java code

Simulating using MATLAB.JMatLink allows to BioUML

workbench to start MATLAB and retrieve simulations results

Java simulation plug-in.Contains ODE solvers ported from odeToJava and methods

for hybrid models support.

… code

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Cyclonet database

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Cyclonet database

Using BioUML workbench we are developing Cyclonet database – a database on cell cycle regulation in eukaryotes. Using BeanExplorer Enterprise Edition database content is available via the Internet.

The database contains information about cell cycle specific genes, proteins, protein complexes and their interactions, diagrams of cell cycle regulation for vertebrates, models of cell cycle and results of their analyses, microarray data, literature references and other related resources.

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Cyclonet database content

Data:for semantic networks- concepts

- relations for pathway diagrams- cells- compartments- genes- proteins- RNAs- substances- reactions- for simulation- constants- equations

Dictionaries:- databases- relation types- species- units- constants

Publications

Resources:- formats- software- sites, etc.

Diagrams Microarray data

Analysis results

EnSmart

GeneOntology

TRANSPATH

TRANSFAC

PASS

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BioUML workbench

Servlet container: Tomcat

Cyclonet system architecture

CyclonetMySQL database

Web browser

JDBC

BeanExplorerEnterprise Edition

Client side:

Server side:

Cyclonet module

GeneOntologyMySQL database

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Biopath (codename) database

Purpose of this project is create formal description of pathogeneses of chronic respiratory diseases and optimization of their treatment.

The work is performed jointly with the Institute of Medical Problems of North (Krasnoyarsk) and the Institute of Pulmonology (Moscow).

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• Graph search engine– Graph search engine completion and testing– adaptation of new graph layout library

• Complete support of SBML level 2 – Time delay– Algebraic rules– Units– SBML semantic tests

• Formula editor• State and transition diagrams.

Current work

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Force directed graph layout(takes nodes size into account)

(lay-out time ~50ms, 300 iterations)

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• Library of predefined kinetic laws• Stochastic modeling• BioPAX support• New diagram type for gene regulatory regions• TRANSPATH support• Microarray data support

Further steps

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Availability

BioUML workbench (including source code) is freely available at www.itcsoftware.com

Cyclonet database } see site Biopath database } for details

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Acknowledgments

Part of this work was partially supported by following grants: Volkswagen-Stiftung (I/75941), INTAS Nr. 03-51-5218 and RFBR Nr. 04-04-49826-а.

Author is grateful to for useful comments, discussions and technical support

Alexander Kel Sergey Zhatchenko

Software developers Annotators

Mikhail Puzanov Igor Tyazhev Ruslan Sharipov Vasiliy Hudyakov Vlad Zhvaleev Elena Cheremushkina Alexandr Koshukov Oleg Onegov Artem Shaidukov

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We hope you enjoyed our presentation !

ITC Software

Tel. +1 978 287 4855info@itcsoftware.comwww.itcsoftware.com