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Category Cross-Omics>Agent-Based Modeling/Simulation/Tools Abstract BioUML is open source integrated Java framework for systems biology. It consists of two (2) parts: 1) BioUML workbench - is an integrated environment that spans a comprehensive range of capabilities including access to databases with experimental data, tools for the formalized description of a biological systems structure and functioning, as well as tools for their visualization, simulation, parameter fittings and analyses; 2) BioUML server - provides access to the databases installed on the server side of the BioUML workbench via the Internet. Visual modeling -- Reconstruction of complex biological systems from a huge amount of experimental data requires a formal language that can be easily understood both by humans and computers. It is known that the 'graphical depiction' of a complex system is one of the most suitable ways of understanding its structure by humans. Graphical notation allows one to completely and formally specify a model so that computer programs can analyze the model and simulate its behavior. This approach is widely used in engineering and computer science. Some examples are: a) MATLAB/Simulink; b) AnyLogic - multi-method simulation software (see G6G Product Number 20438); and c) UML - one of the best known graphical languages for computer science. The BioUML workbench adopted the ‘visual modeling’ approach for the formal description and simulation of complex biological systems. Other distinctive features of the BioUML workbench are the tight integration with databases of biological pathways, a query engine that allows users to find interacting components of the system and shows results as an editable graph. Meta-model -- The core of BioUML is a Meta-model. It provides an abstract layer (compartmentalized attributed graph) for the comprehensive formal description of a wide range of biological and other complex systems. The contents of databases of biological pathways, SBML and CellML models (see G6G Product Number 20293), as well as biological pathways in the BioPAX format can be expressed in terms of this Meta- model and used by the BioUML workbench. This formal description can be used for both the visual depiction and editing of biological system structures and for the automated generation of code to simulate a models behavior. The Meta-model is a neutral problem domain which splits the systems description into three (3) interconnected levels: 1) Graph structure - the system structure is described as a compartmentalized graph; 2) Database level - each graph element can contain reference to some database object; 3) Mathematical model - any graph element can be an element of the mathematical model. BioUML supports the following mathematical elements: variable, formula, equation, event, state and transition. Diagram type -- Diagram type defines: 1) Types of biological components and their interactions that can be shown in the diagram; 2) Diagram view builder - it generates a view (image) for each graph element taking into account the problem domain peculiarities; 3) Semantic controller - provides semantic integrity of the diagram during its editing. It also takes into account problem domain constraints. Diagram type can be defined (created) two (2) ways: 1) Programmatically - as Java class implementing a special interface. There are five (5) predefined diagram types that allow you to describe complex biological systems on the cellular level with different levels of detail and formality; 2) Declaratively - as an XML document. BioUML workbench provides a Graphic Notation Editor that allows advanced users to create and edit diagram types. BioUML workbench provides three (3) main diagram types for modeling metabolic pathways, signal transduction pathways and gene networks: 1) Semantic network - this diagram type is used to describe semantic relationships between system components, system states, and related problem domain concepts. This diagram type is also convenient as an overview. 2) Pathway - this diagram type is used for the formalized description of a biological pathway structure (metabolic pathway or gene network). 3) Pathway simulation - is an extension of the Pathway diagram type, where variables are associated with graph nodes and differential equations (DEs) with graph edges. This allows the BioUML workbench to automatically generate mathematical model(s) of the system and simulate its dynamics. Simulation engine -- BioUML workbench provides two (2) alternative simulation engines: 1) Java simulation engine - it automatically generates and compiles Java code on the bases of the visual model (diagram) of a biological system. For simulation the manufacturer has adopted the odeToJava library (Patterson and Spiteri, 2003) that provides methods for numerical solutions of both stiff and non-stiff systems of ODEs. For solving algebraic equations Newton solver is used. 2) MATLAB simulation engine - workbench automatically generates code for MATLAB and invokes the MATLAB engine to simulate a models behavior using the JMatlink library. Database -- The database contains multiple database types: 1) Data types (gene, protein, RNA, substance, reaction, etc.) that is stored in the database; 2) Mapping of the database content into 'diagram elements' and 'diagram types' that can be used with the database; 3) Diagram types that can be used to present the database content as a set of diagrams. 4) A Query engine to find interacting components of the system. Search results can be shown as a graph and edited by user. Search engines -- BioUML workbench provides three (3) types of search engines for working with its databases: 1) Data search (filter) - this search engine maps the database content into Java objects and filters these Java objects according to filtering conditions for each property, for example name = "TP53". 2) Full text search - this search engine uses the Lucene full text search engine. For this feature the database content is also mapped into Java objects and then these Java objects are indexed by Lucene. 3) Graph search - this search engine finds interacting pathway components and displays the results as an editable graph. BioUML server -- Security support - BioUML server supports secure access to databases. The server administrator can configure security settings for access to each database installed on the server. User interface - From a user’s point of view, databases installed on the server side (remote databases) look similar to databases installed locally and the users can use remote databases the same way as local databases: 1) Remote database content can be shown in a repository tree; 2) A user can add, edit and remove records from a remote database; 3) A user can open and edit diagrams from a remote database; 4) All search engines (Data search, Full text search, Graph search) can work with remote databases via a special protocol; 5) The simulation engine can store simulation results and plots in a remote database. System Requirements BioUML workbench v. 0.8.6 requires JDK 6 or JRE 6 and will Not work with earlier versions of Java. Manufacturer
Institutskaya 6, Novosibirsk, 630090 Russia Tel/Fax: +7 (383) 330 3070 E-mail: fedor@biouml.org
http://www.biouml.org/ Price Contact manufacturer G6G Product Number 20446 G6G Manufacturer Number 104074 |
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