Difference between revisions of "BioUML development history"

• 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

• 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

• 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

• 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)

• 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

• 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.

• 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

• 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

• 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

• 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

• R integration
  • improved interface and bug fixes
  • possibility to call BioUML from R using rbiouml package (http://cran.r-project.org/web/packages/rbiouml)

• JavaScript support (web version)
  • new JavaScript editor, CodeMirror (http://codemirror.net/).

• GTRD database
  • perspective
  • special start page
  • improved web interface

• New methods for analysis of transcription factor binding sites

• Simulation engine
  • SBML level 3 packages:
    • Hierarchical Model Composition
    • Flux Balance Constraints

(Workbench)

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:

• convert table: ability to use column for ID
• filter table: ability to select top N or bottom N entries

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

(Web edition)

(Workbench; beta)

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.

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

• new system for authorization and access rights: BioStore (https://bio-store.org)
• ChIP-SEQ pipeline (available only on test server yes)

(Web edition)

June 14, 2011

(Workbench; beta)

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:

• 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

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)

(Web edition)

September 13, 2010

(Workbench; alpha)

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 of up/down regulated genes using different statistical criteria
  • gene set enrichment analysis (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)
• 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

(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

August 7, 2009 (beta)

• 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

February 17, 2009 (beta)

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

• 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:

• 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.

hierarchical models, block component (proof of concept)

JavaScript functions for:

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

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

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>

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

March 20, 2008 (beta)

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)

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

Performance improvements. ODE solver for stiff problems.

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

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.