Open Source Python Scientific/Engineering Software - Page 70

SuperG is a code library written in Python intended to quickly enable programmers in a scientific environment to manage data files created by dispersed scientific instrumentation.

This repository is the home of the Superstaq development team's open-source work. Our quantum software platform is optimized across the quantum stack and enables users to write quantum programs in Cirq or Qiskit and target a variety of quantum computers and simulators.

SureFit generates 3D mesh surfaces (in VTK and Caret formats) from 3D structural MRI volumes (in formats such as Analyze, AFNI, raw).

Surya is an open‑source, AI‑based foundation model for heliophysics developed collaboratively by NASA (via the IMPACT AI team) and IBM. Named after the Sanskrit word for “sun,” Surya is trained on nine years of high‑resolution solar imagery from NASA’s Solar Dynamics Observatory (SDO). It is designed to forecast solar phenomena—such as flares, solar wind, irradiance, and active region behavior—by predicting future solar images with a sophisticated long–short vision transformer architecture, thereby enabling improved space weather forecasting. Foresees solar flares, wind, EUV spectra, and active region formation in advance. Achieves approximately 16% improvement in forecasting accuracy over traditional methods. 366-million‑parameter foundation model capturing general-purpose solar representations.

This project simulates a multi-agent system (swarm) behavior both graphically and not. The purpose of this project is to research the properties suggested in "stability analysis of swarms" V.Gazi & K.M.Passino. Using the vpython library for 3D modeling

Swift Numerics is a foundational library that extends the Swift standard library with essential numerical protocols, types, and functions needed for scientific and systems programming. It defines generic abstractions over real and complex numbers so algorithms can be written once and work across concrete floating-point types. The package includes RealModule utilities and a full Complex type with the expected arithmetic and transcendental functions, bridging a long-standing gap for numerics in Swift. API design follows Swift’s emphasis on value semantics and protocol-oriented programming, enabling compiler optimizations and predictable performance. The modules are factored to keep dependencies minimal and to allow adopters to pull in only what they need. As a result, Swift Numerics underpins higher-level libraries in simulation, signal processing, and machine learning written in pure Swift.

This is an archive of old releases of SyMAT. The latest version is found at the official website.

Sylli is a universal syllabifier. Developed for Italian, it can easily be adapted to any language that is claimed to respect the SSP. Sylli divides timit, strings, files and directories into syllables.

Symath is a symbolic algebra utility that manipulates expressions as you would by hand. The aim is to provide a utility for students to use to solve complex systems as well as learn how it is done.

SynBioLib -- your toolkit for synthetic biology applications. SynBioLib aims to establish a platform on which the Synthetic Biology community can develop and share code that is common to many tasks and programs.

Synthetic Biology Software Suite (SynBioSS) is composed of a wiki for biochemical kinetic constants, a graphical interface for simulating synthetic biological pathways, and a simulator that runs on either a desktop or supercomputer.

Syzygy is a toolkit for the analysis of targeted (pooled/individual) resequencing datasets.

This project is intended to provide Git access to the code of the original project, TA-Lib, which uses Subversion. It is intended for system integrators wishing to use TA-Lib in their Git-managed project through Git submodules or subtrees. No actual development is being done here; all development happens in the original project.

The Toolkit for Advanced Discriminative Modeling (TADM) is a C++ implementation for estimating the parameters of discriminative models, such as maximum entropy models. It uses the PETSc and TAO toolkits to provide high performance and scalability.

TANGO is an object oriented control system for Linux and Windows. It provides a framework in C++, Java and Python for implementing distributed control objects an accessing them via a well-defined API. This sourceforge project a

A bioinformatics tool for the annotation and tag-counting of next-gen Illumina Solexa datasets. TASE works with CASAVA 1.0 builds, providing annotation, tag counts and visualization in a rapid manner.

TCellXTalk is a comprehensive database of experimentally detected phosphorylation, ubiquitination and acetylation sites in human T cells. The web-app at www.TCellXTalk.org makes TCellXTalk accessible from Internet, and enables the in silico prediction of potential co-modified peptides to facilitate their experimental detection, using targeted or directed mass spectrometry, for the study of protein post-translational modification cross-talk. More detailed information on TCellXTalk and the people at the CSIC/UAB Proteomics Laboratory behind it can be obtained at https://www.tcellxtalk.org/about/ - Casanovas, A., Gallardo, Ó., Carrascal, M., Abian, J., TCellXTalk facilitates the detection of co-modified peptides for the study of protein post-translational modification cross-talk in T cells. Bioinformatics 2019, 35-8, 1404–1413, DOI 10.1093/bioinformatics/bty805 ( https://doi.org/10.1093/bioinformatics/bty805 )

TEACUP automates many aspects of running TCP performance experiments in a specially-constructed physical testbed. TEACUP enables repeatable testing of different TCP algorithms over a range of emulated network path conditions, bottleneck rate limits and bottleneck queuing disciplines. TEACUP utilises a text-based configuration file to define experiments as combinations of parameters specifying desired network path and end host conditions. When multiple values are provided (e.g. for TCP congestion control algorithm), an experiment is made up of multiple tests. For each experiment and test, TEACUP collects a range of data, such as tcpdump files of traffic seen or TCP stack information (e.g. using Web10G). TEACUP also collects a variety of metadata from the end hosts and bottleneck router, such as the actual OS/kernel version(s) used. TEACUP also provides some simple tools for analysing the results of experiments, such as plotting a flow's experienced RTT over time.

Turku Event Extraction System (TEES) is a free and open source natural language processing system developed for the extraction of events and relations from biomedical text. It is written mostly in Python, and should work in generic Unix/Linux environments. Currently, the TEES source code repository still remains on GitHub at http://jbjorne.github.com/TEES/ where there is also a wiki with more information.

TI2BioP allows mainly the calculation of topological indices (spectral moments) derived from inferred and artificial 2D structures of DNA, RNA and proteins being possible to carry out a structure-function correlation irrespective of sequence alignments. TI2BioP version 3.0 is a python platform with a graphical interface designed for Windows, Linux and Mac OS.

Visit [http://www.gmfg.buffalo.edu] GMFG website for More information. A user guide for TITAN is made available on GMFG website. We strongly recommend all the users to register with GMFG website for future updates

TORCH is a web enabled electronic health record (EHR) application. TORCH is usable in single practitioner offices and scalable up to multi-site practices.

Open Source Web-based Application for System & Software Requirement Management and Traceability

Metropolis is a visualization tool for TRANSIMS traffic simulation output. It specializes in viewing the dynamic outputs of the micro-simulator, such as vehicle motion and other time-varying data.