compile

The following is a list of compile dependencies for this project. These dependencies are required to compile and run the application:

compile

The following is a list of compile dependencies for this project. These dependencies are required to compile and run the application:

runtime

The following is a list of runtime dependencies for this project. These dependencies are required to run the application:

Dependency Tree

• org.draegerlab:sbscl:jar:2.1

  Systems Biology Simulation Core Library (SBSCL)

  Description: The Systems Biology Simulation Core Library provides an efficient and exhaustive Java™ implementation of methods to interpret the content of models encoded in the Systems Biology Markup Language (SBML) and its numerical solution. This library is based on the JSBML project. It can be used on every operating system for which a Java Virtual Machine is available. Version 2.0 and beyond support simulation in three frameworks: constraint-based analysis, stochastic simulation, and ordinary differential equation systems. SBSCL supports SED-ML and COMBINE archives in OMEX format. URL: https://github.com/draeger-lab/SBSCL/ Project Licenses: GNU Lesser General Public License

  • junit:junit:jar:4.13.1 (compile)

    JUnit
    Description: JUnit is a unit testing framework for Java, created by Erich Gamma and Kent Beck. URL: http://junit.org Project Licenses: Eclipse Public License 1.0

    • org.hamcrest:hamcrest-core:jar:1.3 (compile)

      Hamcrest Core
      Description: This is the core API of hamcrest matcher framework to be used by third-party framework providers. This includes the a foundation set of matcher implementations for common operations. URL: https://github.com/hamcrest/JavaHamcrest/hamcrest-core Project Licenses: New BSD License

  • org.sbml.jsbml:jsbml:jar:1.5 (compile)

    JSBML
    Description: JSBML is a community-driven project to create a free, open-source, pure Java library for reading, writing, and manipulating SBML files and data streams. URL: http://www.sbml.org/Software/JSBML Project Licenses: LGPL License, Licensing and Distribution Terms for JSBML

    • org.sbml.jsbml:jsbml-core:jar:1.5 (compile)

      jsbml-core
      Description: JSBML is a community-driven project to create a free, open-source, pure Java library for reading, writing, and manipulating SBML files and data streams. URL: http://www.sbml.org/Software/JSBML/jsbml-core Project Licenses: LGPL License, Licensing and Distribution Terms for JSBML

      • org.apache.logging.log4j:log4j-core:jar:2.3 (compile)

        Apache Log4j Core
        Description: The Apache Log4j Implementation URL: http://logging.apache.org/log4j/2.x/log4j-core/ Project Licenses: The Apache Software License, Version 2.0

        • org.apache.logging.log4j:log4j-api:jar:2.3 (compile)

          Apache Log4j API
          Description: The Apache Log4j API URL: http://logging.apache.org/log4j/2.x/log4j-api/ Project Licenses: The Apache Software License, Version 2.0

      • org.apache.logging.log4j:log4j-1.2-api:jar:2.3 (compile)

        Apache Log4j 1.x Compatibility API
        Description: The Apache Log4j 1.x Compatibility API URL: http://logging.apache.org/log4j/2.x/log4j-1.2-api/ Project Licenses: The Apache Software License, Version 2.0

      • com.fasterxml.woodstox:woodstox-core:jar:5.0.1 (compile)

        Woodstox
        Description: Woodstox is a high-performance XML processor that implements Stax (JSR-173), SAX2 and Stax2 APIs URL: https://github.com/FasterXML/woodstox Project Licenses: The Apache License, Version 2.0

        • org.codehaus.woodstox:stax2-api:jar:3.1.4 (compile)

          Stax2 API
          Description: tax2 API is an extension to basic Stax 1.0 API that adds significant new functionality, such as full-featured bi-direction validation interface and high-performance Typed Access API. URL: http://wiki.fasterxml.com/WoodstoxStax2 Project Licenses: The BSD License

      • org.w3c.jigsaw:jigsaw:jar:2.2.6 (compile)

