Debian Med Project
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Summary
Physics
пакет для медицинских физиков

Этот метапакет содержит зависимости для коллекции программного обеспечения и документации, которая полезна для медицинской физики в радиационной онкологии, создании диагностических изображений и в смежных областях.

Description

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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

Biosig-tools
format conversion tools for biomedical data formats
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Based on BioSig library, this package provides command line tools, such as

  • save2gdf: converter between different file formats, including but not limited to SCP-ECG(EN1064), HL7aECG (FDA-XML), GDF, EDF, BDF, CWFB. save2gdf can be also used to upload or retrieve data from a bscs server.
Please cite: Alois Schlögl and Clemens Brunner: BioSig: A Free and Open Source Software Library for BCI Research. (eprint) Computer 41(10):44-50 (2008)
Gdf-tools
IO library for the GDF -- helper tools
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GDF (General Dataformat for Biosignals) is intended to provide a generic storage for biosignals, such as EEG, ECG, MEG etc.

This package provides the tool shipped with the library (gdf_merger).

Octave
язык для вычислений численными методами GNU Octave
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Octave — среда, использующая язык программирования высокого уровня, совместимый с Matlab(R). Применяется в основном для численных вычислений. Имеет интерфейс командной строки для численного решения линейных и нелинейных математических задач.

Octave можно динамически расширять пользовательскими модулями на C++.

The package is enhanced by the following packages: liboctave-dev octave-doc texmacs
Please cite: John W. Eaton, David Bateman, Søren Hauberg and Rik Wehbring: GNU Octave version 4.2.0 manual: a high-level interactive language for numerical computations. (2016)
Registry entries: SciCrunch 
Paw
Physics Analysis Workstation - a graphical analysis program
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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.

Screenshots of package paw
Paw++
Physics Analysis Workstation (Lesstif-enhanced version)
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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
система статистических расчетов и построения графиков GNU R
Maintainer: Dirk Eddelbuettel
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R — это система для статистических расчётов, состоящая из языка и рабочего окружения с графикой, отладчиком, доступом к некоторым системным функциям и возможностью запуска сценариев, хранимых в отдельных файлах.

На разработку R сильное влияние оказали два существующих языка: S Бекера, Чамберса и Уилкса, и Scheme Сассмана. Несмотря на то, что внешне получившийся язык очень сильно похож на S, его реализация и семантика произошли из Scheme.

Ядро R представляет собой интерпретируемый язык программирования, который позволяет реализовать ветвления и циклы, а также модульное программирование с использованием функций. Большинство функций R, видимых пользователю, написаны на R. Также существует возможность обращаться к процедурам, написанным на C, C++ или FORTRAN для большей эффективности, и многие базовые функции R это делают. Дистрибутив R позволяет осуществлять множество статистических операций и лежащих в их основе прикладных математических вычислений. Также присутствует большой набор функций, обеспечивающих гибкое графическое окружение для создания различных графических представлений данных.

Дополнительно, несколько тысяч «пакетов» с расширениями доступны на CRAN, Comprehensive R Archive Network. Многие из них также собраны в виде пакетов Debian, называющихся 'r-cran-<имя пакета>'

Настоящий пакет является метапакетом, облегчающим переход с R версий, меньших 1.5.0, которые поставлялись в виде одного большого пакета r-base. После установки, его можно спокойно удалить; apt-get будет автоматически обновлять установленные компоненты R при последующих обновлениях. Предоставление r-base как метапакета позволяет пользователям устанавливать только пакет r-base-core (меньший по объёму), если они этого пожелают.

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

Official Debian packages with lower relevance

Libbiosig-dev
I/O library for biomedical data - development files
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BioSig is a library for accessing files in several biomedical data formats (including EDF, BDF, GDF, BrainVision, BCI2000, CFWB, HL7aECG, SCP_ECG (EN1064), MFER, ACQ, CNT(Neuroscan), DEMG, EGI, EEG1100, FAMOS, SigmaPLpro, TMS32). The complete list of supported file formats is available at http://pub.ist.ac.at/~schloegl/biosig/TESTED .

This package provides header files and static library.

Please cite: Alois Schlögl and Clemens Brunner: BioSig: A Free and Open Source Software Library for BCI Research. (eprint) Computer 41(10):44-50 (2008)
Octave-biosig
Octave bindings for BioSig library
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This package provides Octave bindings for BioSig library. Primary goal -- I/O interface to variety of biomedical file formats, including but not limited to SCP-ECG(EN1064), HL7aECG (FDA-XML), GDF, EDF.

Please cite: Alois Schlögl and Clemens Brunner: BioSig: A Free and Open Source Software Library for BCI Research. (eprint) Computer 41(10):44-50 (2008)
Paw-demos
Physics Analysis Workstation examples and tests
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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.

Python-multipletau
multiple-tau algorithm for Python/NumPy
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Multipe-tau correlation is computed on a logarithmic scale (less data points are computed) and is thus much faster than conventional correlation on a linear scale such as numpy.correlate

An online reference is available at http://paulmueller.github.io/multipletau

This is the Python 2 version of the package

Python3-biosig
Python3 bindings for BioSig library
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This package provides Python3 bindings for BioSig library. Primary goal -- I/O interface to variety of biomedical file formats, including but not limited to SCP-ECG(EN1064), HL7aECG (FDA-XML), GDF, EDF.

Please cite: Alois Schlögl and Clemens Brunner: BioSig: A Free and Open Source Software Library for BCI Research. (eprint) Computer 41(10):44-50 (2008)

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

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 195839