Summary
Biology
Debian Science - Pakete für die Biologie
Dieses Metapaket wird der Biologie zugeordnete Pakete von Debian Science
installieren. Auch mit dem Debtag field::biology markierte Pakete sind
vielleicht interessant für Sie.
Dieses Metapaket verwendet die Pakete med-bio und med-bio-dev (zur
Entwicklung von biologischen Anwendungen), die von Debian Med - einem
anderen Debian Pure Blend - verwaltet werden. Wenn Sie ein Biologe sind,
werden Sie wahrscheinlich am Projekt Debian Med interessiert sein, das sich
viel detaillierter mit Biologie und Medizin beschäftigt, als es das
allgemeinere Debian Science macht.
Description
For a better overview of the project's availability as a Debian package, each head row has a color code according to this scheme:
If you discover a project which looks like a good candidate for Debian Science
to you, or if you have prepared an unofficial Debian package, please do not hesitate to
send a description of that project to the Debian Science mailing list
Links to other tasks
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Debian Science Biology packages
Official Debian packages with high relevance
bauble
??? missing short description for package bauble :-(
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Versions of package bauble |
Release | Version | Architectures |
jessie | 0.9.7-2 | all |
stretch | 0.9.7-2.1 | all |
Debtags of package bauble: |
field | biology |
interface | x11 |
role | program |
uitoolkit | gtk |
use | organizing |
x11 | application |
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License: DFSG free
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critterding
Sich entwickelndes Künstliches Leben
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Versions of package critterding |
Release | Version | Architectures |
bookworm | 1.0-beta12.1-1.3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.0-beta12.1+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 1.0-beta12.1+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
experimental | 1.0-beta14+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,s390x |
buster | 1.0-beta12.1-1.3 | amd64,arm64,armhf,i386 |
bullseye | 1.0-beta12.1-1.3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 1.0-beta12.1-1.2 | amd64,armel,armhf,i386 |
stretch | 1.0-beta12.1-1.3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
Debtags of package critterding: |
interface | 3d, x11 |
role | program |
uitoolkit | sdl |
use | simulating |
x11 | application |
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License: DFSG free
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Critterding ist ein Petrischalen-Universum in 3D, das demonstriert, wie
sich künstliches Leben entwickelt. Critter starten mit komplett zufälligen
Hirnen und Körpern, entwickeln sich jedoch automatisch weiter in etwas mit
viel besseren Überlebensfähigkeiten.
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med-bio
Debian Med - Bioinformatikpakete
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Versions of package med-bio |
Release | Version | Architectures |
buster | 3.3 | all |
bullseye | 3.7 | all |
sid | 3.8.1 | all |
trixie | 3.8.1 | all |
bookworm | 3.8.1 | all |
jessie | 2.0 | all |
stretch | 3.0.1 | all |
Debtags of package med-bio: |
field | biology |
role | metapackage |
suite | debian |
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License: DFSG free
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Dieses Metapaket wird Debian-Pakete installieren, die in der
Molekularbiologie, Strukturbiologie und weiteren biologischen
Fachrichtungen verwendet werden.
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nmodl
Code generation engine for the NEURON modeling language
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Versions of package nmodl |
Release | Version | Architectures |
bookworm | 0.5-1 | amd64,arm64,mips64el,ppc64el,s390x |
trixie | 0.6-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 0.6-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
upstream | 1.0-alpha-llvm |
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License: DFSG free
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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
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nrn-mod2c
NMODL to C converter for CoreNEURON
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Versions of package nrn-mod2c |
Release | Version | Architectures |
sid | 0.9+git220919-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 0.9+git220919-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 0.9+git220919-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
upstream | 8.2.2 |
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License: DFSG free
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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.
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Official Debian packages with lower relevance
libinterviews-dev
InterViews 3.1 for the NEURON simulator
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Versions of package libinterviews-dev |
Release | Version | Architectures |
sid | 3.1+git20221204-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 3.1+git20221204-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 3.1+git20221204-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
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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.
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med-bio-dev
Debian Med - Entwicklungspakete für Bioinformatik-Anwendungen
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Versions of package med-bio-dev |
Release | Version | Architectures |
bullseye | 3.7 | all |
buster | 3.3 | all |
stretch | 3.0.1 | all |
trixie | 3.8.1 | all |
sid | 3.8.1 | all |
bookworm | 3.8.1 | all |
jessie | 2.0 | all |
Debtags of package med-bio-dev: |
field | biology |
role | metapackage |
suite | debian |
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License: DFSG free
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Dieses Metapaket wird Debian-Pakete installieren, die bei der Entwicklung
von Programmen für die biologische Forschung hilfreich sein könnten.
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python3-nmodl
Python support for the NEURON modeling language engine
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Versions of package python3-nmodl |
Release | Version | Architectures |
sid | 0.6-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 0.6-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 0.5-1 | amd64,arm64,mips64el,ppc64el,s390x |
upstream | 1.0-alpha-llvm |
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License: DFSG free
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The NMODL Framework is a code generation engine for the
NEURON MODeling Language (NMODL).
This package contains support for using nmodl from Python.
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siconos
modeling and simulation of nonsmooth dynamical systems (simulation runner tool)
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Versions of package siconos |
Release | Version | Architectures |
bullseye | 4.3.1+dfsg-2 | all |
bookworm | 4.4.0+dfsg-2 | all |
sid | 4.4.0+dfsg-4 | all |
upstream | 4.5.0 |
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License: DFSG free
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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.
Please cite:
Vincent Acary and Bernard Brogliato:
The SICONOS Platform
:443-488
(2008)
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siconos-mechanics-tools
modeling and simulation of nonsmooth dynamical systems (mechanics tools)
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Versions of package siconos-mechanics-tools |
Release | Version | Architectures |
bookworm | 4.4.0+dfsg-2 | all |
bullseye | 4.3.1+dfsg-2 | all |
sid | 4.4.0+dfsg-4 | all |
upstream | 4.5.0 |
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License: DFSG free
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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.
Please cite:
Vincent Acary and Bernard Brogliato:
The SICONOS Platform
:443-488
(2008)
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Packaging has started and developers might try the packaging code in VCS
genesis
general-purpose neural simulator
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Versions of package genesis |
Release | Version | Architectures |
VCS | 2.3+dfsg-1 | all |
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License: free
Debian package not available
Version: 2.3+dfsg-1
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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.
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