Open Source Python Scientific/Engineering Software - Page 56

The OpenVCT project is designed to provide a common platform for performing Virtual Clinical Trials of medical imaging. OpenVCT provides tools for simulation of patient accrual and reader studies of medical imaging devices, simulating by simulating cohorts of patients and readers. OpenVCT uses common data standards, such as DICOM, to ensure inter-compatibility.

OpenWWTP is wastewater treatment plant simulator based on (modified) Activated Sludge Model (ASM2d) The project is in very beginning stage (help wanted).

The purpose of this project is to make available a variety of tools written in Python.

Orca Core is the central Python control framework for the ORCA Hand, an open-source dexterous robotic hand designed to replicate human-like manipulation capabilities. It provides a high-level abstraction layer over the underlying hardware, allowing developers to interact with the robotic system through simplified joint-space commands rather than low-level motor instructions. The software includes a suite of scripts for calibration, tensioning, and positioning, ensuring that the physical hand operates accurately and consistently across different configurations. It is designed to integrate seamlessly with hardware models defined through configuration files, enabling flexible deployment across variations of the ORCA Hand. The framework also supports real-time control and testing, allowing users to connect to the device, enable torque, and issue precise joint movement commands programmatically.

Oree - Optimum Real-time Estimation of Events of Interaction: real-time reconstruction of photon interaction events in Gamma Cameras. Optionally making use of a CUDA enable GPU, Oree achieves reconstruction of over 1M events/sec.

The purpose of this workshop is to share the tools created as an aid to our everyday work with students, enthusiasts and specialists interested in the development and use of new technologies including (but not limited to) geomatics, mapping, web mapping services (WMS), drafting, remote sensing, GIS and related occult sciences of Gaia. Check out the NBR (dn2nbr) and NDVI (dn2ndvi) calculating tools for GRASS GIS at the top menu!!!

Ouroborus is an artificial life framework for mobile agents on a background of cellular automata. It can be used to teach and research topics such as population genetics, ecology and evolution. The demo includes a curses view and live Csound audio.

OVERVIEW is a framework for optimization that integrates the visualization of complex fluid solutions and geometries taking advantage of the high performance and cutting edge rendering techniques of modern graphic cards.

A simple tool to compute extent of spatial overlap associated with electronic transitions based on natural transition orbitals (NTOs)

Convert maps from Ozi Explorer format to Geotiff

P2TK, the Penn Phonetics Toolkit, developed in the University of Pennsylvania Linguistics Department Phonetics Lab, is a collection of Python scripts and other tools to aid speech research.

Bisulfite sequencing (BSseq) processing is among the most cumbersome next generation sequencing (NGS) applications. Though some BSseq processing tools are available, they are scattered, require puzzling parameters and are running-time and memory-usage demanding. We have developed P3BSseq, a parallel processing pipeline for fast, accurate and automatic analysis of BSseq reads that trims, aligns, annotates, records the intermediate results, performs bisulfite conversion quality assessment, generates BED methylome and report files following the NIH standards. P3BSseq outperforms the known BSseq mappers regarding running time, computer hardware requirements. We optimized the P3BSseq parameters for both directional and non-directional libraries, and for both single-end and paired-end reads of Whole Genome and Reduced Representation BSseq. P3BSseq is a user-friendly streamlined solution for BSseq upstream analysis, requiring only basic computer and NGS knowledge.

This algorithm written in Python solves at least a subset of the Hamilton Circuit problem, which is NP complete, in n^3 time.

PAGC is a command line and web service C library for performing postal address geocoding. A postal address geocoder takes a sufficiently detailed postal addresses and produces a digital map that displays the spatial location of those addresses.

PAIDA is pure Python scientific analysis package and supports AIDA (Abstract Interfaces for Data Analysis). PAIDA can create/plot histograms and functions etc. The parameter optimization and its error evaluation are also supported. Can use with Jython!

A module for Python which provides interface to the PARI/GP computing library. We propose to write programs for PARI using Python scripting language. Python makes code much more clean, readable and manageable than the old-style PARI scripts.

PARs is a bioinformatics tool for the analysis of cis-regulatory DNA sequences. Composed of two parts: a suite of sequence analysis algorithms for predicting cis-binding sites in DNA sequences and a GUI for visualisation and exploration of the results.

This currently hosts two projects created and maintained by Adam English. PBJelly - the genome upgrading tool. PBHoney - the structural variation discovery tool Both are contained within the PBSuite code found in downloads. ----- PBJelly ----- Read The Paper http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047768 PBJelly is a highly automated pipeline that aligns long sequencing reads (such as PacBio RS reads or long 454 reads in fasta format) to high-confidence draft assembles. PBJelly fills or reduces as many captured gaps as possible to produce upgraded draft genomes. ----- PBHoney ----- Read The Paper http://www.biomedcentral.com/1471-2105/15/180/abstract PBHoney is an implementation of two variant-identification approaches designed to exploit the high mappability of long reads (i.e., greater than 10,000 bp). PBHoney considers both intra-read discordance and soft-clipped tails of long reads to identify structural variants.

Physiologically based toxicokinetic (PBTK) modeling offers great promise in environmental risk assessment, potentially speeding up dose-response studies while minimizing animal testing. Some limitations exist in the PBTK field, such as difficulty of model development and a lack of application specific software tools to help modelers. Some parameters used in PBTK models, such as tissue weights, are easily measure. Other parameters can be determined through in-vitro experiments or through extrapolation using published equations. When it is impractical to use these methods to estimate a parameter, techniques can be used to optimize parameters so that model results best fit validation data. This tool was designed to optimize a user-specified list of parameters to a user-specified PBTK model. The user also controls validation data and optimization algorithms. In addition to optimized parameters, the tool outputs statistical information about the fit of the optimized model.

The Poll and Command Service (PCS) project aim is to develop a management and interfacing system for the Khepera III and Koala robots.

This software has moved to http://www.poissonboltzmann.org/

Esse projeto é uma reimplementação dos processadores hipotéticos descritos no livro "Fundamentos de Arquitetura de Computadores" de Raul Fernando Weber, usados em diversas faculdades no sul do Brasil, incluindo o Instituto de Informática da UFRGS.

Image processing tool that encodes pixel data as indices within the first 16.7 million digits of PI (π). Features high-performance Numba-accelerated search and a signature 'film-grain' aesthetic upon reconstruction. ZIP also include 16 MB file with 16,7 mil numbers of PI Benchmark(Single-Thread): Hardware & Environment Apple Silicon: Apple M2 (Mac mini/MacBook) x86_64 Platform: Intel Core Ultra 5 225F (Arrow Lake, 10 Cores) OS 1: Fedora 43 (GNOME) OS 2: Windows 11 Pro (23H2/24H2) Software: Python 3.14.3 + Numba JIT (latest) Results (Lower is better) Platform / OS CPU Time (Seconds) macOS (Native) Apple M2 52.151311 s (in default setup) Fedora Linux Intel Core Ultra 5 225F 58.536457 s (in default Power Management: Balanced) Windows 11 Intel Core Ultra 5 225F 59.681427 s (important! Power Management set as High Performance .. in Balanced is slow)

The Microchip PICkit 2 has the ability to act as a logic analyzer and I/O probe. This project provides a reverse engineered libusb user space device driver and GUI to provide this functionality for users of unsupported operating systems.

PLAtypus's goal is to give people with poor communications skills an opportunity to learn and improve. With the guidance of a tutor, people will be able to learn new signs, sounds or icons and associate them with real life concepts that will, hopefully, help them to better express they needs.