CyberUnits is a cross-platform class library for rapid programming of high-performance computer simulations in life sciences. It supports modelling for biomedical cybernetics and systems biology with Object Pascal, S and Matlab.
Bioconductor is an open source, open development software project to provide tools for the analysis and comprehension of high-throughput genomic data. It is based primarily on the R programming language.
The Bioconductor release version is updated twice each year, and is appropriate for most users. There is also a development version, to which new features and packages are added prior to incorporation in the release. A large number of meta-data packages provide pathway, organism, microarray and other annotations.
DeVIDE, or the Delft Visualisation and Image processing Development Environment, is a cross-platform software framework for the rapid prototyping, testing and deployment of visualisation and image processing algorithms. The software was developed within the Visualisation group. DeVIDE's primary (and currently only) front-end is a data-flow boxes-and-lines network editor. In this regard, it is very similar to AVS, OpenDX, Khoros or VISSION. DeVIDE integrates functionality from libraries such as VTK, ITK, GDCM, DCMTK, numpy and matplotlib. It is being very actively developed.
SPINA (structure parameter inference approach) is a method for calculating constant structure parameters of endocrine feedback control systems in vivo from hormone levels obtained from serum or plasma.
A first successful implementation applies to evaluation of thyroid function. It allows for calculating the thyroid's maximum secretory capacity (GT or SPINA-GT) and the sum activity of peripheral 5'-deiodinases (GD or SPINA-GD) from levels of TSH, (F)T4 and (F)T3 that have been determined once only (SPINA Thyr).
SimThyr is a simulation program for thyroid homeostasis. It is based on a published nonlinear parametric isomorphic model of thyrotropic feedback control. Applications of SimThyr cover generation of hypotheses for biomedical research, education and presentation. Binaries and sourcecode are available for Mac OS, Mac OS X, Windows, Linux and other Unix derivatives.
The PUMA Repository (Pascal units for medical applications) is a collection of reusable source code for bioinformatics. It is compatible with Lazarus and Free Pascal, parts of the source code can also be used with Delphi and winsoft Pocket Studio.
Components of the PUMA repository include a unit converter for transforming instrumentation readouts consisting of a numerical value and a measurement unit, and an HL7 engine for reading, parsing, compiling and writing HL7 messages.
Spectroscopic Image Visualization and Computing (SIVIC) is an open-source, standards-based software framework and application suite for processing and visualization of DICOM MR Spectroscopy data. Through the use of DICOM, SIVIC aims to facilitate the application of MRS in medical imaging studies.
The Arden Syntax as a standardized language to represent medical knowledge can be used to express medical knowledge.
Arden2ByteCode is a open source compiler for the Arden Syntax. Arden2ByteCode runs on Java Virtual Machines (JVM) and translates Arden Syntax directly to Java bytecode (JBC)
executable on JVMs. It also serves as runtime environment for execution of the compiled bytecode.
The Image-Guided Surgery Toolkit is a high-level, component-based framework which provides a common functionality for image-guided surgery applications. The framework is a set of high-level components integrated with low-level open source software libraries and application programming interfaces (API) from hardware vendors.
DicomBrowser is an application for inspecting and modifying DICOM metadata in many files at once. A single imaging session can produce thousands of DICOM files; DicomBrowser allows users to view and edit a whole session—or even multiple sessions—at once. Users can save the original or modified files to disk, or send them across a network to a DICOM C-STORE service class provider, such as a PACS or an XNAT.