Tool

MDAnalysis tool to calculate membrane curvature

Membrane Curvature This is an MDAnalysis module to calculate membrane curvature from molecular dynamics simulations. The MDAkit for membrane curvature analysis is part of the Google Summer of Code program and it is linked to a Code of Conduct. Abstract Elements of differential geometry enable us to quantify the curvature of a surface. The core elements of biological membranes, phospholipids, provide tridimensional configurations from which a surface can be derived to calculate curvature descriptors. We would like to integrate to […]

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Data Analysis

A Python library to analyze molecular dynamics trajectories

MDAnalysis MDAnalysis is a Python library for the analysis of computer simulations of many-body systems at the molecular scale, spanning use cases from interactions of drugs with proteins to novel materials. It is widely used in the scientific community and is written by scientists for scientists. It works with a wide range of popular simulation packages including Gromacs, Amber, NAMD, CHARMM, DL_Poly, HooMD, LAMMPS and many others — see the lists of supported trajectory formats and topology formats. MDAnalysis also […]

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Maps

Solving the Traveling Salesman Problem using Self-Organizing Maps with python

som-tsp Solving the Traveling Salesman Problem using Self-Organizing Maps This repository contains an implementation of a Self Organizing Map that can be used to find sub-optimal solutions for the Traveling Salesman Problem. The instances of the problems that the program supports are .tsp files, which is a widespread format in this problem. All the source code can be found in the src directory, while a report and brief presentation slides (in Spanish) can be found in the report folder. To […]

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Monitoring

A python module for monitoring memory consumption

Memory Profiler This is a python module for monitoring memory consumption of a process as well as line-by-line analysis of memory consumption for python programs. It is a pure python module which depends on the psutil module. Installation Install via pip: $ pip install -U memory_profiler The package is also available on conda-forge. To install from source, download the package, extract and type: $ python setup.py install Usage line-by-line memory usage The line-by-line memory usage mode is used much in […]

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Natural Language Processing

Super easy library for BERT based NLP models with python

Fast-Bert Supports LAMB optimizer for faster training. Please refer to https://arxiv.org/abs/1904.00962 for the paper on LAMB optimizer. Supports BERT and XLNet for both Multi-Class and Multi-Label text classification. Fast-Bert is the deep learning library that allows developers and data scientists to train and deploy BERT and XLNet based models for natural language processing tasks beginning with Text Classification. The work on FastBert is built on solid foundations provided by the excellent Hugging Face BERT PyTorch library and is inspired by […]

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Hardware

A Python package that generates hardware pinout diagrams as SVG images

pinout SVG diagram creation from Python code – pinout provides an easy method of creating pin-out diagrams for electronic hardware. Please visit pinout.readthedocs.io for the full quick start tutorial and detailed documentation on all options provided by the pinout package. Quick start pinout can be easily installed with pip and provides some sample files that demonstrate key features. Install Using a virtual environment is recommended; Start by installing the pinout package. Either clone this repo and pip install it or […]

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Data Analysis

X-ray Analysis for Synchrotron Applications using Python

Larch Larch is an open-source library and set of applications for processing and analyzing X-ray absorption and fluorescence spectroscopy data and X-ray fluorescence and diffraction image data from synchrotron beamlines. It is especially focussed on X-ray absorption fine-structure spectroscopy (XAFS) including X-ray absorption near-edge spectroscopy (XANES) and extended X-ray absorption fine-structure spectroscopy (EXAFS). It also supports visualization and analysis tools for X-ray fluorescence (XRF) spectra and XRF and X-ray diffraction (XRD) images as collected at scanning X-ray microprobe beamlines. Larch […]

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Django

Self hosted FLOSS fitness/workout, nutrition and weight tracker written with Django

wger wger (ˈvɛɡɐ) Workout Manager is a free, open source web application that help you manage your personal workouts, weight and diet plans and can also be used as a simple gym management utility. It offers a REST API as well, for easy integration with other projects and tools. Mobile app Installation These are the basic steps to install and run the application locally on a Linuxsystem. There are more detailed instructions, other deployment options as wellas an administration guide […]

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Command-line Tools

A Python based toolkit for creating Command-Line Interface app

Quo Quo is a Python based toolkit for writing Command-Line Interface(CLI) applications. Quo improves programmer’s productivity because it’s easy to use and supports auto completion which means less time will be spent debugging. Simple to code, easy to learn, and does not come with needless baggage Quo requires Python 3.6 or later. Installation You can install quo via the Python Package Index (PyPI) $ pip install -U quo Example 1 import quo quo.echo(‘Hello, World!’) Example 2 import quo quo.flair(f’Hello, World!’, […]

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Editor

A simple editor for beginner Python programmers Written in Python and Qt5

Mu – A Simple Python Code Editor Mu is a simple code editor for beginner programmers based on extensive feedback from teachers and learners. Having said that, Mu is for anyone who wants to use a simple “no frills” editor. Mu is a modal editor with modes for many different ways to use Python to create cool and interesting things. Mu is written in Python and works on Windows, macOS, Linux and Raspberry Pi. The project’s public facing website is […]

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