Difference between revisions of "BioUML development history"

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BioUML has been continuously developed by scientists from the Institute of Systems Biology in Novosibirsk, Russia, since 2002.
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[[BioUML]] has been continuously developed by the scientific group of Dr. Fedor Kolpakov in Novosibirsk, Russia, since 2002.
  
−
The BioUML project was started by [[User:Fkolpakov@gmail.com|Fedor Kolpakov]] in February 2002, during his work with [http://www.developmentontheedge.com/ 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 BioUML project was started by [[User:Fkolpakov@gmail.com|Fedor Kolpakov]] in February 2002, during his work with [http://www.developmentontheedge.com/ Development On The Edge.com, LLC] in Novosibirsk, Russia. In March 2008, the [http://biosoft.ru/ BIOSOFT.RU], LLC was formed as a specialized subsidiary of Development On The Edge.com, LLC and became the main BioUML developer.
  
 
The current version of the platform is {{BioUML current version}}.  
 
The current version of the platform is {{BioUML current version}}.  
  
 
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.
 +
==2023==
 +
{|class="wikitable"
 +
!width="15%"|Date!!width="5%"|Release!!width="75%"|Description
 +
|- style="background-color: Lavender"
 +
|Sep, 2023
 +
|style="background-color:Gainsboro"| v. 2023.3
 +
|
 +
*General
 +
** Export\import research project
 +
** Export\import optimization document to sbex format
 +
** Overall performance improved, bugs fixed
 +
* Python library
 +
** Created python library [http://wiki.biouml.org/index.php/Bioumlsim| bioumlsim], providing python API for BioUML simulation tools
 +
* Diagrams
 +
** Improved mathematical formulas representation in models description
 +
** Improved visual representation of model variables including concentration\amount notation.
 +
** Improved tabs for model elements editing
 +
* Parameter Identifiability analysis improved to calculate confidence intervals more correctly
 +
* Antimony support:
 +
** new elements: constraints, algebraic equations, subtypes, logical nodes, propagated ports, units (unit definitions, initializations with unit and keyword has), database references, phenotypes
 +
** keyword substanceOnly and initial quantity type (e.g. s1 = 5.0 / C)
 +
** text highlight improved
 +
** autoupdate mode
 +
** Custom annotation added to antimony
 +
*** SBGN annotation to specify:
 +
**** species type: macromolecule, simple chemical, etc.
 +
**** structure: complex elements, multiple modifications, units of information
 +
**** reaction type: process, inhibition etc.
 +
**** modifier type: catalysis, modulation etc.
 +
**** species clones
 +
**** port titles
 +
*** Glycan annotation to specify structure
 +
*** Smiles annotation to specify structure
 +
*** Multimers
 +
* A bunch of complex modular models has recently been constructed in BioUML and published describing:
 +
** [https://doi.org/10.3389/fphys.2021.746300 | blood pressure regulation]
 +
** [https://doi.org/10.3389/fphys.2022.1070115 | antihypertensive therapy]
 +
** [https://doi.org/10.3390/ijms221910353 | skeletal muscle metabolism]
 +
** [https://doi.org/10.3390/math10111925 | SARS-CoV-2 distribution in human organs]
 +
** [https://doi.org/10.1038/s41598-023-40008-9 | COVID-19 epidemiology]
 +
** [https://doi.org/10.1038/s41598-023-40008-9 | PBPK modeling of nanoparticles delivery to solid tumors in mice]
 +
|}
  
−
== Predecessors ==
+
==2020==
−
 
+
{|class="wikitable"
−
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]]
+
−
 
+
−
 
+
−
==2003 - 2007==
+
−
 
+
−
 
+
−
 
+
−
{| class="wikitable"
+
 
!width="15%"|Date!!width="5%"|Release!!width="75%"|Description
 
!width="15%"|Date!!width="5%"|Release!!width="75%"|Description
 
|- style="background-color: Lavender"
 
|- style="background-color: Lavender"
−
|June 13, 2003
+
|Dec, 2020
−
|style="background-color:Gainsboro"| v. 0.7.0
+
|style="background-color:Gainsboro"| v. 2020.4
−
|Plug-in based architecture using Eclipse runtime, SBML format support, ontology diagram type, Html editor for diagram description, etc.
+
|
−
|-
+
*Simulation
−
|September 1, 2003
+
**New simulation document allowing user to vary model parameters and immediately observe changes in simulation results.
−
|style="background-color:Gainsboro "| v. 0.7.1
+
*Diagrams
−
|Shell mode, JavaScript custom functions and host objects, JavaScript help, SBW integration using JavaScript.
+
**Reaction creation dialog is more compact with a separate tab for reaction law editing.
 +
**Export\Import enhanced. Now models can be exported along with all its submodels and related data tables in one archive.**
 +
**New tab to edit variables.
 +
**Species can be renamed.
 +
**Nodes movement improved.
 +
**Initial variable values can be set to diagrams from external tables (e.g. parameter fitting result).
 +
*Parameter fitting
 +
**Optimization can use table data (e.g. result of another parameter fitting) as a starting point.
 +
**During parameter fitting intermediate results (a table with the current  best fitted parameter values) can be saved without stopping the process.
 +
**Results of parameter fitting can be saved as autogenerated plot.
 +
*Web
 +
**Integration with Jupyter improved.
 +
**Default project can be set.
 +
**Variables to plot during model simulation can be edited through more convenient  dialog.
 +
**Complex can be more easily selected with all its elements by double click.
 +
**New tab to work with Flux Balance Analysis.
 +
|}
 +
==2019==
 +
{|class="wikitable"
 +
!width="15%"|Date!!width="5%"|Release!!width="75%"|Description
 
|- style="background-color: Lavender"
 
|- style="background-color: Lavender"
−
|  
+
|Dec, 2019
−
|style="background-color:Gainsboro"| v. 0.7.2
+
|style="background-color:Gainsboro"| v. 2019.4
−
|GeneNet module, database search, diagram editor enhancements, graph layouts and graph search support.
+
|
 +
*General:
 +
**Headless version of BioUML refined and improved. More information and example scripts can be found [http://wiki.biouml.org/index.php/Headless_BioUML here]
 +
**All Curated Biomodels tested to be imported and simulated
 +
**Automatically select imported data element in repository tree
 +
*Formats:
 +
**SBGN Process Description Level 1 version 2.0 supported: shapes of simple chemical and variable changed, equivalence operator implemented (not affecting simulation for now)
 +
**Better Reactome support (full support of new ID format, various fixes)
 +
**Option to use score satisfying UCSC сonventions during export to BED, GTF and GFF formats
 +
*Tables:
 +
**Table importer: fixed quotes processing, better processing of incomplete lines (with empty trailing values)
 +
**Info about matching path is shown in the results of the table converting (with versions of used databases)
 +
*Web version:
 +
**More precise edge selection in diagrams
 +
**Selected edges are highlighted with pink color
 +
**Move nodes on diagram using Ctrl+Arrow keys for 1px and Shift + Arrow keys for 5px shift
 +
**Copy and clone diagram element actions are separated
 +
**Initial integration with Jupyter
 +
**Track finder (user can set conditions and search for tracks in database (Ensembl, GTRD), the results can be added to the genome browser view from the tab)
 
|-
 
|-
−
|  
+
|Aug, 2019
−
|style="background-color:Gainsboro"| v. 0.7.3
+
|style="background-color:Gainsboro"| v. 2019.2
−
|Database modules: KEGG, TRANSPATH. Using relational database for data storage, client/server mode.
+
|
 +
*General
 +
*BioPAX support greatly enhanced
 +
*Diagrams
 +
**New SBGN EX diagram type, extending SBGN with semantic relations
 +
**Compartment shape can be selected apart from its inner nodes which facilitates its resizing
 +
**Reaction name can be set by user upon creation
 +
**Reaction participants can be edited, added and removed after reaction is created.
 +
**More convenient (non-modal) edit dialog for diagram elements
 +
*Analysis
 +
**All analysis methods in BioUML were rearranged into 35 categories
 +
*Web version
 +
**Search for analyses by name or description
 +
**Start page with analysis categories and quick guide
 +
**Multiple plots for simulation results presented in one panel.
 +
**Simulation can be stopped, special button added
 +
**Edges can be edit in drop down menu
 +
*Bugs fixed
 
|- style="background-color: Lavender"
 
|- style="background-color: Lavender"
−
|October 10, 2004
+
|Apr, 2019
−
|style="background-color:Gainsboro"| v. 0.7.4
+
|style="background-color:Gainsboro"| v. 2019.1
−
|MathML support, SBML level 2 support, CellML support,
+
|
−
Java simulation engine, rule and event concepts,  
+
*General
 +
**Installation process for linux systems improved
 +
*Diagrams
 +
**“Fit to screen” option added in toolbar for diagrams
 +
**Create edges from reactions to newly added nodes on diagram, if edge information is present in reaction prototype
 +
**Copy&paste diagram nodes to specified location
 +
**Copy all elements of one diagram to another via drag-and-drop
 +
**Nodes shape size is now editable from info panel
 +
**User can remove parameters from Parameters view part
 +
*Simulation
 +
**More convenient way to show on plot variables from modules several levels deep in the hierarchy
 +
*Visualization
 +
**Nodes and compartments may be visualized using custom images uploaded by user, image width and length can be set in percents of original image
 +
**Reactome Image library supported
 +
*Layout
 +
**Pin/unpin diagram elements via dropdown menu
 +
**Save and remember used automatic layouter for given diagram
 +
**Incremental layout of elements elements added from search
 +
*Expression filters
 +
**All SBGN diagrams support filters (e.g. expression filter)
 +
**Display expression filter as gradient aura on diagrams
 +
**NaN values for expression filters supported
 +
*Web version
 +
**Show multiple simulation plots in one window, stop simulation if plots are closed
 +
**Collapsible array attributes in info block
 +
**Highlight inner nodes of complex in Keynodes visualization
 +
**Selected info template is remembered for elements of the same type
 +
**Import improved
 +
*Analysis
 +
**More user-friendly Identifiability analysis interface (absolute value of deviation instead of chi-square quantile, select parameters for analysis in optimization version)
 +
*Formats
 +
**Partial support of VCF4.3 on import/export, FILTER property for .VCF track files supported
 +
*External libraries
 +
**jfreechart update 1.0.18 -> 1.5.0
 +
**jcommon updated 1.0.22 -> 1.0.24
 +
**underscore.js update 1.2.2 -> 1.9.1
 +
*Many bugs were fixed
 +
|}
  
