Open Source Python Scientific/Engineering Software - Page 54

Path Sim contains a collection of tools for analysing Biochemical pathways with respect to stochastic behavior and cell-to-cell variations.

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.

Pena is an acronym for "Pena Encryption for Automata". This framework will help you to run encrypted representations of programs.

Peptide Vaccine Analysis Tool (PVAT) is an optimization software that predicts the best possible peptide stretches in a given protein sequence based on two factors: 1. the surface exposure of the peptide stretches, and 2. their susceptibility to mutation.

Retrieve statistics from SNMP-aware devices, store them in a database and graphically display them for monitoring and notification purposes.

This (Python) tool allows you to easily create FPGA bitfiles for your embedded system, from several Open Source IPs (compatibles with the OpenCores Wishbone bus) . It will also generates the corresponding drivers (currently only Linux ones).

PetriKit is a modular toolkit for Petri Net analysis. It allows the extraction of basic properties, extraction of invariants, and generation of reachability graph. Results can be formatted in plain text, HTML or XML files.

Pfem is a python-based finite element program aimed at solving solid mechanics and heat transfer problems with flexibility, efficiency and sound object-oriented design.

Phaistos is a framework for all-atom Monte Carlo simulations of proteins. It incorporates several advanced probabilistic models of protein structure for conformational sampling, efficient move-algorithms and the OPLS and PROFASI forcefields.

Phase Space is born out of the need of a simple yet powerful open source tool to study dynamical systems. PhaseSpace allows you to plot the phase space of the dynamical system you are studying, its critical points and the curves of slope zero and infinite.It can also plot the solutions of the system and it's vector field. To use PhaseSpace you'll need to have Python installed along with Matplotlib and Numpy.

PhiCAD is a LGPL'd , cross-platform software intended to provide to community an eclectic suite of CAD such as EDA to solve physics problems.

Concurrent vision processing system; Toolkit for easy implementation of software concurrent vision processing sub-system. Aimed at robotic applications w/best effort realtime. System includes: capture,processing and displaying.

Phobos is to be used for recording rodents' behavior during the thigmotaxis (open-field) and the elevated plus-maze tests. Phobos provides the possibility to easily calculate all possible experimental parameters at once immediately after the evaluation of the fear/anxiety level of each animal. All extracted files can be readily combined to one in order for statistical analyses to be performed. If you use Phobos for your research, please cite: Telonis AG, Margarity M.Phobos: a novel software for recording rodents' behavior during the thigmotaxis and the elevated plus-maze test. Neurosci Lett (2015) doi: 10.1016/j.neulet.2015.05.045 Paper link: http://www.sciencedirect.com/science/article/pii/S0304394015004103 For support, questions or feedback: atelonis@users.sourceforge.net

The Visual Annotator from Health Information Technologies Research Laboratory at The University of Sydney. http://hitrl.it.usyd.edu.au/

Phylogenetic Representativeness is a method for estimating adequacy of taxon sampling for phylogenetic studies. Through a series of statistics generated by PhyRe, it is possible to evaluate taxon coverage within a given group.

A python/C++ framework for Bayesian phylogenetic analysis.

PhyloTrack is a JavaScript--based software tool that integrates the D3.js library for data visualization with the JBrowse tool for genome browser representation. It requires a phylogenetic tree of the common Newick data format as input, as well as three meta data files for samples, clade-defining nodes and clade color definitions - all in tab delimited format. Functionality within PhyloTrack shows the informative markers at each node in the phylogenetic tree, therefore highlighting clade-defining polymorphism. This functionality has been implemented using the tabix tool on the server side, providing simple and rapid access to the information at each tree node, including informative SNPs stored in VCF-similar files. These informative variants have been established by comparing allele frequencies between strain-types using ancestral node comparisons and FST measures of population differentiation.

Como técnico en informática en un Instituto de Física con el tiempo surgió la necesidad de tener que crear distintas piezas de software para ir resolviendo situaciones diarias. En este proyecto iré agregando pequeños programas en Python 2.7 que voy escribiendo para dar soluciones a algunos de los problemas que surgen día a día en el laboratorio, como ser comunicación con algunos dispositivos o rutinas para ordenar o modificar datos de forma recursiva algunos cálculos matemáticos, creación de gráficas etc. La finalidad principal del proyecto es poder poner a disposición de aquel que lo necesite mi trabajo tanto dentro del Instituto donde trabajo como fuera del mismo. Asi como tambien recibir la mayor cantidad de criticas, consejos e ideas posibles para poder mejorar mi trabajo. Podrán ver que parte de los programas están mas documentados que otros tratare de ir poniéndome al día comentando el código y escribiendo la documentación de los distintos scripts.

Physical Symbolic Optimization (Φ-SO) - A symbolic optimization package built for physics. Symbolic regression module uses deep reinforcement learning to infer analytical physical laws that fit data points, searching in the space of functional forms.

Mind this project is no longer maintained. You might be interested in having a look at http://pythonhosted.org/plasduino/ instead. Framework for data acquisition through the parallel port, suitable for performing simple didactic physics experiment.

We are trying to create a very complete physics teaching program. So, we would be pleased if you could suggest any improvement or create any module for us. To use any of these sources you need python 2.2, pygame and scipy.

PhysikPy ist ein Modul welches Physikalische Berechnungen durchführen soll. Dabei wird auf die Einfachheit aber auch Funktionalität gearbeitet. Es soll so bleiben das man mit Python einfach aber doch mächtige Programme schreiben kann.

A simulation and visualization of random walks based on the digits pi. This program also has a settings menu.

Read the temperature, display it on this neat little 10-LED muticolor array. The array has, in order, BGGGGYYYRR LEDs. This first version is a trivial program that scans the CPU temp and uses 10 GPIO pins, one for each LED.