Free Desktop version of BioDatomics

We have provided a version of BioDatomics for a chance to try for yourself the huge functionality and wide range of tools that can deepen your discovery possibilities and open your eyes to a new era in the world of bioinformatics and computational analysis.

Installation notes:

First, make sure you have the latest JDK or JRE on you computer. 
Note : V.0.9.3 requires JDK 6 or later and will not work with earlier versions of Java.

You may download JDK 6 from Sun Microsystems Inc web site 
start BioUML workbench installer using command line:

java -jar biouml-install-2011_10_31.jar

Note: for some methods of data analyses you will need to install R and Bioconductor

Here are the main download links:

Release notes:

This is a brief overview of new features and changes in BioUML version 0.9.3:

Major changes
  • Core update
  • Eclipse runtime is updated to Equinox version 3.6.0
  • Java 7
  • Improved Windows 7 compatibility
SED-ML (Simulation Experiment Description Markup Language) support (alpha version)
import and handling of SED-ML files
run and edited as workflows
used to generate simulation plots
Improved BioPAX support
BioPAX import/export, level 2, 3 (alpha version)
display BioPAX pathways in SBGN notation
graph search, full text search
Graph search enhancements 
flexible merging of previous search results
improved graph layout: hierarchical layout, orthogonal layout
Diagram state refactoring
using transactions for compound edits
possibility to remove transaction from changes
Data import/export improvements:
FTP upload - possibility to upload huge data from user’s ftp site
text and html files can be imported 
several image formats can be imported and viewed (jpg, png, etc.)
results can be exported as generic, text, html, or image files.
special document types for user data: text, images, html
Data handling improvements
multiple tables can be joined
columns with identical names may be merged automatically
Workflow improvements
now possible to include JavaScripts into workflows
more comfortable handling of folders and result files
handling of circular processes
Algorithms for NGS and sequence analysis
Bowtie wrapper
peak detection MACS (update)
motif discovery wrapper for ChIPMunk
motif discovery IPS-align
motif logo (on the base of PWM)
errors estimation: false positive, FDR, ROC curves
Embedded chat for collaborative work and on-line consultations (pilot version) 
(you need to register before at
BioUML server
new system for authorization and access rights: Biostore (
ChIP-SEQ pipeline (available only on test server)

Available videos about BioDatomics:

YouTube Video

YouTube Video

YouTube Video

YouTube Video

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