−
update for Eclipse 3.0, JavaHelp support (only few help topics were written).
+
==2018==
−
 
+
{|class="wikitable"
−
State and transition concept support.
+
!width="15%"|Date!!width="5%"|Release!!width="75%"|Description
 +
|- style="background-color: Lavender"
 +
|Oct, 2018
 +
|style="background-color:Gainsboro"| v. 2018.3
 +
|
 +
*General
 +
**Diagram can be created in any generic folder
 +
*SBGN and visualization
 +
**Shrink node titles (if option enabled)
 +
**Dynamically highlight nodes (equations, reactions, species, etc.), containing selected variables and parameters
 +
*Web
 +
**Import of several files from local computer and generic files from repository
 +
**Wait dialog appears when several elements are deleted
 +
*Simulation
 +
**Plotting of simulation result reworked. Now variables to plot are specified in separate tab. User may create multiple plots and define different variables for axes. Example models with plots are included in the build.
 +
**Show in plot and line spec are removed from "Variables" and "Parameters" tabs.
 +
*SBML
 +
**Unit definitions from the model may be set to parameters (previously only for species)
 +
*Cytoscape
 +
**Import and export diagrams in Cytoscape JSON format (.cx)
 +
*External libraries
 +
**org.jsoup updated (1.7.1 -> 1.11.3)
 +
*Bug fixing
 
|-
 
|-
−
|January 14, 2005
+
|Jun, 2018
−
|style="background-color:Gainsboro"| v. 0.7.5
+
|style="background-color:Gainsboro"| v. 2018.2
−
|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.)
+
*SBGN
 +
**Visualization erros fixed
 +
**Automatic creation of complexes from string (e.g. “A:B”)
 +
**PantherDB and CellDesigner models support improved (as SBGN diagrams)
 +
*SBML
 +
**L3v2 supported, including:
 +
***rateOf, rem, quotinent functions, min and max with arbitrary number of arguments
 +
***boolean values now may be mixed with numeric (e.g. x = false + 10)
 +
***find more details [http://sbml.org/Documents/Specifications here]
 +
***All tests from current test suite passed successfully (see details [http://sbml.org/Facilities/Database/Submission/Details/108 here])
 +
**Constraints supported (3 options: ignore them, stop simulation or just log message)
 +
*Diagrams
 +
**Copy\paste of diagram elements
 +
*Antimony
 +
**gene <-> species conversion fixed
 +
*Simulation
 +
**Fast reactions handling enhanced: user can select whether to handle them as algebraic systems or as ODE systems with very high rate
 +
**Automatic detection of species variable type implemented (Not used, Calculated, Differential, Algebraic, Discrete, Parameter)
 +
**Parameters identifiability analysis: added option to select type of image (png or chart)
 +
*Workflows:
 +
**Option to ignore failed steps and continue if possible
 +
**Option to skip steps if they were completed on previous runs
 +
**Visualization erros fixed
 +
*Data analysis and tables
 +
**TreeMap on Functional classification on Gene Ontology
 +
**Tabular data visualization using pie chart or bar chart.
 +
**Super Annotate Table (annotates one table by another)
 +
**Export tables with images to zhtml file
 +
*Unused libraries excluded from build
 +
*Bugs fixed
 +
|}
  
−
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)
+
==2017==
−
SBW 2.0.0
+
{|class="wikitable"
 +
!width="15%"|Date!!width="5%"|Release!!width="75%"|Description
 
|- style="background-color: Lavender"
 
|- style="background-color: Lavender"
−
|May 10, 2005
+
|Septeber, 2017
−
|style="background-color:Gainsboro"| v. 0.7.6
+
|style="background-color:Gainsboro"| v. 2017.2
−
|User interface improvements: preferences, possibility to load and change look & feel, user interface for editing rules and events.  
+
|
−
Performance improvements.
+
*Mathematical modeling
−
ODE solver for stiff problems.
+
**Identifiability Analysis improved
 +
*Visualization
 +
**Fixed reading and processing 3D mol structures (MDL Molfile)
 +
*Modular modeling
 +
**Split model action: automatic separation of selected model elements into submodel
 +
**User may change type of the port (input, output or contact) after it is added to the model
 +
**User may refresh content of submodels in composite model without its reloading
 +
*Bug fixing
 +
|}
 +
 
 +
==2016==
 +
{|class="wikitable"
 +
!width="15%"|Date!!width="5%"|Release!!width="75%"|Description
 +
|- style="background-color: Lavender"
 +
|December, 2016
 +
|style="background-color:Gainsboro"| v. 2016.4
 +
|
 +
*Analysis
 +
**Parameters identifiability analysis (Raue et al., 2009)
 +
**Generating models population using Metropolis algorithm
 +
**Key node sensitivity analysis
 +
**New result types for Steady State: table, simulation result
 +
*Simulation
 +
**Automatic generation of kinetik laws from SBO
 +
**Option to set different output type for variables (quantity or concentration)
 +
**Options for algebraic solvers
 +
*SBML
 +
**Level 2 version 5 supported
 +
**All tests from SBML test suite v. 3.2.0 passed
 +
*BioUML IDE
 +
**NetBeans version updated to 8.2
 +
*BioUML web edition
 +
**fixed bug with openning SBGN Composite diagrams
 +
**fixed bug with missed icons for SBGN Composite diagrams
 +
**fixed bug with incorrect reverting of the diagram element position (after unacceptable moving)
 
|-
 
|-
−
|October 24, 2007
+
|July, 2016
−
|style="background-color:Gainsboro"| v. 0.7.7
+
|style="background-color:Gainsboro"| v. 2016.2
−
|Full text search engine (uses Lucene), graph search, graph layout improvements
+
|
 +
*Modeling
 +
**Custom styles for diagram elements rendering for all types of models (see SBGN examples)
 +
**Automatic detection of model parameter types (Unused, ODE, Algebraic, Descrete, Parameter)
 +
**Converter: SBML-SBGN diagram -> SBML-SBGN composite diagram
 +
*Databases
 +
**CHEBI support enhanced
 +
*Analysis
 +
**Flux balance analysis enhanced
 +
|}
  
−
BioPAX format - import/export, OBO format - import/export
+
==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.
  
−
Ensembl support (spike solution)
+
|-
 +
|February, 2015
 +
|style="background-color:Gainsboro"| v. 0.9.9
 +
|
 +
*BioUML IDE
 +
**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
 +
|-
 +
|}
  
−
Clipboard pane
+
==2014==
 +
{|class="wikitable"
 +
!width="15%"|Date!!width="5%"|Release!!width="75%"|Description
 +
|- style="background-color: Lavender"
 +
|September, 2014
 +
|style="background-color:Gainsboro"| v. 0.9.8
 +
|
 +
*Visual modelling and simulation
 +
**population based modelling (beta version, see article [http://virtual-biology.org/vb/article/view/15 BioUML: plugin for population-based modeling])
 +
**refactoring of code generation for model simulation
 +
**graph layout improvements (orthogonal path finder, hierarchical path finder)
 +
**creating edges via drag & drop
 +
**new analysis for diagram comparison
 +
*Server
 +
**integration with Galaxy ToolShed
  
−
CDK library is used to visualize chemical structures on diagrams
+
|-
−
arbitrary images (GIF, PNG, etc.) for graph nodes
+
|April, 2014
−
 
+
|style="background-color:Gainsboro"| v. 0.9.7
−
Client-server architecture, BioUML can be started as standalone server or as a servlet
+
|
−
 
+
*Visual modelling and simulation
−
BioUML network edition
+
**population based modelling (nlme plug-in)
−
 
+
***special graphic notation
−
New installer based on IzPack
+
***automated Java and R code generation
−
 
+
***integration with R nlme package for solving non-linear mixed effect models
−
Initial draft of user manual
+
**optimized Java code generator for huge models (10 000+ species and 10 000+ reactions)
 +
**Gurobi solver for fbc analyses (need to separately install [http://www.gurobi.com  Gurobi Optimizer])
 +
**started simulations are shown in "Tasks" tab
 +
**visualisation of dependency edges - these edges link equations and used there variables
 +
**visualisation of glycan structures on the base their structure
 +
**possibility to hide elements on a diagram ("visible" node property)
 +
**analyses "ShareComplexMolecules" makes clones for substances involved into many reactions
 +
**new actions on toolbar to align selected nodes (top, bottom, etc.
 +
**BioNetGen plugin improvements:
 +
*** Importer/Exporter for .bngl files
 +
*** Support for Molecule Types
 +
*** Built-in functions
 +
*** Highlight selected diagram element in corresponding BioNetGen code
 +
*Server
 +
**BioUML node for cluster/cloud architecture
 +
**cloud version support for Amazon EC2 (alpha)
 +
**improved task manager
 
|}
 
|}
  
−
 
+
==2012 - 2013==
−
==2008==
+
{|class="wikitable"
−
 
+
−
{| class="wikitable"
+
 
!width="15%"|Date!!width="5%"|Release!!width="75%"|Description
 
!width="15%"|Date!!width="5%"|Release!!width="75%"|Description
 
|- style="background-color: Lavender"
 
|- style="background-color: Lavender"
−
|January 28, 2008 (alpha)
+
|2013, November 18
−
+
|style="background-color:Gainsboro"|v. 0.9.6
−
March 20, 2008 (beta)
+
|
−
|style="background-color:Gainsboro"| v. 0.7.8
+
*BioUML workbench (desktop version)
−
|Graphic notation editor, SBGN (alpha version)
+
**integration of Galaxy
 +
**rule based modelling (implementation of BioNetGen approach, [[BioNetGen|details]])
 +
**Antimony support ([[Antimony|details]])
 +
**Synchronisation between textual and graphical model representation (BioNetGen, Antimony)
  
