Framework for Systems Biology
The Systems Biology Workbench(SBW) is a framework for application intercommunications. It uses a broker-based, distributed, message-passing architecture, supports many languages including Java, C++, Perl & Python, and runs under Linux,OSX & Win32. It comes with a large number of modules, encompassing the whole modeling cycle: creating computational models, simulating and analyzing them, visualizing the information, in order to improve the models. All using community standards, such as SED-ML, SBML and MIRIAM.
It's possible for machines to become self-aware.
We believe that it's possible for machines to become self-aware, but may not exhibit human-like thought processes. This project is a quest for conscious artificial intelligence. We will develop prototypes while we go for our main goal. Our steps will be 1) Develop a Learning/Predictive Module. 2) Develop a Planning Module based on the learning/predictive module. 3) Develop a Plan Optimization Module so plans built in the previous module can be optimized. 4) Develop a Decision Making Engine based on previous planning. 5) Develop prototypes of the artificial creature. 6) Publish some academic papers. And there is the video: 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 optimizing plans.
This site hosts the source code for C++ version of the Broker for SBW, NOM module, advanced simulation suite, analysis applications and model editors.
Units for computational cybernetics
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, S and Matlab.
Pascal Units for Medical Applications
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 converting functions for measurement units 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.
biOP [bio~ObjectPascal/bio~Delphi] bioinformatics libraries
Structure parameter inference approach for endocrine feedback control
SPINA is software for determining constant structure-parameters of endocrine feedback control systems from hormone levels obtained in vivo. The first version of this cybernetic approach allows for evualuating the functional status of the thyroid gland, i.e. thyroid's secretory capacity (GT or SPINA-GT) and sum activity of peripheral deiodinases (GD or SPINA-GD).
Clad organizes a tree of biological species, allowing the user to add scientific and popular names, origin, distribution, apomorphies and other information such as pictures or if the clade is extinct. Browsing through the trees is easy and educative.
iMate is a win32 / Linux desktop mate programme. It offers more features than the already existing desktop mate (AI, learning capacity, growth and limited lifeTime, third party tools to add new behaviour, ...).
Software for working with and managing nucleotide sequences in multiple formats. The features include format conversion, sequence viewer, sequence editor, oligonucleotides alignment, restriction analysis, pattern searching, retrieval from servers, multi
This software uses data gathered from published biodiversity inventories, together with physical and vegetational maps, to build a biodiversity map (darkening geographical landscape according with the richness/diversity of species).
The Canopy project is an initiative to merge and expand the functionality of Perl-speaks-NONMEM (PsN), Census, Xpose and PopED. The goal is to produce a coherent, inclusive and convenient platform for pharmacometric data analysis.
Frankenstein Project: Hack the Genome A collection of valuable tools needed for genome analysis, such as: - molecule, protein 3d structure viewer - protein alignement machine - cloner - DNA manipulating tools - DNA-to-Protein translator and more
MLPA Analyzer is a workflow and analysis environment for Multiplex Ligation-dependent Probe Amplification
Natural Family Planning Software - Written in Delphi for Windows; It provides a free support method to help with fertility awareness.
Statistical algorithms for life sciences
Collection of algorithms for computational statistics in life sciences
Scientific table server and relay
Refinery is a scientific table server for relaying between data sources and statistical software.
Bioinformatics program for analysing two (currently) or more (in the future) protein sequences and compare them using a Smith-Waterman and/or Needleman-Wunsch algorithms. Also set on gathering inherent statistical analysis from the process and displaying
TI2BioP allows mainly the calculation of topological indices (spectral moments) derived from inferred and artificial 2D structures of DNA, RNA and proteins being possible to carry out a structure-function correlation irrespective of sequence alignments. TI2BioP version 2.1 is a python platform with a graphical interface designed for Linux OS.
The Hairdresser enables removal of sequences of desired length/subset from metagenomic sequence database, renames sequences and calculates thermostability index of database entries.
"T-Station" is software designed to colect , store and manage measured temperatures from DS1820 sensors in "micro LAN" topology.
A set of computational chemistry modules and programs to perform ab initio calculations of various properties of small molecules. The system will use GRID technology for large computations. The system will use C++ and Qt, running on Win32 and Linux
A set of very useful utilities from icon extraction tool for everyday use to free encryption tools and sound analysis software aimed at any healthcare professional interested in improving his/her cardiac auscultation skills.
utilities for fst genome scans
Give names to the colors your eyes see, watch the computer learn and suggest names for new randomic colors. It gives the RGB components of each colors and list the memory so on, saving it into a text file with your name.