Summary
Biology
Debian Science Biology packages
This metapackage will install Debian Science packages related to
Biology. You might also be interested in the field::biology debtag.
This metapackage makes use of the packages med-bio and med-bio-dev
(for development of biological applications) which are maintained
by Debian Med - another Debian Pure Blend. If you are a biologist
you are most probably interested in the Debian Med project which
deals with biology and medicine in much more detail then the more
general Debian Science.
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
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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 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.
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med-bio
Debian Med bioinformatics packages
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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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This metapackage will install Debian packages for use in molecular biology,
structural biology and other biological sciences.
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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 packages for development of bioinformatics applications
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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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This metapackage will install Debian packages which might be helpful
for development of applications for biological research.
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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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