−
Library of predefined kinetic law functions (SBO)
+
*Interface improvements
 +
**display name and actions for table cell values
  
−
BioModels - comparison with other simulators (Copasi, CVODE, RoadRunner, Jarnac, JSim, Oscill8 Core, SBWOdeSolver, MathSBML)
+
*R integration
 +
**improved interface and bug fixes
 +
**possibility to call BioUML from R using rbiouml package (http://cran.r-project.org/web/packages/rbiouml)
  
−
Database references editor
+
*JavaScript support (web version)
 +
** new JavaScript editor, CodeMirror (http://codemirror.net/).
  
−
Equations editor
+
*GTRD database
 +
**perspective
 +
**special start page
 +
**improved web interface
  
−
Microarray plug-in (alpha version)
+
*New methods for analysis of transcription factor binding sites
 
|-
 
|-
−
|July 2, 2008
+
|2013, June 15
−
|style="background-color:White"| v. 0.8.0
+
|style="background-color:Gainsboro"|v. 0.9.5
−
|Composite database module
+
|
 +
* Simulation engine
 +
**SBML level 3 packages:
 +
***Hierarchical Model Composition
 +
***Flux Balance Constraints
 +
|- style="background-color: Lavender"
 +
|2013, March 20
  
−
Database module editor
+
(Workbench)
 +
|style="background-color:Gainsboro"| v. 0.9.4
 +
|'''BioUML web:'''
  
−
SBML extensions for BioModels database (experiment, simulation, parameters, result, plot)
+
Collaborative work on diagram (like Google documents)
  
−
XML diagram type
+
UI improvements:
 +
* automatic suggestions in search pane
 +
* automatic opening of uploaded files
 +
* select several elements to remove in repository tree
  
−
Experiments
+
'''BioUML core (both workbench and web version):'''
  
−
Loading of modules from BioUML server:
+
History of diagram editing (like CVS or SVN)
  
−
EBI data pack (Ensembl, UniProt, ChEBI, IntAct, BioModels) - free databases from EBI as BioUML modules
+
Simulation engine
−
|- style="background-color: Lavender"
+
* stochastic modeling, following solvers were implemented:
−
|July 22, 2008
+
** Gillespie (Gillespie, D.T. 1977)
−
|style="background-color:White"| v. 0.8.1
+
** Gibson-Bruck (Gibson, J. Bruck 2000)
−
|Workbench update from the site
+
** Max Time step (Puchalka, J., Kierzek, A.M. 2004)
 +
** Tau-leaping (Yang, C. et al. 2006)
 +
* Discrete Stochastic Models Test Suite (DSMTS) was passed succesfully
 +
* agent based modelling - new agent with ability to produce descendants. Is used to simulate cell population behaviour.
  
−
Third party libraries update: JFreeChart,  Lucene, Rhino,  JHelp
+
SBML support:
 +
* bug fixing
 +
* flux balance constraint models support (using org.apache.common.math3)
 +
* all non composite tests from test-suite 2.3.2 (2013-02-04) passed.
  
−
UI improvements: graphics (for simulation results) - now node titles instead of node IDs are used
+
Visual modelling
 +
* composite diagrams improvements
 +
* MathDiagramType - new diagram type for describing physial procsses. Automatically generates dependencies between equations.
  
−
Several HTML tags can be used in titles for graph nodes: <nowiki><br>, <sub>, <sup>, <b>, <i>, <font color, size></nowiki>
+
Model analysis
−
|-
+
* model reduction
−
|August 9, 2008
+
* [[Metabolic Control Analysis|MCA]] (Metabolic Control Analysis, alpha version)
−
|style="background-color:White"| v. 0.8.2
+
−
|Graphic notation skins: KEGG notation for metabolic pathway diagrams, Regensburg notation for metabolic pathway diagrams
+
  
−
Simple line path editor
+
Analyses:
 +
* [[Convert table (analysis)|convert table]]: ability to use column for ID
 +
* [[Filter table (analysis)|filter table]]: ability to select top N or bottom N entries
  
−
Microarray data and analysis results as documents (they are opened in tabs similar with diagrams)
+
User interface improvements
 +
* [[perspective]]s - allows to group and filter UI components for specific user's tasks
 +
* tree table component
 +
* drag & drop for annotations
  
−
Microarray analysis - identification up/down regulated genes using t-statistics and hyperheometric distribution
+
[[Genome browser]] improvements
−
|- style="background-color: Lavender"
+
* better navigation (chromosome switch, position input box, drag-and-scroll, zoom selection, mouse wheel support, etc.)
−
|August 28, 2008
+
* improved sites information tab
−
|style="background-color:White"| v. 0.8.3
+
* BAM tracks support
−
|Authorization subsystem (login)
+
* gene structure can be shown in a table cell (only web)
 +
* improved and new styles for genes structure visualization
  
−
hierarchical models, block component (proof of concept)
+
Improved support of DAS protocol
 +
* support for 1.53 and 1.6
 +
* support for non positional features
 +
* interactions
 +
* ontologies
  
−
JavaScript functions for:
+
Integration with JMOL for visualization of 3D structures
−
* data access,
+
−
* operations on data sets (union, overlap, etc.),
+
−
* microarray statistical analyses
+
−
|-
+
−
|December 12, 2008
+
−
|style="background-color:White"| v. 0.8.4
+
−
|New database modules on BioUML server (pilot version):
+
  
−
* SABIO-RK ([http://sabio.villa-bosch.de/ System for the Analysis of Biochemical Pathways Reaction Kinetics])
+
'''BioUML server'''
−
* EHMN ([http://wwwtest.bioinformatics.ed.ac.uk/wiki/PublicCSB/EHMN Edinburgh Human Metabolic Network])
+
−
* LipidMAPS ([http://www.lipidmaps.org/data/structure/ LIPID Metabolites And Pathways Strategy])
+
−
* KEGG LIGAND
+
−
* KEGG Pathways
+
−
* TRANSPATH
+
  
−
General refactoring - now tabs in repository are called:
+
{{Galaxy}} support
−
* Databases (instead of Modules)
+
−
* Data
+
−
* Analyses
+
  
−
New architecture for methods of analyses:
+
new section "Galaxy" in analysis tab allows to use all methods from [[Using Galaxy in BioUML|Galaxy platform]]
−
* extension point, registry for methods of analyses
+
|-
−
* methods are shown in analyses tab
+
|2012
−
* new version of dialog for microarray analyses
+
  
−
Parameters fitting (initial version)
+
(Web edition)
−
 
+
|style="background-color:Gainsboro"| v. 0.9.4
−
Refinements, bug fixing:
+
|Integration with [[BioStore]] (www.bio-store.org) for control of access rights and downloading
−
* authorization subsystem
+
−
* repository tree
+
−
 
+
−
Setup wizard - wizard to configure BioUML on first start.
+
 
|}
 
|}
−
 
−
 
−
==2009==
 
  
 +
==2011==
 
{|class="wikitable"
 
{|class="wikitable"
 
!width="15%"|Date!!width="5%"|Release!!width="75%"|Description
 
!width="15%"|Date!!width="5%"|Release!!width="75%"|Description
 
|- style="background-color: Lavender"
 
|- style="background-color: Lavender"
−
|January 28, 2009 (alpha)
+
|October 31, 2011
  
−
February 17, 2009 (beta)
+
(Workbench; beta)
−
|style="background-color:White"| v. 0.8.5
+
|style="background-color:Gainsboro"| v. 0.9.3
−
|SBGN 1.0 implementation - alpha version
+
|'''BioUML core:'''
  
−
KEGG improvements:
+
Core update
−
* graph layout improvements, orthogonal path finder
+
* Eclipse runtime is updated to Equinox version 3.6.0
−
* labels location
+
* Java 7
−
* graph search engine improvements
+
* fixed problems for Windows 7
  
−
UI improvements:
+
[http://www.sed-ml.org/ SED-ML] (Simulation Experiment Description Markup Language) support (alpha version)
−
* grid
+
* import and handling of SED-ML files
−
* snap to grid
+
* run and edited as workflows
−
* arrows and lines selection
+
* used to generate simulation plots
−
* keyboard navigation for diagram editing
+
−
* repository tree shows database status using icons (public, free, log-in, preloaded, etc.)
+
−
* possibility to edit diagrams on display without saving for read only databases
+
  
−
Parameters fitting (alpha version)
+
Improved BioPAX support
 +
* BioPAX import/export, level 2, 3 (alpha version)
 +
* display BioPAX pathways in SBGN notation
 +
* graph search, full text search
  
−
Bug fixing:
+
Graph search enhancements
−
* MATLAB simulation engine - pass SBML semantic test suite again
+
* flexible merging of previous search results
 +
* improved graph layout: hierarchical layout, orthogonal layout
  
−
JavaHelp refactoring: new tool for help writing - Help&Manual 5
+
Diagram state refactoring
−
* introduction
+
* using transactions for compound edits
−
* installation and configuration
+
* possibility to remove transaction from changes
−
* databases
+
−
|-
+
−
|July 31, 2009 (alpha)
+
  
−
August 7, 2009 (beta)
+
Data import/export improvements:
−
|style="background-color:White"| v. 0.8.6
+
* [[Upload from FTP (analysis)|FTP upload]] - possibility to upload huge data from user’s ftp site
−
|JavaScript:
+
* [[Text file|text]] and [[HTML file|html]] files can be imported
 +
* several [[Image file|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: {{Type link|text}}, {{Type link|image}}s, {{Type link|html}}
  
−
* editor - JavaScript files can be opened and edited in BioUML workbench
+
Data handling improvements:
−
* debugger
+
* multiple tables can be [[Join several tables (analysis)|joined]];
−
* new functions:  plot, view
+
* columns with identical names may be merged automatically.
  
