|
This document is an outline of releases for BioUML project for near
future. In parallel we will work on user guide, developer documentation,
and bug fixing.
|
Release |
|
Description |
|
Date |
v. 0.7.0
|
|
Plug-in based architecture using Eclipse runtime, SBML format support,
ontology diagram type, Html editor for diagram description, etc. |
|
June 13, 2003
release notes
|
v. 0.7.1
|
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Shell mode, JavaScript custom functions and host objects, JavaScript
help, SBW integration using JavaScript. |
|
September 1, 2003
release notes
|
| v. 0.7.2 |
|
GeneNet module, database search,
diagram editor enhancements, graph layouts and graph search support.
|
|
|
| v. 0.7.3 |
|
Database modules: KEGG, TRANSPATH.
Using relational database for data storage, client/server mode.
|
|
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| v. 0.7.4 |
|
MathML support, SBML level 2 support, CellML
support,
Java simulation engine, rule and event concepts,
update for Eclipse
3.0, JavaHelp support (only few help topics were written).
State and transition concept support.
|
|
October 10, 2004
release notes
|
| v. 0.7.5 |
|
Matlab and Java simulation engines passed 100% SBML semantic test suite 100%.
Support of algebraic equations, delay, piece wise functions, all MathML
functions (factorial, sh, tgh, ctgh, ash, atgh, etc.)
SBML semantic suite now is part of BDK (BioUML Development Kit)
Support of diagram import (SBML, CellML, GinSim) and export (PNG, JPEG,
SVG, GXL, SBML)
SBW 2.0.0
|
|
January 14, 2005
release notes |
| v. 0.7.6 |
|
User interface improvements: preferences, possibility to load and
change look & feel, user interface for editing rules and events.
Performance improvements.
ODE solver for stiff problems.
|
|
May 10, 2005
release notes |
| v. 0.7.7 |
|
Full text search engine (uses Lucene), graph search, graph layout improvements
BioPAX format - import/export,
OBO format - import/export
Ensembl support (spike solution)
Clipboard pane
CDK library is used to visualize chemical structures on diagrams
arbitrary images (GIF, PNG, etc.) for graph nodes
Client-server architecture, BioUML can be started as standalone server or
as a servlet
BioUML network edition
New installer based on IzPack
Initial draft of user manual
|
|
October 24, 2007
release notes |
| v. 0.7.8 |
|
Graphic notation editor, SBGN (alpha version)
Library of predefined kinetic law functions (SBO)
BioModels - comparison with other simulators (Copasi, CVODE, RoadRunner,
Jarnac, JSim, Oscill8 Core, SBWOdeSolver, MathSBML)
Database references editor
Equations editor
Microarray plug-in (alpha version)
|
|
January 28, 2008 (alpha)
March 20, 2008 (beta)
release notes |
| v. 0.8.0 |
|
Composite database module
Database module editor
SBML extensions for BioModels database (experiment, simulation, parameters,
result, plot)
XML diagram type
Experiments
Loading of modules from BioUML server:
EBI data pack (Ensembl, UniProt, ChEBI, IntAct, BioModels) - free databases
from EBI as BioUML modules
|
|
July 2, 2008
release notes |
| v. 0.8.1 |
|
Workbench update from the site
Third party libraries update: JFreeChart, Lucene, Rhino, JHelp
UI improvements: graphics (for simulation results) - now node titles
instead of node IDs are used
Several HTML tags can be used in titles for graph nodes: <br>,
<sub>, <sup>, <b>, <i>, <font color, size>
|
|
July 22, 2008
release notes |
| v. 0.8.2 |
|
Graphic notation skins: KEGG notation for metabolic pathway diagrams, Regensburg notation for metabolic pathway
diagrams
Simple line path editor
Microarray data and analysis results as documents (they are opened in tabs
similar with diagrams)
Microarray analysis - identification up/down regulated genes using
t-statistics and hyperheometric distribution
|
|
August 9, 2008
release notes |
| v. 0.8.3 |
|
Authorization subsystem (login)
hierarchical models, block component (proof of concept)
JavaScript functions for:
data access,
operations on data sets (union, overlap, etc.),
microarray statistical analyses
|
|
August 28, 2008
release notes |
| v. 0.8.4 |
|
JavaScript editor, debugger
JavaScript functions: for plot, simulation
Refinements, bug fixing
- BSA (biological sequence analyses)
+ sequences, + import
+ matrixes, - import
+ profiles, - import, -new, -edit
- result (predicted sites)
- map document
- map view
- sequence filter
- site filter
- view options
|
|
September, 2008
in progress |
| v. 0.8.5 |
|
Integration with R, further integration with Matlab
Data editing history
BioUML server:
- network repository for group working
- remote tasks for execution on server side
- installation of EBI databases
|
|
September, 2008 |
| v. 0.8.6 |
|
Major refactoring: complex, macromolecule state, reaction
SBGN notation - refinements
BioUML server:
- BioHub - new technology for database integration on the base of
cross references
Graph search engine refactoring
|
|
October, 2008 |
| v. 0.8.7 |
|
MSigDB database
Literature editor
|
|
October, 2008 |
| v. 0.9.0 |
|
Document type for sequence maps
Nucleotide sequence analysis - site search
|
|
October, 2008 |
| v. 0.9.1 |
|
Agent based modeling
Parameters optimization
|
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November, 2008 |
| v. 0.9.2 |
|
Bug fixing
Documentation, help improvements
|
|
|
| v. 1.0.0 |
|
Official release
|
|
|
Features listed below can be implemented in future. You are welcome with your comments and suggestion about new features as well as
feature implementation priorities. Please
use BioUML forum for
this purpose: you can write a letter to biouml@yahoogroups.com
or post your message. We
are really needed in your feedback.
| Features for future |
|
Priority |
|
BioPAX 3.0 support |
|
medium |
| SED-ML support |
|
medium |
| BIND support |
|
medium |
| SBML graph layout extension support |
|
medium |
| Stochastic modeling |
|
medium |
| Petri nets |
|
medium |
| Diagram HTML publishing |
|
medium |
| Markov models |
|
low |
|
