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| BioUML development roadmap |
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This document is an outline of releases for BioUML project for near
future. In parallel we will work on user guide, developer documentation,
and bug fixing.
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Release |
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Description |
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Date |
v. 0.7.0
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Plug-in based architecture using Eclipse runtime, SBML format support,
ontology diagram type, Html editor for diagram description, etc. |
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June 13, 2003
release notes
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v. 0.7.1
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Shell mode, JavaScript custom functions and host objects, JavaScript
help, SBW integration using JavaScript. |
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September 1, 2003
release notes
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| v. 0.7.2 |
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GeneNet module, database search,
diagram editor enhancements, graph layouts and graph search support.
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| v. 0.7.3 |
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Database modules: KEGG, TRANSPATH.
Using relational database for data storage, client/server mode.
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| v. 0.7.4 |
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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.
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October 10, 2004
release notes
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| v. 0.7.5 |
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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
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January 14, 2005
release notes |
| v. 0.7.6 |
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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.
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May 10, 2005
release notes |
| v. 0.7.7 |
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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
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October 24, 2007
release notes |
| v. 0.7.8 |
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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)
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January 28, 2008 (alpha)
March 20, 2008 (beta)
release notes |
| v. 0.8.0 |
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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
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July 2, 2008
release notes |
| v. 0.8.1 |
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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>
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July 22, 2008
release notes |
| v. 0.8.2 |
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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
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August 9, 2008
release notes |
| v. 0.8.3 |
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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
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August 28, 2008
release notes |
| v. 0.8.4 |
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New database modules on BioUML server (pilot version):
- SABIO-RK (System for the Analysis of Biochemical Pathways Reaction Kinetics)
- EHMN (Edinburgh Human Metabolic Network)
- LipidMAPS (LIPID Metabolites And Pathways Strategy)
- KEGG LIGAND
- KEGG Pathways
- TRANSPATH
General refactoring - now tabs in repository are called: 1)
- 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.
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December 12, 2008
release notes |
| v. 0.8.5 |
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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
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January 28, 2009 (alpha)
February 17, 2009 (beta)
release notes
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| v. 0.8.6 |
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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
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July 31, 2009 (alpha)
August 7, 2009 (beta)
release notes |
| v. 0.9.0 |
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BioUML web edition
first public versionSBGN:
- 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
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Web edition:
November 30, 2009
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| v. 0.9.0 |
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BioUML core (common for workbench and web edition):
Data analysis - a lot of new methods for analyses
microarray data and gene regulatory regions
- microarray analyses
- data normalisation
- identification up/down regulated genes using
different statistical criteria
- gene set enrichment analyses (using GO and
MSigDB databases)
- building gene regulation models on the base of
microarray time series
- cluster analysis
- master regulatory nodes
- search for transcription factors binding sites
- ChiP-seq analyses (MACS algorithm)
- Venn diagrams
SBML
- support L2v4, L3V1
- simulation engine passed all SBML tests
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)
Reproducible research
- research journal (collects all user actions related with data
analyses)
- research diagram (graphical representation of research journal)
- workflow support
User interface
- filtering table rows according to some JavaScript condition
BioUML workbench:
- 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
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Web edition:
July 2, 2010 |
| v. 0.9.1 |
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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
BioUML web edition:
- diagrams export (sbml, sbgn)
- diagrams import into custom folders (sbml)
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| v. 0.9.2 |
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BioUML core:
Simulation engine
- hierarchical models
- stochastic modeling
- agent based modeling
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| v. 0.9.3 |
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BioUML core:
Improved graph search engine
SBGN
- support for BioPAX
BioUML server:
- remote tasks for execution on server side
- security refactoring
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| v. 0.9.x |
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BioUML core:
Major refactoring: complex, macromolecule state, reaction
BioHub - new technology for database integration on the base of
cross references
Implementation of OQL subset for access to databases via BioUML object
model
SBML and related issues:
- SBML hierarchical models - pilot version
- SED-ML support
- SBRML support
Further integration with Matlab
KEGG improvements:
- omics data visualisation
- graph search engine improvements (not include small molecules, search for
related maps)
- organism - filter and highlighter
- visualization of chemical structure for substances
- diagram editing
- diagram export (KGML, BioPAX, SBML, +SVG, +PNG, +JPEG)
- set up wizard
BioUML server:
- history of data editing
- synchronization of BioUML client with BioUML server
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| v. 0.9.9 |
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Bug fixing
Documentation, help improvements
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| v. 1.0.0 |
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Official release
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Features listed below can be implemented in future. You are welcome with your comments and suggestion about new features as well as
feature implementation priorities. Please
use BioUML forum for
this purpose: you can write a letter to biouml@yahoogroups.com
or post your message. We
are really needed in your feedback.
| Features for future |
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Priority |
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BioPAX 3.0 support |
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medium |
| BIND support |
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medium |
| SBML graph layout extension support |
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medium |
| Diagram HTML publishing |
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medium |
| Petri nets |
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low |
| Markov models |
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low |
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BioUML tutorial
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October 10, 8.30-12.30 a.m - tutorial
"BioUML - integrated platform for building virtual cell and virtual physiological human"
on ICSB 2010 conference.
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SBML tests passed 100%
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BioUML version 0.9.0 have passed all tests from SBML test suite version 2.0 (SBML L1v2, L2v1-4, L3v1)
Test details.
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SBGN super-hackathon
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Materials for virtual participation of BioUML team in
SBGN super-hackathon in Okinawa.
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Have questions?
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If you have any questions please contact us at
info@Biosoft.Ru
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