Open Source Python Scientific/Engineering Software - Page 63

Basic and intermediate examples to read, modify and write DICOM files with Python code using Jupyter - To install Jupyter - https://jupyter.org/install ====== All examples are based on Pydicom. An open source library - https://pydicom.github.io/

Pydusa is a package for parallel programming using Python. It contains a module for doing MPI programming in Python. We have added parallel solver packages such as Parallel SuperLU for solving sparse linear systems.

Allows one to program fablab (factory and/or laboratory) in the same way as we program computer. Imagine commands like: "dim screw12 as new screw" or "mold(form_piston_081212, brass)" or ''gear(3)=lasercut(steel2,"biggear.gc")". This approach will let us program highly automated and self-deploying or even self-replicating factories. I am more engineer than programmer and just beginner in python. So it looks like community help will be needed :)

This repository is outdated. Please visit https://github.com/RegulatoryGenomicsUPF/pyicoteo/tags

Pylero is an open-source Python-based text generator.

Pymerase is a tool intended to generate a python object model, relational database, and an object-relational model connecting the two. However it has been extended to also output webpages and can be easily extended to output whatever else you might like.

Python Trust Metrics. Implementation of Ford-Faulkersson Maximum Flow algorithm and mod_virgule's Trust Metrics code, in python

Command-line, Entrez, NCBI e-utilities client, written in Python; developed for Linux

Comman-line client to Entrez, e-utilities, written in Python, developed for Linux

Pyphant is a framework for scientific data analysis. It features a flexible plugin architecture allowing for the application in many different fields. For the analysis a graph of processing steps is constructed, that can be applied via the cli as well.

PySCeS is the Python Simulator of Cellular Systems. For a network of coupled reactions it does a stoichiometric matrix analysis, calculates the time course and steady state, and does a complete control analysis.

UPDATE: After some bug fixes, I've ditched Pysimony for Javamony: https://sourceforge.net/projects/javamony/ Given Python's beauty, I know that someday I will have to finish Pysimony. A student's first attempt at a phylogenetic inference program, written in the simplistic yet elegant Python. Pysimony reads a FASTA file (only ATGC accepted) specified as its only argument. Basic testing has shown that it is slow, inaccurate and most definitely inefficient. An unlikely-to-be-the-most-parsimonious tree is printed upon completion in basic Newick tree format. As all parts of the program are the original work of a beginner programmer, this may represent one of the worst approaches to solving the phylogenetic problem. I have clearly avoided object-oriented programming. Nevertheless, I distribute this imagining it might someday be slightly educational or at least provide a laugh at the pathetic attempt it makes to reinvent the wheel

Python Arrays is a project to reimplement the existing Python Numeric module which adds the ability to efficiently manipulate large numeric arrays in ways similar to Matlab and IDL.

This program is a User Interface to run command-line applications in any python-enabled system. Batch execution is available for files in a folder or in subfolders.

This is a Python package for general Bayesian inference.

Functions to convert to and from decimal to Canonical Signed Digit representation. Handles fractional numbers. Useful for multiplierless hardware blocks on ASICs, FPGAs etc.

Python Champollion Electronic utilities

A lightweight, browsing-based, 100% Python, federated data integration framework. Users may create custom schemas for disparate sources, query and expand results across sources to find related data; for use in fields such as bioinformatics and datamining

Python FFTW as the name suggests are Python bindings to the FFTW3 C-library from http://www.fftw.org. They use numpy and python ctypes, and often offer about twice the performance compared to the fft routines included in numpy.

The Python Genetic Programming Project implements a Genetic Programming System a la J Koza in Python.

This project provides a library written in Python for reading and eventually writing ISO8211 files. ISO8211 is a format used for various GIS systems (geographic data), including SDTS, the format used by the US Geological Survey.

A Python library for easy creation and manipulation of Google Earth KML and KMZ placemark files. Please get your copy from http://pykml.cvs.sourceforge.net/viewvc/pykml/pykml/?view=tar

A toolkit of Python software useful in a laboratory data acquisition and analysis environment. Includes support for such protocols as VXI-11 (and its extension, LXI), Vernier LabPro (now very old), and National Instruments DSTP (now very old). Also includes data analysis and modelling tidbits. Python3 updates are on the way in the very near future for the biggest packages. the vxi11 package is fully up-to-date, although see the blog post about python 3.13

The project is a suite of utilities to manage grammars, monolingual dictionaries and translation manuals for as many as possible languages.

A python module aimed to automate routine lab calculating and formatting tasks.