|
|
|
|
|
| BioUML development roadmap |
|
This document is an outline of releases for BioUML project for near
future. In parallel we will work on user guide, developer documentation,
and bug fixing.
|
Release |
|
Description |
|
Date |
v. 0.7.0
|
|
Plug-in based architecture using Eclipse runtime, SBML format support,
ontology diagram type, Html editor for diagram description, etc. |
|
June 13, 2003
release notes
|
v. 0.7.1
|
|
Shell mode, JavaScript custom functions and host objects, JavaScript
help, SBW integration using JavaScript. |
|
September 1, 2003
release notes
|
| v. 0.7.2 |
|
GeneNet module, database search,
diagram editor enhancements, graph layouts and graph search support.
|
|
|
| v. 0.7.3 |
|
Database modules: KEGG, TRANSPATH.
Using relational database for data storage, client/server mode.
|
|
|
| v. 0.7.4 |
|
MathML support, SBML level 2 support, CellML
support,
Java simulation engine, rule and event concepts,
update for Eclipse
3.0, JavaHelp support (only few help topics were written).
State and transition concept support.
|
|
October 10, 2004
release notes
|
| v. 0.7.5 |
|
Matlab and Java simulation engines passed 100% SBML semantic test suite 100%.
Support of algebraic equations, delay, piece wise functions, all MathML
functions (factorial, sh, tgh, ctgh, ash, atgh, etc.)
SBML semantic suite now is part of BDK (BioUML Development Kit)
Support of diagram import (SBML, CellML, GinSim) and export (PNG, JPEG,
SVG, GXL, SBML)
SBW 2.0.0
|
|
January 14, 2005
release notes |
| v. 0.7.6 |
|
User interface improvements: preferences, possibility to load and
change look & feel, user interface for editing rules and events.
Performance improvements.
ODE solver for stiff problems.
|
|
May 10, 2005
release notes |
| v. 0.7.7 |
|
Full text search engine (uses Lucene), graph search, graph layout improvements
BioPAX format - import/export,
OBO format - import/export
Ensembl support (spike solution)
Clipboard pane
CDK library is used to visualize chemical structures on diagrams
arbitrary images (GIF, PNG, etc.) for graph nodes
Client-server architecture, BioUML can be started as standalone server or
as a servlet
BioUML network edition
New installer based on IzPack
Initial draft of user manual
|
|
October 24, 2007
release notes |
| v. 0.7.8 |
|
Graphic notation editor, SBGN (alpha version)
Library of predefined kinetic law functions (SBO)
BioModels - comparison with other simulators (Copasi, CVODE, RoadRunner,
Jarnac, JSim, Oscill8 Core, SBWOdeSolver, MathSBML)
Database references editor
Equations editor
Microarray plug-in (alpha version)
|
|
January 28, 2008 (alpha)
March 20, 2008 (beta)
release notes |
| v. 0.8.0 |
|
Composite database module
Database module editor
SBML extensions for BioModels database (experiment, simulation, parameters,
result, plot)
XML diagram type
Experiments
Loading of modules from BioUML server:
EBI data pack (Ensembl, UniProt, ChEBI, IntAct, BioModels) - free databases
from EBI as BioUML modules
|
|
July 2, 2008
release notes |
| v. 0.8.1 |
|
Workbench update from the site
Third party libraries update: JFreeChart, Lucene, Rhino, JHelp
UI improvements: graphics (for simulation results) - now node titles
instead of node IDs are used
Several HTML tags can be used in titles for graph nodes: <br>,
<sub>, <sup>, <b>, <i>, <font color, size>
|
|
July 22, 2008
release notes |
| v. 0.8.2 |
|
Graphic notation skins: KEGG notation for metabolic pathway diagrams, Regensburg notation for metabolic pathway
diagrams
Simple line path editor
Microarray data and analysis results as documents (they are opened in tabs
similar with diagrams)
Microarray analysis - identification up/down regulated genes using
t-statistics and hyperheometric distribution
|
|
August 9, 2008
release notes |
| v. 0.8.3 |
|
Authorization subsystem (login)
hierarchical models, block component (proof of concept)
JavaScript functions for:
data access,
operations on data sets (union, overlap, etc.),
microarray statistical analyses
|
|
August 28, 2008
release notes |
| v. 0.8.4 |
|
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.
|
|
December 12, 2008
release notes |
| 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
|
|
January 28, 2009 (alpha)
February 17, 2009 (beta)
release notes
|
| 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
|
|
July 31, 2009 (alpha)
August 7, 2009 (beta)
release notes |
| 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
|
|
Web edition:
November 30, 2009
|
| 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
- 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
- search for transcription factors binding sites
- ChiP-seq analyses (MACS algorithm)
- Venn diagrams
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:
- 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
|
|
Web edition:
July 2, 2010
Workbench:
September 13, 2010 (alpha)
release notes |
| 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)
|
|
October 13, 2010
|
| 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)
Workflow 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:
- 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
|
|
Web edition:
May 7, 2011
Workbench:
June 14, 2011 (beta)
release notes |
| 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: text, images, html
Data handling improvements:
- multiple tables can be joined;
- columns with identical names may be merged automatically.
Workflow 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
- new system for authorization and access rights: Biostore (https://biostore.biouml.org)
- ChIP-SEQ pipeline (available only on test server yes)
|
|
Workbench
October 31, 2011 (beta)
release notes
|
| v. 0.9.4 |
|
BioUML web:
Collaborative work on diagram (like Google documents)
BioUML core:
History of diagram editing (like CVS or SVN)
Integration with Biostore for control of access rights
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
Composite diagrams improvements
Model analysis
- model reduction
- MCA (Metabolic Control Analysis, alpha version)
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
- gene structure can be shown in a table cell
- improved and new styles for genes structure visualization
BioUML server
Galaxy support (pilot version, available only on dedicated server)
new section "Galaxy" in analyses tab
allows to use all methods from Galaxy
platform .
|
|
December, 2011 |
| v. 0.9.5 |
|
BioUML core:
Simulation engine
- stochastic modeling
Optimization refactoring
- optimization process as a workflow
- save optimization results as the diagram state
BioUML server:
- synchronization of BioUML client with BioUML server
|
|
January, 2012 |
| v. 0.9.x |
|
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:
- 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:
- remote tasks for execution on server side
|
|
|
| v. 0.9.9 |
|
Bug fixing
Documentation, help improvements
|
|
|
| v. 1.0.0 |
|
Official release
|
|
|
Features listed below can be implemented in future. You are welcome with your comments and suggestion about new features as well as
feature implementation priorities. Please
use BioUML forum for
this purpose: you can write a letter to biouml@yahoogroups.com
or post your message. We
are really needed in your feedback.
|
|
|
|
|
|
Version 0.9.3
|
|
BioUML workbench version 0.9.3 (alpha) was released at October 31, 2010.
More...
|
| |
|
SBML tests passed 100%
|
BioUML version 0.9.0 have passed all tests from SBML test suite version 2.0 (SBML L1v2, L2v1-4, L3v1)
Test details.
|
| |
|
SBGN super-hackathon
|
Materials for virtual participation of BioUML team in
SBGN super-hackathon in Okinawa.
|
| |
|
Have questions?
|
|
If you have any questions please contact us at
info@Biosoft.Ru
|
| |
|
