Features

The core of this project is open source BioDatomics platform (http://www.biouml.org) which consists of three parts:

Server - provides access to the integrated data and analyses methods installed on the server side.
Workbench - Java application that can work standalone or as "thick" client for the BioDatomics server.
Web Edition - "thin" client, it uses AJAX and HTML5 canvas technology for data visualization.

Here are some of the many specific features we offer in BioDatomics:

Database Repository

The data repository provides a storage for raw and processed data on specialized servers to facilitate collaborative work. Additional features of the repository include security systems that allow the control of user access rights and security of user data. A repository can be populated with data by a number of methods including import and export in a variety of formats and is expected to run at around 500 Terabytes but this is all extendable and can be tailor-made for the demands of the research in hand.

Database Access

The BioDatomics platform provides uniform access, full text search and retrieval of information from any of the biological databases that are installed on the server side. Information from these databases is also used for automated annotation of raw data uploaded from laboratory equipment.

Data Processing and Analysis

BioDatomics is a comprehensive processing and analysis platform which includes many plug-ins covering a broad array of analysis. We are working to add more and introduce 3rd Party plugins as part of the platform in the near future.
  • R/Bioconductor/MATLAB - Current plug-ins provide integration of R/Bioconductor and MATLAB for processing, visualizing and statistical analysis of high throughput data; including microarrays and NGS.
  • Galaxy - The platform includes all methods provided by Galaxy and you can use it to configure files directly. The platform provides powerful user interface for scripts and workflows to automate such analysis.

Plug-in Based Architecture

BioDatomics has an innovative plugin architecture that extends the capabilities of this software considerably. Based on the Eclipse runtime system we can add a myriad of plugins as coded by some of the best bio-researchers and programmers in the world. Tools we have already incorporated as plugins include: SBW, R, Matlab, CDK, Lucene – but there are many, many more. 

We are introducing new plugins regularly and invite anyone who codes such tools to approach us so that we can port their tool into BioDatomics if you are interested click here.

Full Support for the Main Standards in Systems Biology

  • SBML - Systems Biology Markup Language. ( SBML Level 1 version 1-2; Level 2 versions 1-4; Level 3 version 1) BioDatomics is the ONLY simulator that has passed all tests from SBML test suite version 2.0 (test details).
  • SBGN - Systems Biology Graphic Notation.  BioDatomics supports Process Diagrams as they are defined by SBGN version 1.0.
  • BioPAX - Biological Pathway Exchange. BioDatomics 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.  BioDatomics supports data in PSI-MI format.
  • OBO - Ontology Flat File Format. BioDatomics can import ontology in OBO 1.2 format. Imported data can be presented as dependencies diagrams.
  • CellML - Cell Markup Language BioDatomics can read and simulated biochemical models presented in CellML 1.0 format.
  • SEDML – Simulation Experiment Description Language
  • MIRIAM -  Minimal Information Required In the Annotation of Models
Support for many Mainstream Biological Databases
  • Catalogs: Ensembl, UniProt, ChEBI, GO
  • Pathways: KEGG, Reactome, EHMN, BioModels, SABIO-RK, TRANSPATH, EndoNet, BMOND
Powerful Search Capabilities
  • Full text search using Apache Lucene
  • Graph search - finds related pathway components and presents results as an editable graph

Graph Layout Engine

The graph layout engine includes a broad range of layout options including:

  • Force-directed layout
  • Hierarchical layout
  • Cross-grid  layout
  • Fast grid layout (Kaname, K., Masao, N. and Satoru, M., 2008: Fast grid layout algorithm for biological networks with sweep calculation)
  • Incremental graph layout support
  • Compartments support
  • Layout preview
  • Layout templates can be created and re-used.

Visual Modeling

BioDatomics contains a comprehensive set of visual modeling tools and features all designed to make the analysis of research data easier to understand and manipulate.

  • Visual Modeling Features:
    • Powerful diagram editor – Our editor allows diagram editing at the finest detail level.
    • 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
    • Differential equation solvers -  we have included a variety of useful tools for solving 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)
  • Model Types: Our visual modeling systems support several different popular model types
    • ODE - ordinary differential equations
    • DAE - differential algebraic equations
    • ODE/DAE with delay
    • 1D PDE (for bloof flow simulation)
    • Hybrid models are supported (with events, states and transitions)
    • Hierarchical models
  • Plot types available (using JFreeChart)
    • Time series
    • Phase portrait

Parameters Fitting Features

  • Experimental data - time courses or steady states
  • Experimental data - exact or relative values of substance or concentrations
  • Multi-experiment fitting
  • Global and local parameters for multi-experiment fitting
  • Constraint support
  • 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

  • Powered by AJAX and HTML5  canvas technologies (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
  • JavaScript editor
  • JavaScript debugger  (workbench only)
  • JavaScript preprocessor (to simplify R: expression embedding)

R Support

  • Connect to R on local or remote machine
  • Convert BioDatomics data to R and save R results as BioDatomics 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 methods
  • Biosequence analysis
  • Gene expression regulation modeling
  • Model optimization
  • Statistics
  • Executing analysis from JavaScript

Microarray Analyses

  • Normalization
  • Annotation
  • Up & Down identification
  • Correlation analysis
  • Hypergeometric meta-analysis
  • Cluster analysis

Workflow, Reproducible Research

  • Actions Journal
  • Analysis
  • JavaScript
  • SQL requests
  • Research Diagrams that allow the presentation of a set of actions
  • Build and execute workflow documents

Reports, Templates

  • Templates for representing data element information in a number of different ways
  • Model reports
    • Overview
    • Reactions
    • Parameters
    • Variables
    • ODE (model as differential equation system)