med-tasks 1.10ubuntu1 / usr / share / tasksel / debian-med-tasks.desc

Task: med-bio
Section: debian-med
Description: Debian Med micro-biology packages
 This metapackage will install Debian packages related to molecular biology,
 structural biology and bioinformatics for use in life sciences.
Relevance: 10
Enhances: t-coffee
Key: 
 med-bio
Packages: list
 altree
 fastdnaml
 njplot
 tree-puzzle
 probalign
 treeviewx
 figtree
 fastlink
 loki
 plink
 r-cran-qtl
 amap-align
 boxshade
 fastx-toolkit
 gff2aplot
 muscle
 sim4
 sibsim4
 tabix
 wise
 maqview
 bwa
 mummer
 blast2
 mafft
 t-coffee
 kalign
 hmmer
 exonerate
 dialign
 dialign-tx
 poa
 probcons
 proda
 sigma-align
 emboss
 embassy-domalign
 embassy-domainatrix
 embassy-domsearch
 clustalx
 clustalw
 mothur
 bowtie
 dotur
 transtermhp
 last-align
 maq
 ssake
 velvet
 infernal
 rnahybrid
 adun.app
 garlic
 gamgi
 gdpc
 ghemical
 jmol
 pymol
 r-other-bio3d
 massxpert
 gromacs
 rasmol
 plasmidomics
 gff2ps
 ncbi-epcr
 ncbi-tools-bin
 ncbi-tools-x11
 perlprimer
 readseq
 tigr-glimmer
 melting
 mipe
 primer3
 gbrowse
 biomaj
 glam2
 raster3d
 phyml
 autodock
 autogrid
 autodock-vina
 mustang
 theseus
 staden-io-lib-utils
 samtools
 bedtools
 filo
 r-bioc-hilbertvis
 r-other-mott-happy
 seq-gen
 mira-assembler
 alien-hunter
 ncoils
 picard-tools
 acedb-other-dotter
 acedb-other-belvu
 acedb-other
 python-cogent
 mrbayes
 squizz
 clonalframe
 jellyfish
 raxml
 mlv-smile
 tm-align
 jalview
 ncbi-blast+
 abacas
 profnet-bval
 profnet-chop
 profnet-con
 profnet-isis
 profnet-md
 profnet-norsnet
 profnet-prof
 profnet-snapfun
 profphd-net
 ampliconnoise
 disulfinder
 populations
 vcftools

Task: med-bio-dev
Section: debian-med
Description: Debian Med packages for development of micro-biology applications
 This metapackage will install Debian packages which might be helpful
 for development of applications for micro-biological research.
Relevance: 10
Key: 
 med-bio-dev
Packages: list
 bioperl
 bioperl-run
 libncbi6-dev
 mcl
 biosquid
 libvibrant6-dev
 python-biopython
 python-cogent
 ruby-bio
 libbiojava-java
 libgenome-1.3-0-dev
 libbio-mage-perl
 libgo-perl
 r-cran-genetics
 r-cran-haplo.stats
 libbio-graphics-perl
 libbio-primerdesigner-perl
 libace-perl
 libbiococoa-dev
 libstaden-read-dev
 libsrf-dev
 seqan-dev
 libbio-mage-utils-perl
 libjebl2-java
 r-bioc-biobase

Task: med-bio-ngs
Section: debian-med
Description: Debian Med bioinformatics applications usable in Next Generation Sequencing
 It aims at gettting packages which specializes in alignment of
 sequences produced by next generation sequencing.
Relevance: 10
Packages: list
 mothur
 mira-assembler

Task: med-bio-phylogeny
Section: debian-med
Description: Debian Med phylogeny packages
 This lists Debian packages related to phylogeny for use in life sciences.
 The purpose of this compilation of packages is to have a handy subset of
 from the med-bio metapackage which contains a lot more than only phylogeny
 related software.
Relevance: 10
Packages: list
 altree
 fastdnaml
 njplot
 tree-puzzle
 probalign
 treeviewx
 muscle
 t-coffee
 kalign
 hmmer
 exonerate
 dialign
 dialign-tx
 poa
 probcons
 proda
 sigma-align
 clustalx
 clustalw
 mustang
 phyml
 tm-align
 mrbayes
 figtree
 populations
 spread

Task: med-cloud
Section: debian-med
Description: Debian Med bioinformatics applications usable in cloud computing
 This metapackage will install Debian packages related to molecular biology,
 structural biology and bioinformatics for use in life sciences, that do not
 depend on graphical toolkits and therefore can fit on system images for use
 in cloud computing clusters, where space can be limited.
Relevance: 10
Key: 
 med-cloud
Packages: list
 clustalw
 autodock
 raster3d
 python-cogent

Task: med-data
Section: debian-med
Description: Debian Med drug databases
 There is at least one free medical drug database packaged for Debian
 which can be installed using this metapackage.  It is supported by the
 GNUmed Electronic Medical Record package.
Relevance: 10
Key: 
 med-data
Packages: list
 freediams
 python-hl7

Task: med-dental
Section: debian-med
Description: Debian Med packages related to dental practice
 This metapackage contains dependencies for a collection of software
 which might be helpful for dentists to manage their practice.
Relevance: 10
Key: 
 med-dental
Packages: list
 imagetooth

Task: med-epi
Section: debian-med
Description: Debian Med epidemiology related packages
 This metapackage will install tools that are useful in epidemiological
 research.  Several packages making use of the GNU R data language for
 statistical investigation.  It might be a good idea to read the paper
 "A short introduction to R for Epidemiology" at
 http://staff.pubhealth.ku.dk/%7Ebxc/Epi/R-intro.pdf
Relevance: 10
Key: 
 med-epi
Packages: list
 epigrass
 r-cran-epibasix
 r-cran-epitools
 r-cran-epi
 r-cran-diagnosismed
 r-cran-epicalc
 r-cran-epir

