The Front page and Main project page will temporarily redirect here while the original wiki server is being restored. Many of the wiki pages are not yet available here.
With PyDSTool we aim to provide a powerful suite of computational tools for the development, simulation, and analysis of dynamical systems that are used for the modeling of physical processes in many scientific disciplines. We place emphasis on the support of data analysis as part of the process of data-driven modeling. Our focus is on models involving ordinary differential equations (ODEs), differential-algebraic equations (DAEs), and discrete maps.
The software package is written primarily in the high-level interpreted language Python, and is freely available under the BSD open-source license from the SourceForge community website. For certain computationally intensive tasks, code written in C and Fortran can be invoked.
In pursuing our aims we have developed a hierarchy of object-oriented programming classes available to the modeler. These classes provide a means for “data abstraction”, that is, to provide the user with intuitive “objects” that encapsulate common data structures and methods for manipulating that data through a well-defined interface. These classes naturally make the software highly modular, and they range from defining hybrid model simulators, to individual data points, to symbolic mathematical expressions, to bifurcation analyzers. Some of these classes are built over classes exported by SciPy. We believe that many of these classes have wider scientific utility.
The PyDSTool software is "research code" in a Beta stage of development, and should not be treated as a complete or comprehensive dynamical systems package, with the associated expectation that its design and implementation have thoroughly stabilized and have been well tested. We have added features as and when we have had a use for them in our own research, and have omitted many important features that we would love to add if time permits us, or if our research so demands.
You might like to submit feature requests, or you may also like to contribute to the code yourself. We are also interested to hear your opinions about the possibility of adding some of our classes to SciPy (perhaps in modified form). Please contact us at the SourceForge open discussion forum or via email.
A dynamical system is defined by a set of rules or transformations for determining how points in a multidimensional space move in time. Time may be either discrete or continuous. The traces of the points as they move in time are called trajectories. The goal of Dynamical Systems Theory is to provide a comprehensive description of the geometric structures arising from these trajectories. In addition to elucidating the dynamics associated with an individual dynamical ssystem, bifurcation theory may be used to describe how the dynamics of a system varies with changes in parameter values.
Interactive numerical and graphical exploration are important tools in dynamical systems research for several reasons:
There is generally no way to obtain trajectory information other than by iteration or numerical integration;
The geometric structures of a dynamical system are often intricate and extremely sensitive to changes in the system parameters, so that interactive computation and graphics are useful in interpreting their meaning;
Exploration of a dynamical system often involves the generation of large quantities of data. Usually, only a small portion of data needs to be saved in order to concisely record the pertinent features of the dynamics. In general it is only through interactive exploration of the dynamics that the most compact and efficient representations of the a system's dynamics can be determined.
Consequently, there is a critical need for computational environments that provide effective tools for exploring dynamical systems with minimial effort on the part of the user. The PyDSTool project attempts to provide such an environment for use by both casual and advanced practitioners of Dynamical Systems Theory.
Our package incorporates:
Efficient and state-of-the-art ODE / DAE / discrete map simulation tools (using dynamically-linked and automatically generated C code, if external compiler available) (see Generators)
Hybrid model and event-driven simulation support (HybridSystems)
Simulations and analysis can be forced to be "bounds safe", e.g. for "non-negativity preservation" (see BoundsSafety)
Bifurcation analysis and continuation tools in-built, via PyCont
Support for data-driven modeling (see DataDrivenModels)
Interactive command-line / script-based interface
"Index-free" and context-heavy data structures, including an enhanced version of arrays (see Pointsets)
Symbolic expression utilities (including evaluation, substitution, derivatives, some simplification) (see Symbolic)
Easy to build complex models using hierarchical object-oriented data structures that contain composable model specifications (see ModelSpec)
Modular code design allows easy expansion to support other algorithms (contributions welcome)
Data structures and toolkits for parameter estimation / model fitting and other time-series and data-driven problems (see Parameter Estimation)
Seamless use with tools in SciPy, Numpy, etc. through dynamic typing
Additional toolboxes for specific applications, including biomechanical modeling, computational neuroscience, and systems biology (see ToolboxDocumentation)
Many tutorial examples and documentation available online at this Wiki
Most of these features are simply not available in the native SciPy ODE integrators.
Users of PyDSTool need to be familiar with working in interactive, command-line environments such as UNIX and Matlab, including the writing of simple command scripts. There is presently no graphical interface for PyDSTool. Our emphasis is on the interactivity of a command-line and the rapid prototyping possibilities of script-based computing.
In building a core library of Python classes, supporting many fundamental concepts in dynamical systems modeling, we provide more than just a glue with which to interface multiple tools. Our classes involve storing and maintaining a "context" that carries a lot of useful mathematical baggage. Through interaction with our Python environment at the script level, users can build complex models in a structured way, and have access to mathematically intuitive information about the models, using the intrinsic context of all the Python objects at the heart of their computations.
