Debian Science Biology packages

Bauble is a software application to help you manage a collection of botanical specimens. It is intended to be used by botanic gardens, herbaria, arboreta, etc. to manage their collection information. It is a open, free, cross-platform alternative to BG-Base and similar software.

Critterding is a "Petri dish" universe in 3D that demonstrates evolving artificial life. Critters start out with completely random brains and bodies, but will automatically start evolving into something with much better survival skills.

This metapackage will install Debian packages for use in molecular biology, structural biology and other biological sciences.

The NMODL Framework is a code generation engine for the NEURON MODeling Language (NMODL). It is designed with modern compiler and code generation techniques to:

• Provide modular tools for parsing, analysing and transforming NMODL
• Provide easy to use, high level Python API
• Generate optimised code for modern compute architectures including CPUs, GPUs
• Flexibility to implement new simulator backends
• Support the full NMODL specification

MOD2C is NMODL to C adapted for CoreNEURON simulator.

NMODl is a description language to specify a model for a physical neuron in terms of simultaneous nonlinear algebraic equations, differential equations, or kinetic schemes.

InterViews is a C++ GUI library from Stanford University and Silicon Graphics with a Motif look and feel.

It is used by the NEURON simulator for legacy UI support, and should not be used by newly written code.

This metapackage will install Debian packages which might be helpful for development of applications for biological research.

The NMODL Framework is a code generation engine for the NEURON MODeling Language (NMODL).

This package contains support for using nmodl from Python.

Siconos is an open-source scientific software primarily targeted at modeling and simulating nonsmooth dynamical systems in C++ and in Python:

• Mechanical systems (rigid or solid) with unilateral contact and Coulomb friction and impact (nonsmooth mechanics, contact dynamics, multibody systems dynamics or granular materials).
• Switched Electrical Circuit such as electrical circuits with ideal and piecewise linear components: power converter, rectifier, Phase-Locked Loop (PLL) or Analog-to-Digital converter.
• Sliding mode control systems.
• Biology (Gene regulatory network). Other applications are found in Systems and Control (hybrid systems, differential inclusions, optimal control with state constraints), Optimization (Complementarity systems and Variational inequalities), Fluid Mechanics, and Computer Graphics.

This package contains the 'siconos' tool allowing to compile and run Siconos programs/scripts in a single command.

Siconos is an open-source scientific software primarily targeted at modeling and simulating nonsmooth dynamical systems in C++ and in Python:

• Mechanical systems (rigid or solid) with unilateral contact and Coulomb friction and impact (nonsmooth mechanics, contact dynamics, multibody systems dynamics or granular materials).
• Switched Electrical Circuit such as electrical circuits with ideal and piecewise linear components: power converter, rectifier, Phase-Locked Loop (PLL) or Analog-to-Digital converter.
• Sliding mode control systems.
• Biology (Gene regulatory network). Other applications are found in Systems and Control (hybrid systems, differential inclusions, optimal control with state constraints), Optimization (Complementarity systems and Variational inequalities), Fluid Mechanics, and Computer Graphics.

This package contains tools to allow running, analysing, manipulating, exporting, and viewing the output of mechanical simulations.

GENESIS is a general purpose simulation platform which was developed to support the simulation of neural systems ranging from complex models of single neurons to simulations of large networks made up of more abstract neuronal components.

GENESIS has provided the basis for laboratory courses in neural simulation at both Caltech and the Marine Biological Laboratory in Woods Hole, MA. Most current GENESIS applications involve realistic simulations of biological neural systems. Although the software can also model more abstract networks, other simulators are more suitable for backpropagation and similar connectionist modeling.