Debian Med Project
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Summary
Physics
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.

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 Physics packages

Official Debian packages with high relevance

Octave
GNU Octave language for numerical computations
Maintainer: Debian Octave Group
Versions of package octave
ReleaseVersionArchitectures
wheezy3.6.2-5+deb7u1amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
jessie3.6.4-4ia64,s390
sid3.6.4-4ia64,s390
experimental3.8.0-2ia64
jessie3.8.1-1amd64,armel,armhf,i386,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390x,sparc
sid3.8.1-1amd64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390x,sparc
Debtags of package octave:
fieldmathematics
roleprogram
suitegnu
Popcon: 1023 users (949 upd.)*
Versions and Archs
License: DFSG free
Git

Octave is a (mostly Matlab (R) compatible) high-level language, primarily intended for numerical computations. It provides a convenient command-line interface for solving linear and nonlinear problems numerically.

Octave can be dynamically extended with user-supplied C++ files.

The package is enhanced by the following packages: texmacs
Screenshots of package octave
Paw
Physics Analysis Workstation - a graphical analysis program
Versions of package paw
ReleaseVersionArchitectures
wheezy2.14.04.dfsg.2-8amd64,armel,i386,ia64,mips,mipsel,powerpc,s390,sparc
jessie2.14.04.dfsg.2-9amd64,armel,armhf,i386,ia64,mips,mipsel,powerpc,s390,s390x,sparc
sid2.14.04.dfsg.2-9amd64,armel,armhf,i386,ia64,mips,mipsel,powerpc,s390,s390x,sparc
Debtags of package paw:
fieldphysics
interfacex11
roleprogram
scopeutility
uitoolkitxlib
useviewing
x11application
Popcon: 34 users (16 upd.)*
Versions and Archs
License: DFSG free
Git

CERNLIB is a suite of data analysis tools and libraries created for use in physics experiments, but also with applications to other fields such as the biological sciences.

PAW is an interactive program providing interactive graphical presentation and statistical and mathematical analysis tools. It is designed to work on objects familiar to physicists such as histograms, event files (Ntuples), vectors, etc.

The program is linked statically against the CERN libraries on 64-bit architectures in order to function properly, as its design is not very 64-bit clean.

Paw++
Physics Analysis Workstation (Lesstif-enhanced version)
Versions of package paw++
ReleaseVersionArchitectures
wheezy2.14.04.dfsg.2-8amd64,armel,i386,ia64,mips,mipsel,powerpc,s390,sparc
jessie2.14.04.dfsg.2-9amd64,armel,armhf,i386,ia64,mips,mipsel,powerpc,s390,s390x,sparc
sid2.14.04.dfsg.2-9amd64,armel,armhf,i386,ia64,mips,mipsel,powerpc,s390,s390x,sparc
Debtags of package paw++:
fieldphysics
interfacex11
roleprogram
scopeutility
uitoolkitmotif
useviewing
x11application
Popcon: 26 users (15 upd.)*
Versions and Archs
License: DFSG free
Git

CERNLIB is a suite of data analysis tools and libraries created for use in physics experiments, but also with applications to other fields such as the biological sciences.

This package includes Paw++, an interactive program for use in analysis and graphical presentation. Paw++ is the same program as PAW (in the "paw" package), but with a more user-friendly Motif-based GUI, compiled against Lesstif in Debian.

The program is linked statically against the CERN libraries on 64-bit architectures in order to function properly, as its design is not very 64-bit clean.

R-base
GNU R statistical computation and graphics system
Maintainer: Dirk Eddelbuettel
Versions of package r-base
ReleaseVersionArchitectures
squeeze2.11.1-6all
wheezy2.15.1-4all
jessie3.0.2-1all
sid3.0.2-1all
jessie3.0.3-1all
sid3.1.0-1all
Debtags of package r-base:
devellang:r
fieldstatistics
roledummy, metapackage
suitegnu
Popcon: 10 users (1 upd.)*
Versions and Archs
License: DFSG free

R is a system for statistical computation and graphics. It consists of a language plus a run-time environment with graphics, a debugger, access to certain system functions, and the ability to run programs stored in script files.

The design of R has been heavily influenced by two existing languages: Becker, Chambers & Wilks' S and Sussman's Scheme. Whereas the resulting language is very similar in appearance to S, the underlying implementation and semantics are derived from Scheme.

