Exploring Open-Source Software for Systems Science and Modeling

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Introduction:

Open-source software plays a crucial role in advancing systems science and modeling by providing accessible tools for practitioners, researchers, and educators across various domains. From decision support and optimization to network analysis and beyond, a diverse array of open-source programs exists to support systems thinking and modeling in a wide range of applications. In this article, we’ll introduce you to some of the key types of open-source software available and provide a meaningful typology to help you navigate the options for your specific needs.

1. Decision Support and Optimization:

Decision support and optimization software help users make informed decisions and optimize complex systems. Programs like OpenSolver, OptaPlanner, and Pyomo offer tools for solving linear programming, integer programming, and nonlinear optimization problems, making them invaluable for decision-makers in business, engineering, and logistics.

2. Data Mining and Machine Learning:

Data mining and machine learning tools enable users to extract insights from data and build predictive models. Platforms like Orange and scikit-learn provide a wide range of algorithms for classification, regression, clustering, and more, empowering users to analyze complex datasets and uncover hidden patterns and relationships.

3. Network Analysis and Visualization:

Network analysis and visualization software allow users to explore and analyze complex networks, such as social networks, biological networks, and transportation networks. Programs like Cytoscape, Graph-tool, and NodeXL offer tools for visualizing network structures, identifying key nodes and connections, and analyzing network properties and dynamics.

4. Probabilistic Programming and Bayesian Inference:

Probabilistic programming languages enable users to build and fit Bayesian statistical models, allowing for uncertainty quantification and inference. Platforms like Stan provide tools for Bayesian modeling, Markov chain Monte Carlo (MCMC) sampling, and variational inference, facilitating robust statistical analysis and decision-making in diverse fields.

5. Simulation and Modeling:

Simulation and modeling software help users simulate and analyze complex systems, allowing for scenario testing, policy evaluation, and strategic planning. Tools like Insight Maker, Vensim, and AnyLogic offer user-friendly interfaces for building and simulating dynamic models, making them suitable for educators, researchers, and practitioners alike.

Conclusion:

As systems science and modeling continue to play an increasingly important role in addressing complex challenges in our interconnected world, open-source software provides essential tools and resources for understanding, analyzing, and managing complex systems. Whether you’re a business analyst, researcher, educator, or student, the wide variety of open-source programs available offer valuable support for your systems thinking and modeling endeavors. By exploring and utilizing these tools, you can enhance your ability to tackle real-world problems and contribute to the advancement of systems science and modeling in your respective field.

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Directory

Here’s a directory of websites dedicated to providing open-source software related to systems science and its subdisciplines:

1. Insight Maker

  • Summary: A web-based modeling and simulation platform that allows users to create and share system dynamics models, agent-based models, and other types of simulations.
  • First Release Date: 2010
  • Programming Language: JavaScript, HTML5
  • Mathematics Involved: System dynamics, agent-based modeling, discrete-event simulation.
  • Web Address: [https://insightmaker.com/]

2. Vensim

  • Summary: A software tool for building and simulating dynamic models, particularly in the field of system dynamics.
  • First Release Date: 1983
  • Programming Language: C
  • Mathematics Involved: System dynamics, differential equations.
  • Web Address: [https://vensim.com/]

3. NetLogo

  • Summary: An open-source programming environment for building agent-based models and simulations, widely used in research and education.
  • First Release Date: 1999
  • Programming Language: Java
  • Mathematics Involved: Agent-based modeling, cellular automata.
  • Web Address: [https://ccl.northwestern.edu/netlogo/]

4. Gephi

  • Summary: An open-source network visualization and analysis tool that helps users explore, analyze, and visualize complex networks.
  • First Release Date: 2008
  • Programming Language: Java
  • Mathematics Involved: Graph theory, statistical analysis.
  • Web Address: [https://gephi.org/]

5. Kumu

  • Summary: A web-based platform for mapping and analyzing relationships in complex systems, offering tools for visualizing networks and conducting network analysis.
  • First Release Date: 2012
  • Programming Language: JavaScript
  • Mathematics Involved: Graph theory, network analysis. 
  • Web Address: [https://kumu.io/]

