Debian Med Project
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Summary
Pharmacology
paquet de Debian Med pour la recherche en pharmacologie

Ce métapaquet contient les dépendances pour une collection de logiciels et de documentations utiles pour la recherche en pharmacologie.

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 Med 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 Med mailing list

Links to other tasks

Debian Med Pharmacology packages

Official Debian packages with high relevance

Chemtool
programme de dessin de structures chimiques
Versions of package chemtool
ReleaseVersionArchitectures
buster1.6.14-3amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
squeeze1.6.12-1amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
wheezy1.6.13-1amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
jessie1.6.14-1amd64,armel,armhf,i386
stretch1.6.14-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
sid1.6.14-6amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye1.6.14-6amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
Debtags of package chemtool:
fieldchemistry
interfacex11
roleprogram
scopeapplication
uitoolkitgtk
useediting, learning
works-withimage, image:vector
works-with-formatsvg
x11application
Popcon: 24 users (12 upd.)*
Versions and Archs
License: DFSG free
Git

Chemtool est un éditeur de structure chimique 2D en GTK+ pour X11. Il prend en charge plusieurs types de liaisons, la plupart des formats de texte nécessaires à l'écriture en chimie et les flèches en forme de cerce, d'arc ou courbées.

Les dessins peuvent être exportés dans les formats MOL et PDB, SVG ou XFig pour des annotations ultérieures, en tant que dessin PiCTex ou comme fichier bitmap ou Postscript (plusieurs de ces formats grâce au programme fig2dev, pendant de XFig).

Le paquet contient également un programme d'aide, cht, pour calculer des formules et des masses moléculaires exactes à partir d'un fichier de dessin chemtool. Cht peut être appelé directement depuis Chemtool ou bien depuis la ligne de commande.

Please cite: Matthias Brüstle: Chemtool - Moleküle zeichnen mit dem Pinguin. (eprint) Nachr. Chem. 49(11):1310-1313 (2001)
Screenshots of package chemtool
R-cran-dosefinding
Planning and Analyzing Dose Finding experiments
Versions of package r-cran-dosefinding
ReleaseVersionArchitectures
jessie0.9-12-1amd64,armel,armhf,i386
stretch0.9-15-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
buster0.9-16-2amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
bullseye0.9-17-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid0.9-17-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
Popcon: 11 users (3 upd.)*
Versions and Archs
License: DFSG free
Git

The DoseFinding GNU R package provides functions for the design and analysis of dose-finding experiments (with focus on pharmaceutical Phase II clinical trials). It provides functions for: multiple contrast tests, fitting non-linear dose-response models (using Bayesian and non-Bayesian estimation), calculating optimal designs and an implementation of the MCPMod methodology.

Please cite: Jose C. Pinheiro, Björn Bornkamp and Frank Bretz: Design and Analysis of Dose-Finding Studies Combining Multiple Comparisons and Modeling Procedures. (PubMed) Journal of Biopharmaceutical Statistics 16(5):639-656 (2006)
R-cran-rpact
Confirmatory Adaptive Clinical Trial Design and Analysis
Versions of package r-cran-rpact
ReleaseVersionArchitectures
buster1.0.0-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
bullseye3.0.3-2amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid3.0.3-2amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
upstream3.0.4
Popcon: 8 users (3 upd.)*
Newer upstream!
License: DFSG free
Git

Design and analysis of confirmatory adaptive clinical trials with continuous, binary, and survival endpoints according to the methods described in the monograph by Wassmer and Brannath (2016). This includes classical group sequential as well as multi-stage adaptive hypotheses tests that are based on the combination testing principle.

Debian packages in contrib or non-free

Raccoon
preparation of in silico drug screening projects
Versions of package raccoon
ReleaseVersionArchitectures
jessie1.0b-1 (contrib)all
wheezy1.0-1 (contrib)all
Popcon: users ( upd.)*
Versions and Archs
License: DFSG free, but needs non-free components
Svn

The field of computational biology is all about modeling physiochemical entities. Structural biology is about how those entities look in 3D and behave. And we have a drug when we can change that behaviour in a way that we want it to be changed - and only that behaviour.

Some good part of the characterisation of promising drug-like compounds for their interaction with a larger protein can be done on computers. This package helps with getting collections of small ligands prepared to be fitted against a particular protein of known structure. That docking itself is then to be performed by autodock or autodock-vina.

Raccoon may not find the drug, but it may well find a lead to it. To have this package with Debian shall help smaller biochemistry labs and grants an opportunity for the general public to educate itself and/or actively join in to help the world .... just a bit.

Please cite: Sandro Cosconati, Stefano Forli, Alex L. Perryman, Rodney Harris, David S. Goodsell and Arthur J. Olson: Virtual screening with AutoDock: theory and practice. (PubMed,eprint) Expert Opinion on Drug Discovery 5(6):597–607 (2010)
Registry entries: OMICtools 
*Popularitycontest results: number of people who use this package regularly (number of people who upgraded this package recently) out of 203033