Merge pull request #53 from hemilpanchiwala/fern

Add stochastic simulation through FERN to SBSCL
draeger-lab · Jul 20, 2020 · 8d5715d · 8d5715d
2 parents c0d1077 + 52e6395
commit 8d5715d
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diff --git a/.gitignore b/.gitignore
@@ -27,4 +27,20 @@ src/test/resources/sbml-test-suite/
 
 # log files
 *.log
+
+# Maven
+target/
+pom.xml.tag
+pom.xml.releaseBackup
+pom.xml.versionsBackup
+pom.xml.next
+release.properties
+dependency-reduced-pom.xml
+buildNumber.properties
+.mvn/timing.properties
+.mvn/wrapper/maven-wrapper.jar
+.flattened-pom.xml
+
+# Eclipse
+**/.metadata
 /bin/
diff --git a/FernMLSchema.xsd b/FernMLSchema.xsd
@@ -0,0 +1,83 @@
+<?xml version="1.0" encoding="utf-8"?>
+<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema">
+  <xsd:element name="fernml" type="FERNML">
+    <xsd:key name="speciesKey">
+      <xsd:selector xpath="./listOfSpecies/species" />
+      <xsd:field xpath="@name" />
+    </xsd:key>
+    <xsd:keyref name="listOfSpecieslistOfReactants" refer="speciesKey">
+      <xsd:selector xpath="listOfReactions/reaction/listOfReactants/speciesReference" />
+      <xsd:field xpath="@name" />
+    </xsd:keyref>
+    <xsd:keyref name="listOfSpecieslistOfProducts" refer="speciesKey">
+      <xsd:selector xpath="listOfReactions/reaction/listOfProducts/speciesReference" />
+      <xsd:field xpath="@name" />
+    </xsd:keyref>
+  </xsd:element>
+  <xsd:complexType name="FERNML">
+    <xsd:complexContent>
+      <xsd:extension base="RNBase">
+        <xsd:sequence>
+          <xsd:element name="listOfSpecies" type="ListOfSpecies" />
+          <xsd:element name="listOfReactions" type="ListOfReactions" />
+        </xsd:sequence>
+        <xsd:attribute name="version" type="xsd:string" use="required" />
+      </xsd:extension>
+    </xsd:complexContent>
+  </xsd:complexType>
+  <xsd:complexType name="ListOfSpecies">
+    <xsd:sequence>
+      <xsd:element name="species" type="Species" minOccurs="1" maxOccurs="unbounded" />
+    </xsd:sequence>
+  </xsd:complexType>
+  <xsd:complexType name="ListOfReactions">
+    <xsd:sequence>
+      <xsd:element name="reaction" type="Reaction" minOccurs="1" maxOccurs="unbounded" />
+    </xsd:sequence>
+  </xsd:complexType>
+  <xsd:complexType name="Species">
+    <xsd:complexContent>
+      <xsd:extension base="RNBase">
+        <xsd:attribute name="initialAmount" type="xsd:float" use="required" />
+        <xsd:attribute name="name" type="xsd:string" use="required" />
+      </xsd:extension>
+    </xsd:complexContent>
+  </xsd:complexType>
+  <xsd:complexType name="Reaction">
+    <xsd:complexContent>
+      <xsd:extension base="RNBase">
+        <xsd:sequence>
+          <xsd:element name="listOfReactants" type="ListOfSpeciesReferences" />
+          <xsd:element name="listOfProducts" type="ListOfSpeciesReferences" />
+        </xsd:sequence>
+        <xsd:attribute name="kineticConstant" type="xsd:float" use="required" />
+        <xsd:attribute name="kineticConstantReversible" type="xsd:float" use="optional" />
+      </xsd:extension>
+    </xsd:complexContent>
+  </xsd:complexType>
+  <xsd:complexType name="ListOfSpeciesReferences">
+    <xsd:sequence>
+      <xsd:element name="speciesReference" type="SpeciesReference" minOccurs="1" maxOccurs="unbounded" />
+    </xsd:sequence>
+  </xsd:complexType>
+  <xsd:complexType name="SpeciesReference">
+    <xsd:attribute name="name" type="xsd:string" use="required" />
+  </xsd:complexType>
+  <xsd:complexType name="RNBase">
+    <xsd:sequence>
+      <xsd:element name="listOfAnnotations" type="ListOfAnnotations" minOccurs="0" />
+    </xsd:sequence>
+  </xsd:complexType>
+  <xsd:complexType name="ListOfAnnotations">
+    <xsd:sequence>
+      <xsd:element name="annotation" type="Annotation" minOccurs="1" maxOccurs="unbounded" />
+    </xsd:sequence>
