cleberecht/singa: singa-all release v0.4.0

In this update we are migrating to our own domain singa.bio for packaging. Correspondingly, the maven group and all packages change from "de.bioforscher.singa" to "bio.singa". Sorry for any inconvinience this might cause.

Starting with this update, all versions will be prefixed by "v".

Updates and features

Mathematics

• affinity propagation clustering optimized

Features

• Identifiers (such as UniProtIdentifier or ECNumber) are now considered to be Features and can be automatically annotated.
• Features are now resolved recursively, if the relevant FeatureProviders are available
• Alternative strategies to resolve Features can be assigned to FeatureProviders

Structure

• Structures can be renumbered consecutively
• Fit3D core algorithm substantially improved (up to 10fold speed-up)
• Quaterion superimposition replaces the Kabsch algorithm

Simulation

The simulation module has been remodeled substantially.

• Modules are now divided into ConcentrationBasedModules and DisplacementBasedModules
• ConcentrationBasedModules apply Updates based on their Scope and Specificity
• DisplacementBasedModules apply updates to the newly introduced agent based simulation layer
• using the agent based simulation layer vesicle movement can be simulated
• this also allows for a macroscopic instead of an implicit definition of membranes
• Compartments are now implemented as Subsections assigned to a Topology
• ComplexBuildingReactions allow for Subsection changing Reactions (e.g. Receptor in Membrane binding Ligand in Cytoplasm)
• ChemicalEnitites can be anchored in membranes, preventing Diffusion
• Gifs of Graphs can be created during simulation for visualization
• ReactionRates have been remodeled

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>0.4.0</version>
</dependency>