6. PythonSciPy

  • Summary: A versatile programming language widely used in systems science and related fields, with numerous libraries and packages for modeling, simulation, data analysis, and visualization.
  • First Release Date: 2001
  • Programming Language: Python
  • Mathematics Involved: Numerical analysis, linear algebra, optimization.
  • Web Address: [https://www.python.org/]

7. R Project for Statistical Computing

  • Summary: An open-source programming language and software environment for statistical computing and graphics, commonly used in systems science research and analysis.
  • First Release Date: 1995
  • Programming Language: R
  • Mathematics Involved: Statistical analysis, data visualization, machine learning. 
  • Web Address: [https://www.r-project.org/]

8. AnyLogic PLE

  • Summary: A free version of AnyLogic, a multi-method simulation software for modeling complex systems using system dynamics, agent-based modeling, and discrete-event simulation.
  • First Release Date: 2000
  • Programming Language: Java
  • Mathematics Involved: System dynamics, agent-based modeling, discrete-event simulation.
  • Web Address: [https://www.anylogic.com/downloads/personal-learning-edition/]

9. SageMath

  • Summary: An open-source mathematics software system that supports a wide range of mathematical operations and computations, including symbolic and numerical mathematics.
  • First Release Date: 2005
  • Programming Language: Python, Cython
  • Mathematics Involved: Algebra, calculus, number theory.
  • Web Address: [https://www.sagemath.org/]

10. GNU Octave

  • Summary: An open-source numerical computing environment similar to MATLAB, widely used for mathematical and scientific computing tasks.
  • First Release Date: 1992
  • Programming Language: C, C++
  • Mathematics Involved: Numerical analysis, linear algebra, signal processing.
  • Web Address: [https://www.gnu.org/software/octave/]

11. SAS University Edition

  • Summary: A free version of SAS software for learning and teaching purposes, offering tools for data analysis, statistical modeling, and predictive analytics.
  • First Release Date: 2014
  • Programming Language: SAS, Python, R
  • Mathematics Involved: Statistical analysis, data mining, machine learning.
  • Web Address: [https://www.sas.com/en_us/software/university-edition.html]

12. SciPy

  • Summary: An open-source scientific computing library for Python, offering tools for optimization, integration, interpolation, and other numerical tasks commonly used in systems science research.
  • First Release Date: 2001
  • Programming Language: Python
  • Mathematics Involved: Numerical analysis, linear algebra, optimization.
  • Web Address: [https://www.scipy.org/]

13. SymPy

  • Summary: An open-source symbolic mathematics library for Python, providing tools for symbolic computation, algebraic manipulation, and calculus operations.
  • Summary: An open-source discrete-event simulation library for Python, offering tools for modeling and simulating complex systems with discrete changes over time.   
  • First Release Date: 2007
  • Programming Language: Python
  • Mathematics Involved: Symbolic computation, algebra, calculus.
  • Web Address: [https://www.sympy.org/]

14. OpenMx

  • Summary: An open-source package for structural equation modeling (SEM) and other advanced statistical methods, implemented in the R programming language.
  • First Release Date: 2007
  • Programming Language: R
  • Mathematics Involved: Structural equation modeling, covariance structure modeling.
  • Web Address: [https://openmx.ssri.psu.edu/]

15. Jupyter Notebook

  • Summary: An open-source web application that allows users to create and share documents containing live code, equations, visualizations, and narrative text, making it an ideal tool for interactive computing and data analysis.
  • First Release Date: 2011
  • Programming Language: Python, JavaScript
  • Mathematics Involved: Interactive computing, data visualization, symbolic mathematics.
  • Web Address: [https://jupyter.org/]

16. Modelica

  • Summary: An open-standard modeling language for describing and simulating complex physical and cyber-physical systems, widely used in engineering and systems science disciplines.
  • First Release Date: 1997
  • Programming Language: Modelica
  • Mathematics Involved: Modeling and simulation of physical systems.
  • Web Address: [https://www.modelica.org/]

