[[Concept:Biology]]

Bioperl: The Bioperl project is a coordinated effort to collect computational methods routinely used in bioinformatics into a set of standard CPAN-style, well-documented, and freely available Perl modules. It is well-accepted throughout the community and used in many high-profile projects, e.g., Ensembl. The recommended packages are needed to run some of the included binaries, for a detailed explanation including the specific Perl modules please see README.Debian. The suggested package enhances the manual pages.

Bioperl-run: Contains scripts from the BioPerl-Run package. This package will also install all wrappable applications packaged in Debian. The ones that are not Free are "Suggested" by this package.

Biskit: Biskit is a python library for structural bioinformatics research. It simplifies the analysis of macromolecular structures, protein complexes, and molecular dynamics trajectories and offers a platform for the rapid integration of external programs.

Blossoc: Blossoc is a linkage disequilibrium association mapping tool that attempts to build (perfect) genealogies for each site in the input, score these according to non-random clustering of affected individuals, and judge high-scoring areas as likely candidates for containing disease affecting variation. Building the local genealogy trees is based on a number of heuristics that are not guaranteed to build true trees, but have the advantage over more sophisticated methods of being extremely fast. Blossoc can therefore handle much larger data sets than more sophisticated tools, but at the cost of sacrificing some accuracy.

Bmrblib: Bmrblib is a Python API abstracting the Biological Magnetic Resonance Data Bank (BioMagResBank or BMRB) NMR-STAR format (http://www.bmrb.wisc.edu/). It allows the writing of NMR-STAR files for BMRB data deposition and the reading and easy extraction of data from files residing in the BMRB data bank, all without knowledge of the Self-Defining Text Archive and Retrieval (STAR) format.

CAGE: A generic and fairly complete cellular automata simulation engine. CAGE is a fairy generic and complete cellular automaton simulation engine in Python. It supports both 1D and 2D automata, a variety of prepackaged rules, and the concept of "agents" which can move about independently on the map for implementing agent behavior. CAGE comes with numerous examples of fully-functional CA systems, including Conway's Game of Life, Langton's self-reproducing automaton, Langton's "vants," and 1D automata rule explorers. It also comes with simple displayers (including a curses interface for 2D automata). Also included is a unique implementation of a finite state machine (ant.py).

CT Sim: Computed Tomography is the technique of estimating the interior of objects from the measurements of radiation projected through the object. That radiation can be transmitted through the object such as in X-ray computed tomography or emitted from internal radiation sources as in nuclear medicine scans. CTSim simulates the transmission of X-rays through phantom objects. These X-ray data are called projections; CTSim reconstructs the original phantom image from the projections using a variety of algorithms. The program also has a wide array of image analysis and image processing functions.

CoaSim: 'CoaSim' is a tool for simulating the coalescent process with recombination and gene conversion under the assumption of exponential population growth. It constructs the ancestral recombination graph for a given number of individuals and uses this to simulate samples of SNP and micro-satellite haplotypes/genotypes. The generated sample can afterwards be separated in cases and controls, depending on states of selected individual markers. The tool can accordingly also be used to construct cases and control data sets for association studies.

CoaSim-gui: 'CoaSim-gui' is a graphical use interface for the coalescence process simulator CoaSIm.

CvEyeTracker: 'cvEyeTracker' is a toolkit for low-cost real-time eye tracking. It is intended to provide a hardware design and a set of software tools useful for the analysis of eye movement data collection using inexpensive, off-the-shelf hardware. Available tools include algorithms to measure eye movements from digital videos, techniques to calibrate the eye tracking system, and example software to facilitate real-time eye-tracking application development.

DataStatix: DataStatix is a free software for GNU/Linux and Windows useful to manage data of every kind (although it has been written to manage biomedical data), to create descriptive statistics and graphs and to export items easily to R environment or to other statistic softwares. In order to handle properly big amount of data and many concurrent users, DataStatix works with MySql database and it has been developed and tested with MySql community edition 5.5. Some features of the software are: users management (create, delete, modify password) within the software; different users levels of data access (administrator, default, read only); user defined templates (models) of data, to create new databases easily; importation and esportation of data in CSV format (used also by Calc and Excel); updating of existing data from a CSV file created with DataStatix; descriptive statistics from every data (some more kind of statistics to come); graphs from every data.