        W3C Jigsaw
        Description: Jigsaw is W3C's leading-edge Web server platform, providing a sample HTTP 1.1 implementation and a variety of other features on top of an advanced architecture implemented in Java. URL: http://www.w3.org/Jigsaw/ Project Licenses: W3C Software License

      • org.biojava:biojava-ontology:jar:4.0.0 (compile)

        biojava-ontology

        Description: BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It provides analytical and statistical routines, parsers for common file formats and allows the manipulation of sequences and 3D structures. The goal of the biojava project is to facilitate rapid application development for bioinformatics. URL: http://maven.apache.org Project Licenses: GNU LGPL v2

        • org.apache.logging.log4j:log4j-slf4j-impl:jar:2.1 (runtime)

          Apache Log4j SLF4J Binding
          Description: The Apache Log4j SLF4J API binding to Log4j 2 Core URL: http://logging.apache.org/log4j/2.x/log4j-slf4j-impl/ Project Licenses: The Apache Software License, Version 2.0

      • com.thoughtworks.xstream:xstream:jar:1.4.9 (compile)

        XStream Core
        Description: XStream is a serialization library from Java objects to XML and back. URL: http://x-stream.github.io/xstream Project Licenses: BSD style

        • xmlpull:xmlpull:jar:1.1.3.1 (compile)

          XML Pull Parsing API
          Description: There is currently no description associated with this project. URL: http://www.xmlpull.org Project Licenses: Public Domain

        • xpp3:xpp3_min:jar:1.1.4c (compile)

          MXP1: Xml Pull Parser 3rd Edition (XPP3)
          Description: MXP1 is a stable XmlPull parsing engine that is based on ideas from XPP and in particular XPP2 but completely revised and rewritten to take the best advantage of latest JIT JVMs such as Hotspot in JDK 1.4+. URL: http://www.extreme.indiana.edu/xgws/xsoap/xpp/mxp1/ Project Licenses: Indiana University Extreme! Lab Software License, vesion 1.1.1, Public Domain

      • com.fasterxml.staxmate:staxmate:jar:2.3.0 (compile)

        StaxMate

        Description: StaxMate is a light-weight framework that adds convenience to streaming XML-processing without significant additional overhead. It builds on top of a Stax (JSR-173) compliant XML processors such as Woodstox or Sjsxp (default Stax implementation of JDK 1.6) and offers two basic abstractions: Cursors, which build on XMLStreamReaders and Output objects, which build on XMLStreamWriters. URL: http://staxmate.codehaus.org Project Licenses: BSD

    • org.sbml.jsbml.ext:jsbml-arrays:jar:1.5 (compile)

      jsbml-arrays
      Description: JSBML is a community-driven project to create a free, open-source, pure Java library for reading, writing, and manipulating SBML files and data streams. URL: http://www.sbml.org/Software/JSBML/ext/jsbml-arrays Project Licenses: LGPL License, Licensing and Distribution Terms for JSBML

    • org.sbml.jsbml.ext:jsbml-comp:jar:1.5 (compile)

      jsbml-comp
      Description: JSBML is a community-driven project to create a free, open-source, pure Java library for reading, writing, and manipulating SBML files and data streams. URL: http://www.sbml.org/Software/JSBML/ext/jsbml-comp Project Licenses: LGPL License, Licensing and Distribution Terms for JSBML

    • org.sbml.jsbml.ext:jsbml-distrib:jar:1.5 (compile)

      jsbml-distrib
      Description: JSBML is a community-driven project to create a free, open-source, pure Java library for reading, writing, and manipulating SBML files and data streams. URL: http://www.sbml.org/Software/JSBML/ext/jsbml-distrib Project Licenses: LGPL License, Licensing and Distribution Terms for JSBML

