Open Source Python Scientific/Engineering Software - Page 59

ProjectQ is an open-source effort for quantum computing. It features a compilation framework capable of targeting various types of hardware, a high-performance quantum computer simulator with emulation capabilities, and various compiler plug-ins.

Course Project

Protein ALignment Optimiser (PALO) is a script for the selection and alignment of the best combination of transcripts among orthologous genes. PALO is mainly written in Python, although other programming languages are also implemented (R, Perl...).

Software to identify cavities and crevices in proteins. The goal is to be able to take a protein structure, and to differentiate between five different types of environments for each residue: buried, surface, interfacial, cavity, or crevice.

The Protein Geometry Database hosts the development code for a flexible database for searching protein geometry, as well as a library for accessing this data for protein modeling & refinement programs.

PepT-IDE is a protein analysis tool that is used for multiple sequence alignment, 3D visualization and displaying protein contact maps for protein sequences and structures. It also has feedback communication between the different views of the protein.

This project implements an algorithm for segmenting protein sequences into smaller meaningful blocks. The method is based on the pure statistical approach and it uses an analogy between proteins and natural language.

Protenix is an open-source, trainable PyTorch reimplementation of AlphaFold 3, developed by ByteDance with the goal of democratizing high-accuracy protein structure prediction for computational biology and drug-discovery research. Protenix provides a complete pipeline for turning protein sequences (with optional MSA / sequence alignment) or structural inputs (e.g. PDB/CIF) into full 3D atomic-level structure predictions. It supports both “full” models and lightweight variants such as “Protenix-Mini,” offering a trade-off between speed/compute cost and predictive accuracy — making structure prediction accessible even in resource-constrained environments. The project also includes support for constraints (e.g., specifying residue- or atom-level contact constraints, or pocket constraints) to guide predictions toward biologically or experimentally relevant conformations, which enhances its utility for tasks like modeling complexes, ligands, or antibody–antigen interactions.

Sign up to our mailing list at http://www.protospacer.com/contact.html. Protospacer allows researchers to build, analyze, and share their own database of CRISPR target-sites. This enables the development of custom libraries and helps to transfer the CRISPR technology to new organisms. Each Protospacer database is a simple catalogue of all possible Cas9 target-sites within a given FASTA sequence, i.e. all NGG/NAG sites. Protospacer then allows the user to sub-select targets from the database by gene ID, by exon/intron/UTR location, by sequence similarity, or by genomic co-ordinate. From here, users are able to evaluate potential off targeting, to export results in FASTA format or tabulated (e.g. for Microsoft Excel), and to connect to the Integrative Genomics Viewer (IGVref) and view target-sites in the context of genomic annotations, amino acid translations, and HT-Seq data (for off-target validation). We provide online video tutorials and a toy database from our main website.

The EU Provenance project developed an architecture to document a data generating process in a distributed environment. The Python Client Side Library (CSL) enables the development of provenance-aware Python applications.

Network grep, on steroids

Command-line, PubChem PUG client, written in Python; developed for Linux

Client to the PubChem Tool (PCT), The Power User Gateway (PUG). Written in Python and developed for use with Linux.

A programmable signal generator and RF synthesizer for scientific experiments, especially quantum computing and quantum information processing. It includes hardware, firmware, software, and documentation, all under an open source license.

Computational electromagnetics software. Uses surface Method of Moments, enhanced by using the Multilevel Fast Multipole Method. Code is parallelized and runs on laptops, desktops and clusters. The code precision is adjustable, it is fast and uses little memory. CFIE is used for closed surfaces, and EFIE for open PEC surfaces. Can function on GMSH, GiD and ANSYS meshes.

A simple and powerful interface for Tightvnc Server, written in python and developed with glade.

Py3DN, is an open-source solution providing innovative tools to analyze 3D data collected with the widely used commercial system Neurolucida (MBF). It allows the construction of mathematical representations of neuronal topology, visualization and a variety of morphometric analysis on the neuronal structures. Above all, it provides a flexible environment where new types of analyses can be easily set up allowing total freedom to test new hypotheses. The application was developed in Python and uses Blender (an open source program) to produce detailed 3D representations of raw and processed data. Py3DN is described in the paper: Aguiar P et al, "Versatile morphometric analysis and visualization of the three-dimensional structure of neurons", Neuroinformatics, 2013, 11(4):393-403 doi: 10.1007/s12021-013-9188-z

(Historical) PyAcad makes Python available as a scripting language to AutoCAD/IntelliCAD. A builtin module "ads" allows to access and control most aspects of AutoCAD/IntelliCAD from Python programs.

PyAero is a toolkit developped at andheo for CFD software : post-processing, curve generation, … Currently PyAero focuses on ONERA's code "Cedre". PyAero is powered by Qt, Python, PySide, enthought and pyLot.

Ant foraging simulation. Ants can be programmed using Python. Actual programme writtenin c++ using SDL

With this Python module (based on C++ code) it is possible to create a Brain Comp. Interface (BCI) and herewith to get EEG data online and evaluate the data while receiving it. - Up to now, this tool relies on the Brain Vision Rec. as EEG software -

PyBrella is a script designed to automate the umbrella sampling process, using the AMBER molecular dynamics package.

Python module for manipulation of Crystallographic Information Framework (CIF) files

Python module to interface the CLIPS expert system shell library.

PyCancerDB is a source code distribution providing a Web-based interface for browsing and updating the Cancer Proteomics Database, together with scripts for maintaining the database.