Datamash: Datamash is a command-line program which performs basic numeric, textual and statistical operations on input textual data files. Datamash is designed to be portable and reliable, and aid researchers to easily automate analysis pipelines, without writing code or even short scripts.

Discosnp: Software discoSnp is designed for discovering Single Nucleotide Polymorphism (SNP) from raw set(s) of reads obtained with Next Generation Sequencers (NGS). Note that number of input read sets is not constrained, it can be one, two, or more. Note also that no other data as reference genome or annotations are needed. The software is composed by two modules. First module, kissnp2, detects SNPs from read sets. A second module, kissreads, enhance the kissnp2 results by computing per read set and for each found SNP: 1) its mean read coverage 2) the (phred) quality of reads generating the polymorphism.

Drmaa: This is a Python implementation of the Distributed Resource Management (DRM) Application API (DRMAA). It provides all high- level functionality necessary to consign a job to a DRM system (e.g. Sun Gridengine), including common operations on jobs, such as termination or suspension.

E-CELL Simulation Environment: E-Cell System is an object-oriented software suite for modelling, simulation, and analysis of large scale complex systems such as biological cells. It allows many components, driven by multiple algorithms with different timescales, to coexist. The core library is written in C++ with a Python binding, and frontend software uses Python.

Edlib: Lightweight, super fast C/C++ library for sequence alignment using edit distance.

Electrocardiognosis: Electrocardiognosis (a.k.a. Ecgnosis) is a software package designed to assist the physician in formulating diagnoses on 24h ambulatory ECG monitoring (Holter) recordings.

EpiR: A package for analysing epidemiological data. Contains functions for directly and indirectly adjusting measures of disease frequency, quantifying measures of association on the basis of single or multiple strata of count data presented in a contingency table, and computing confidence intervals around incidence risk and incidence rate estimates. Miscellaneous functions for use in meta-analysis, diagnostic test interpretation, and sample size calculations.

FastDNAml: 'fastDNAml' estimates maximum likelihood phylogenetic trees from nucleotide sequences. It is derived from Joseph Felsenstein's version 3.3 DNAML (part of his PHYLIP package). 'fastDNAml' tries to solve the same problem as DNAML, but to do so faster and using less memory, so that larger trees and/or more bootstrap replicates become tractable. Much of fastDNAml is merely a recoding of the PHYLIP 3.3 DNAML program from PASCAL to C.

FastQC: FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis. The main functions of FastQC are * Import of data from BAM, SAM or FastQ files (any variant) * Providing a quick overview to tell you in which areas there may be problems * Summary graphs and tables to quickly assess your data * Export of results to an HTML based permanent report * Offline operation to allow automated generation of reports without running the interactive application

FreeLIMS: FreeLIMS is a Laboratory Information Management System ( LIMS ). Manage samples; create sample types from methods & parameters; easily generate reports & certificates; fine tune user rights. FreeLIMS is Open Source and Free.

FreeMED: FreeMED is a Web-based medical records (EMR) and patient management system with a printing system, patient scheduling, an HL7 interface, a billing system, XML-RPC Web services, and many other features. It has an extensible modular architecture, allowing it to be customized based on individual practices without having to rewrite core components of the system. It is HIPAA compliant.

GAUL: The Genetic Algorithm Utility Library (GAUL) is a programming library designed to assist in the development of code requiring genetic algorithms. The steady-state, generation based and the island model of evolution are supported, using the Darwinian, Lamarkian or Baldwininan evolutionary schemes. Standard mutation, crossover and selection operators are provided, while code hooks additionally allow custom operators. It provides data structures and functions for handling and manipulation of the data required for a genetic algorithm. Additional stochastic algorithms are provided for comparison to the genetic algorithms. Much of the functionality is also available through a simple S-Lang interface.

GENtle: GENtle is bioinformatics software for everyday molecular biology tasks. It features DNA and amino acid sequence display and editing, database management, plasmid maps, restriction and ligation, alignments, sequencer data import, calculators, gel image display, primer design, virtual PCR, online database access, and more.

Genometools: The GenomeTools genome analysis system is a free collection of bioinformatics tools.