    • org.sbml.jsbml.ext:jsbml-dyn:jar:1.5 (compile)

      jsbml-dyn
      Description: JSBML is a community-driven project to create a free, open-source, pure Java library for reading, writing, and manipulating SBML files and data streams. URL: http://www.sbml.org/Software/JSBML/ext/jsbml-dyn Project Licenses: LGPL License, Licensing and Distribution Terms for JSBML

    • org.sbml.jsbml.ext:jsbml-fbc:jar:1.5 (compile)

      jsbml-fbc
      Description: JSBML is a community-driven project to create a free, open-source, pure Java library for reading, writing, and manipulating SBML files and data streams. URL: http://www.sbml.org/Software/JSBML/ext/jsbml-fbc Project Licenses: LGPL License, Licensing and Distribution Terms for JSBML

    • org.sbml.jsbml.ext:jsbml-groups:jar:1.5 (compile)

      jsbml-groups
      Description: JSBML is a community-driven project to create a free, open-source, pure Java library for reading, writing, and manipulating SBML files and data streams. URL: http://www.sbml.org/Software/JSBML/ext/jsbml-groups Project Licenses: LGPL License, Licensing and Distribution Terms for JSBML

    • org.sbml.jsbml.ext:jsbml-layout:jar:1.5 (compile)

      jsbml-layout
      Description: JSBML is a community-driven project to create a free, open-source, pure Java library for reading, writing, and manipulating SBML files and data streams. URL: http://www.sbml.org/Software/JSBML/ext/jsbml-layout Project Licenses: LGPL License, Licensing and Distribution Terms for JSBML

    • org.sbml.jsbml.ext:jsbml-multi:jar:1.5 (compile)

      jsbml-multi
      Description: JSBML is a community-driven project to create a free, open-source, pure Java library for reading, writing, and manipulating SBML files and data streams. URL: http://www.sbml.org/Software/JSBML/ext/jsbml-multi Project Licenses: LGPL License, Licensing and Distribution Terms for JSBML

    • org.sbml.jsbml.ext:jsbml-qual:jar:1.5 (compile)

      jsbml-qual
      Description: JSBML is a community-driven project to create a free, open-source, pure Java library for reading, writing, and manipulating SBML files and data streams. URL: http://www.sbml.org/Software/JSBML/ext/jsbml-qual Project Licenses: LGPL License, Licensing and Distribution Terms for JSBML

    • org.sbml.jsbml.ext:jsbml-render:jar:1.5 (compile)

      jsbml-render
      Description: JSBML is a community-driven project to create a free, open-source, pure Java library for reading, writing, and manipulating SBML files and data streams. URL: http://www.sbml.org/Software/JSBML/ext/jsbml-render Project Licenses: LGPL License, Licensing and Distribution Terms for JSBML

    • org.sbml.jsbml.ext:jsbml-req:jar:1.5 (compile)

      jsbml-req
      Description: JSBML is a community-driven project to create a free, open-source, pure Java library for reading, writing, and manipulating SBML files and data streams. URL: http://www.sbml.org/Software/JSBML/ext/jsbml-req Project Licenses: LGPL License, Licensing and Distribution Terms for JSBML

    • org.sbml.jsbml.ext:jsbml-spatial:jar:1.5 (compile)

      jsbml-spatial
      Description: JSBML is a community-driven project to create a free, open-source, pure Java library for reading, writing, and manipulating SBML files and data streams. URL: http://www.sbml.org/Software/JSBML/ext/jsbml-spatial Project Licenses: LGPL License, Licensing and Distribution Terms for JSBML

    • org.sbml.jsbml.modules:jsbml-tidy:jar:1.5 (compile)

      jsbml-tidy
      Description: JSBML is a community-driven project to create a free, open-source, pure Java library for reading, writing, and manipulating SBML files and data streams. URL: http://www.sbml.org/Software/JSBML/modules/jsbml-tidy Project Licenses: LGPL License, Licensing and Distribution Terms for JSBML

