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Framework for Systems Biology

 


BioUML Powerpoint Presentations >>

Introduction

 

BioUML is a free, open source, extensible software framework for systems biology.

 

"Systems biology" can be narrowly defined as the "mathematical modeling of biological systems," Luke V. Schneider >> or more broadly as "the synergistic application of experiment, theory and modeling towards understanding biological processes as whole systems instead of isolated parts," Herbert M. Sauro >> "Using the analogy of an automobile, systems biology is like understanding the different parts of a car and how the different parts work together to achieve motion" >>

 

BioUML spans the entire range of capabilities including access to databases with experimental data, tools for formalized description of biological system's structures and functions, as well as tools for their visualization and simulations.

 

The language is similar to UML to define biological systems. Users can create diagrams from the set of predefined elements and specify a relationship between them.Similar to UML, the language defines a set of diagrams to describe any biological system as a whole. There are the following types of diagrams:

  1. Structural diagrams on organism, organ/tissue and cell level.

    • For one species

    • For group of related species

    • For different pathology and anomalies.

  2. Classification diagram for organs, tissues, cells etc. as a hierarchical tree.

  3. Maps of genes, genomes, viruses and prokaryotes.

  4. Biological systems state and transition graphs.

  5. Stepwise description of the assembly and functioning of multi-component biological systems, e.g. ribosome, RNA-polymerase, DNA reparation.

  6. Development and life cycles for organisms, organs and cells.

BioUML is an open source extensible workbench based on Eclipse runtime from IBM. BioUML is integrated with many biological databases and new databases can be easily added. BioUML supports many formats: SBML (level 1 and 2 completely), CellML, GXL, BioPAX (under development).


Overview

Currently BioUML framework consists of the following parts:

bullet

Meta model - provides an abstract layer to present structure of any biological system as a clustered graph.

bullet

Viewer - a universal viewer to visualize graphs of biological systems structure as diagrams.

bullet

Editor - universal diagram editor.

bullet

Search engine - provides searching of components with the specified properties in biological pathway databases. The search result can be presented as graph and further edited by a user using BioUML editor.

bullet

Modeler - allows a user to model/simulate dynamics of biological systems using block diagrams.

bullet

Standard diagram and data types - an attempt to standardize data types and graphic notations for biological pathways.

bullet

Database modules - provides incorporation of different databases biological pathways into BioUML framework.


Free Access

 

BioUML specifications will be free for all users.
BioUML referential implementation will be free for non-profit organizations.
For commercial use please contact us at info(at)itcsoftware.com.

BioUML workbench 0.8.5 (alpha) - 22.1MB - >>>

Installation notes:

install JDK 6 or JRE 6 on you computer.

BioUML workbench v. 0.8.5 requires JDK 6 or JRE 6 and will not work with early version of Java.

You may download JDK 6 from Sun Microsystems Inc web site: http://java.sun.com/javase/downloads/?intcmp=1281

start BioUML workbench installer using command line:

java -jar BioUML-install-2009_01_28.jar

BioUML set up wizard, tab "Load databases" allows you to connect with BioUML server and use databases installed there in test mode.

Main part of the databases are configured with "read-only" access for guest but commercial databases TRANSPATH and TRANSPATH-demo requires correct user name and password to see their content.

Early access Download >>


Acknowledgements

BioUML has been sponsored in part by a grant of the Volkswagen-Stiftung (I/75941) and DOTE.


Abstract | Quickstart | Presentations | Achitecture | Meta Model | Diagram Markup Language | Extension Points | SBML Support | BioUML Download | Release Notes | Development Roadmap | Cyclonet Project | Team: Systems Modeling   Scientific Advisory Board

 

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