−
Integration with R - special R object in JavaScript allows to evaluate R expressions as well as to show R graphic output
+
[[Workflows]] improvements:
 +
* possibility to include JavaScripts into workflows
 +
* more comfortable handling of folders and result files
 +
* handling of circular processes
  
−
Genome viewer (alpha version):
+
Algorithms for NGS and sequence analysis:
−
* Ensembl tracks initial support (genes, repeats)
+
* [http://bowtie-bio.sourceforge.net/index.shtml Bowtie] wrapper
−
* map document - displays sequences and sites grouped by tracks
+
* peak detection [http://liulab.dfci.harvard.edu/MACS/ MACS] (update)
−
* project pane - the project HTML description
+
* motif discovery wrapper for [http://line.imb.ac.ru/smbsm/librettos/libretto_chipmunk/chipmunk_home.rhtml ChIPMunk]
−
* regions pane - allows to specify sequence regions to be visualized as well as sequence visualization options
+
* motif discovery IPS-align
−
* tracks pane - allows to specify tracks to be visualized as well as site visualization options
+
* motif logo (on the base of PWM)
−
* sites pane - shows the list of site displayed on the map document
+
* errors estimation: false positive, FDR, ROC curves
  
−
Sequence analysis (alpha version):
+
Embedded chat for collaborative work and on-line consultations (pilot version)
−
* special section in repository: Data/Sequence analyses
+
−
* sequences import
+
''(you need to register before at https://biostore.biouml.org)''
  
−
SBML level 2 version 2-4 support
+
'''BioUML server'''
−
 
+
* new system for authorization and access rights: [[BioStore]] (https://bio-store.org)
−
Parameters fitting (beta version)
+
* ChIP-SEQ pipeline (available only on test server yes)
−
 
+
|-
−
JavaHelp:
+
|May 12, 2011
−
* new chapter: JavaScript (pane, editor, shell, functions)
+
|colspan="2"| '''''the first [http://www.biodatomics.com/home BioDatomics] release (built around the [[BioUML]] platform)'''''
−
* new chapter: R
+
−
* new chapter: parameters fitting
+
 
|- style="background-color: Lavender"
 
|- style="background-color: Lavender"
−
|November 30, 2009
+
|May 7, 2011
  
 
(Web edition)
 
(Web edition)
−
|style="background-color:Gainsboro"|v. 0.9.0
 
−
|'''BioUML web edition:'''
 
  
−
first public version
+
June 14, 2011
  
−
'''BioUML core:'''
+
(Workbench; beta)
 +
|style="background-color:Gainsboro"| v. 0.9.2
 +
|'''BioUML core (common for workbench and web edition):'''
  
−
SBGN:
+
Import for Process Diagrams in CellDesigner 4.0/4.1 format
−
* SBGN - graphic notation update
+
−
* <sbgn> extension for SBML
+
−
* support for BioModels 
+
−
* support for TRANSPATH
+
  
−
Databases:
+
Data analysis
−
* BioModels are installed on BioUML server (public)
+
* a lot of new methods for analyses of microarray data,  import data in different formats and other
−
* EndoNet database support (pilot version, protected)
+
* JavaScript API to work with models and simulation engine (JavaScript host objects model and simulationEngine)
  
−
Graph layout improvements:
+
[[Workflows]] support (beta version)
−
* PathwayLayouter is used as decorator for other graphs to take into account compartments and peculiarities of diagrams
+
* improved graphic editor
 +
* cycles
 +
* patterns for input/output parameters
 +
* automatic orthogonal layout for edges
  
−
(for example all math elements are located on the top of diagram)  
+
Simulation engine
−
* layout preview
+
* composite models (beta version)
−
* possibility to reuse layout for similar diagrams
+
** graphic notation improvements
 +
** special preprocessor to generate flat model
 +
* agent based models - improved, new elements
  
−
New graph layout algorithms:
+
User interface improvements:
−
* cross grid layout - Kato,M. et al. (2005) Automatic drawing of biological networks using cross cost.
+
* a lot of new icons
−
* fast grid layout - Kaname, K., Masao, N. and Satoru, M. (2008) Fast grid layout algorithm for biological networks with sweep calculation.
+
* drag & drop support
 +
* improved filter for tables (user can filter rows using some expression) 
 +
* improved graph layout
 +
** hierarchical layout
 +
** orthogonal layout
 +
* mathematical expressions
 +
** special editor for all mathematical expressions
 +
** user can use node title (instead of its name/identifier) in math expressions
 +
** different modes to show variable names (using id or title)
  
−
UI improvements:
+
Coloring diagram using omics data (redesigned)
−
* quick search field in repository pane
+
−
* quick search for diagrams that contain specified component
+
−
* templates for HTML generation for list of species, reactions, variables, parameters and equations
+
−
* database loading dialog - possibility to specify login/password to see the list of protected databases.
+
−
 
+
−
Simulation engine:
+
−
* JVODE solvers (ported to Java version of CVODE)
+
−
* bug fixing (correct reading of piecewise from SBML)
+
  
 
'''BioUML server:'''
 
'''BioUML server:'''
−
* network repository for group working
+
* PantherDB pathways in CellDesigner 4.1 format (ftp://ftp.pantherdb.org/pathway/current_release/CD4.1.zip)
 +
* Reactome database
 +
** direct access using SQL
 +
** display diagrams in SBGN graphic notation
 +
* security improvements
 +
|-
 +
|May 6, 2011
 +
|colspan="2"| '''''Version 1.0 of the [[geneXplain]] platform (based on [[BioUML]])'''''
 
|}
 
|}
−
 
  
 
==2010==
 
==2010==
−
 
 
{|class="wikitable"
 
{|class="wikitable"
 
!width="15%"|Date!!width="5%"|Release!!width="75%"|Description
 
!width="15%"|Date!!width="5%"|Release!!width="75%"|Description
 
|- style="background-color: Lavender"
 
|- style="background-color: Lavender"
 +
|October 13, 2010
 +
|style="background-color:Gainsboro"| v. 0.9.1
 +
|'''BioUML core (common for workbench and web edition):'''
 +
 +
Simulation engine:
 +
* composite models (beta version, apoptosis model as an example)
 +
* agent based modeling (beta version, cardiovascular system as an example)
 +
 +
Chemoinformatics support (on the base of CDK and JChemPaint):
 +
* import 2D structures (SDF, MOL and other format)
 +
* special document type  for 2D structures
 +
* 2D structures rendering and editing
 +
* JavaScript API for CDK
 +
* PASS (Prediction of Activity Spectra for Substances) integration
 +
 +
Tasks manager:
 +
* tasks list as a special viewpart
 +
* tasks management (interrupt, see status and results)
 +
 +
'''BioUML web edition:'''
 +
* diagrams export (sbml, sbgn)
 +
* diagrams import into custom folders (sbml)
 +
|-
 
|July 2, 2010
 
|July 2, 2010
  
Line 333: Line 672:
 
* microarray analyses
 
* microarray analyses
 
** data normalisation
 
** data normalisation
−
** identification up/down regulated genes using different statistical criteria
+
** identification of [[Up and Down Identification (analysis)|up/down regulated genes]] using different statistical criteria
−
** gene set enrichment analyses (using GO and MSigDB databases)
+
** [[Enrichment analysis|gene set enrichment analysis]] (using GO and MSigDB databases)
 
** building gene regulation models on the base of microarray time series
 
** building gene regulation models on the base of microarray time series
−
** cluster analysis
+
** [[Cluster analysis by K-means (analysis)|cluster analysis]]
−
* search for transcription factors binding sites
+
* [[Site search on track (analysis)|search for transcription factors binding sites]]
−
* ChiP-seq analyses (MACS algorithm)
+
* ChiP-seq analyses ([[Run MACS 1.3.7 on ChiP-Seq (analysis)|MACS algorithm]])
−
* Venn diagrams
+
* [[Venn diagrams (analysis)|Venn diagrams]]
  
 
Reproducible research
 
Reproducible research
 
* research journal (collects all user actions related with data analyses)
 
* research journal (collects all user actions related with data analyses)
 
* research diagram (graphical representation of research journal)
 
* research diagram (graphical representation of research journal)
−
* workflow support
+
* [[workflows]] support
  
 
User interface
 
User interface
Line 355: Line 694:
 
'''BioUML web edition:'''
 
'''BioUML web edition:'''
 
* data analyses
 
* data analyses
−
* genome browser
+
* [[genome browser]]
 
* diagrams export (png, gif, jpeg, svg, sbml, sbgn, dml)
 
* diagrams export (png, gif, jpeg, svg, sbml, sbgn, dml)
−
* diagrams import (sbml)
+
* diagrams import ([[SBML (file format)|sbml]])
−
* tables import (csv) and export (csv)
+
* tables import ([[Tabular (file format)|csv]]) and export (csv)
  