      • net.sf.jtidy:jtidy:jar:r938 (compile)

        JTidy

        Description: JTidy is a Java port of HTML Tidy, a HTML syntax checker and pretty printer. Like its non-Java cousin, JTidy can be used as a tool for cleaning up malformed and faulty HTML. In addition, JTidy provides a DOM interface to the document that is being processed, which effectively makes you able to use JTidy as a DOM parser for real-world HTML. URL: http://jtidy.sourceforge.net Project Licenses: Java HTML Tidy License

  • org.jdom:jdom2:jar:2.0.5 (compile)

    JDOM
    Description: A complete, Java-based solution for accessing, manipulating, and outputting XML data URL: http://www.jdom.org Project Licenses: Similar to Apache License but with the acknowledgment clause removed

  • org.jmathml:jmathml:jar:2.1.0 (compile)

    JMathml library
    Description: Supports the subset of MathML that is used in systems biology standard data formats. URL: http://www.jmathml.org Project Licenses: MIT

    • org.jdom:jdom:jar:1.1 (compile)

      JDOM

      Description: JDOM is, quite simply, a Java representation of an XML document. JDOM provides a way to represent that document for easy and efficient reading, manipulation, and writing. It has a straightforward API, is a lightweight and fast, and is optimized for the Java programmer. It's an alternative to DOM and SAX, although it integrates well with both DOM and SAX. URL: http://www.jdom.org/ Project Licenses: No licenses are defined for this project.

    • commons-io:commons-io:jar:1.4 (compile)

      Commons IO
      Description: Commons-IO contains utility classes, stream implementations, file filters, file comparators and endian classes. URL: http://commons.apache.org/io/ Project Licenses: The Apache Software License, Version 2.0

  • org.jlibsedml:jlibsedml:jar:2.2.3 (compile)

    Jlibsedml library
    Description: Java library for reading, writing, validating and working with SED-ML files. URL: http://jlibsedml.sf.net/jlibsedml Project Licenses: MIT

    • org.slf4j:slf4j-api:jar:1.7.13 (compile)

      SLF4J API Module
      Description: The slf4j API URL: http://www.slf4j.org Project Licenses: MIT License

    • commons-lang:commons-lang:jar:2.6 (compile)

      Commons Lang
      Description: Commons Lang, a package of Java utility classes for the classes that are in java.lang's hierarchy, or are considered to be so standard as to justify existence in java.lang. URL: http://commons.apache.org/lang/ Project Licenses: The Apache Software License, Version 2.0

    • jaxen:jaxen:jar:1.1.1 (compile)
      • dom4j:dom4j:jar:1.6.1 (compile)

        dom4j
        Description: dom4j: the flexible XML framework for Java URL: http://dom4j.org Project Licenses: No licenses are defined for this project.

      • jdom:jdom:jar:1.0 (compile)

        jdom
        Description: There is currently no description associated with this project. Project Licenses: No licenses are defined for this project.

      • xml-apis:xml-apis:jar:1.3.02 (compile)

        xml-apis
        Description: There is currently no description associated with this project. URL: http://xml.apache.org/commons/#external Project Licenses: No licenses are defined for this project.

      • xerces:xercesImpl:jar:2.6.2 (compile)

        xercesImpl
        Description: There is currently no description associated with this project. Project Licenses: No licenses are defined for this project.

    • xom:xom:jar:1.2.5 (compile)

      XOM
      Description: The XOM Dual Streaming/Tree API for Processing XML URL: http://xom.nu Project Licenses: The GNU Lesser General Public License, Version 2.1

      • xalan:xalan:jar:2.7.0 (compile)

        xalan
        Description: There is currently no description associated with this project. Project Licenses: No licenses are defined for this project.

