Open Source Python Scientific/Engineering Software - Page 52

Medical Image Computing Workflow (MICFlow) is a simple, easy but flexible, extensible and powerful workflow system to automate medical image computing tasks such as segmentation, registration and analysis. It's pure Python so can be used on any platform

The MeqTree project provides a modelling, simulation and calibration toolkit aimed at (but not exclusive to) radioastronomical applications.

MerDAQ is a data acquisition GUI and other tools for collecting and storing time dependent. Originally designed to collect 4 temperature data vs. time and plot one of the temperatures in real time with matplotlib. Ideal for use with Arduino.

Metaboflux is a generic approach for predicting flux distribution in metabolic networks under multiple and various constraints deducted from the experiments, to increase the biological relevance of the model.

We have moved to https://github.com/MetPX everything on sourceforge is obsolete. metpx is the Meteorological Product Exchanger. Intended for use in industrial/government weather forecast operations, for exchange of meteorological bulletins over TCP/IP.

MethyMer is a Python-based tool aimed at selecting specific primers for amplification of complete CpG islands. These regions are difficult in terms of selection appropriate primers because of their low-complexity, polyN-, CG-richness, etc. MethyMer have a flexible scoring system capable of selecting primers in problematic regions (e.g. SpG islands) and includes specificity test (based on bowtie alignment against bisulfite-treated genome). It also incorporates TCGA CpG methylation (microarrays) and gene expression (RNA-Seq) data, as well as methylation-expression correlation analysis results for 20 human cancer types. ENCODE genome regions annotation data are also integrated in MethyMer

The Microarray Integrator is freely available programs to integrate heterogeneous Affymetrix microarrays for human and mouse. The cell-type-specific genes or condition-specific genes can be screened in the integrated microarrays by MAI result.

We developed a novel clustering-free method, microarray-associated motif analyzer (MAMA), to predict novel cis-acting elements based on weighted sequence similarities and gene expression profiles in microarray analyses. Simulation of gene expression was performed using a support vector machine and based on the presence of predicted motifs and motif pairs. The accuracy of simulated gene expression was used to evaluate the quality of prediction and to optimize the parameters used in this method. After optimization, MAMA accurately simulated more than 87% of gene expression. See Kakei Y, Ogo Y, Itai RN, et al. (2013) Development of a novel prediction method of cis-elements to hypothesize collaborative functions of cis-element pairs in iron-deficient. Rice 6(1): 22.

MicrobeGPS is a bioinformatics tool for the analysis of metagenomic sequencing data. The goal is to profile the composition of metagenomic communities as accurately as possible and present the results to the user in a convenient manner. One main focus is reliability: the tool calculates quality metrics for the estimated candidates and allows the user to identify false candidates easily.

XMIPP is an image processing suite for 3D-reconstruction of biological specimens from transmission electron microscopy data. NOTE that stable releases (including binaries) are longer stored at Sourceforge, but are available at http://xmipp.cnb.csic.es

Software package for stochastic and hybrid simulation of microtubule dynamics and the effects of anti-mitotic drugs and microtubule regulatory proteins.

a customizable cellular automata program written in c++

Mix is a tool that combines two or more draft assemblies, without relying on a reference genome and has the goal to reduce contig fragmentation and thus speed-up genome finishing. The proposed algorithm builds an extension graph where vertices represent extremities of contigs and edges represent existing alignments between these extremities. These alignment edges are used for contig extension. The resulting output assembly corresponds to a path in the extension graph that maximizes the cumulative contig length. Please note that Mix has moved to: https://github.com/massyah/MIX

For making various mixtures, like homemade alcohol, brine or e-liquids. Add a components, set a percentage in total, set how much I want a given mixture and save, share or print recipe.

Benchmark instances for multiobjective combinatorial optimization

MoDAVE aims at providing data analysis and visualization extensions to Mosaic datasets, including cubed sphere data, to the Climate Data Analysis Tools (CDATA) in particular.

MoViT is a distributed software suite for the virtualization of mobile wireless networks. MoViT provides researchers and developers with a virtualized environment for developing and testing mobile applications and protocols for any hardware and software platform that can be virtualized. The distributed nature of MoViT allows for the emulation of mobile networks of arbitrary size. Additionally, the network connectivity is shaped transparently such that the connectivity observed by each virtual node resembles that of a physical mobile network.

remote control your mobile phone currently supported: SonyEricsson K800i, SonyEricsson W810i, Siemens S65, SonyEricsson T630, ...

Modama is a new software project for processing and analysing 2d detector data (images) provided by any available detectors, mainly SAX and WAX.

Model Builder is a graphical tool for designing, simulating and analyzing Mathematical models consisting of a system of ordinary differential equations(ODEs).

Graphical interface for ModelTest and MrModelTest written in Python, for Windows, Linux and Mac OSX

A modular, network transparent and realtime capable C++ framework for controlling robots and other kind of hardware.

The Modular toolkit for Data Processing (MDP) is a Python data processing framework. From the user's perspective, MDP is a collection of supervised and unsupervised learning algorithms and other data processing units that can be combined into data processing sequences and more complex feed-forward network architectures. From the scientific developer's perspective, MDP is a modular framework, which can easily be expanded. The implementation of new algorithms is easy and intuitive. The new implemented units are then automatically integrated with the rest of the library. The base of available algorithms is steadily increasing and includes signal processing methods (Principal Component Analysis, Independent Component Analysis, Slow Feature Analysis), manifold learning methods ([Hessian] Locally Linear Embedding), several classifiers, probabilistic methods (Factor Analysis, RBM), data pre-processing methods, and many others.

This a python based Molecular simulator in the first stages of devlopment,right now the little simulator engine is capable of: viewing of .MOL files with rendering ,Analyses of bend length,Calculation of Energies

Mos2Gnu is a conversion utility to generate a GNU MathProg description file, understandable by the GNU Linear Programming Kit from the proprietary X-Press Mosel's file format