Debian Med: Medical research

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

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 to you, or if you have prepared an unofficial Debian package, please do not hesitate to send a description of that project to the mailing list.

Official Debian packages

python-pyepl
http://pyepl.sourceforge.net/ 		License: LGPL
Official Debian package

PyEPL is a stimuli delivery and response registration toolkit to be used for generating psychology (as well as neuroscience, marketing research, and other) experiments.

It provides

  • presentation: both visual and auditory stimuli
  • responses registration: both manual (keyboard/joystick) and sound (microphone) time-stamped
  • sync-pulsing: synchronizing your behavioral task with external acquisition hardware
  • flexibility of encoding various experiments due to the use of Python as a description language
  • fast execution of critical points due to the calls to linked compiled libraries

This toolbox is here to be an alternative for a widely used commercial product E'(E-Prime).

Unofficial Debian packages

phpESP
http://www.butterfat.net/wiki/Projects/phpESP/ 		License: BSD
Unofficial Debian package
phpESP is a package for PHP that provides an easy to use web-based interface to design surveys, deploy them on your web site, and export data. It features multiple users and user groups, with data isolation and hiding between groups. It is suitable for use by a single person, a department, or an entire organization. The surveys created by phpESP can be easily embedded into existing HTML templates with one or two new lines.

Debian packages not available

The Virtual Medical School Project at the Hammersmith Hospital
http://www.soundray.de/vms/ 		License: GPL
Debian package not available
Storing every imaging study digitally together with the radiologist's report resulted in a huge database of diseases and their imaging presentations as well as normal anatomy. This database is, of course, an immensely valuable resource for teaching. The Virtual Medical School Project was initiated with the intention to convert this image database into a knowledge base. This knowledge base will form the foundation of a digital network based teaching system for the whole of medicine at every level: the "Virtual Medical School". It is based heavily on free software (Apache-Cocoon).
International Classification for Diseases (ICD-9 and ICD-10)
http://www.cdc.gov/nchs/icd9.htm 		License: Public Domain
Debian package not available
There are two related classifications of diseases with similar titles. The International Classification of Diseases (ICD) is the classification used to code and classify mortality data from death certificates. The International Classification of Diseases, Clinical Modification (ICD-CM) is used to code and classify morbidity data from the in-patient and out-patient records, physician offices, and most NCHS surveys.
EpiTools
http://www.epitools.net/ 		License: GPL
Debian package not available

Freely available numerical tools and methods of epidemiology. The primary target audience is public health epidemiologists and data analysts. Using R, an open source programming language and environment for statistical computing and graphics, there are provided numerial tools and programming solutions that have been used and tested in real-world epidemiologic applications.

Many practical problems in the analysis of public health data require programming or special software, and investigators in different locations may duplicate programming efforts done elsewhere. Often, simple analyses, such as the construction of confidence intervals, are not calculated and thereby complicate appropriate statistical inferences for small geographic areas. There are many examples of simple and useful numerical tools that would enhance the work of epidemiologists at local health departments and yet are not readily available for the problem in front of them (e.g., exact confidence intervals for low incidence rates, statistical pooling methods for meta-analysis, lifetime risk calculations, etc.). The availability of these tools will encourage wider use of appropriate methods and promote evidence-based public health practices.

Surveillance
http://www.statistik.lmu.de/~hoehle/software/surveillance/ 		License: GPL
Debian package not available
The intention of the R-package surveillance is to provide a test-bench for surveillance algorithms. It allows users to test new algorithms and compare their results with those of standard surveillance methods. Among others the package contains an implementation of the procedures described by Stroup et al. (1989), Farrington et al. (1996) and the system used at the Robert Koch Institute (RKI), Germany. For evaluation purposes, the package contains example datasets drawn from the SurvStat@RKI Database maintained by the RKI, Germany. More comprehensive comparisons using simulation studies are possible by methods for simulating point source outbreak data using a hidden Markov model. To compare the algorithms, benchmark numbers like sensitivity, specificity and detection delay can be computed for entire sets of surveillance time series.
OHF STEM
http://www.eclipse.org/ohf/components/stem/ 		License: Free
Debian package not available
The Spatiotemporal Epidemiological Modeler (STEM) tool is designed to help scientists and public health officials create and use spatial and temporal models of emerging infectious diseases. These models could aid in understanding, and potentially preventing, the spread such diseases. STEM is part of the Open Healthcare Framework.