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singa-all release v0.5.0

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@cleberecht cleberecht released this 11 Dec 09:56
· 308 commits to master since this release
v0.5.0
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cleberecht Christoph Leberecht
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SiNGA now uses JUnit 5 for testing. All SBML parsing and associated libraries have been dropped, since most export and import operations for the simulation module are now maintained in the singa-exchange repository.

Updates and features

Mathematics

  • added implementation of the Flood fill algorithm for grids
  • added implementation of the Sutherland–Hodgman algorithm to clip polygons.
  • added possibility to apply transformations to matrices and vectors (such as z score and min max)
  • added support for bit vectors and corresponding operations
  • many improvements and small additions to the geometry part of the package

JavaFx

  • added support for swing based renderer
  • arrowheads are now drawn for directed graphs

Features

  • added the UnitRegistry, which allows to transform and scale units and quantities based on default units
  • generalized FeatureOrigin to Evidence

Chemistry

  • added support to parse sequence variants and entry names from UniProt

Structure

  • added support to write MMTF structures
  • added support for all substitution matrices that are currently supported by NCBI BLAST

Simulation

  • added multiple modules for endo- and exocytosis phenomena
  • reimplemented dynamic reactions (reactions with kinetics given by functions), which were disabled in the last releases
  • GO terms can now be assigned to subsections and regions
  • observing deltas (changes from modules) now returns the average of the deltas since the last observation instead of only the delta of the last observation
  • sampling and variation of features allows to quickly set up multiple similar simulations
  • the simulation manager provides more settings to fine tune the computation of your simulations
  • SBML parsing is now part of singa-exchange
  • added possibility to record data to trajectory objects

Installation

You can add SiNGA to your project by adding the following dependency to your pom.xml.

<dependency>
    <groupId>bio.singa</groupId>
    <artifactId>'artifact'</artifactId>
    <version>0.5.0</version>
</dependency>
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