Gnotary: Gnotary is an asynchronous peer-to-peer digital notary service based on email. The server polls POP3 mail boxes scanning for specified key words in the subject line. A digital signature of the email body is returned to the sender. The main purpose is to allow medical practitioners to establish a peer-to-peer based notary service for their electronic health records.

Gnumed: GNUmed is a a comprehensive medical management solution written by medical professionals. Its purpose is to enable doctors to keep a medically sound record on their patients’ health. It is intended to become a sophisticated decision support system that will elevate the quality of medical care that can be delivered. GNUmed operates in a client-server environment where the client and the server are physically two different machines. Each software component i.e. Client / Server are distributed separately. It is alongside GNU Health, one of the medical solution of the GNU project.

HASAS: HASAS (HydroAcoustic Signal Analysis System) is a modular system for passive sonar signal analysis. It can be used for biological research or surveillance, for example. The soundcard is used as input device, and it currently includes all the very basic functionality; beamforming, direction finding, level histogram, LOFAR/DEMON (narrowband spectrogram), wideband spectrogram, and raw audio.

Health

GNU Health is a program designed for hospitals, offering the following functionalities:

Electronic Medical Record (EMR)
Hospital Information System (HIS)
Health Information System

It has a strong focus on family medicine and primary care, along with socio-economic circumstances. It uses the following disease and medical procedure standards: (ICD-10 / ICD-10-PCS). There are facilities to aid in choosing medicines; prescription writing; patient, hospital finacial, and lab administration tools; a database of 4,200 disease-related genes; epidemiological reporting; and much more. GNU Health is part of GNU Solidario, an NGO offering health and education to the underpriveledged through free software: http://www.gnusolidario.org

HealthBox: HealthBox is a convenient way to manage health information. Instead of each app having to record inforamtion within it's own ecosystem, HealthBox creates a place for developers to centralize health information. Say you have a program that records your steps, one that monitors work outs, and a third program to track your nutrient intake. Typically, if you wanted to access your information, you'd have to use each respective service's interface. With HealthBox, those developers would be able to store all the information in one place, making it much easier for you to compare different health metrics, and share information between services.

Homoeopim: This is a toy homoeopathy software using a database, an expert system and a suit of CGI programs to search for homoeopathic remedies depending on symptoms entered. There is an iteration mode where questions are asked in a attempt to refine the search. This is an ongoing project, but with 47,000+ mapping entries between remedies and symptoms, it should be marginally usable.

INFOTOPO: Programs for Information Topology Data Analysis Information Topology is a program written in Python (compatible with Python 3.4.x), with a graphic interface built using TKinter [1], plots drawn using Matplotlib [2], calculations made using NumPy [3], and scaffold representations drawn using NetworkX [4]. It computes all the results on information presented in the study [5], that is all the usual information functions: entropy, joint entropy between k random variables (Hk), mutual informations between k random variables (Ik), conditional entropies and mutual informations and provides their cohomological (and homotopy) visualisation in the form of information landscapes and information paths together with an approximation of the minimum information energy complex [5]. It is applicable on any set of empirical data that is data with several trials-repetitions-essays (parameter m), and also allows to compute the undersampling regime, the degree k above which the sample size m is to small to provide good estimations of the information functions [5]. The computational exploration is restricted to the simplicial sublattice of random variable (all the subsets of k=n random variables) and has hence a complexity in O(2^n). In this simplicial setting we can exhaustively estimate information functions on the simplicial information structure, that is joint-entropy Hk and mutual-informations Ik at all degrees k=<n and for every k-tuple, with a standard commercial personal computer (a laptop with processor Intel Core i7-4910MQ CPU @ 2.90GHz * 8) up to k=n=21 in reasonable time (about 3 hours). Using the expression of joint-entropy and the probability obtained using equation and marginalization [5], it is possible to compute the joint-entropy and marginal entropy of all the variables. The alternated expression of n-mutual information given by equation then allows a direct evaluation of all of these quantities. The definitions, formulas and theorems are sufficient to obtain the algorithm [5]. We will further develop a refined interface (help welcome) but for the moment it works like this, and requires minimum Python use knowledge. Please contact pierre.baudot [at] gmail.com for questions, request, developments (etc.): [1] J.W. Shipman. Tkinter reference: a gui for python. . New Mexico Tech Computer Center, Socorro, New Mexico, 2010. [2] J.D. Hunter. Matplotlib: a 2d graphics environment. Comput. Sci. Eng., 9:22–30, 2007. [3] S. Van Der Walt, C. Colbert, and G. Varoquaux. The numpy array: a structure for efficient numerical computation. Comput. Sci. Eng., 13:22– 30, 2011. [4] A.A. Hagberg, D.A. Schult, and P.J. Swart. Exploring network structure, dynamics, and function using networkx. Proceedings of the 7th Python in Science Conference (SciPy2008). Gel Varoquaux, Travis Vaught, and Jarrod Millman (Eds), (Pasadena, CA USA), pages 11–15, 2008. [5] M. Tapia, P. Baudot, M. Dufour, C. Formisano-Tréziny, S. Temporal, M. Lasserre, J. Gabert, K. Kobayashi, JM. Goaillard . Information topology of gene expression profile in dopaminergic neurons doi: https://doi.org/10.1101/168740 http://www.biorxiv.org/content/early/2017/07/26/168740

