Debian Science Project
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

Debian Science Biology packages

Official Debian packages with high relevance

bauble
biodiversity collection manager software application
Versions of package bauble
ReleaseVersionArchitectures
stretch0.9.7-2.1all
jessie0.9.7-2all
Debtags of package bauble:
fieldbiology
interfacex11
roleprogram
uitoolkitgtk
useorganizing
x11application
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Versions and Archs
License: DFSG free

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
Evolving Artificial Life
Versions of package critterding
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bookworm1.0-beta12.1-1.3amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie1.0-beta12.1-1.3amd64,arm64,armel,armhf,i386,mips64el,ppc64el,s390x
sid1.0-beta12.1-1.3amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
buster1.0-beta12.1-1.3amd64,arm64,armhf,i386
bullseye1.0-beta12.1-1.3amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
experimental1.0-beta14+dfsg-2amd64,arm64,armel,armhf,i386,mips64el,ppc64el,s390x
jessie1.0-beta12.1-1.2amd64,armel,armhf,i386
stretch1.0-beta12.1-1.3amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
upstream1.0-beta14
Debtags of package critterding:
interface3d, x11
roleprogram
uitoolkitsdl
usesimulating
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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.

Screenshots of package critterding
med-bio
Debian Med bioinformatics packages
Versions of package med-bio
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buster3.3all
bullseye3.7all
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trixie3.8.1all
bookworm3.8.1all
jessie2.0all
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fieldbiology
rolemetapackage
suitedebian
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This metapackage will install Debian packages for use in molecular biology, structural biology and other biological sciences.

Remark of Debian Science team: Maintained by Debian Med Blend

For more information see http://debian-med.alioth.debian.org/tasks/bio

nmodl
Code generation engine for the NEURON modeling language
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sid0.6-2amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
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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
nrn-mod2c
NMODL to C converter for CoreNEURON
Versions of package nrn-mod2c
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sid0.9+git220919-2amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
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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.

Official Debian packages with lower relevance

libinterviews-dev
InterViews 3.1 for the NEURON simulator
Versions of package libinterviews-dev
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sid3.1+git20221204-2amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
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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.

med-bio-dev
Debian Med packages for development of bioinformatics applications
Versions of package med-bio-dev
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jessie2.0all
buster3.3all
stretch3.0.1all
trixie3.8.1all
sid3.8.1all
bookworm3.8.1all
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Debtags of package med-bio-dev:
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rolemetapackage
suitedebian
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This metapackage will install Debian packages which might be helpful for development of applications for biological research.

Remark of Debian Science team: Maintained by Debian Med Blend

For more information see http://debian-med.alioth.debian.org/tasks/bio-dev

python3-nmodl
Python support for the NEURON modeling language engine
Versions of package python3-nmodl
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upstream1.0-alpha-llvm
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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.

siconos
modeling and simulation of nonsmooth dynamical systems (simulation runner tool)
Versions of package siconos
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sid4.4.0+dfsg-4all
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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)
siconos-mechanics-tools
modeling and simulation of nonsmooth dynamical systems (mechanics tools)
Versions of package siconos-mechanics-tools
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upstream4.5.0
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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)

Packaging has started and developers might try the packaging code in VCS

genesis
general-purpose neural simulator
Versions of package genesis
ReleaseVersionArchitectures
VCS2.3+dfsg-1all
Versions and Archs
License: free
Debian package not available
Git
Version: 2.3+dfsg-1

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.

*Popularitycontest results: number of people who use this package regularly (number of people who upgraded this package recently) out of 235799