Open Source Mac Medical Software

Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology. For instructions and documentations, please refer to the wiki page. MAGeCK is developed by Wei Li and Han Xu from Dr. Xiaole Shirley Liu's lab at Dana-Farber Cancer Institute/Harvard School of Public Health, and is maintained by Wei Li lab at Children's National Medical Center. We thank the support from Claudia Adams Barr Program in Innovative Basic Cancer Research and NIH/NHGRI to develop MAGeCK.

These R packages are developed for data analysis of PK/PD modeling & simulation, bioequivalence/bioavailability (BE/BA), drug stability, in-vitro and in-vivo correlation (ivivc), as well as therapeutic drug monitoring (TDM).

OpenCell is a user interface for working with CellML models. Features: * Integrate models made up of ODEs. * Supports CellML 1.0 and 1.1, allowing you to build complex models using imports. * Plot and edit graphs. * And more ...

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.

This is a sophisticated & integrated simulation and analysis environment for dynamical systems models of physical systems (ODEs, DAEs, maps, and hybrid systems). It supports symbolic math, optimization, continuation, data analysis, biological apps...

The new version of MinimPy (MinimPy2) is available for download at: https://osdn.net/dl/minimpy2/MinimPy2.zip Please send your feedback about this new version to mahmood.saghaei@gmail.com (include MinimPy2 in the subject) ============================================================ MinimPy is a desktop application program for sequential allocation of subjects to treatment groups in clinical trials by using the method of minimization. Comprehensive reference help is available at http://minimpy.sourceforge.net MinimPy has been fully described in the following article: Saghaei, M. and Saghaei, S. (2011) Implementation of an open-source customizable minimization program for allocation of patients to parallel groups in clinical trials. Journal of Biomedical Science and Engineering, 4, 734-739. doi: 10.4236/jbise.2011.411090. Available at: http://www.scirp.org/journal/PaperInformation.aspx?PaperID=8518

Parallel Iterative Deconvolution is a multithreaded ImageJ plugin for iterative image deblurring.

Based on MinimPy (http://sourceforge.net/projects/minimpy/), QMinim is a web-based minimization application, for allocation of subject to different arms of a clinical trial. It is an alternative to randomization, with the advantage of balancing arms of trial with respect to preselected prognostic factors. All aspects of minimization procedure including treatments, factors, minimization protocole, and including a preload can be customized using QMinim.

Parallel Spectral Deconvolution is a multithreaded ImageJ plugin for spectral image deblurring.

A java based neural network framework. The Auratus network is built around an XML messaging system, allowing for a complete MVC design. Additionally, Auratus networks are constructed and at the node/edge level, allowing for advanced topologies.

The Biopsychology Nonlinear Toolbox is a MATLAB toolbox that combines established analysis routines in one easy to use graphical user interface.

The purpose of the project is to develop a quantitative medical imaging & visualization program for use on brain MR, DTI and MRS data. It is a joint project of the Kennedy Krieger Institute & the Johns Hopkins University, Psychiatric Neuroimaging Lab

The continuous medial representation is a method for object representation and shape analysis. Hosted on Sourceforge are the source code for routines that fit medial models to anatomical objects.

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.

This software is a tool for measurement kyphosis, lordosis and scoliosis. LoB Analytics was developed in Python.

MASyV (Multi-Agent System Visualization) enables one to write agent-based models/cellular automata, eg. in C, visualize them in real time & capture to movie file with MASyVs GUI & message passing lib. Includes examples: Hello World, ants, viral infection

Our goal is to surpass the performance of the Matching Pursuit and Best Basis algorithms and provide progressive time-frequency analysis.

A topological data structure to handle 2D, surfaces and 3D simplicial meshes. This data structure is implemented in C++ using templates. It is based on Corner-Table and CGAL data structure.

Parallel HRRT Deconvolution is a multithreaded ImageJ plugin for motion correction of PET brain images.

PopED (Population Experimental Design) is a software tool for computing optimal experimental designs. The software has been developed with an emphasis on drug trials based on population models (non-linear mixed effects models).

This will be a place to release tools that have not yet been added to SciPy (or will not be added for whatever reason). Currently an interface to ImageMagick is here.

A collection of code, bundled into a single R package, to perform several aspects of data management, image pre-processing, data analysis and statistical inference related to the quantitative analysis of dynamic contrast-enhanced MRI (DCE-MRI).

A topological data structure to handle 2D simplicial meshes (using the Morse operators published by authors). This data structure is implemented using C++ and it is based on the classical Half-Edge. This code started in 2002 and it has been used in many

A tool set for registering and statistically analyzing medical images with special focus on the human skeleton.

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.