Debian Med Project
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pacchetti Debian Med per la ricerca farmaceutica

Questo metapacchetto contiene le dipendenze per una raccolta di software e documentazione che è utile per la ricerca farmacologica.


For a better overview of the project's availability as a Debian package, each head row has a color code according to this scheme:

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Debian Med Pharmacology packages

Official Debian packages with high relevance

programma per il disegno di strutture chimiche
Versions of package chemtool
Debtags of package chemtool:
useediting, learning
works-withimage, image:vector
Popcon: 49 users (27 upd.)*
Versions and Archs
License: DFSG free

Chemtool è un editor 2D per X11 per strutture chimiche basato su GTK+. Supporta molti stili per i legami, la maggior parte dei tipi di testo necessari per impaginare testi chimici e spline/archi/frecce curve.

I disegni possono essere esportati in formato MOL e PDB, in formato SVG * XFig per ulteriori annotazioni, come disegni PiCTex, come bitmap o file PostScript (molti di questi grazie a transfig, il programma compagno di Xfig).

Il pacchetto contiene anche un programma di aiuto, cht, per calcolare le formule somma e il peso molecolare (esatto) a partire da un file di disegno di chemtool. Cht può essere invocato direttamente da Chemtool o dalla console.

Please cite: Matthias Brüstle: Chemtool - Moleküle zeichnen mit dem Pinguin. (eprint) Nachr. Chem. 49(11):1310-1313 (2001)
Screenshots of package chemtool
pianificazione e analisi di esperimenti di determinazione della dose
Versions of package r-cran-dosefinding
Popcon: 15 users (16 upd.)*
Newer upstream!
License: DFSG free

Il pacchetto GNU R DoseFinding fornisce funzioni per la progettazione e l'analisi di esperimenti di determinazione della dose (con attenzione agli studi clinici farmaceutici di fase II). Fornisce funzioni per: test con contrasti multipli, fit di modelli dose-risposta non lineari (usando stime bayesiane e non bayesiane), calcolo del design ottimale e implementazione della metodologia MCPMod.

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
sid1.0b-2 (contrib)all
Popcon: 4 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. Assume a specific behaviour (and only this) of a drug can be changed in a defined way.

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 193664