ImageJ: ImageJ is a public domain Java image processing program inspired by NIH Image for the Macintosh. It runs, either as an online applet or as a downloadable application, on any computer with a Java 1.4 or later virtual machine.

Interval RPN Calculator: This terminal app runs on PCs or laptops running Windows, OSX or GNU/Linux. It attempts to mimic the functionality of an HP ReversePolishNotation [RPN] calculator with the added enhancement of interval output. So along with your answer, you get a good idea of its trustworthiness.

KNIME: KNIME [naim] is a user-friendly graphical workbench for the entire analysis process: data access, data transformation, initial investigation, powerful predictive analytics, visualisation and reporting. The open integration platform provides over 1000 modules (nodes), including those of the KNIME community and its extensive partner network.

Librsb: librsb is a library for sparse matrix computations featuring the Recursive Sparse Blocks (RSB) matrix format. This format allows cache efficient and multi-threaded (that is, shared memory parallel) operations on large sparse matrices. The most common operations necessary to iterative solvers are available, e.g.: matrix-vector multiplication, triangular solution, rows/columns scaling, diagonal extraction / setting, blocks extraction, norm computation, formats conversion. The RSB format is especially well suited for symmetric and transposed multiplication variants. On these variants, librsb has been found to be faster than Intel MKL's implementation for CSR. Most numerical kernels code is auto generated, and the supported numerical types can be chosen by the user at build time. librsb implements the Sparse BLAS standard, as specified in the BLAS Forum documents.

Minfx: The minfx project is a Python package for numerical optimisation, being a large collection of standard minimisation algorithms. This includes the line search methods: steepest descent, back-and-forth coordinate descent, quasi-Newton BFGS, Newton, Newton-CG; the trust-region methods: Cauchy point, dogleg, CG-Steihaug, exact trust region; the conjugate gradient methods: Fletcher-Reeves, Polak-Ribiere, Polak-Ribiere +, Hestenes-Stiefel; the miscellaneous methods: Grid search, Simplex, Levenberg-Marquardt; and the augmented function constraint algorithms: logarithmic barrier and method of multipliers (or augmented Lagrangian method).

Mondo Health Monitor: Mondo is a system health monitor daemon for GNU/Linux, capable of running specific commands whenever alarm conditions get tripped. Mondo can do things like send e-mails and shut your system down if a fan fails, voltage rails start to go haywire, or your system just seems warmer than it should be. It can actually run any command of your choice to handle an alarm condition

NUT nutrition software: This software help you record what you eat and then analyzes your meals for nutrient levels in terms of the USDA "Daily Value" (the standard for food labeling in the US.

Network Extraction from Images: NEFI is an extensible computer vision tool that analyzes images that contain networks and extracts the graph. Examples are leaf venations, insect wings, slime molds, mud crack patterns etc. It determines topological information as well as properties such as edge length and width.

NeuroScope: NeuroScope is an advanced viewer for electrophysiological and behavioral data (with limited editing capabilities): it can display local field potentials (EEG), neuronal spikes, behavioral events, and the position of the animal in the environment.

