singa-all release v0.6.0

We changed the license from GPL 3.0 (GNU General Public License v3.0) to MIT. This update brings major changes to the simulation package.

Updates and features

Mathematics

• added possibility to concatenate bitvectors
• fixed problem with directed graphs in the subgraph isomorphism algorithm
• added parser for Newick strings resulting in tree structures
• added traversal of trees with lambda functions
• added predicate-based graph methods for easier graph modification
• added algorithm to determine touching sides of polygons and overlapping regions

Chemistry

• added implementation for the RECAP fragmentation algorithm
• complex chemical entities are now stored in a tree data structure and can be parsed from Newick-like strings
• writing of smiles strings is now supported via beam

Features

• changed feature handling and scaling
• features are now split into QualitativeFeatures and QuantitativeFeatures
• ScalableQualitativeFeatures are automatically rescaled to the units specified in the UnitRegistry - this also works for complex units; e.g. the default space unit is milli metre and a feature is given in liter the scaled quantity will be in milli metere cubed
• features are now maintained centrally and referenced in modules, entities using the FeatureRegistry, where any feature is referenced upon creation
• it is now possible to annotate a list of evidences to a feature
• added formatters that display quantities in human readable format
• updated units of measurement reference implementation to indriya

Simulation

• switch internally from calculations with concentration quantities to primitive doubles, which results in about two-fold speedup
• the concentration handling api has not changed, concentrations can still be initialized and retrieved in arbitrary concentration quantities
• fixed a problem in the simulation of clathrin mediated endocytosis, where aborting pits were not correctly removed
• added modules for point like agents to change state when interacting with line like agents
• added modules for point like agents to change state when interacting with volume like agents
• added uniform reaction equation and kinetic law formatting for export purposes in plain text or latex (using the chemfig package)
• reaction module implementations are now streamlined using composite and behavioural patterns
• it is now possible to use pre- or user defined kinetic laws for every reaction type
• it is now possible to formulate rule based reactions with dynamic reactants
• this is made possible by storing complex entities as trees that are traversed and modified according to modifications applied by dynamic reactions
• it is also possible to mix and match static and dynamic components
• every reaction is created using the ReactionBuilder
• a global error of the simulation is now evaluated in addition to the local error, this increases numerical stability for the combined simulation of fast and slow modules
• added simulation status class for easy simulation monitoring
• restructured and refactored observation of simulations, which is now separated in FlatUpdateRecorder and NestedUpdateRecorder
• it is now possible to singa-simulation with openjdk
• added builder pattern for the creation of membranes
• diffusion now also takes the geometry of adjacent spatial representations of nodes into account
• added module to simulate diffusion through porous membranes
• added builder pattern for concentration initialization
• added possibility to inject concentration into the simulation at arbitrary time points

Structure

• added possibility to retrieve gene name from uniprot
• added possibility to retrieve go terms from uniprot
• adapted updated EC numbering pattern

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>0.6.0</version>
</dependency>