Our UI model is for users to interactively "query" objects for basic information (known in Python-speak as introspection), and also to be able to treat them as unitary objects of computation for use with tools and utilities such as optimizers, parameter estimators, and so forth.
We believe it is crucial for users to be able to combine the application of tools in a nested or interleaved fashion, in order to make the most flexible and dynamic manipulations of a model. Such rich combinations are practically impossible in disjointed software environments, and we believe our community is eager to be able to smoothly set-up and maintain such situations for their own modeling projects. It is a challenge to cleanly and efficiently interface different legacy algorithms with the core Python code in order to maximize the use and re-use of the context associated with the core objects.
Users are provided with an interface for the specification of both simple and complex dynamical systems models, using minimal programming syntax, and a range of options in converting these abstract specifications into instantiated numerical solvers for a specific system. Within the same interactive session, users have immediate access to analysis tools for continuation, parameter estimation, optimization, and so on. These tools are each tailored for use with the core PyDSTool structures to ensure the user has to write as little additional computer code as possible. Extensive documentation for the project has been provided online on this wiki.
A key aspect in the design of PyDSTool is the provision of adequate diagnostic information and querying utilities for data structures and computations. Users can expect helpful information regarding the status of their model development and computations beyond the guidance of the online documentation, through in-built querying commands and detailed error messages. The object-oriented nature of the software also provides inherent protection of the users’ conceptualization of data-flow and control in their PyDSTool scripts. See the UserDocumentation for more details.
Python has several benefits as a platform for our package. It is an open-source language, enthusiastically developed by a large community of people drawn from both academic and commercial backgrounds. The powerful object-oriented and dynamic typing features of the language greatly aid in the development of flexible and intuitive data structures and user interface (UI) elements. Being a high level language its interactive mode of UI, via a prompt, follows the same principle as that of Matlab, and shares the same advantages for quick prototyping, querying and scripting of complex object manipulations and computations.
In our design we have emphasized modularized data structures and interface design that facilitates data-driven approaches to the modeling of physical processes, and we have built upon standard numerical, scientific and graphics libraries for Python (for instance, SciPy and MatPlotLib). These, in turn, make use of well-established and efficient legacy codes for numerical integration of ODEs, and for dealing with linear algebra, optimization, and root solving (for instance, the LAPACK and MINPACK Fortran libraries). These legacy codes are typically interfaced using SWIG. The low-level languages of these codes provide the computational speed that Python itself lacks, in the places for which computation is most intensive.
All of the code involved in the PyDSTool project is open source, and we have aimed to create as few dependencies on external software packages as possible. In particular, the package can be used with Microsoft Windows, Mac OS X and Linux machines.
On top of the third-party libraries we have added several new tools and capabilities. We have enhanced legacy numerical integration code for ordinary differential equations to perform various additional tasks of use in hybrid systems modeling, implemented at the C-code level for maximal efficiency. This includes supporting discrete event detection during dynamical evolution. Adding arbitrary user-specified event detection to a model permits ODEs and maps to be used in combination as "hybrid" dynamical systems. Also, the inclusion of data-based time series inputs to a dynamical system’s evolution equations is a feature that aids data-driven modeling.
Utilities have been added that allow the movement of data and model specifications both in and out of PyDSTool, for sharing in other software environments. As well as basic importing and exporting of numerical data as text files, this also includes more systems-level interfacing. For instance, a user can export a dynamical model’s definition to a Matlab environment in which Automatic Differentiation is available for parameter sensitivity calculations (via the package ADMC++). Also, PyDSTool can be interfaced with the systems biology modeling package SloppyCell, through which PyDSTool inherits access to an interface with the Systems Biology Markup Language (SBML) for model specification, and the LaTeX mathematical markup language. Further interfaces to packages are in active development, such as to the original DsTool and to other simulation tools such as XPP or NEURON.
For the most up to date information about these, see the page ComingAttractions.
Support for delayed systems is currently limited to dirac delta function pulses, as part of a hybrid system (see HybridSystems). DDE integrators written by Hairer and Wanner follow the same interfacing pattern as our existing integrators and will be added soon.
Automatic differentiation and Taylor-series integration capabilities will be added once we can get a working interface to an open-source AD package such as ADOL-C. In the meantime, we provide a model export tool to interface PyDSTool models to work with the ADMC++ environment in Matlab, a package that was also developed at Cornell (by Eric Phipps). See this paper about ADMC++ and its application to parameter estimation for periodic orbits.
Although adequately supported in the underlying numerics of Python and SciPy, PyDSTool does not presently support dynamical systems having phase spaces ranging over the complex numbers. The application of PyDSTool to date has been to certain types of model in the physical sciences which have not required expressions of complex dynamics. It is hoped that at some point this can be redressed with explicitly complex dynamical systems. In the meantime, complex dynamics must be represented using two-dimensional real number phase spaces, and complex arithmetic implemented using auxiliary user-defined functions on 2D reals.
