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Intrinsic Noise Analyzer Changelog

What's new in Intrinsic Noise Analyzer 0.4.3

Mar 20, 2014
  • Added user warning about unsaved and modified models.
  • Avoided unneeded collapsing of complete tree
  • Enabled MAT-file export for all analysis results
  • Enhanced syntax error reporting for SBMLsh
  • Made task tree-item visible on auto-show
  • Compatibility with Eigen 3.2.0
  • Dead code clean up
  • Fix: Giant memory leak in SSA paramater scan
  • Fix: Partial rewrite of the reaction editor fixing an uncaught exception and an error due undefined species or compartments in user defined propensity
  • Fix: Handle “Close all models” entry in “File” menu
  • Fix: Expression editors to handle undefined variables properly
  • Fix: Specification reaction modifiers on SBML export.
  • Fix: Weird crash under MacOS X when exporting SBML
  • Fix: SSA time-course analysis ignoring thread count
  • Fix: Check for invalid ids
  • Fix: Catch unhandled exceptions in Expand/Collapse Reversible Reactions
  • Fix: Restore model if expansion/collapse of reversible reactions fails
  • Fix: Handling of unit identifiers
  • Fix: Export units of parameters
  • Fix: Failure of conservation analysis on models w/o conserved cycles.

New in Intrinsic Noise Analyzer 0.4.2 (Jul 3, 2013)

  • OpenMP support for MacOS X
  • New feature: View conserved quantities
  • New feature: Wizard for editing any plot
  • Change default behavior: import of substance units when all species have substance units
  • Allow TeX in species selection list
  • Switch automatically to new analyses results
  • Select current model in analysis wizard
  • Fix: Fano factor plot now available in parameter scans involving the volume parameter
  • Fix: Display of large integers
  • Fix: Task duration now measured in real time
  • Fix: Auto-completion caused GUI crash
  • Fix: Freeze in SSE wizard for large models
  • Fix: Handle MaxIterationsReached exception in SSE parameter scan
  • Fix: Exceptions for models defining zero volumes
  • Fix: Resize all table colums to content size
  • Fix: Parameters defined as Sqrt() cannot be correctly substituted
  • Fix: Missing error handling in redefinition of variables
  • Fix: Missing filename when downloading a model
  • Fix: Legend in plots
  • Fix: Axis origin in plots
  • Fix: Accept reaction names with white-spaces in reaction editor

New in Intrinsic Noise Analyzer 0.4.1 (Mar 16, 2013)

  • SSA parameter scan
  • More efficient SSE parameter scan using bytecode interpreter or LLVM
  • Drag & drop models into side panel for import
  • Enabling Customized Plots for Windows using bytecode interpreter
  • Allow log messages to be saved to file or copied to clip board
  • Level filter for log messages
  • Lower threshold for autocompletion
  • Notification if identifier cannot be changed
  • Notification if expression cannot be parsed
  • Allow for moving local parameters into the global scope
  • Adjust Makefile for compilation with LLVM 3.2
  • Allow TeX in Plot labels
  • Center plot titles on axis not the figure
  • Fix: Segmentation fault when expanding reversible reactions
  • Fix: Export expressions using exp() to SBML
  • Fix: Color of axis tick labels
  • Fix: Font size in SVG export
  • Fix: Remove Fano plot for volume parameter scan
  • Fix: Several memory leaks
  • Fix: Wrong parser handling of associative operators
  • Fix: Serialization of big integers abs()>1e6
  • Fix: Update kinetic law/chem eq view after reaction update
  • Fix: Exception handling for volume 0
  • Fix: Allow unknown TeX symbols in Customized Plot
  • Fix: Exception for empty model analysis
  • Fix: Update reaction view if parameter name or identifier was changed
  • Fix: Layout of TeX superscript
  • Fix: Function calls in expression writer
  • Fix: Vertical alignment of line and label in plot legends
  • Fix: Units for reaction parameters
  • Fix: Customized Plot missing plot legends
  • Fix: Handling of unicode filenames
  • Fix: Export of substance units to SBML
  • Fix: Parsing substance units in SBMLsh
  • Fix: Background of rendered expressions.
  • Fix: Adjusted mouse cursor hoovering for model units to indicate that they are editable. Also add a tooltip.
  • Fix: Window title in SBML-SH editor
  • Fix: Colors in steady state tables (being non-selectable)

New in Intrinsic Noise Analyzer 0.4.0 (Nov 10, 2012)

  • Parameter scans - The latest feature of iNA's analyses allows you to access the parametric dependence of steady state fluctuations in biochemical networks. It provides invaluable information such as coefficients of variations that are difficult to obtain from stochastic simulations.
  • Model editing capabilities - The current release introduces advanced stochastic model manipulation. It allows you to edit existing SBML models, convert them into a format suitable for stochastic analysis, or simply create your own model from scratch. Learn more.
  • SBML-sh support - iNA now imports and exports the easy to read & write file format SBML shorthand allowing rapid generation of the essential SBML model structure. Learn more.
  • Improved reaction & expression rendering - iNA improves the overall readability of the mathematical model representation by introducing a new renderer of mathematical expressions and reaction equations. Learn more.
  • Customized plots - Beside predefined plots this release introduces customized plots allowing you to produce high quality visualization easily from spreadsheet analysis data (Linux and MacOS builds only).
  • Export vector graphics - iNA now lets you export lossless vector graphics using the popular SVG file format.