Difference between revisions of "BioUML development history"
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Further below one can find the history of its development, where each record includes the version number, date of release and a concise description of the updates in the release. The records are listed in chronological order and grouped by year. | Further below one can find the history of its development, where each record includes the version number, date of release and a concise description of the updates in the release. The records are listed in chronological order and grouped by year. | ||
+ | |||
+ | ==2015== | ||
+ | {|class="wikitable" | ||
+ | !width="15%"|Date!!width="5%"|Release!!width="75%"|Description | ||
+ | |- style="background-color: Lavender" | ||
+ | |December, 2015 | ||
+ | |style="background-color:Gainsboro"| v. 0.9.10 | ||
+ | | | ||
+ | *Server | ||
+ | **integration with Galaxy CloudMan | ||
+ | **cloud/grid version - further development and improvements | ||
+ | **repository - packages for Debian and CentOS | ||
+ | *Web interface | ||
+ | **mobile version (for web-browser) | ||
+ | **web interface improvements diagrams | ||
+ | *SBGN-ML import and exported supported | ||
+ | *SBML | ||
+ | ** built-in constants pi and exponentiale | ||
+ | ** fbc 1.2 supported (except gene products). Now boundaries can be specified by parameters | ||
+ | *Simulation | ||
+ | ** dynamic fbc implemented - flux balance analysis can be performed continuosly during ODE simulation. Special engine implemented. | ||
+ | |||
+ | |- | ||
+ | |February, 2015 | ||
+ | |style="background-color:Gainsboro"| v. 0.9.9 | ||
+ | | | ||
+ | *BioUML IDE<br>new branch of BioUML platform based on NetBeans IDE | ||
+ | *General diagrams | ||
+ | **automatic redraw of diagram objects on mouse dragging | ||
+ | **context actions on right click: edit element, rotate | ||
+ | *SBGN diagrams reworked and enhanced | ||
+ | **special action for clone creation: user can choose for which reactions clone will be created. | ||
+ | **"oriented" reactions with one input edge for products and one output edge for reactants. | ||
+ | **Creation of phenotypes as processes with modifiers | ||
+ | **entity pool node and process types can be selected from drop boxes rather then typed | ||
+ | **complexes can be transformed to other EPNs and vice-versa | ||
+ | **separate fonts for node titles. | ||
+ | *SBML | ||
+ | **species are saved with the same name as correspondent node on diagram without auomaic prepending of "compartmentName_". | ||
+ | **Unit definitions can be created and changed via BioUML interface. | ||
+ | **SBO terms can be set for reactions, equations, functions etc. | ||
+ | **random variables with normal, unifrom and binomial distributions. Support of custom annotation (also supported by COPASI, Jarnac, Roadrunner). | ||
+ | **"time", "avogadro" and "delay" csymbols. | ||
+ | *SedML l1v2 supported | ||
+ | *Antimony | ||
+ | **added support for visual arrangment of species (complexes, state variables, different types of EPN) | ||
+ | **fixed bug with disabling of "close document" action. | ||
+ | *Agent-based modeling: introuced script-agents. Supported script languages: R, MATLAB, java-script. | ||
+ | *Server | ||
+ | *integration with DropBox, Google Drive, Microsoft One Drive | ||
+ | |- | ||
+ | |} | ||
==2014== | ==2014== | ||
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**cloud version support for Amazon EC2 (alpha) | **cloud version support for Amazon EC2 (alpha) | ||
**improved task manager | **improved task manager | ||
− | |||
|} | |} | ||
Revision as of 18:47, 11 March 2016
BioUML has been continuously developed by scientists from the Institute of Systems Biology in Novosibirsk, Russia, since 2002.
The BioUML project was started by Fedor Kolpakov in February 2002, during his work with Development On The Edge.com, LLC in Novosibirsk, Russia. In 2005 the Institute of Systems Biology, LLC was formed as a specialized subsidiary of Development On The Edge.com, LLC.
The current version of the platform is 2023.3.
Further below one can find the history of its development, where each record includes the version number, date of release and a concise description of the updates in the release. The records are listed in chronological order and grouped by year.
