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

Avida-base
Auto-adaptive genetic system for Artificial Life research
Maintainer: Miriam Ruiz (Bas Zoetekouw)
Versions of package avida-base
ReleaseVersionArchitectures
squeeze2.0b7-4.2amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
Popcon: 1 users (0 upd.)*
Versions and Archs
License: DFSG free

Avida is an auto-adaptive genetic system designed primarily for use as a platform in Digital or Artificial Life research. In lay terms, Avida is a digital world in which simple computer programs mutate and evolve.

Avida allows us to study questions and perform experiments in evolutionalry dynamics and theoretical biology that are intractable in real biological system.

Homepage http://dllab.caltech.edu/avida/

Bauble
biodiversity collection manager software application
Versions of package bauble
ReleaseVersionArchitectures
jessie0.9.7-2all
stretch0.9.7-2.1all
buster0.9.7-2.1all
sid0.9.7-2.1all
squeeze0.9.7-2all
wheezy0.9.7-2all
Debtags of package bauble:
fieldbiology
interfacex11
roleprogram
uitoolkitgtk
useorganizing
x11application
Popcon: 8 users (3 upd.)*
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
ReleaseVersionArchitectures
wheezy1.0-beta12.1-1.2amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
jessie1.0-beta12.1-1.2amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x
stretch1.0-beta12.1-1.3amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
buster1.0-beta12.1-1.3amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
sid1.0-beta12.1-1.3amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,powerpc,ppc64el,s390x
experimental1.0-beta14+dfsg-2amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,powerpc,ppc64el,s390x
squeeze1.0-beta12.1-1amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
upstream1.0-beta14
Debtags of package critterding:
interface3d, x11
roleprogram
uitoolkitsdl
usesimulating
x11application
Popcon: 11 users (3 upd.)*
Newer upstream!
License: DFSG free
Git

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
ReleaseVersionArchitectures
sid3.0.1all
squeeze1.8all
wheezy1.13.2all
jessie2.0all
stretch3.0.1all
buster3.0.1all
Debtags of package med-bio:
fieldbiology
rolemetapackage
suitedebian
Popcon: 8 users (2 upd.)*
Versions and Archs
License: DFSG free
Git

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

Official Debian packages with lower relevance

Med-bio-dev
Debian Med packages for development of bioinformatics applications
Versions of package med-bio-dev
ReleaseVersionArchitectures
stretch3.0.1all
sid3.0.1all
squeeze1.8all
jessie2.0all
buster3.0.1all
wheezy1.13.2all
Debtags of package med-bio-dev:
fieldbiology
rolemetapackage
suitedebian
Popcon: 3 users (0 upd.)*
Versions and Archs
License: DFSG free
Git

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

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 200581