 
'''BioUML server:'''
 
'''BioUML server:'''
Line 366: Line 705:
 
* new chapters: Genome browser, Optimisation
 
* new chapters: Genome browser, Optimisation
 
* updated chapters: Simulation
 
* updated chapters: Simulation
−
|-
 
−
|October 13, 2010
 
−
|style="background-color:Gainsboro"| v. 0.9.1
 
−
|'''BioUML core (common for workbench and web edition):'''
 
−
 
−
Simulation engine:
 
−
* composite models (beta version, apoptosis model as an example)
 
−
* agent based modeling (beta version, cardiovascular system as an example)
 
−
 
−
Chemoinformatics support (on the base of CDK and JChemPaint):
 
−
* import 2D structures (SDF, MOL and other format)
 
−
* special document type  for 2D structures
 
−
* 2D structures rendering and editing
 
−
* JavaScript API for CDK
 
−
* PASS (Prediction of Activity Spectra for Substances) integration
 
−
 
−
Tasks manager:
 
−
* tasks list as a special tab
 
−
* tasks management (interrupt, see status and results)
 
−
 
−
'''BioUML web edition:'''
 
−
* diagrams export (sbml, sbgn)
 
−
* diagrams import into custom folders (sbml)
 
 
|}
 
|}
  
−
 
+
==2009==
−
==2011==
+
−
 
+
 
{|class="wikitable"
 
{|class="wikitable"
 
!width="15%"|Date!!width="5%"|Release!!width="75%"|Description
 
!width="15%"|Date!!width="5%"|Release!!width="75%"|Description
 
|- style="background-color: Lavender"
 
|- style="background-color: Lavender"
−
|May 6, 2011
+
|November 30, 2009
−
|colspan="2"| '''''Version 1.0 of the [[geneXplain]] platform (based on [[BioUML]])'''''
+
−
|-
+
−
|May 7, 2011
+
  
 
(Web edition)
 
(Web edition)
 +
|style="background-color:Gainsboro"|v. 0.9.0
 +
|'''BioUML web edition:'''
  
−
June 14, 2011
+
first public version
  
−
(Workbench; beta)
+
'''BioUML core:'''
−
|style="background-color:Gainsboro"| v. 0.9.2
+
−
|'''BioUML core (common for workbench and web edition):'''
+
  
−
Import for Process Diagrams in CellDesigner 4.0/4.1 format
+
SBGN:
 +
* SBGN - graphic notation update
 +
* <sbgn> extension for SBML
 +
* support for BioModels 
 +
* support for TRANSPATH
  
−
Data analysis
+
Databases:
−
* a lot of new methods for analyses of microarray data,  import data in different formats and other
+
* BioModels are installed on BioUML server (public)
−
* JavaScript API to work with models and simulation engine (JavaScript host objects model and simulationEngine)
+
* EndoNet database support (pilot version, protected)
  
−
Workflow support (beta version)
+
Graph layout improvements:
−
* improved graphic editor
+
* PathwayLayouter is used as decorator for other graphs to take into account compartments and peculiarities of diagrams
−
* cycles
+
−
* patterns for input/output parameters
+
−
* automatic orthogonal layout for edges
+
  
−
Simulation engine
+
(for example all math elements are located on the top of diagram)  
−
* composite models (beta version)
+
* layout preview
−
** graphic notation improvements
+
* possibility to reuse layout for similar diagrams
−
** special preprocessor to generate flat model
+
−
* agent based models - improved, new elements
+
  
−
User interface improvements:
+
New graph layout algorithms:
−
* a lot of new icons
+
* cross grid layout - Kato,M. et al. (2005) Automatic drawing of biological networks using cross cost.
−
* drag & drop support
+
* fast grid layout - Kaname, K., Masao, N. and Satoru, M. (2008) Fast grid layout algorithm for biological networks with sweep calculation.
−
* improved filter for tables (user can filter rows using some expression) 
+
−
* improved graph layout
+
−
** hierarchical layout
+
−
** orthogonal layout
+
−
* mathematical expressions
+
−
** special editor for all mathematical expressions
+
−
** user can use node title (instead of its name/identifier) in math expressions
+
−
** different modes to show variable names (using id or title)
+
  
−
Coloring diagram using omics data (redesigned)
+
UI improvements:
 +
* quick search field in repository pane
 +
* quick search for diagrams that contain specified component
 +
* templates for HTML generation for list of species, reactions, variables, parameters and equations
 +
* database loading dialog - possibility to specify login/password to see the list of protected databases.
 +
 
 +
Simulation engine:
 +
* JVODE solvers (ported to Java version of CVODE)
 +
* bug fixing (correct reading of piecewise from SBML)
  
 
'''BioUML server:'''
 
'''BioUML server:'''
−
* PantherDB pathways in CellDesigner 4.1 format (ftp://ftp.pantherdb.org/pathway/current_release/CD4.1.zip)
+
* network repository for group working
−
* Reactome database
+
−
** direct access using SQL
+
−
** display diagrams in SBGN graphic notation
+
−
* security improvements
+
−
|- style="background-color: Lavender"
+
−
|May 12, 2011
+
−
|colspan="2"| '''''the first [http://www.biodatomics.com/home BioDatomics] release (built around the [[BioUML]] platform)'''''
+
 
|-
 
|-
−
|October 31, 2011
+
|July 31, 2009 (alpha)
  
−
(Workbench; beta)
+
August 7, 2009 (beta)
−
|style="background-color:Gainsboro"| v. 0.9.3
+
|style="background-color:Gainsboro"| v. 0.8.6
−
|'''BioUML core:'''
+
|JavaScript:
  
−
Core update
+
* editor - JavaScript files can be opened and edited in BioUML workbench
−
* Eclipse runtime is updated to Equinox version 3.6.0
+
* debugger
−
* Java 7
+
* new functions:  plot, view
−
* fixed problems for Windows 7
+
  
−
[http://www.sed-ml.org/ SED-ML] (Simulation Experiment Description Markup Language) support (alpha version)
+
Integration with {{R}} - special R object in JavaScript allows to evaluate R expressions as well as to show R graphic output
−
* import and handling of SED-ML files
+
−
* run and edited as workflows
+
−
* used to generate simulation plots
+
  
−
Improved BioPAX support
+
Genome viewer (alpha version):
−
* BioPAX import/export, level 2, 3 (alpha version)
+
* Ensembl tracks initial support (genes, repeats)
−
* display BioPAX pathways in SBGN notation
+
* map document - displays sequences and sites grouped by tracks
−
* graph search, full text search
+
* project pane - the project HTML description
 +
* regions pane - allows to specify sequence regions to be visualized as well as sequence visualization options
 +
* tracks pane -  allows to specify tracks to be visualized as well as site visualization options
 +
* sites pane - shows the list of site displayed on the map document
  
−
Graph search enhancements
+
Sequence analysis (alpha version):
−
* flexible merging of previous search results
+
* special section in repository: Data/Sequence analyses
−
* improved graph layout: hierarchical layout, orthogonal layout
+
* sequences import
  
−
Diagram state refactoring
+
SBML level 2 version 2-4 support
−
* using transactions for compound edits
+
−
* possibility to remove transaction from changes
+
  
−
Data import/export improvements:
+
Parameters fitting (beta version)
−
* 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:
+
JavaHelp:  
−
* multiple tables can be joined;
+
* new chapter: JavaScript (pane, editor, shell, functions)
−
* columns with identical names may be merged automatically.
+
* new chapter: R
 +
* new chapter: parameters fitting
 +
|- style="background-color: Lavender"
 +
|January 28, 2009 (alpha)
  
−
Workflow improvements:
+
February 17, 2009 (beta)
−
* possibility to include JavaScripts into workflows
+
|style="background-color:Gainsboro"| v. 0.8.5
−
* more comfortable handling of folders and result files
+
|SBGN 1.0 implementation - alpha version
−
* handling of circular processes
+
  
−
Algorithms for NGS and sequence analysis:
+
KEGG improvements:
−
* [http://bowtie-bio.sourceforge.net/index.shtml Bowtie] wrapper
+
* graph layout improvements, orthogonal path finder
−
* peak detection [http://liulab.dfci.harvard.edu/MACS/ MACS] (update)
+
* labels location
−
* motif discovery wrapper for [http://line.imb.ac.ru/smbsm/librettos/libretto_chipmunk/chipmunk_home.rhtml ChIPMunk]
+
* graph search engine improvements
−
* 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)
+
UI improvements:
−
+
* grid
−
''(you need to register before at https://biostore.biouml.org)''
+
* snap to grid
 +
* arrows and lines selection
 +
* keyboard navigation for diagram editing
 +
* repository tree shows database status using icons (public, free, log-in, preloaded, etc.)
 +
* possibility to edit diagrams on display without saving for read only databases
  
−
'''BioUML server'''
+
Parameters fitting (alpha version)
−
* new system for authorization and access rights: [[BioStore]] (https://bio-store.org)
+
−
* ChIP-SEQ pipeline (available only on test server yes)
+
  
 +
Bug fixing:
 +
* MATLAB simulation engine - pass SBML semantic test suite again
 +
 +
JavaHelp refactoring: new tool for help writing - Help&Manual 5
 +
* introduction
 +
* installation and configuration
 +
* databases
 
|}
 
|}
  
−
==2012 - 2013==
+
==2008==
−
 
+
{| class="wikitable"
−
{|class="wikitable"
+
 
!width="15%"|Date!!width="5%"|Release!!width="75%"|Description
 
!width="15%"|Date!!width="5%"|Release!!width="75%"|Description
 
|- style="background-color: Lavender"
 
|- style="background-color: Lavender"
−
|2012
+
|December 12, 2008
 +
|style="background-color:Gainsboro"| v. 0.8.4
 +
|New database modules on BioUML server (pilot version):
  