+  </xsd:complexType>
+  <xsd:complexType name="Annotation">
+    <xsd:simpleContent>
+      <xsd:extension base="xsd:string">
+        <xsd:attribute name="name" type="xsd:string" use="required" />
+      </xsd:extension>
+    </xsd:simpleContent>
+  </xsd:complexType>
+</xsd:schema>
diff --git a/README.md b/README.md
@@ -1,67 +1,67 @@
-# The Systems Biology Simulation Core Library
-
-[![License (LGPL version 3)](https://img.shields.io/badge/license-LGPLv3.0-blue.svg?style=plastic)](http://opensource.org/licenses/LGPL-3.0)
-[![Latest version](https://img.shields.io/badge/Latest_version-1.4.0-brightgreen.svg?style=plastic)](https://github.com/draeger-lab/SBSCL/releases/)
-[![DOI](https://img.shields.io/badge/DOI-10.1186%2F1752--0509--7--55-blue.svg?style=plastic)](https://doi.org/10.1186/1752-0509-7-55)
-[![Build Status](https://travis-ci.com/draeger-lab/SBSCL.svg?branch=master&style=plastic)](https://travis-ci.com/draeger-lab/SBSCL)
-
-*Authors*: [Roland Keller](https://github.com/RolandKeller5), [Andreas Dräger](https://github.com/draeger), [Shalin Shah](https://github.com/shalinshah1993), [Matthias König](https://github.com/matthiaskoenig), [Alexander Dörr](https://github.com/a-doerr), [Richard Adams](https://github.com/otter606), [Nicolas Le Novère](https://github.com/lenov), [Max Zwiessele](https://github.com/mzwiessele)
-
-*Contributors to predecessor projects:* Philip Stevens, Marcel Kronfeld, Sandra Saliger, Simon Schäfer, Dieudonné Motsou Wouamba, Hannes Borch
-
-#### Description
-The Systems Biology Simulation Core Library (SBSCL) provides an efficient and exhaustive Java™ implementation of methods to interpret the content of models encoded in the Systems Biology Markup Language ([SBML](http://sbml.org)) and its numerical solution. This library is based on the [JSBML](http://sbml.org/Software/JSBML) project and can be used on every operating system for which a Java Virtual Machine is available. Please note that this project does not contain any user interface, neither a command-line interface, nor a graphical user interface. This project has been developed as a pure programming library. To support the [MIASE](http://co.mbine.org/standards/miase) effort, it understands [SED-ML](http://sed-ml.org) files. Its abstract type and interface hierarchy facilitates the implementation of further community standards, such as [CellML](https://www.cellml.org).
-
-When using this library, please cite: http://www.biomedcentral.com/1752-0509/7/55.
-
-#### Categories
-Bio-Informatics, Libraries, Simulations
-
-#### Features
-* Numerical simulation
-* Ordinary differential equation solver
-* Time-course analysis
-* Systems Biology Markup Language
-* Application programming interface
-
-#### Licensing terms
-
-This file is part of Simulation Core Library, a Java-based library for efficient numerical simulation of biological models.
-
-Copyright (C) 2007 jointly held by the individual authors.
-
-This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation. A copy of the license agreement is provided in the file named "LICENSE.txt" included with this software distribution and also available online as http://www.gnu.org/licenses/lgpl-3.0-standalone.html.
-
-Please cite the original work and the authors when using this program. See the [project homepage](https://draeger-lab.github.io/SBSCL/) for details.
-
-## Getting started
-
-For an introduction of how to use this library, please open the javadoc [homepage](https://draeger-lab.github.io/SBSCL/apidocs/overview-summary.html). There you can find instructions and source code examples, including some use cases. Once a maven build is ran, the binaries will be generated in the target folder. This folder will also include a JAR files of the simulation core library to work with.
-
-## File structure
-
-Just a brief explanation of the folders and files contained in this distribution.
