Debian Med Project
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Summary
Pharmacology
Debian Med packages for pharmaceutical research

This metapackage contains dependencies for a collection of software and documentation which is useful for pharmaceutical research.

The list to the right includes various software projects which are of some interest to the Debian Med Project. Currently, only a few of them are available as Debian packages. It is our goal, however, to include all software in Debian Med which can sensibly add to a high quality Debian Pure Blend.

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
chemical structures drawing program
Versions of package chemtool
ReleaseVersionArchitectures
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,arm64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,ppc64el,s390,s390x,sparc
sid1.6.14-1amd64,arm64,armel,armhf,hurd-i386,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,ppc64el,s390,s390x,sparc
Debtags of package chemtool:
fieldchemistry
interfacex11
roleprogram
scopeapplication
uitoolkitgtk
useediting, learning
works-withimage, image:vector
works-with-formatsvg
x11application
Popcon: 74 users (56 upd.)*
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License: DFSG free
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Chemtool is a GTK+ based 2D chemical structure editor for X11. It supports many bond styles, most forms of text needed for chemical typesetting and splines/arcs/curved arrows.

Drawings can be exported to MOL and PDB format, SVG or XFig format for further annotation, as a PiCTeX drawing, as a bitmap or as Postscript files (several of these through XFig's companion program transfig).

The package also contains a helper program, cht, to calculate sum formula and (exact) molecular weight from a chemtool drawing file. Cht can either be called directly by Chemtool or on the console.

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
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jessie0.9-9-1ia64,sparc
sid0.9-9-1ia64
jessie0.9-11-1amd64,armel,armhf,i386,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,ppc64el,s390x
sid0.9-11-1hurd-i386
sid0.9-12-1amd64,armel,armhf,i386,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,ppc64el,s390x,sparc
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License: DFSG free
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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)

Debian packages in contrib or non-free

Raccoon
preparation of in silico drug screening projects
Versions of package raccoon
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wheezy1.0-1 (contrib)all
jessie1.0b-1 (contrib)all
sid1.0b-1 (contrib)all
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License: DFSG free, but needs non-free components
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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)
*Popularitycontest results: number of people who use this package regularly (number of people who upgraded this package recently) out of 170477