−
(Web edition)
+
* SABIO-RK ([http://sabio.villa-bosch.de/ System for the Analysis of Biochemical Pathways Reaction Kinetics])  
−
|style="background-color:Gainsboro"| v. 0.9.4
+
* EHMN ([http://wwwtest.bioinformatics.ed.ac.uk/wiki/PublicCSB/EHMN Edinburgh Human Metabolic Network])
−
|Integration with [[BioStore]] (www.bio-store.org) for control of access rights and downloading
+
* LipidMAPS ([http://www.lipidmaps.org/data/structure/ LIPID Metabolites And Pathways Strategy])
 +
* KEGG LIGAND
 +
* KEGG Pathways
 +
* TRANSPATH
 +
 
 +
General refactoring - now tabs in repository are called:
 +
* Databases (instead of Modules)
 +
* Data
 +
* Analyses
 +
 
 +
New architecture for methods of analyses:
 +
* extension point, registry for methods of analyses
 +
* methods are shown in analyses tab
 +
* new version of dialog for microarray analyses
 +
 
 +
Parameters fitting (initial version)
 +
 
 +
Refinements, bug fixing:
 +
* authorization subsystem
 +
* repository tree
 +
 
 +
Setup wizard - wizard to configure BioUML on first start.
 
|-
 
|-
−
|March 20, 2013
+
|August 28, 2008
 +
|style="background-color:Gainsboro"| v. 0.8.3
 +
|Authorization subsystem (login)
  
−
(Workbench)
+
hierarchical models, block component (proof of concept)
−
|style="background-color:Gainsboro"| v. 0.9.4
+
−
|'''BioUML web:'''
+
  
−
Collaborative work on diagram (like Google documents)
+
JavaScript functions for:
 +
* data access,
 +
* operations on data sets (union, overlap, etc.),
 +
* microarray statistical analyses
 +
|- style="background-color: Lavender"
 +
|August 9, 2008
 +
|style="background-color:Gainsboro"| v. 0.8.2
 +
|Graphic notation skins: KEGG notation for metabolic pathway diagrams, Regensburg notation for metabolic pathway diagrams
  
−
UI improvements:
+
Simple line path editor
−
* automatic suggestions in search pane
+
−
* automatic opening of uploaded files
+
−
* select several elements to remove in repository tree
+
  
−
'''BioUML core (both workbench and web version):'''
+
Microarray data and analysis results as documents (they are opened in tabs similar with diagrams)
  
−
History of diagram editing (like CVS or SVN)
+
Microarray analysis - identification up/down regulated genes using t-statistics and hyperheometric distribution
 +
|-
 +
|July 22, 2008
 +
|style="background-color:Gainsboro"| v. 0.8.1
 +
|Workbench update from the site
  
−
Simulation engine
+
Third party libraries update: JFreeChart, Lucene, Rhino,  JHelp
−
* stochastic modeling, following solvers were implemented:
+
−
** Gillespie (Gillespie, D.T. 1977)
+
−
** Gibson-Bruck (Gibson, J. Bruck 2000)
+
−
** Max Time step (Puchalka, J., Kierzek, A.M. 2004)
+
−
** Tau-leaping (Yang, C. et al. 2006)
+
−
* Discrete Stochastic Models Test Suite (DSMTS) was passed succesfully
+
−
* agent based modelling - new agent with ability to produce descendants. Is used to simulate cell population behaviour.
+
  
−
SBML support:
+
UI improvements: graphics (for simulation results) - now node titles instead of node IDs are used
−
* bug fixing
+
−
* flux balance constraint models support (using org.apache.common.math3)
+
−
* all non composite tests from test-suite 2.3.2 (2013-02-04) passed.
+
  
−
Visual modelling
+
Several HTML tags can be used in titles for graph nodes: <nowiki><br>, <sub>, <sup>, <b>, <i>, <font color, size></nowiki>
−
* composite diagrams improvements
+
|- style="background-color: Lavender"
−
* MathDiagramType - new diagram type for describing physial procsses. Automatically generates dependencies between equations.
+
|July 2, 2008
 +
|style="background-color:Gainsboro"| v. 0.8.0
 +
|Composite database module
  
−
Model analysis
+
Database module editor
−
* model reduction
+
−
* MCA (Metabolic Control Analysis, alpha version)
+
  
−
Analyses:
+
SBML extensions for BioModels database (experiment, simulation, parameters, result, plot)
−
* [[Convert table (analysis)|convert table]]: ability to use column for ID
+
−
* [[Filter table (analysis)|filter table]]: ability to select top N or bottom N entries
+
  
−
User interface improvements
+
XML diagram type
−
* [[perspective]]s - allows to group and filter UI components for specific user's tasks
+
−
* tree table component
+
−
* drag & drop for annotations
+
  
−
[[Genome browser]] improvements
+
Experiments
−
* better navigation (chromosome switch, position input box, drag-and-scroll, zoom selection, mouse wheel support, etc.)
+
−
* improved sites information tab
+
−
* BAM tracks support
+
−
* gene structure can be shown in a table cell (only web)
+
−
* improved and new styles for genes structure visualization
+
  
−
Improved support of DAS protocol
+
Loading of modules from BioUML server:
−
* support for 1.53 and 1.6
+
−
* support for non positional features
+
−
* interactions
+
−
* ontologies
+
  
−
Integration with JMOL for visualization of 3D structures
+
EBI data pack (Ensembl, UniProt, ChEBI, IntAct, BioModels) - free databases from EBI as BioUML modules
 +
|-
 +
|January 28, 2008 (alpha)
 +
 +
March 20, 2008 (beta)
 +
|style="background-color:Gainsboro"| v. 0.7.8
 +
|Graphic notation editor, SBGN (alpha version)
  
−
'''BioUML server'''
+
Library of predefined kinetic law functions (SBO)
  
−
{{Galaxy}} support
+
BioModels - comparison with other simulators (Copasi, CVODE, RoadRunner, Jarnac, JSim, Oscill8 Core, SBWOdeSolver, MathSBML)
  
−
new section "Galaxy" in analysis tab allows to use all methods from [[Using Galaxy in BioUML|Galaxy platform]]
+
Database references editor
 +
 
 +
Equations editor
 +
 
 +
Microarray plug-in (alpha version)
 
|}
 
|}
 +
 +
==2003 - 2007==
 +
{| class="wikitable"
 +
!width="15%"|Date!!width="5%"|Release!!width="75%"|Description
 +
|- style="background-color: Lavender"
 +
|October 24, 2007
 +
|style="background-color:Gainsboro"| 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
 +
|style="background-color:Gainsboro"| 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.
 +
|- style="background-color: Lavender"
 +
|January 14, 2005
 +
|style="background-color:Gainsboro"| 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
 +
|style="background-color:Gainsboro"| 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.
 +
|- style="background-color: Lavender"
 +
|
 +
|style="background-color:Gainsboro"| v. 0.7.3
 +
|Database modules: KEGG, TRANSPATH. Using relational database for data storage, client/server mode.
 +
|-
 +
|
 +
|style="background-color:Gainsboro"| v. 0.7.2
 +
|GeneNet module, database search, diagram editor enhancements, graph layouts and graph search support.
 +
|- style="background-color: Lavender"
 +
|September 1, 2003
 +
|style="background-color:Gainsboro "| v. 0.7.1
 +
|Shell mode, JavaScript custom functions and host objects, JavaScript help, SBW integration using JavaScript.
 +
|-
 +
|June 13, 2003
 +
|style="background-color:Gainsboro"| 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]]
 +
  
 
==See also==
 
==See also==
Line 601: Line 996:
 
* [[Features]]
 
* [[Features]]
 
* [[BioUML development roadmap]]
 
* [[BioUML development roadmap]]
 +
 +
[[Category:BioUML history]]

Latest revision as of 16:37, 27 October 2023

BioUML has been continuously developed by the scientific group of Dr. Fedor Kolpakov 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 March 2008, the BIOSOFT.RU, LLC was formed as a specialized subsidiary of Development On The Edge.com, LLC and became the main BioUML developer.

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

[edit] 2023

Date Release Description
Sep, 2023 v. 2023.3
  • General
    • Export\import research project
    • Export\import optimization document to sbex format
    • Overall performance improved, bugs fixed
  • Python library
    • Created python library bioumlsim, providing python API for BioUML simulation tools
  • Diagrams
    • Improved mathematical formulas representation in models description
    • Improved visual representation of model variables including concentration\amount notation.
    • Improved tabs for model elements editing
  • Parameter Identifiability analysis improved to calculate confidence intervals more correctly
  • Antimony support:
    • new elements: constraints, algebraic equations, subtypes, logical nodes, propagated ports, units (unit definitions, initializations with unit and keyword has), database references, phenotypes
    • keyword substanceOnly and initial quantity type (e.g. s1 = 5.0 / C)
    • text highlight improved
    • autoupdate mode
    • Custom annotation added to antimony
      • SBGN annotation to specify:
        • species type: macromolecule, simple chemical, etc.
        • structure: complex elements, multiple modifications, units of information
        • reaction type: process, inhibition etc.
        • modifier type: catalysis, modulation etc.
        • species clones
        • port titles
      • Glycan annotation to specify structure
      • Smiles annotation to specify structure
      • Multimers
  • A bunch of complex modular models has recently been constructed in BioUML and published describing:

[edit] 2020

Date Release Description
Dec, 2020 v. 2020.4
  • Simulation
    • New simulation document allowing user to vary model parameters and immediately observe changes in simulation results.
  • Diagrams
    • Reaction creation dialog is more compact with a separate tab for reaction law editing.
    • Export\Import enhanced. Now models can be exported along with all its submodels and related data tables in one archive.**
    • New tab to edit variables.
    • Species can be renamed.
    • Nodes movement improved.
    • Initial variable values can be set to diagrams from external tables (e.g. parameter fitting result).
  • Parameter fitting
    • Optimization can use table data (e.g. result of another parameter fitting) as a starting point.
    • During parameter fitting intermediate results (a table with the current best fitted parameter values) can be saved without stopping the process.
    • Results of parameter fitting can be saved as autogenerated plot.
  • Web
    • Integration with Jupyter improved.
    • Default project can be set.
    • Variables to plot during model simulation can be edited through more convenient dialog.
    • Complex can be more easily selected with all its elements by double click.
    • New tab to work with Flux Balance Analysis.