Neuron Health: Neuron is an EHR tool kit that supports inpatient and ambulatory care using a smart longitudinal patient record.

OASIS: OASIS is a novel linkage disequilibrium clustering algorithm that can potentially address false positives and negatives in genome-wide association studies (GWAS) in complex disorders. OASIS is a unique method that can be widely applied for mining existing GWAS datasets to identify new genes and loci in an efficient, low cost way.

Open BEAGLE: Open BEAGLE is an evolutionary computation framework. It provides an Object-Oriented software environment enabling the implementation of almost any kind of evolutionary algorithm, such as genetic algorithms and genetic programming. The only necessary condition is to have a population of individuals to which a sequence of evolving operations is iteratively applied. So far, two specialized frameworks have been implemented: genetic algorithms and genetic programming. An evolution strategies framework is also planned for a future release.

Open Source Ventilator Remote Monitor Project: Our goal is to quickly develop a remote monitoring interface for low-cost rapidly-manufactured ventilators currently being developed to provide emergency relief in the Covid-19 Pandemic. We strive for a lightweight, interoperable, and reliable interface. Currently the interface provides ventilator remote monitoring only (no control). This software is not approved to be used in a medical setting.

OpenChrom: OpenChrom is data analysis a tool for gas chromatography and mass spectrometry. Its functionality and algorithms can be extended using a flexible plugin approach. File formats from various vendors are supported.

Openfight: It's a webapp, easily and highly configurable, that makes it available for governments of third world countries, to provide their citizens with an self-diagnosis tool that also offers openData (anonymized) that can be used by data-scientist and machine learning experts.

Orthanc: Orthanc aims at providing a simple, yet powerful standalone DICOM server. It is designed to improve the DICOM flows in hospitals and to support research about the automated analysis of medical images. Orthanc can turn any computer running Windows or GNU/Linux into a DICOM store (in other words, a mini-PACS system). Its architecture is lightweight and standalone, meaning that no complex database administration is required, nor the installation of third-party dependencies. What makes Orthanc unique is the fact that it provides a RESTful API. Thanks to this major feature, it is possible to drive Orthanc from any computer language. The DICOM tags of the stored medical images can be downloaded in the JSON file format. Furthermore, standard PNG images can be generated on-the-fly from the DICOM instances by Orthanc. Orthanc lets its users focus on the content of the DICOM files, hiding the complexity of the DICOM format and of the DICOM protocol.

Pathomx: Pathomx is a workflow-based tool for the analysis and visualisation of experimental data. Initially created as a tool for metabolomic data analysis is has been extended and can now be used for any scientific and non-scientific data analysis. The software functions as a hybrid of workflow and script-based approaches to analysis. Using workflows it is possible to construct rapid, reproducible analysis constructs for experimental data. By combining this with custom inline scripting it is possible to perform any analysis imaginable. Workflows can be dynamically re-arranged to test different approaches and saved to track the development of your approach. Saved workflows can also be shared with other users or groups, allowing instant reproduction of results and methods. Tools can export images as publication-ready high resolution images in common formats.

PerlPrimer: 'PerlPrimer' designs primers for standard PCR, bisulphite PCR, real-time PCR (QPCR), and sequencing by automating and simplifying the process of primer design. Current features include calculation of possible primer-dimers, retrieval of genomic or CDNA sequences from Ensembl, the ability to BLAST search primers using the NCBI server, ORF, and CpG island detection algorithms, the ability to add cloning sequences to primers, automatically adjusted to be in-frame, and QPCR primer design without manual intron-exon boundary entry.

Phylographer: PhyloGrapher helps you visualize and study evolutionary relationships within families of homologous genes or proteins (elements). It is a drawing tool that generates custom graphs for the given set of elements. It can be used to visualize any type of interactions between elements you want. Each gene or protein on a graph is represented as a colored node (vertex) and connected to other nodes (vertices) by lines (edges) of variable thickness and color based on the similarity of genes or proteins (distance matrix). The user positions these nodes in such a way as to optimize visualization of the inter-relationships between the nodes. Unlike classical phylogenetic trees, the physical distances on the graph between nodes have no information content. The level of similarity between genes or proteins on PhyloGrapher's graphs is indicated by color and line thickness.

