Debian Med Project
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Debian Med: Pakete für die pharmazeutische Forschung

Dieses Metapaket enthält Abhängigkeiten für eine Sammlung von Software und Dokumentation, die für die pharmazeutische Forschung geeignet sind.

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

Zeichenprogramm für chemische Strukturen
Versions of package chemtool
Debtags of package chemtool:
useediting, learning
works-withimage, image:vector
Popcon: 58 users (60 upd.)*
Versions and Archs
License: DFSG free

Chemtool ist ein zweidimensionaler GTK+-basierter Editor für chemische Strukturen für X11. Er unterstützt viele Bindungstypen, die meisten Formen von Text, der für chemischen Schriftsatz benötigt wird, und Splines, Bögen und gekrümmte Pfeile.

Zeichnungen können in das MOL-, PDB-, SVG- und XFig-Format zur weiteren Kommentierung, so wie in eine PiCTeX-Zeichnung, als Bitmap oder als PostScript-Dateien (die meisten dieser durch das XFig-Begleitprogramm transfig) exportiert werden.

Das Paket beinhaltet auch das Hilfsprogramm »cht«, um Summenformeln und ein (exaktes) Molekulargewicht aus einer Chemtool-Zeichnung berechnen zu können. »cht« kann entweder von Chemtool direkt oder von der Konsole aufgerufen werden.

Please cite: Matthias Brüstle: Chemtool - Moleküle zeichnen mit dem Pinguin. (eprint) Nachr. Chem. 49(11):1310-1313 (2001)
Screenshots of package chemtool
Planning and Analyzing Dose Finding experiments
Versions of package r-cran-dosefinding
Popcon: 8 users (2 upd.)*
Versions and Archs
License: DFSG free

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

preparation of in silico drug screening projects
Versions of package raccoon
wheezy1.0-1 (contrib)all
jessie1.0b-1 (contrib)all
sid1.0b-1 (contrib)all
Popcon: 1 users (2 upd.)*
Versions and Archs
License: DFSG free, but needs non-free components

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 167387