-
-Most importantly, see 
- * the [`INSTALL.md`](INSTALL.md) file for instruction to run maven build
- * the docs folder containing an exhaustive documentation under apidocs
-
-The package structure in more detail:
-```
- /
- |- docs           -> Contains code for the maven built website
- |- src            -> The main source folder containing all the code and test files
-    |- assembly    -> assembly files for maven plugins
-    |- lib         -> 3rd party libraries needed for compilation and execution
-    |- main        -> Core java files of simulation library
-    |- test        -> JUnit test files along with resources required
-    |- site        -> Contains markup files, old javadoc, site.xml and other website 
-                      resources 
- |- LICENSE.txt    -> the license, under which this project is distributed
- |- pom.xml        -> Maven file for building the project
- |- README.md      -> this file
-```
-
-## Troubleshooting
-
-Please e-mail any bugs, problems, suggestions, or issues regarding this library to the bug tracker at https://github.com/draeger-lab/SBSCL/issues
+# The Systems Biology Simulation Core Library
+
+[![License (LGPL version 3)](https://img.shields.io/badge/license-LGPLv3.0-blue.svg?style=plastic)](http://opensource.org/licenses/LGPL-3.0)
+[![Latest version](https://img.shields.io/badge/Latest_version-1.4.0-brightgreen.svg?style=plastic)](https://github.com/draeger-lab/SBSCL/releases/)
+[![DOI](https://img.shields.io/badge/DOI-10.1186%2F1752--0509--7--55-blue.svg?style=plastic)](https://doi.org/10.1186/1752-0509-7-55)
+[![Build Status](https://travis-ci.com/draeger-lab/SBSCL.svg?branch=master&style=plastic)](https://travis-ci.com/draeger-lab/SBSCL)
+
+*Authors*: [Roland Keller](https://github.com/RolandKeller5), [Andreas Dräger](https://github.com/draeger), [Shalin Shah](https://github.com/shalinshah1993), [Matthias König](https://github.com/matthiaskoenig), [Alexander Dörr](https://github.com/a-doerr), [Richard Adams](https://github.com/otter606), [Nicolas Le Novère](https://github.com/lenov), [Max Zwiessele](https://github.com/mzwiessele)
+
+*Contributors to predecessor projects:* Philip Stevens, Marcel Kronfeld, Sandra Saliger, Simon Schäfer, Dieudonné Motsou Wouamba, Hannes Borch
+
+#### Description
+The Systems Biology Simulation Core Library (SBSCL) provides an efficient and exhaustive Java™ implementation of methods to interpret the content of models encoded in the Systems Biology Markup Language ([SBML](http://sbml.org)) and its numerical solution. This library is based on the [JSBML](http://sbml.org/Software/JSBML) project and can be used on every operating system for which a Java Virtual Machine is available. Please note that this project does not contain any user interface, neither a command-line interface, nor a graphical user interface. This project has been developed as a pure programming library. To support the [MIASE](http://co.mbine.org/standards/miase) effort, it understands [SED-ML](http://sed-ml.org) files. Its abstract type and interface hierarchy facilitates the implementation of further community standards, such as [CellML](https://www.cellml.org).
+
+When using this library, please cite: http://www.biomedcentral.com/1752-0509/7/55.
+
+#### Categories
+Bio-Informatics, Libraries, Simulations
+
+#### Features
+* Numerical simulation
+* Ordinary differential equation solver
+* Time-course analysis
+* Systems Biology Markup Language
+* Application programming interface
+
+#### Licensing terms
+
+This file is part of Simulation Core Library, a Java-based library for efficient numerical simulation of biological models.
+
+Copyright (C) 2007 jointly held by the individual authors.
+
+This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation. A copy of the license agreement is provided in the file named "LICENSE.txt" included with this software distribution and also available online as http://www.gnu.org/licenses/lgpl-3.0-standalone.html.
+
+Please cite the original work and the authors when using this program. See the [project homepage](https://draeger-lab.github.io/SBSCL/) for details.
+
+## Getting started
+
+For an introduction of how to use this library, please open the javadoc [homepage](https://draeger-lab.github.io/SBSCL/apidocs/overview-summary.html). There you can find instructions and source code examples, including some use cases. Once a maven build is ran, the binaries will be generated in the target folder. This folder will also include a JAR files of the simulation core library to work with.
+
+## File structure
+
+Just a brief explanation of the folders and files contained in this distribution.
+
+Most importantly, see 
+ * the [`INSTALL.md`](INSTALL.md) file for instruction to run maven build
+ * the docs folder containing an exhaustive documentation under apidocs
+
+The package structure in more detail:
+```
+ /
+ |- docs           -> Contains code for the maven built website
+ |- src            -> The main source folder containing all the code and test files
+    |- assembly    -> assembly files for maven plugins
+    |- lib         -> 3rd party libraries needed for compilation and execution
+    |- main        -> Core java files of simulation library
+    |- test        -> JUnit test files along with resources required
+    |- site        -> Contains markup files, old javadoc, site.xml and other website 
+                      resources 
+ |- LICENSE.txt    -> the license, under which this project is distributed
+ |- pom.xml        -> Maven file for building the project
+ |- README.md      -> this file
+```
+
+## Troubleshooting
+
+Please e-mail any bugs, problems, suggestions, or issues regarding this library to the bug tracker at https://github.com/draeger-lab/SBSCL/issues