BioUML consists of 3 parts:

• BioUML server - provides access to data and analyses methods installed on the server side for BioUML clients (workbench and web edition) via the Internet.
   
• BioUML workbench - Java application that can work standalone or as "thick" client for BioUML server.
   
• BioUML web edition - "thin" client for BioUML server (you just need to start web browser) that provides most of functionality of BioUML workbench. It uses AJAX and HTML5 <canvas> technology for visual modeling and interactive data editing.

Main BioUML features

• supports main standards in systems biology
   
  • SBML - Systems Biology Markup Language. 
    BioUML supports SBML Level 1 version 1-2; Level 2 versions 1-4; Level 3 version 1. 
    BioUML is the only simulator that have passed all tests from SBML test suite version 2.0 (test details).
     
  • SBGN - Systems Biology Graphic Notation. 
    BioUML supports Process Diagrams as they are defined by SBGN version 1.0.
     
  • BioPAX - Biological Pathway Exchange. 
    BioUML can import data in BioPAX 2.0 format. Imported data can be stored as native BioPAX file, SQL or text database.
     
  • PSI-MI - The Proteomics Standards Initiative Molecular Interaction XML format. 
    BioUML supoorts data in PSI-MI format.
     
  • OBO - Ontology Flat File Format. 
    BioUML can import ontology in OBO 1.2 format. Imported data can be presented as dependences diagram.
     
  • CellML - Cell Markup Language BioUML can read and simulated biochemical models presented in CellML 1.0 format.
     
• support main biological databases
  • catalolgs: Ensembl, UniProt, ChEBI, GO
  • pathways: KEGG, Reactome, EHMN, BioModels, SABIO-RK, TRANSPATH, EndoNet, BMOND
   
• powerful search possibilities
  • full text search (Apache Lucene is used)
  • graph search - finds related pathway components and presents results as an editable graph
   
• graph layout engine
  • includes different layout algorithms:
    • force directed layout
    • hierarchical layout
    • cross grid layout (Kato,M. et al., 2005: Automatic drawing of biological networks using cross cost)
    • fast grid layout (Kaname, K., Masao, N. and Satoru, M., 2008: Fast grid layout algorithm for biological networks with sweep calculation)
  • support incremental graph layout
  • support compartments
  • layout preview
  • possibility to reuse layout for similar diagrams
   
• visual modeling
  • powerful diagram editor
  • virtual experiment - variations of diagram to simulate different experimental conditions, knock-outs, etc.
  • automated generation of optimized Java code for model simulation from corresponding pathway diagram
  • different solvers for differential equations:
    • JVODE - ported to Java version of CVODE
    • RADAU IIA - (implicit Runge-Kutta method for stiff delay differential equations)
    • Imex - (implicit Runge-Kutta method for stiff differential equations)
    • Dormand-Prince - (explicit Runge-Kutta method)
    • Euler (for debugging complex models)
  • supports different model types:
    • ODE - odinary differential equations
    • DAE - differential algebraic equations
    • ODE/DAE with delay
    • 1D PDE (for bloof flow simulation)
    • hybrid models support (with events, states and transitions)
    • hierarchical models
  • plots (using JFreeChart)
    • time series
    • phase portrait
   
• parameters fitting
  • experimental data - time courses or steady states
  • experimental data - exact or relative values of substance or concentrations
  • multiexperiment fitting
  • global and local parameters for multiexperiment fitting
  • constraint support
  • different optimization methods
    • Adaptive Simulating Annealing
    • Cellular genetic algorithm
    • Evolution strategy (SRES)
    • GLBSOLVE
    • Particle swarm optimization
    • Quadratic Hill-climbing
  • optimization and parallelization of computations
  • JavaScript API for parameters fitting
   
• genome browser
  • uses AJAX and HTML5 <canvas> technologies (BioUML web edition)
  • interactive - dragging, semantic zoom
  • DAS support (Distributed Annotation System)
  • tracks support
    • Ensembl tracks
    • DAS tracks
    • user-loaded BED/GFF/Wiggle files
   
• JavaScript support
  • script console
  • JavaSsript editor
  • JavaScript debugger (BioUML workbench only)
  • JavaScript preprocessor (allows to embed easily R expressions)
   
• R support
  • connect to R on local or remote machine
  • convert BioUML data to R and save R results as BioUML data
  • R graphics support
  • R preprocessor for JavaScript
   
• SQL support
  • SQL console
  • direct SQL access to analysis results tables
   
• data analyses
  • supports a set of analysis method
    • biosequence analysis
    • gene expression regulation modeling
    • model optimization
    • statistics
  • executing analysis from JavaScript
   
• microarray analyses
  • normalization
  • annotation
  • up and down identification
  • correlation analysis
  • hypergeometric meta-analysis
  • cluster analysis
   
• workflow, reproducible research
  • actions journal
    • Analysis
    • JavaScript
    • SQL requests
  • allows to present set of actions in research diagram
  • allows to build and execute workflow document
   
• reports, templates
  • different templates for representing data element info
  • model reports
    • Overview
    • Reactions
    • Parameters
    • Variables
    • ODE(model as differential equation system)
   
• plug-in based architecture
  • based on Eclipse runtime
  • allows to integrate other tools: SBW, R, Matlab, CDK, Lucene, ...