Prime-phylo: PrIME (Probabilistic Integrated Models of Evolution) is a package supporting inference of evolutionary parameters in a Bayesian framework using Markov chain Monte Carlo simulation. A distinguishing feature of PrIME is that the species tree is taken into account when analyzing gene trees. The input data to PrIME is a multiple sequence alignment in FASTA format and the output data contains trees in Newick format.

Primer Pooler: This is a program for cancer researchers and others who want to use Multiplex PCR (polymerase chain reaction) to study DNA samples, and wish to optimize their combinations of primers. It can handle thousands of primers without being slow, and can also handle degenerate primers and automatically check for overlaps.

Project-Mindfulness: Project Mindfulness is an initiative to improve societal understanding of mindfulness by way of data science and computer programming. This project is 100% free (as in freedom) and open source. Feel free to contribute! Mindfulness: observing (physical or mental, positive or negative) followed by describing (internally or externally). A person skilled in mindfulness will then fully bring the mind back to baseline through an act of awareness while simultaneously accepting the observation without judgment. Click on the supplied URL and check out the README.md!

Py-ACQUA 2: PY ACQUA is the first Italian Free Source software dedicated to the to the world of the acquariophilia. Py-Acqua traks all events of an Aquarium Tanks (see the ScreenShots of the program), from the insertion date of the species of plants and fish, to the water values control. The program has special alarms that perceives the owner of a tank of the presence of anomalous values of water assuring him a more careful management of his aquarium.

PyMOL: PyMOL is a molecular visualization system created by Warren Lyford DeLano and commercialized initially by DeLano Scientific LLC, which was a private software company dedicated to creating useful tools that become universally accessible to scientific and educational communities. It is currently commercialized by Schrödinger, Inc. PyMOL can produce high-quality 3D images of small molecules and biological macromolecules, such as proteins. PyMOL is one of a few free visualization tools available for use in structural biology. The Py portion of the software's name refers to the fact that it extends, and is extensible by the Python programming language. PyMOL uses OpenGL Extension Wrangler Library (GLEW) and Freeglut, and can solve Poisson–Boltzmann equations using the Adaptive Poisson Boltzmann Solver.

Pycomedi: This package provides an object-oriented interface to the Comedi drivers. The standard Python interface bundled with Comedilib is a simple SWIG clone of the C interface. In pycomedi, we convert the functions into class methods (see pycomedi.classes), so you don't have to worry about dragging around opaque types like comedi_t * device pointers. We also bundle related constants together in _Enums and _Flags (see pycomedi.constants), to make handling common operations like flag manipulations simpler. Finally, there are a number of utility classes (see pycomedi.utility) to make common tasks like creating instructions or reading hardware-timed analog input easier.

QDist: 'QDist' implements the O(n log^2 n) time method for computing the quartet distance between unrooted evolutionary trees. It takes as input two trees in newick format over the same set of species and computes the quartet distance between them.

RIGEL: A lightweight evolutionary algorithms engine, capable of handling any user-defined genome, with both genetic-algorithm and evolutionary-strategy optimisation paradigms.

Relax: relax is a program designed for the study of molecular dynamics of organic molecules, proteins, RNA, DNA, sugars, and other biomolecules through the analysis of experimental NMR data. It supports exponential curve fitting for the calculation of the R1 and R2 relaxation rates, calculation of the NOE, reduced spectral density mapping, the Lipari and Szabo model-free analysis, study of domain motions via the N-state model or ensemble analysis and frame order dynamics theories using anisotropic NMR parameters such as RDCs and PCSs, the investigation of stereochemistry in dynamic ensembles, and the analysis of relaxation dispersion.

Rstudio: An integrated development environment (IDE) for R. R is a programming language and software environment. RStudioIt includes a console, syntax-highlighting editor that supports direct code execution, tools for plotting, history, debugging and workspace management.

