Open Source Object Pascal Bio-Informatics Software

The Free DELTA Project is a free, open-source, software alternative for a generic system to the processing of taxonomic descriptions based on the DELTA (DEscription Language for TAxonomy) format.

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.

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 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.

This project is a quest for conscious artificial intelligence. A number of prototypes will be developed as the project progresses. This project has 2 subprojects: Object Pascal based CAI NEURAL API - https://github.com/joaopauloschuler/neural-api Python based K-CAI NEURAL API - https://github.com/joaopauloschuler/k-neural-api A video from the first prototype has been made: http://www.youtube.com/watch?v=qH-IQgYy9zg Above video shows a popperian agent collecting mining ore from 3 mining sites and bringing to the base. At the time the agent is born, it doesn't know how to walk nor it knows that it feels pleasure by mining. He has tact only (blind agent). The video shows learning, planning, executing and plan optimization.

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

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.