[edit] 2019

Date Release Description
Dec, 2019 v. 2019.4
  • General:
    • Headless version of BioUML refined and improved. More information and example scripts can be found here
    • All Curated Biomodels tested to be imported and simulated
    • Automatically select imported data element in repository tree
  • Formats:
    • SBGN Process Description Level 1 version 2.0 supported: shapes of simple chemical and variable changed, equivalence operator implemented (not affecting simulation for now)
    • Better Reactome support (full support of new ID format, various fixes)
    • Option to use score satisfying UCSC сonventions during export to BED, GTF and GFF formats
  • Tables:
    • Table importer: fixed quotes processing, better processing of incomplete lines (with empty trailing values)
    • Info about matching path is shown in the results of the table converting (with versions of used databases)
  • Web version:
    • More precise edge selection in diagrams
    • Selected edges are highlighted with pink color
    • Move nodes on diagram using Ctrl+Arrow keys for 1px and Shift + Arrow keys for 5px shift
    • Copy and clone diagram element actions are separated
    • Initial integration with Jupyter
    • Track finder (user can set conditions and search for tracks in database (Ensembl, GTRD), the results can be added to the genome browser view from the tab)
Aug, 2019 v. 2019.2
  • General
  • BioPAX support greatly enhanced
  • Diagrams
    • New SBGN EX diagram type, extending SBGN with semantic relations
    • Compartment shape can be selected apart from its inner nodes which facilitates its resizing
    • Reaction name can be set by user upon creation
    • Reaction participants can be edited, added and removed after reaction is created.
    • More convenient (non-modal) edit dialog for diagram elements
  • Analysis
    • All analysis methods in BioUML were rearranged into 35 categories
  • Web version
    • Search for analyses by name or description
    • Start page with analysis categories and quick guide
    • Multiple plots for simulation results presented in one panel.
    • Simulation can be stopped, special button added
    • Edges can be edit in drop down menu
  • Bugs fixed
Apr, 2019 v. 2019.1
  • General
    • Installation process for linux systems improved
  • Diagrams
    • “Fit to screen” option added in toolbar for diagrams
    • Create edges from reactions to newly added nodes on diagram, if edge information is present in reaction prototype
    • Copy&paste diagram nodes to specified location
    • Copy all elements of one diagram to another via drag-and-drop
    • Nodes shape size is now editable from info panel
    • User can remove parameters from Parameters view part
  • Simulation
    • More convenient way to show on plot variables from modules several levels deep in the hierarchy
  • Visualization
    • Nodes and compartments may be visualized using custom images uploaded by user, image width and length can be set in percents of original image
    • Reactome Image library supported
  • Layout
    • Pin/unpin diagram elements via dropdown menu
    • Save and remember used automatic layouter for given diagram
    • Incremental layout of elements elements added from search
  • Expression filters
    • All SBGN diagrams support filters (e.g. expression filter)
    • Display expression filter as gradient aura on diagrams
    • NaN values for expression filters supported
  • Web version
    • Show multiple simulation plots in one window, stop simulation if plots are closed
    • Collapsible array attributes in info block
    • Highlight inner nodes of complex in Keynodes visualization
    • Selected info template is remembered for elements of the same type
    • Import improved
  • Analysis
    • More user-friendly Identifiability analysis interface (absolute value of deviation instead of chi-square quantile, select parameters for analysis in optimization version)
  • Formats
    • Partial support of VCF4.3 on import/export, FILTER property for .VCF track files supported
  • External libraries
    • jfreechart update 1.0.18 -> 1.5.0
    • jcommon updated 1.0.22 -> 1.0.24
    • underscore.js update 1.2.2 -> 1.9.1
  • Many bugs were fixed

[edit] 2018

Date Release Description
Oct, 2018 v. 2018.3
  • General
    • Diagram can be created in any generic folder
  • SBGN and visualization
    • Shrink node titles (if option enabled)
    • Dynamically highlight nodes (equations, reactions, species, etc.), containing selected variables and parameters
  • Web
    • Import of several files from local computer and generic files from repository
    • Wait dialog appears when several elements are deleted
  • Simulation
    • Plotting of simulation result reworked. Now variables to plot are specified in separate tab. User may create multiple plots and define different variables for axes. Example models with plots are included in the build.
    • Show in plot and line spec are removed from "Variables" and "Parameters" tabs.
  • SBML
    • Unit definitions from the model may be set to parameters (previously only for species)
  • Cytoscape
    • Import and export diagrams in Cytoscape JSON format (.cx)
  • External libraries
    • org.jsoup updated (1.7.1 -> 1.11.3)
  • Bug fixing
Jun, 2018 v. 2018.2
  • SBGN
    • Visualization erros fixed
    • Automatic creation of complexes from string (e.g. “A:B”)
    • PantherDB and CellDesigner models support improved (as SBGN diagrams)
  • SBML
    • L3v2 supported, including:
      • rateOf, rem, quotinent functions, min and max with arbitrary number of arguments
      • boolean values now may be mixed with numeric (e.g. x = false + 10)
      • find more details here
      • All tests from current test suite passed successfully (see details here)
    • Constraints supported (3 options: ignore them, stop simulation or just log message)
  • Diagrams
    • Copy\paste of diagram elements
  • Antimony
    • gene <-> species conversion fixed
  • Simulation
    • Fast reactions handling enhanced: user can select whether to handle them as algebraic systems or as ODE systems with very high rate
    • Automatic detection of species variable type implemented (Not used, Calculated, Differential, Algebraic, Discrete, Parameter)
    • Parameters identifiability analysis: added option to select type of image (png or chart)
  • Workflows:
    • Option to ignore failed steps and continue if possible
    • Option to skip steps if they were completed on previous runs
    • Visualization erros fixed
  • Data analysis and tables
    • TreeMap on Functional classification on Gene Ontology
    • Tabular data visualization using pie chart or bar chart.
    • Super Annotate Table (annotates one table by another)
    • Export tables with images to zhtml file
  • Unused libraries excluded from build
  • Bugs fixed


[edit] 2017

Date Release Description
Septeber, 2017 v. 2017.2
  • Mathematical modeling
    • Identifiability Analysis improved
  • Visualization
    • Fixed reading and processing 3D mol structures (MDL Molfile)
  • Modular modeling
    • Split model action: automatic separation of selected model elements into submodel
    • User may change type of the port (input, output or contact) after it is added to the model
    • User may refresh content of submodels in composite model without its reloading
  • Bug fixing

[edit] 2016

Date Release Description
December, 2016 v. 2016.4
  • Analysis
    • Parameters identifiability analysis (Raue et al., 2009)
    • Generating models population using Metropolis algorithm
    • Key node sensitivity analysis
    • New result types for Steady State: table, simulation result
  • Simulation
    • Automatic generation of kinetik laws from SBO
    • Option to set different output type for variables (quantity or concentration)
    • Options for algebraic solvers
  • SBML
    • Level 2 version 5 supported
    • All tests from SBML test suite v. 3.2.0 passed
  • BioUML IDE
    • NetBeans version updated to 8.2
  • BioUML web edition
    • fixed bug with openning SBGN Composite diagrams
    • fixed bug with missed icons for SBGN Composite diagrams
    • fixed bug with incorrect reverting of the diagram element position (after unacceptable moving)
July, 2016 v. 2016.2
  • Modeling
    • Custom styles for diagram elements rendering for all types of models (see SBGN examples)
    • Automatic detection of model parameter types (Unused, ODE, Algebraic, Descrete, Parameter)
    • Converter: SBML-SBGN diagram -> SBML-SBGN composite diagram
  • Databases
    • CHEBI support enhanced
  • Analysis
    • Flux balance analysis enhanced

[edit] 2015

Date Release Description
December, 2015 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 v. 0.9.9
  • BioUML IDE
    • 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

[edit] 2014

Date Release Description
September, 2014 v. 0.9.8
  • Visual modelling and simulation
    • population based modelling (beta version, see article BioUML: plugin for population-based modeling)
    • refactoring of code generation for model simulation
    • graph layout improvements (orthogonal path finder, hierarchical path finder)
    • creating edges via drag & drop
    • new analysis for diagram comparison
  • Server
    • integration with Galaxy ToolShed
April, 2014 v. 0.9.7
  • Visual modelling and simulation
    • population based modelling (nlme plug-in)
      • special graphic notation
      • automated Java and R code generation
      • integration with R nlme package for solving non-linear mixed effect models
    • optimized Java code generator for huge models (10 000+ species and 10 000+ reactions)
    • Gurobi solver for fbc analyses (need to separately install Gurobi Optimizer)
    • started simulations are shown in "Tasks" tab
    • visualisation of dependency edges - these edges link equations and used there variables
    • visualisation of glycan structures on the base their structure
    • possibility to hide elements on a diagram ("visible" node property)
    • analyses "ShareComplexMolecules" makes clones for substances involved into many reactions
    • new actions on toolbar to align selected nodes (top, bottom, etc.
    • BioNetGen plugin improvements:
      • Importer/Exporter for .bngl files
      • Support for Molecule Types
      • Built-in functions
      • Highlight selected diagram element in corresponding BioNetGen code
  • Server
    • BioUML node for cluster/cloud architecture
    • cloud version support for Amazon EC2 (alpha)
    • improved task manager