SPINA: SPINA is free software that facilitates the calculation of constant structure parameters of endocrine feedback control systems. A first successful implementation applies to the 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). This method is increasingly used in experimental research. SPINA Thyr has been evaluated in clinical trials covering more than 10,000 subjects with various disorders of thyroid homeostasis. Additional applications targeting other endocrine feedback loops are currently being developed or prepared, respectively. SPINA Thyr is a free application that calculates GT and GD. Source code is provided for Lazarus and Free Pascal. The program is compatible with most desktop GNU/Linux distributions, Mac OS X and Windows.

SigmaPi Neurosimulator: SigmaPi is a simulator for recurrent neural networks of arbitrary topology. It uses the LSTM neuron model, and implements a training algorithm based on RTRL with some extensions taken from RProp.

SimThyr: SimThyr is a continuous simulation program for pituitary-thyroid feedback control. Applications of this program cover research, including development of hypotheses, and education of students in biology and medicine, nurses and patients. SimThyr is based on a physiologically-grounded nonlinear mathematical theory of thyroid homeostasis. The application supports simulation in time domain and various methods of sensitivity analysis. Source code is provided for Lazarus and Free Pascal. The program is compatible with most desktop GNU/Linux distributions, Mac OS X and Windows.

Simple World: Simple World is the simulation of a world and the bugs that live on it. Simple World tries to reproduce the basic elements that define a simple world. The objective of the project is to observe the evolution of this world and of these bugs.

SimulaBeta: SimulaBeta is a numeric simulation program for insulin-glucose feedback control. It is based on a nonlinear MiMe-NoCoDI model.

Sispread: Sispread allows users to simulate the dynamics of an hypothetical infectious disease within a contact network of connected people. It is intended to help people concerned by public health to easily perform epidemic simulations and to analyze their results.

Slither: Slither is an application designed to track the movement of C. elegans worms in a laboratory environment. You can either use video footage you've already captured from your dissection microscope camera, or you can allow Slither to capture new footage for you.

Snackmix: Snack is a meal design tool and calculator that will facilitate achieving your health goals and objectives by first helping you understand your food intake and second by allowing you to create new food intake options that are healthier, flavorful and satisfying. With Snack I can: *quantify food intake *prepare customized meals that meet specific requirements *quantify any popular diet for comparison and research purposes *facilitate learning/teaching anyone with interest in nutrition *track any nutrient, compound or value that has an impact on health *create food exchange lists *compare food intake options *keep a food journal and track progress *is free and open source software

Split-Dist: 'Split-Dist' calculates the number of splits (edges) that differs for two trees. When you construct phylogenetic trees using slightly different methods, or from slightly different input data, the trees will not completely agree on the topology. When they differ, it is interesting to know where they differ (which edges can be found in both trees and which cannot).

Tkfp: Tkfp is a clinical medical information system suitable for a solo or small group practice. A search engine, SSL secure web server and browser, and a PostGres database are all built in. This package is not maintained anymore. It was originally written and maintained by the family doctor and amateur Tcl programmer Alex Caldwell.

Xmedcon: The Medical Image Conversion library consists of a library, a command line utility, and a GUI interface for converting and manipulating medical images. It can convert between commonly used formats in (freely available) research tools, while preserving medical parameters like patient information, slice orientation, voxel dimension and pixel quantitation. The program can also read unsupported files without compression, print pixel values, or extract/reorder specified images. The library can also be used as a framework for your own image format.

Yanuca: YaNuCa is a JavaScript web tool to calculate plans for artificial nutrition (enteral+parenteral) in intensive care patients, with special regard to the different phases of critical illness, stress metabolism and stages of rehabilitation. Proper nutrition can be crucial for the outcome of critically ill patients at every stage of treatment and rehabilitation. This tool has been successfully used for years by two intensive care units at the University Clinic for Internal Medicine in Heidelberg/Germany. It is based on the ESPEN Guidelines for parenteral nutrition in intensive care (ESPEN = European Society for Clinical Nutrition and Metabolism).

Z--PeerLibrary: PeerLibrary is an free software project developing a collaborative online community where scholars and researchers can discover, read, and discuss scholarly literature all within one site. This project focuses on expediting access to publications, enabling public recordings of analysis and insights on said publications, and encouraging collaboration and openness in the development of science.

Free Software Foundation!

Semantic search

Query log

Navigation menu

Personal tools

Namespaces

Variants

Views

More

Search

Interaction

Navigation

Creation

Print

Tools