Open Source Pascal Bio-Informatics Software

SPINA is software for the rapid, reliable and accurate determination of constant structure parameters of endocrine feedback control systems. It is a class of static function tests that require nothing more than steady-state concentrations of hormones or metabolites obtained in vivo. The first version of this cybernetic approach had been developed for the evaluation of the functional status of the thyroid gland, i.e. thyroid's secretory capacity (gain of thyroid, GT or SPINA-GT) and sum activity of peripheral deiodinases (GD or SPINA-GD). A second version has been established for insulin-glucose homeostasis. It delivers the secretory capacity of pancreatic beta cells (SPINA-GBeta), an estimate for the insulin receptor amplification (SPINA-GR) and a static disposition index as a measure for the loop gain of the feedback loop (SPINA-DI). Both implementations of SPINA have been validated in more than 50 clinical studies based on large cohorts.

The PUMA Repository is a collection of Pascal units for medical informatics. It contains reusable source code for a wide field of health-care application development. The code includes a support engine for the European Data Format (EDF and EDF+), converting functions for units of measurement and an HL7 engine. PUMA is compatible with Lazarus and Free Pascal. Some of the units also support other Pascal implementations including Delphi, winsoft Pocket Studio and other compilers.

Boxshade is a program for creating good looking printouts from multiple- aligned protein or DNA sequences.

SimThyr is a continuous simulation program for the human pituitary-thyroid feedback control system. Applications of this program cover research, including development of hypotheses, and education of students in biology and medicine, nurses and patients.

The TMpred program makes a prediction of membrane-spanning regions and their orientation. The algorithm is based on the statistical analysis of TMbase, a database of naturally occuring transmembrane proteins.

Avian Freeware Suite (AFS) provides two things: Developers with libraries for Java Swing Widgets, XML handling, Fortran95 and Pascal; End users (Medical students, doctors, scientists) with productivity tools they can use (quizzes, XML databasing & PDF)

CyberUnits is a cross-platform class library for rapid development of high-performance computer simulations in life sciences. It supports modelling for biomedical cybernetics and systems biology with Object Pascal.

Diktyologia is software for investigating complex systems with advanced methods of network theory. The package allows for analysing statistical properties of directed intercausal networks that are represented in form of cy.prus XML files.

Palibino is a class library for Object Pascal supporting bioinformatics, large-scale genomic analysis in life sciences and computational biology.

Collection of algorithms for computational statistics in life sciences

ROC.KIT is an application for health sciences that automatically calculates ROC curves (receiver operating charateristic plots) from continuous medical data like laboratory results.

Tempomat is software that supports statistical analysis of time series in the life sciences.

cy.prus is a cross platform simulation environment for medical cybernetics and systems biology. Its purpose is to provide both a facility for simulating life and a GUI for easily constructing biological information processing structures based on XML.

The program fuses 2 sets of molecules. It tries different relative positions of molecules before binding them, so that there is no or minimal intersection in the resulting molecule. The atom to be fused in a molecule is labeled with an R symbol.

An open access program for the optimisation of AFLP scoring parameters, closely related with the tinyFLP software

A software for automatic peak selection and scoring of AFLP data tables witten by Wolfgang Arthofer, University of Innsbruck. Austria.