Contents |
2015
Date | Release | Description |
---|---|---|
December, 2015 | v. 0.9.10 |
|
February, 2015 | v. 0.9.9 |
|
2014
Date | Release | Description |
---|---|---|
September, 2014 | v. 0.9.8 |
|
April, 2014 | v. 0.9.7 |
|
2012 - 2013
Date | Release | Description |
---|---|---|
2013, November 18 | v. 0.9.6 |
|
2013, June 15 | v. 0.9.5 |
|
2013, March 20
(Workbench) |
v. 0.9.4 | BioUML web:
Collaborative work on diagram (like Google documents) UI improvements:
BioUML core (both workbench and web version): History of diagram editing (like CVS or SVN) Simulation engine
SBML support:
Visual modelling
Model analysis
Analyses:
User interface improvements
Genome browser improvements
Improved support of DAS protocol
Integration with JMOL for visualization of 3D structures BioUML server Galaxy support new section "Galaxy" in analysis tab allows to use all methods from Galaxy platform |
2012
(Web edition) |
v. 0.9.4 | Integration with BioStore (www.bio-store.org) for control of access rights and downloading |
2011
Date | Release | Description |
---|---|---|
October 31, 2011
(Workbench; beta) |
v. 0.9.3 | BioUML core:
Core update
SED-ML (Simulation Experiment Description Markup Language) support (alpha version)
Improved BioPAX support
Graph search enhancements
Diagram state refactoring
Data import/export improvements:
Data handling improvements:
Workflows improvements:
Algorithms for NGS and sequence analysis:
Embedded chat for collaborative work and on-line consultations (pilot version) (you need to register before at https://biostore.biouml.org) BioUML server
|
May 12, 2011 | the first BioDatomics release (built around the BioUML platform) | |
May 7, 2011
(Web edition) June 14, 2011 (Workbench; beta) |
v. 0.9.2 | BioUML core (common for workbench and web edition):
Import for Process Diagrams in CellDesigner 4.0/4.1 format Data analysis
Workflows support (beta version)
Simulation engine
User interface improvements:
Coloring diagram using omics data (redesigned) BioUML server:
|
May 6, 2011 | Version 1.0 of the geneXplain platform (based on BioUML) |
2010
Date | Release | Description |
---|---|---|
October 13, 2010 | v. 0.9.1 | BioUML core (common for workbench and web edition):
Simulation engine:
Chemoinformatics support (on the base of CDK and JChemPaint):
Tasks manager:
BioUML web edition:
|
July 2, 2010
(Web edition) September 13, 2010 (Workbench; alpha) |
v. 0.9.0 | BioUML core (common for workbench and web edition):
Simulation engine
Optimisation engine
SBML
Data analysis - a lot of new methods for analyses microarray data and gene regulatory regions
Reproducible research
User interface
BioUML workbench:
BioUML web edition:
BioUML server:
JavaHelp:
|
2009
Date | Release | Description |
---|---|---|
November 30, 2009
(Web edition) |
v. 0.9.0 | BioUML web edition:
first public version BioUML core: SBGN:
Databases:
Graph layout improvements:
(for example all math elements are located on the top of diagram)
New graph layout algorithms:
UI improvements:
Simulation engine:
BioUML server:
|
July 31, 2009 (alpha)
August 7, 2009 (beta) |
v. 0.8.6 | JavaScript:
Integration with R - special R object in JavaScript allows to evaluate R expressions as well as to show R graphic output Genome viewer (alpha version):
Sequence analysis (alpha version):
SBML level 2 version 2-4 support Parameters fitting (beta version) JavaHelp:
|
January 28, 2009 (alpha)
February 17, 2009 (beta) |
v. 0.8.5 | SBGN 1.0 implementation - alpha version
KEGG improvements:
UI improvements:
Parameters fitting (alpha version) Bug fixing:
JavaHelp refactoring: new tool for help writing - Help&Manual 5
|
2008
Date | Release | Description |
---|---|---|
December 12, 2008 | v. 0.8.4 | New database modules on BioUML server (pilot version):
General refactoring - now tabs in repository are called:
New architecture for methods of analyses:
Parameters fitting (initial version) Refinements, bug fixing:
Setup wizard - wizard to configure BioUML on first start. |
August 28, 2008 | v. 0.8.3 | Authorization subsystem (login)
hierarchical models, block component (proof of concept) JavaScript functions for:
|
August 9, 2008 | 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 |
July 22, 2008 | 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 2, 2008 | 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 |
January 28, 2008 (alpha)
March 20, 2008 (beta) |
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) |
2003 - 2007
Date | Release | Description |
---|---|---|
October 24, 2007 | 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 |
May 10, 2005 | 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. |
January 14, 2005 | 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 |
October 10, 2004 | 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. |
v. 0.7.3 | Database modules: KEGG, TRANSPATH. Using relational database for data storage, client/server mode. | |
v. 0.7.2 | GeneNet module, database search, diagram editor enhancements, graph layouts and graph search support. | |
September 1, 2003 | v. 0.7.1 | Shell mode, JavaScript custom functions and host objects, JavaScript help, SBW integration using JavaScript. |
June 13, 2003 | v. 0.7.0 | Plug-in based architecture using Eclipse runtime, SBML format support, ontology diagram type, Html editor for diagram description, etc. |
Predecessors
Prior to the first BioUML release a number of attempts had been undertaken to create versatile and convenient tools for retrieval, analysis, modelling and visualization of biological (particularly, genetic) data:
- MGL
- TRRD viewer
- Computer system "GeneNet"
- Transplorer