The core of R is an interpreted computer language which allows branching and looping as well as modular programming using functions. Most of the user-visible functions in R are written in R. It is possible for the user to interface to procedures written in the C, C++, or FORTRAN languages for efficiency, and many of R's core functions do so. The R distribution contains functionality for a large number of statistical procedures and underlying applied math computations. There is also a large set of functions which provide a flexible graphical environment for creating various kinds of data presentations.

Additionally, several thousand extension "packages" are available from CRAN, the Comprehensive R Archive Network, many also as Debian packages, named 'r-cran-'.

This package is a metapackage which eases the transition from the pre-1.5.0 package setup with its larger r-base package. Once installed, it can be safely removed and apt-get will automatically upgrade its components during future upgrades. Providing this package gives a way to users to then only install r-base-core if they so desire.

The package is enhanced by the following packages: texmacs
Screenshots of package r-base

Official Debian packages with lower relevance

Paw-demos
Physics Analysis Workstation examples and tests
Versions of package paw-demos
ReleaseVersionArchitectures
wheezy2.14.04.dfsg.2-8all
jessie2.14.04.dfsg.2-9all
sid2.14.04.dfsg.2-9all
Debtags of package paw-demos:
develexamples, testing-qa
fieldphysics
interfacecommandline, x11
roleprogram
x11application
Popcon: 24 users (16 upd.)*
Versions and Archs
License: DFSG free
Git

CERNLIB is a suite of data analysis tools and libraries created for use in physics experiments, but also with applications to other fields such as the biological sciences.

This package includes example scripts for use by PAW or Paw++, and test scripts to make sure that the PAW or Paw++ programs behave correctly. You may run the examples and tests with the included paw-demos program.

No known packages available but some record of interest (WNPP bug)

Biosig - wnpp
library for biomedical signal processing
Responsible: NeuroDebian Team
License: GPL
Debian package not available

BioSig is an open source software library for biomedical signal processing, featuring for example the analysis of biosignals such as the electroencephalogram (EEG), electrocorticogram (ECoG), electrocardiogram (ECG), electrooculogram (EOG), electromyogram (EMG), respiration, and so on. Major application areas are: Neuroinformatics, brain-computer interfaces, neurophysiology, psychology, cardiovascular systems and sleep research. The aim of the BioSig project is to foster research in biomedical signal processing by providing open source software tools for many different applications. Generally, many concerns have to be addressed in this scientific field. BioSig handles this by providing solutions for data acquisition, artifact processing, quality control, feature extraction, classification, modeling, data visualization, and so on.

BioSig consists of some (more or less) coherent parts, for more details take a look at the project page:

  • BioSig for Octave and Matlab (biosig4octmat): A toolbox for Octave and Matlab with powerful data import and export filters, feature extraction algorithms, classification methods, and a powerful viewing and scoring software.
  • BioSig for C/C++ (biosig4c++) containing: reading and writing routines for different biosignal data formats.
  • libbiosig - a library for reading and writing of a number of data formats. libbiosig is used by save2gdf, mexSLOAD and SigViewer
  • save2gdf - a converter between different data formats, and can be used to show the header information
  • mexSLOAD is a MEX-interface for loading biosignal data into Octave (its much faster than the pure M-tools from biosig4octmat). It requires Octave-headers and libbiosig
  • SigViewer (sigviewer): A stand-alone viewing and scoring software for biosignals (especially for EEG signals) based on C++ and the platform-independent GUI toolkit Qt 4.
  • rtsBCI (rtsbci): A real-time BCI system implemented in Matlab and Simulink.
  • BioProFeed (bioprofeed)
  • BCIx (bcix)
Gate - wnpp
Geant4 Application for Emission Tomography
Responsible: Nicolas Spalinger
License: LGPL
Debian package not available

GATE incorporates the Geant4 libraries in a modular, versatile, and scripted simulation toolkit which is adapted to the field of nuclear medicine both in PET (Positron Emission Tomography) and SPECT (Single Photon Emission Computer Tomography). It allows the accurate description of time-dependent phenomena such as source or detector movement and source decay kinetics. The ability to synchronize all time-dependent components allows a coherent description of the acquisition process. It makes it possible to perform realistic simulations of data acquisitions in time.

Openvibe - wnpp
platform for the design, test and use of BCI
License: LGPL
Debian package not available
Language: C++

OpenViBE enables to design, test and use Brain-Computer Interfaces (BCI). OpenViBE is a software for real-time neurosciences (that is, for real-time processing of brain signals). It can be used to acquire, filter, process, classify and visualize brain signals in real time.

*Popularitycontest results: number of people who use this package regularly (number of people who upgraded this package recently) out of 167678