Task: med-imaging
Section: debian-med
Description: Debian Med imaging packages
 This metapackage will install Debian packages which might be useful in
 medical image processing.
 .
 It installs several packages supporting DICOM (Digital Imaging and
 Communications in Medicine) which is the de-facto standard for medical
 image management. The standard defines data structures and services for
 the exchange of medical images and related information. The latest release
 has been published in 2008 and consists of 18 parts.
 .
 For more information, you can visit the NEMA homepage
 http://medical.nema.org/ .
 .
 The status of the official DICOM base standard plus all the
 supplements and correction items are summarized at David Clunie's webpage:
 http://www.dclunie.com/dicom-status/status.html
 where you'll find direct links to the most recent yearly edition
 ftp://medical.nema.org/medical/dicom/2008/ .
Relevance: 10
Key: 
 med-imaging
Packages: list
 amide
 ctsim
 ctn
 dicomnifti
 imagej
 minc-tools
 medcon
 python-nifti
 xmedcon
 dcmtk
 nifti-bin
 aeskulap
 via-bin
 gwyddion
 sofa-apps
 python-mvpa
 python-nipy
 python-nipype
 caret
 libgdcm-tools
 dicom3tools
 dicomscope
 pixelmed-java
 gofigure2
 ginkgocadx
 openslide-tools
 mricron
 voxbo
 mrtrix
 mriconvert
 connectomeviewer
 sigviewer
 tifffile
 openmeeg-tools
 plastimatch
 biosig-tools
 python-nitime
 python-dipy

Task: med-imaging-dev
Section: debian-med
Description: Debian Med packages for medical image development
 This metapackage will install Debian packages which might be useful
 for developing applications for medical image processing.
Relevance: 10
Key: 
 med-imaging-dev
Packages: list
 ctn-dev
 cimg-dev
 libminc-dev
 libmdc2-dev
 libnifti-dev
 libigstk4-dev
 libinsighttoolkit3-dev
 libvolpack1-dev
 libgdcm2-dev
 python-gdcm
 python-mvpa
 python-nipy
 python-nipype
 python-nitime
 libvia-dev
 libcv-dev
 libvxl1-dev
 libteem1-dev
 gmic
 libgiftiio-dev
 python-dicom
 libopenmeeg-dev
 python-nibabel
 libgdf-dev
 python-dipy
 libbiosig-dev
 libactiviz.net5.6-cil
 python-cfflib
 libopenslide-dev

Task: med-oncology
Section: debian-med
Description: Debian Med packages for oncology
 This metapackage will install tools that are useful for radiation
 oncology.
Relevance: 10
Key: 
 med-oncology
Packages: list
 dicompyler

Task: med-pharmacy
Section: debian-med
Description: Debian Med packages for pharmaceutical research
 This metapackage contains dependencies for a
 collection of software and documentation which is useful for
 pharmaceutical research.
Relevance: 10
Key: 
 med-pharmacy
Packages: list
 chemtool

Task: med-physics
Section: debian-med
Description: Debian Med packages for medical physicists
 This metapackage contains dependencies for a
 collection of software and documentation which is useful for
 medical physicists in radiation oncology, diagnostics imaging
 and related fields.
Relevance: 10
Key: 
 med-physics
Packages: list
 paw++
 paw
 octave3.2
 r-base

Task: med-practice
Section: debian-med
Description: Debian Med packages for practice management
 This metapackage contains dependencies for a collection of software
 which might be helpful for practitioners to manage their practice.
Relevance: 10
Key: 
 med-practice
Packages: list
 gnumed-client
 gnumed-server
 libchipcard-tools
 ginkgocadx
 freediams
 r-cran-medadherence

Task: med-psychology
Section: debian-med
Description: Debian Med packages for psychology
 This metapackage contains dependencies for a collection of software
 which might be helpful for psychological research.
Relevance: 10
Key: 
 med-psychology
Packages: list
 python-pyepl
 praat
 r-cran-foreign
 psignifit
 r-cran-psy
 psychopy

Task: med-rehabilitation
Section: debian-med
Description: Debian Med packages for rehabilitation technologies
 This metapackage will install tools that are useful for
 rehabilitation and therapy.
Relevance: 10
Key: 
 med-rehabilitation
Packages: list
 sitplus

Task: med-statistics
Section: debian-med
Description: Debian Med statistics
 This metapackage will install packages which are helpful to do statistics
 with a special focus on tasks in medical care.
Relevance: 10
Key: 
 med-statistics
Packages: list
 r-bioc-edger
 r-bioc-limma
 r-cran-qvalue
 r-cran-randomforest
 r-cran-pvclust

Task: med-tools
Section: debian-med
Description: Debian Med several tools
 This metapackage will install tools for several purposes in health care.
 Currently it contains some simple programs for Personal Health.
Relevance: 10
Key: 
 med-tools
Packages: list
 pcalendar
 pondus
 wgerman-medical
 hunspell-de-med
 quitcount
 workrave
 edfbrowser

Task: med-typesetting
Section: debian-med
Description: Debian Med support for typesetting and publishing
 This metapackage will install Debian packages that might be helpful
 for typesetting and publishing in medical care and structural
 biology.
Relevance: 10
Key: 
 med-typesetting
Packages: list
 texlive-science
 texlive-latex-extra