med-tasks 2.1ubuntu4 / usr / share / tasksel / descs / 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
 r-cran-genabel
 amap-align
 boxshade
 fastx-toolkit
 gff2aplot
 muscle
 sim4
 sibsim4
 tabix
 tophat
 wise
 maqview
 bwa
 mummer
 blast2
 ncbi-blast+
 mafft
 sra-toolkit
 t-coffee
 kalign
 hmmer
 exonerate
 dialign
 dialign-tx
 poa
 probcons
 proda
 sigma-align
 emboss
 embassy-domalign
 embassy-domainatrix
 embassy-domsearch
 clustalo
 clustalw
 mothur
 bowtie
 bowtie2
 transtermhp
 last-align
 maq
 ssake
 velvet
 qiime
 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
 phyml
 autodock
 autogrid
 autodock-vina
 mustang
 probabel
 theseus
 staden-io-lib-utils
 samtools
 bedtools
 filo
 r-bioc-hilbertvis
 r-other-mott-happy.hbrem
 seq-gen
 snp-sites
 mira-assembler
 alien-hunter
 seqan-apps
 ncoils
 picard-tools
 acedb-other-dotter
 acedb-other-belvu
 acedb-other
 python-cogent
 velvetoptimiser
 mrbayes
 pdb2pqr
 squizz
 clonalframe
 dssp
 jellyfish
 pynast
 raxml
 mlv-smile
 cd-hit
 r-bioc-cummerbund
 grinder
 jalview
 reprof
 tm-align
 norsnet
 norsp
 predictnls
 prime-phylo
 proftmb
 profbval
 profisis
 hhsuite
 ffindex
 flexbar
 neobio
 ray
 ugene
 logol-bin
 soapdenovo
 soapdenovo2
 microbiomeutil
 chimeraslayer
 nast-ier
 wigeon
 minia
 trimmomatic
 saint
 rtax
 rate4site
 rna-star
 scythe
 sickle
 aegean
 arden
 fitgcp
 gasic
 giira
 ipig
 aevol
 anfo
 aragorn
 barrnap
 bamtools
 cassiopee
 cdbfasta
 clearcut
 ecopcr
 edtsurf
 fasttree
 fastaq
 fastqc
 freecontact
 genometools
 gwama
 hmmer2
 idba
 kissplice
 ltrsift
 kmer
 macs
 macsyfinder
 progressivemauve
 mauve-aligner
 metastudent
 microbegps
 mrs
 ncbi-seg
 paraclu
 parsinsert
 perm
 phyutility
 prank
 predictprotein
 proalign
 prodigal
 pycorrfit
 pyscanfcs
 r-bioc-rtracklayer
 r-bioc-gviz
 r-bioc-biostrings
 r-cran-phangorn
 r-cran-seqinr
 r-cran-vegan
 relion-bin
 rdp-alignment
 rdp-readseq
 rdp-classifier
 seqprep
 seqtk
 smalt
 staden
 stacks
 subread
 swarm
 toppred
 transdecoder
 uc-echo
 vsearch
 zalign
 discosnp
 mapsembler2
 dnaclust
 concavity
 conservation-code
 r-cran-ape
 abacas
 profnet-bval
 profnet-chop
 profnet-con
 profnet-isis
 profnet-md
 profnet-norsnet
 profnet-prof
 profnet-snapfun
 profphd-net
 profphd-utils
 profphd
 ampliconnoise
 disulfinder
 circos
 populations
 librg-utils-perl
 snap
 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
 python-screed
 ruby-bio
 libbiojava-java
 libbiojava3-java
 libbiojava4-java
 libgenome-1.3-dev
 libmuscle-3.7-dev
 libmems-1.6-dev
 libai-fann-perl
 libbio-mage-perl
 libnhgri-blastall-perl
 libtfbs-perl
 libfreecontact-dev
 libfreecontact-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
 libzerg0-dev
 libzerg-perl
 librg-reprof-bundle-perl
 python-corepywrap
 librcsb-core-wrapper0-dev
 seqan-dev
 libbio-mage-utils-perl
 libchado-perl
 libpal-java
 libjebl2-java
 r-bioc-biobase
 libffindex0-dev
 librostlab3-dev
 librostlab-blast0-dev
 librg-blast-parser-perl
 libsort-key-top-perl
 libhmsbeagle-dev
 libbambamc-dev
 libbamtools-dev
 python-mmtk
 libgenometools0-dev
 librdp-taxonomy-tree-java
 python-biom-format
 python-rdkit
 libgenome-perl
 libgenome-model-tools-music-perl
 pyfai
 libhts-dev
 python-htseq
 python-csb
 python-freecontact
 libkmer-dev
 libsnp-sites1-dev
 libssm-dev
 librelion-dev
 python-pysam
 python-cobra
 python-ruffus