[edit] 2012 - 2013

Date Release Description
2013, November 18 v. 0.9.6
  • BioUML workbench (desktop version)
    • integration of Galaxy
    • rule based modelling (implementation of BioNetGen approach, details)
    • Antimony support (details)
    • Synchronisation between textual and graphical model representation (BioNetGen, Antimony)
  • Interface improvements
    • display name and actions for table cell values
  • GTRD database
    • perspective
    • special start page
    • improved web interface
  • New methods for analysis of transcription factor binding sites
2013, June 15 v. 0.9.5
  • Simulation engine
    • SBML level 3 packages:
      • Hierarchical Model Composition
      • Flux Balance Constraints
2013, March 20

(Workbench)

v. 0.9.4 BioUML web:

Collaborative work on diagram (like Google documents)

UI improvements:

  • automatic suggestions in search pane
  • automatic opening of uploaded files
  • select several elements to remove in repository tree

BioUML core (both workbench and web version):

History of diagram editing (like CVS or SVN)

Simulation engine

  • stochastic modeling, following solvers were implemented:
    • Gillespie (Gillespie, D.T. 1977)
    • Gibson-Bruck (Gibson, J. Bruck 2000)
    • Max Time step (Puchalka, J., Kierzek, A.M. 2004)
    • Tau-leaping (Yang, C. et al. 2006)
  • Discrete Stochastic Models Test Suite (DSMTS) was passed succesfully
  • agent based modelling - new agent with ability to produce descendants. Is used to simulate cell population behaviour.

SBML support:

  • bug fixing
  • flux balance constraint models support (using org.apache.common.math3)
  • all non composite tests from test-suite 2.3.2 (2013-02-04) passed.

Visual modelling

  • composite diagrams improvements
  • MathDiagramType - new diagram type for describing physial procsses. Automatically generates dependencies between equations.

Model analysis

  • model reduction
  • MCA (Metabolic Control Analysis, alpha version)

Analyses:

User interface improvements

  • perspectives - allows to group and filter UI components for specific user's tasks
  • tree table component
  • drag & drop for annotations

Genome browser improvements

  • better navigation (chromosome switch, position input box, drag-and-scroll, zoom selection, mouse wheel support, etc.)
  • improved sites information tab
  • BAM tracks support
  • gene structure can be shown in a table cell (only web)
  • improved and new styles for genes structure visualization

Improved support of DAS protocol

  • support for 1.53 and 1.6
  • support for non positional features
  • interactions
  • ontologies

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

[edit] 2011

Date Release Description
October 31, 2011

(Workbench; beta)

v. 0.9.3 BioUML core:

Core update

  • Eclipse runtime is updated to Equinox version 3.6.0
  • Java 7
  • fixed problems for Windows 7

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: Type-text-icon.png text, Type-image-icon.png images, Type-html-icon.png html

Data handling improvements:

  • multiple tables can be joined;
  • columns with identical names may be merged automatically.

Workflows improvements:

  • possibility 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 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

  • a lot of new methods for analyses of microarray data, import data in different formats and other
  • JavaScript API to work with models and simulation engine (JavaScript host objects model and simulationEngine)

Workflows support (beta version)

  • improved graphic editor
  • cycles
  • patterns for input/output parameters
  • automatic orthogonal layout for edges

Simulation engine

  • composite models (beta version)
    • graphic notation improvements
    • special preprocessor to generate flat model
  • agent based models - improved, new elements

User interface improvements:

  • a lot of new icons
  • drag & drop support
  • improved filter for tables (user can filter rows using some expression)
  • improved graph layout
    • hierarchical layout
    • orthogonal layout
  • mathematical expressions
    • special editor for all mathematical expressions
    • user can use node title (instead of its name/identifier) in math expressions
    • different modes to show variable names (using id or title)

Coloring diagram using omics data (redesigned)

BioUML server:

May 6, 2011 Version 1.0 of the geneXplain platform (based on BioUML)

[edit] 2010

Date Release Description
October 13, 2010 v. 0.9.1 BioUML core (common for workbench and web edition):

Simulation engine:

  • composite models (beta version, apoptosis model as an example)
  • agent based modeling (beta version, cardiovascular system as an example)

Chemoinformatics support (on the base of CDK and JChemPaint):

  • import 2D structures (SDF, MOL and other format)
  • special document type for 2D structures
  • 2D structures rendering and editing
  • JavaScript API for CDK
  • PASS (Prediction of Activity Spectra for Substances) integration

Tasks manager:

  • tasks list as a special viewpart
  • tasks management (interrupt, see status and results)

BioUML web edition:

  • diagrams export (sbml, sbgn)
  • diagrams import into custom folders (sbml)
July 2, 2010

(Web edition)

September 13, 2010

(Workbench; alpha)

v. 0.9.0 BioUML core (common for workbench and web edition):

Simulation engine

  • fast reactions support
  • new ODE/DAE solver - RADAU IIA
  • refactoring and bug fixing

Optimisation engine

  • refactoring
  • support for steady state
  • optimisation document (to handle all data related with optimisation)
  • JavaScript API
  • performance optimisation (now it much faster then COPASI)

SBML

  • support L2v4, L3V1
  • simulation engine passed all SBML tests

Data analysis - a lot of new methods for analyses microarray data and gene regulatory regions

Reproducible research

  • research journal (collects all user actions related with data analyses)
  • research diagram (graphical representation of research journal)
  • workflows support

User interface

  • filtering table rows according to some JavaScript condition

BioUML workbench:

  • new tabs in setup wizard (SQL settings, connect DAS, Load project, Create project)
  • literature editor (refactoring and bugfixing)

BioUML web edition:

  • data analyses
  • genome browser
  • diagrams export (png, gif, jpeg, svg, sbml, sbgn, dml)
  • diagrams import (sbml)
  • tables import (csv) and export (csv)

BioUML server:

  • sandbox for JavaScript

JavaHelp:

  • new chapters: Genome browser, Optimisation
  • updated chapters: Simulation

[edit] 2009

Date Release Description
November 30, 2009

(Web edition)

v. 0.9.0 BioUML web edition:

first public version

BioUML core:

SBGN:

  • SBGN - graphic notation update
  • <sbgn> extension for SBML
  • support for BioModels
  • support for TRANSPATH

Databases:

  • BioModels are installed on BioUML server (public)
  • EndoNet database support (pilot version, protected)

Graph layout improvements:

  • PathwayLayouter is used as decorator for other graphs to take into account compartments and peculiarities of diagrams

(for example all math elements are located on the top of diagram)

  • layout preview
  • possibility to reuse layout for similar diagrams

New graph layout algorithms:

  • 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.

UI improvements:

  • quick search field in repository pane
  • quick search for diagrams that contain specified component
  • templates for HTML generation for list of species, reactions, variables, parameters and equations
  • database loading dialog - possibility to specify login/password to see the list of protected databases.

Simulation engine:

  • JVODE solvers (ported to Java version of CVODE)
  • bug fixing (correct reading of piecewise from SBML)

BioUML server:

  • network repository for group working
July 31, 2009 (alpha)

August 7, 2009 (beta)

v. 0.8.6 JavaScript:
  • editor - JavaScript files can be opened and edited in BioUML workbench
  • debugger
  • new functions: plot, view

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):

  • Ensembl tracks initial support (genes, repeats)
  • map document - displays sequences and sites grouped by tracks
  • project pane - the project HTML description
  • regions pane - allows to specify sequence regions to be visualized as well as sequence visualization options
  • tracks pane - allows to specify tracks to be visualized as well as site visualization options
  • sites pane - shows the list of site displayed on the map document

Sequence analysis (alpha version):

  • special section in repository: Data/Sequence analyses
  • sequences import

SBML level 2 version 2-4 support

Parameters fitting (beta version)

JavaHelp:

  • new chapter: JavaScript (pane, editor, shell, functions)
  • new chapter: R
  • new chapter: parameters fitting
January 28, 2009 (alpha)

February 17, 2009 (beta)

v. 0.8.5 SBGN 1.0 implementation - alpha version

KEGG improvements:

  • graph layout improvements, orthogonal path finder
  • labels location
  • graph search engine improvements

UI improvements:

  • grid
  • snap to grid
  • arrows and lines selection
  • keyboard navigation for diagram editing
  • repository tree shows database status using icons (public, free, log-in, preloaded, etc.)
  • possibility to edit diagrams on display without saving for read only databases

Parameters fitting (alpha version)

Bug fixing:

  • MATLAB simulation engine - pass SBML semantic test suite again

JavaHelp refactoring: new tool for help writing - Help&Manual 5

  • introduction
  • installation and configuration
  • databases

[edit] 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:

  • Databases (instead of Modules)
  • Data
  • Analyses

New architecture for methods of analyses:

  • extension point, registry for methods of analyses
  • methods are shown in analyses tab
  • new version of dialog for microarray analyses

Parameters fitting (initial version)

Refinements, bug fixing:

  • authorization subsystem
  • repository tree

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:

  • data access,
  • operations on data sets (union, overlap, etc.),
  • microarray statistical analyses
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)

[edit] 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.

[edit] 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:


[edit] See also

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