    • org.jdom:jdom-contrib:jar:1.1.3 (compile)

      JDOM
      Description: A complete, Java-based solution for accessing, manipulating, and outputting XML data URL: http://www.jdom.org Project Licenses: Similar to Apache License but with the acknowledgment clause removed

  • org.apache.commons:commons-math:jar:2.2 (compile)

    Commons Math
    Description: The Math project is a library of lightweight, self-contained mathematics and statistics components addressing the most common practical problems not immediately available in the Java programming language or commons-lang. URL: http://commons.apache.org/math/ Project Licenses: The Apache Software License, Version 2.0

  • org.apache.commons:commons-lang3:jar:3.7 (compile)

    Apache Commons Lang
    Description: Apache Commons Lang, a package of Java utility classes for the classes that are in java.lang's hierarchy, or are considered to be so standard as to justify existence in java.lang. URL: http://commons.apache.org/proper/commons-lang/ Project Licenses: Apache License, Version 2.0

  • org.jfree:jfreechart:jar:1.0.19 (compile)

    JFreeChart
    Description: JFreeChart is a class library, written in Java, for generating charts. Utilising the Java2D APIs, it currently supports bar charts, pie charts, line charts, XY-plots and time series plots. URL: http://www.jfree.org/jfreechart/ Project Licenses: GNU Lesser General Public Licence

    • org.jfree:jcommon:jar:1.0.23 (compile)

      JCommon
      Description: JCommon is a free general purpose Java class library that is used in several projects at www.jfree.org, including JFreeChart and JFreeReport. URL: http://www.jfree.org/jcommon/ Project Licenses: GNU Lesser General Public Licence

  • com.blazegraph:colt:jar:2.1.4 (compile)

    Blazegraph Colt

    Description: Blazegraph Modifications to the Colt libraries to remove hep.aida. Forked under LGPL 2.1 from the original license: Copyright (c) 1999 CERN - European Organization for Nuclear Research. Permission to use, copy, modify, distribute and sell this software and its documentation for any purpose is hereby granted without fee, provided that the above copyright notice appear in all copies and that both that copyright notice and this permission notice appear in supporting documentation. CERN makes no representations about the suitability of this software for any purpose. It is provided "as is" without expressed or implied warranty. URL: http://www.blazegraph.com/colt/ Project Licenses: GNU LESSER GENERAL PUBLIC LICENSE Version 2.1

    • concurrent:concurrent:jar:1.3.4 (compile)

      Dough Lea's util.concurrent package
      Description: There is currently no description associated with this project. Project Licenses: Public domain, Sun Microsoystems

  • scpsolver:SCPSolver:jar:1.0v2 (compile)

    SCPSolver
    Description: POM was created from install:install-file Project Licenses: No licenses are defined for this project.

  • scpsolver:GLPKSolverPack:jar:4.35v2 (compile)

    GLPKSolverPack
    Description: POM was created from install:install-file Project Licenses: No licenses are defined for this project.

  • scpsolver:LPSOLVESolverPack:jar:5.5.2.5 (compile)

    LPSOLVESolverPack
    Description: POM was created from install:install-file Project Licenses: No licenses are defined for this project.

  • kisao:libkisao:jar:1.0.3.1-rc (compile)

    libkisao
    Description: POM was created from install:install-file Project Licenses: No licenses are defined for this project.

  • de.uni-rostock.sbi:CombineArchive:jar:1.3.6 (compile)

    CombineArchive
    Description: Library to read/create/write/manipulate/... COMBINE archives URL: http://sems.uni-rostock.de/projects/combinearchive/ Project Licenses: BSD 3Clause

    • de.binfalse:BFLog:jar:1.3.3 (compile)

      BFLog
      Description: Simple but efficient logging facility URL: https://github.com/binfalse/BFLog Project Licenses: The Clear BSD License

    • com.googlecode.json-simple:json-simple:jar:1.1.1 (compile)

      JSON.simple
      Description: A simple Java toolkit for JSON URL: http://code.google.com/p/json-simple/ Project Licenses: The Apache Software License, Version 2.0