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
 qiime
 mira-assembler
 kissplice
 uc-echo

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
 clustalw
 mustang
 phyml
 tm-align
 mrbayes
 figtree
 populations
 proalign

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
 altree
 clearcut
 fastdnaml
 fasttree
 parsinsert
 phyml
 phyutility
 alien-hunter
 fastlink
 loki
 gasic
 genometools
 plink
 amap-align
 blast2
 biosquid
 boxshade
 cassiopee
 cdbfasta
 cd-hit
 bamtools
 bedtools
 fastx-toolkit
 flexbar
 picard-tools
 samtools
 anfo
 bowtie
 bowtie2
 bwa
 last-align
 maq
 perm
 tophat
 smalt
 mapsembler2
 idba
 minia
 mira-assembler
 ssake
 velvet
 ampliconnoise
 arden
 fastqc
 discosnp
 dnaclust
 fitgcp
 giira
 grinder
 kissplice
 macs
 mothur
 aragorn
 infernal
 rnahybrid
 rtax
 autodock
 autodock-vina
 autogrid
 concavity
 dssp
 freecontact
 melting
 mipe
 ncbi-epcr
 primer3
 acedb-other
 disulfinder
 ncbi-tools-bin
 ncoils
 python-cogent
 aevol
 biomaj
 bioperl
 bioperl-run
 cain
 clonalframe
 circos
 datamash
 filo

Task: med-cms
Section: debian-med
Description: Debian Med content management systems
 Here you can find software that is useful to build a
 content management system for medical care.
Relevance: 10
Packages: list

Task: med-data
Section: debian-med
Description: Debian Med drug databases
 This metapackage will install free drug databases and related
 applications. The database can be accessed by any EMR using
 the application.
Relevance: 10
Key: 
 med-data
Packages: list
 freediams
 freemedforms-freedata
 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
 openmolar
 imagetooth
 entangle

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
 r-cran-seroincidence

Task: med-his
Section: debian-med
Description: Debian Med suggestions for Hospital Information Systems
 This metapackage contains dependencies for software and that could
 be useful ro run a Hospital Information System.  While there is
 continuous work going on to package a ready to install system currently
 only preconditions are finished but hopefully helpful in hospitals
 anyway.
Relevance: 10
Key: 
 med-his
Packages: list
 fis-gtm

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
 medcon
 python-nibabel
 python-dicom
 xmedcon
 dcmtk
 nifti-bin
 aeskulap
 fslview
 gwyddion
 sofa-apps
 python-mvpa2
 python-nipy
 python-nipype
 caret
 dicom3tools
 imagevis3d
 dicomscope
 pixelmed-apps
 openslide-tools
 conquest-common
 orthanc
 teem-apps
 mricron
 voxbo
 mrtrix
 mriconvert
 mia-tools
 mialmpick
 mia-viewit
 ismrmrd-tools
 sigviewer
 openmeeg-tools
 biosig-tools
 python-surfer
 king
 gdf-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
 libvtk5-dev
 libnifti-dev
 libvolpack1-dev
 python-mvpa2
 python-nipy
 python-nipype
 python-nitime
 python-casmoothing
 libcv-dev
 libvxl1-dev
 libteem-dev
 gmic
 libgiftiio-dev
 libactiviz.net-cil
 libvistaio-dev
 libmia-2.2-dev
 libmiaviewit-dev
 libmialm-dev
 python-mia
 r-cran-rniftilib
 python-dicom
 libopenmeeg-dev
 python-nibabel
 libgdf-dev
 octave-gdf
 python-pyxnat
 python-dipy
 libbiosig-dev
 python-cfflib
 libopenslide-dev
 python-openslide
 libpapyrus3-dev
 python-mne
 libvigraimpex-dev
 python-vigra
 libedf-dev
 libismrmrd-dev

Task: med-laboratory
Section: debian-med
Description: Debian Med suggestions for medical laboratories
 This metapackage contains dependencies for software and that could
 be useful ro run a medical laboratory.
Relevance: 10
Key: 
 med-laboratory
Packages: list
 opencfu

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
 r-cran-dosefinding

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
 octave
 r-base
 biosig-tools
 gdf-tools

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
 freediams
 freemedforms-emr
 r-cran-medadherence
 clinica
 entangle
 qrisk2

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-bioc-qvalue
 r-cran-randomforest
 r-cran-beeswarm
 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
 hunspell-en-med
 python-clips
 cronometer
 python-fitbit
 nut-nutrition

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
 king