18. PyDSTool

  • Summary: An open-source simulation and modeling toolkit for dynamical systems, offering tools for analyzing and simulating complex systems described by ordinary differential equations (ODEs) and differential algebraic equations (DAEs).
  • First Release Date: 2004
  • Programming Language: Python
  • Mathematics Involved: Dynamical systems theory, differential equations.
  • Web Address: [https://pydstool.github.io/]

19. OpenSolver

  • Summary: An open-source Excel add-in for optimization modeling and solving, allowing users to build and solve linear, nonlinear, and integer optimization problems directly within Microsoft Excel.
  • First Release Date: 2008
  • Programming Language: Excel VBA (Visual Basic for Applications)
  • Mathematics Involved: Linear programming, integer programming, nonlinear optimization.
  • Web Address: [https://opensolver.org/]

20. OptaPlanner

  • Summary: An open-source constraint satisfaction solver and optimization engine for Java, offering tools for solving planning and scheduling problems, resource allocation, and other optimization challenges.
  • First Release Date: 2011
  • Programming Language: Java
  • Mathematics Involved: Constraint satisfaction, metaheuristic optimization
  • Web Address: [https://www.optaplanner.org/]

21. Orange

  • Summary: An open-source data mining and machine learning toolkit, offering tools for visual programming, data visualization, predictive modeling, and knowledge discovery.
  • First Release Date: 1996
  • Programming Language: Python
  • Mathematics Involved: Machine learning algorithms, statistical methods.
  • Web Address: [https://orange.biolab.si/]

22. Cytoscape

  • Summary: An open-source platform for visualizing and analyzing complex networks, widely used in bioinformatics, systems biology, and social network analysis.
  • First Release Date: 2002
  • Programming Language: Java
  • Mathematics Involved: Graph theory, network analysis.
  • Web Address: [https://cytoscape.org/]

23. Graph-tool

  • Summary: An open-source Python library for statistical analysis of graphs and networks, offering tools for network modeling, analysis, and visualization.
  • First Release Date: 2004
  • Programming Language: C++, Python
  • Mathematics Involved: Graph theory, statistical analysis.
  • Web Address: [https://graph-tool.skewed.de/]

24. NodeXL

  • Summary: An open-source Excel add-in for network analysis and visualization, providing tools for exploring and analyzing social networks, organizational networks, and other network datasets.
  • First Release Date: 2008
  • Programming Language: C#, .NET
  • Mathematics Involved: Graph theory, social network analysis.
  • Web Address: [https://www.smrfoundation.org/nodexl/]

25. Pyomo

  • Summary: An open-source Python optimization modeling language for building and solving mathematical optimization models, offering tools for linear programming, mixed-integer programming, and nonlinear optimization.
  • First Release Date: 2008
  • Programming Language: Python
  • Mathematics Involved: Mathematical optimization, linear algebra.
  • Web Address: [http://www.pyomo.org/]

26. Stan

  • Summary: An open-source probabilistic programming language for Bayesian statistical modeling, offering tools for building and fitting hierarchical models, Markov chain Monte Carlo (MCMC) sampling, and variational inference.
  • First Release Date: 2012
  • Programming Language: C++, R, Python
  • Mathematics Involved: Bayesian statistics, probability theory.
  • Web Address: [https://mc-stan.org/]

27. Pajek

  • Summary: An open-source program for large network analysis and visualization, offering tools for exploring and analyzing large-scale networks, with applications in social network analysis, citation analysis, and more.
  • First Release Date: 1996
  • Programming Language: C++
  • Mathematics Involved: Graph theory, network analysis.
  • Web Address: [http://mrvar.fdv.uni-lj.si/pajek/]

These open-source software tools cover a range of applications in decision support, knowledge management, business analysis, optimization, network analysis, and hierarchy analysis. Whether you’re interested in solving optimization problems, analyzing networks, or building predictive models, these platforms offer valuable resources to support your work and research.

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