We have successfully tested an update of our automatic generation and compilation of C-code, although it does not yet avoid Python's distutils package by using Scons or autoconf / automake. This updated improves the efficiency of C-based vector field support and will make them more easily configured in new installations of Python/SciPy/PyDSTool.
We look forward to adding a range of other standard tools that are available in other packages for dynamical systems, such as phase-plane analysis, Poincare maps, Lyapunov exponent calculations, support for symbolic dynamics and complex dynamics, BVP solvers, averaging tools, invariant manifold computations, and so on.
Approximately ten years ago the original DsTool package was written here at Cornell, and has provided many years of functionality to the applied mathematics community. We have decided to write a new package from the ground up, as our concept of what is needed in our community has evolved. Our new project is different from existing approaches because it attempts to combine a large array of tools under one, centralized umbrella. We wish to support both straightforward simulation tools, such as numerical integrators of differential equations, and sophisticated analysis tools such as continuators and parameter estimation / sensitivity tools.
Individually, several examples of the software tools to implement these algorithms exist in the world of scientific computing. However, there has not yet been a one-stop solution to providing mathematically sophisticated users with a combined suite of such tools that are highly integrated and interactively operated. For instance, Matlab is geared much less towards applied mathematicians in this regard as it is to physicists and engineers. It is still typical for applied scientists to need to use a variety of separate programs to achieve their dynamical systems modeling goals, but increasingly sophisticated questions are being asked of the models, which are ever-harder to answer when the tools are not integrated. Example domains that will benefit from PyDSTool are computational neuroscience, biomechanics and robotics, and advanced engineering projects.
In the broadest terms, we believe PyDSTool combines or extends a range of features from packages such as Matlab, XPP, AUTO, and NEURON into an integrated and open environment.
PyDSTool provides dynamical systems-specific tools that Matlab does not.
Other science and data analysis tools are present in the working environment of PyDSTool through access to Scipy, Numeric, and Pylab. Many of these are ultimately imported from the same standard C or Fortran libraries that Matlab uses.
PyDSTool retains many of the advantages of the interactive environment that is Matlab's shell.
PyDSTool's numerical integrators are faster and more richly-featured than Matlab's and support a wider range of ODE, DAE, DDE and discrete map models.
PyDSTool model building scripting language and "index free" data structures make simulations and model exploration easy.
PyDSTool provides no graphical interface to its data structures.
See also this comparison of the NumPy library to Matlab.
PyDSTool supports arbitrarily large systems, and supports a representation of their inherent structure through our compositional model-building scripting language. This facilitates building such large models.
PyDSTool supports a wider range of differential equation right-hand side expressions.
PyDSTool supports long names (more than 9 characters).
Continuation and bifurcation analysis is more closely integrated with core PyDSTool tools and data structures.
Simulations and analysis can be embedded inside other algorithms, and automated using interactive or "intelligent" scripts. This is because PyDSTool is an "open environment".
XPP supports general delay-differential systems, a wider variety of ODE integrators, and a BVP solver.
XPP provides a fully-graphical user interface, postscript output, visualization tools for arrays, phase-plane analysis tools, GUI with a subset of AUTO, and a lot of other good stuff.
PyDSTool offers a suite of common continuation tools (via PyCont), but cannot yet be considered comprehensive.
PyDSTool/PyCont is an "open environment", like Matcont. This facilitates data exchange between different packages.
PyDSTool offers closer integration of continuation with the rest of the working environment.
PyCont is written in pure Python (except for the interface to AUTO), and is unlikely to work as fast as AUTO, although it is competitive with Matcont. The dynamically-linked C code for periodic orbit continuation re-uses components of AUTO directly. Because we create a C-code version of a vector field, PyCont+AUTO is technically a little faster than the most recent full native release of AUTO for continuation of periodic orbits, which uses Python callbacks to evaluate user-supplied functions.
PyDSTool provides a centralized, general purpose environment.
Python has a strong object-oriented capability.
PyDSTool utilizes automatically-generated and dynamically-linked C code for fast execution of user-defined vector fields. Hand-written modifications to this C code, or externally written DLL code can also be utilized.
Python's dynamic typing makes embedding PyDSTool objects inside other Python computations very simple to set up.
Python's interactive environment (i.e. interpreted language) is excellent for exploration of a mathematical system, and introspection of the associated PyDSTool objects.
A PyDSTool toolkit for compartmental modeling provide templates of data structures and utilities for sophisticated hierarchical and composable model building, using a modern object-oriented model specification language built in to PyDSTool (including symbolic expression handling).
The PyDSTool templates are not comprehensive, and are not as fully-featured as some of those designed for use with Neuron or Genesis. We are working to broaden the support for different types of model.
PyDSTool source code is hosted by SourceForge: