ToeholdTools is a Python package and desktop app designed to facilitate analyzing and designing toehold switches, created as part of the 2021 iGEM competition.

Related tags

Data Analysispythonbioinformaticsbiologyrnaamino-acidsbiotechnologytoehold-switches
Overview

ToeholdTools

Category Status
Repository GitHub Documentation Status
Package Python PyPI PyPI - Downloads
Build Build GitHub Workflow Status (event) GitHub Workflow Status (event) Codecov
Quality Language grade: Python Language grade: JavaScript LGTM Alerts

A library for the analysis of toehold switch riboregulators created by the iGEM team City of London UK 2021.

What is ToeholdTools?

ToeholdTools is a Python package and desktop app designed to facilitate analyzing and designing toehold switches, created as part of the 2021 iGEM competition. As of 2021 this is the only software of its kind! It's still in the making, so please leave a feature request if there is anything else you would like to see!

Features

  • An easy-to-use programmatic API for investigating the target RNA specificity of toehold switches.
  • A desktop app complete with a graphical user interface for users who prioritise ease over configuration.
  • Full offline support in both the desktop app and the API, with offline support for the latest release of miRBase as well.
  • Progress–tracking support in both the desktop app and the API.
  • Support for Pandas to allow further data-processing.

Documentation

Installation instructions, the full API reference and all available developer notes can be found here.

License

ToeholdTools is licensed under the terms of the GPLv3. However, the distributed app is bundled with several third party projects. Please see third_party/NOTICES.md for more information.

© Copyright 2021, Lucas Ng.

You might also like...
Unsub is a collection analysis tool that assists libraries in analyzing their journal subscriptions.
Unsub is a collection analysis tool that assists libraries in analyzing their journal subscriptions.

About Unsub is a collection analysis tool that assists libraries in analyzing their journal subscriptions. The tool provides rich data and a summary g

null 9 Nov 16, 2022
Developed for analyzing the covariance for OrcVIO

about This repo is developed for analyzing the covariance for OrcVIO environment setup platform ubuntu 18.04 using conda conda env create --file envir

Sean 1 Dec 8, 2021
Data Competition: automated systems that can detect whether people are not wearing masks or are wearing masks incorrectly
Data Competition: automated systems that can detect whether people are not wearing masks or are wearing masks incorrectly

Table of contents Introduction Dataset Model & Metrics How to Run Quickstart Install Training Evaluation Detection DATA COMPETITION The COVID-19 pande

Thanh Dat Vu 1 Feb 27, 2022
Created covid data pipeline using PySpark and MySQL that collected data stream from API and do some processing and store it into MYSQL database.
Created covid data pipeline using PySpark and MySQL that collected data stream from API and do some processing and store it into MYSQL database.

Created covid data pipeline using PySpark and MySQL that collected data stream from API and do some processing and store it into MYSQL database.

null 2 Nov 20, 2021
CaterApp is a cross platform, remotely data sharing tool created for sharing files in a quick and secured manner.
CaterApp is a cross platform, remotely data sharing tool created for sharing files in a quick and secured manner.

CaterApp is a cross platform, remotely data sharing tool created for sharing files in a quick and secured manner. It is aimed to integrate this tool with several more features including providing a User Interface.

Ravi Prakash 3 Jun 27, 2021
Repository created with LinkedIn profile analysis project done
Repository created with LinkedIn profile analysis project done

EN/en Repository created with LinkedIn profile analysis project done. The datase

Mayara Canaver 4 Aug 6, 2022
Package for decomposing EMG signals into motor unit firings, as used in Formento et al 2021.

EMGDecomp Package for decomposing EMG signals into motor unit firings, created for Formento et al 2021. Based heavily on Negro et al, 2016. Supports G

null 13 Nov 1, 2022
A python package which can be pip installed to perform statistics and visualize binomial and gaussian distributions of the dataset

GBiStat package A python package to assist programmers with data analysis. This package could be used to plot : Binomial Distribution of the dataset p

Rishikesh S 4 Oct 17, 2022
A Python package for Bayesian forecasting with object-oriented design and probabilistic models under the hood.
A Python package for Bayesian forecasting with object-oriented design and probabilistic models under the hood.

Disclaimer This project is stable and being incubated for long-term support. It may contain new experimental code, for which APIs are subject to chang

Uber Open Source 1.6k Dec 29, 2022
Releases(v1.0.0)
Owner
GitHub Repository
Python script to automate the plotting and analysis of percentage depth dose and dose profile simulations in TOPAS.

topas-create-graphs A script to automatically plot the results of a topas simulation Works for percentage depth dose (pdd) and dose profiles (dp). Dep

Sebastian Schäfer 10 Dec 08, 2022
An Aspiring Drop-In Replacement for NumPy at Scale

Legate NumPy is a Legate library that aims to provide a distributed and accelerated drop-in replacement for the NumPy API on top of the Legion runtime. Using Legate NumPy you do things like run the f

Legate 502 Jan 03, 2023
Pip install minimal-pandas-api-for-polars

Minimal Pandas API for Polars Install From PyPI: pip install minimal-pandas-api-for-polars Example Usage (see tests/test_minimal_pandas_api_for_polars

Austin Ray 6 Oct 16, 2022
Exploratory data analysis

Exploratory data analysis An Exploratory data analysis APP TAPIWA CHAMBOKO 🚀 About Me I'm a full stack developer experienced in deploying artificial

tapiwa chamboko 1 Nov 07, 2021
Udacity - Data Analyst Nanodegree - Project 4 - Wrangle and Analyze Data

WeRateDogs Twitter Data from 2015 to 2017 Udacity - Data Analyst Nanodegree - Project 4 - Wrangle and Analyze Data Table of Contents Introduction Proj

Keenan Cooper 1 Jan 12, 2022
peptides.py is a pure-Python package to compute common descriptors for protein sequences

peptides.py Physicochemical properties and indices for amino-acid sequences. 🗺️ Overview peptides.py is a pure-Python package to compute common descr

Martin Larralde 32 Dec 31, 2022
Sample code for Harry's Airflow online trainng course

Sample code for Harry's Airflow online trainng course You can find the videos on youtube or bilibili. I am working on adding below things: the slide p

102 Dec 30, 2022
MDAnalysis is a Python library to analyze molecular dynamics simulations.

MDAnalysis Repository README [*] MDAnalysis is a Python library for the analysis of computer simulations of many-body systems at the molecular scale,

MDAnalysis 933 Dec 28, 2022
Candlestick Pattern Recognition with Python and TA-Lib

Candlestick-Pattern-Recognition-with-Python-and-TA-Lib Goal Look at the S&P500 to try and get a better understanding of these candlestick patterns and

Ganesh Jainarain 11 Oct 07, 2022
PyEmits, a python package for easy manipulation in time-series data.

PyEmits, a python package for easy manipulation in time-series data. Time-series data is very common in real life. Engineering FSI industry (Financial

Thompson 5 Sep 23, 2022
Wafer Fault Detection - Wafer circleci with python

Wafer Fault Detection Problem Statement: Wafer (In electronics), also called a slice or substrate, is a thin slice of semiconductor, such as a crystal

Avnish Yadav 14 Nov 21, 2022
Hue Editor: Open source SQL Query Assistant for Databases/Warehouses

Hue Editor: Open source SQL Query Assistant for Databases/Warehouses

Cloudera 759 Jan 07, 2023
A tool to compare differences between dataframes and create a differences report in Excel

similarpanda A module to check for differences between pandas Dataframes, and generate a report in Excel format. This is helpful in a workplace settin

Andre Pretorius 9 Sep 15, 2022
A collection of robust and fast processing tools for parsing and analyzing web archive data.

ChatNoir Resiliparse A collection of robust and fast processing tools for parsing and analyzing web archive data. Resiliparse is part of the ChatNoir

ChatNoir 24 Nov 29, 2022
Project under the certification "Data Analysis with Python" on FreeCodeCamp

Sea Level Predictor Assignment You will anaylize a dataset of the global average sea level change since 1880. You will use the data to predict the sea

Bhavya Gopal 3 Jan 31, 2022
Python Package for DataHerb: create, search, and load datasets.

The Python Package for DataHerb A DataHerb Core Service to Create and Load Datasets.

DataHerb 4 Feb 11, 2022
Zipline, a Pythonic Algorithmic Trading Library

Zipline is a Pythonic algorithmic trading library. It is an event-driven system for backtesting. Zipline is currently used in production as the backte

Quantopian, Inc. 15.7k Jan 07, 2023
Convert monolithic Jupyter notebooks into Ploomber pipelines.

Soorgeon Join our community | Newsletter | Contact us | Blog | Website | YouTube Convert monolithic Jupyter notebooks into Ploomber pipelines. soorgeo

Ploomber 65 Dec 16, 2022
This creates a ohlc timeseries from downloaded CSV files from NSE India website and makes a SQLite database for your research.

NSE-timeseries-form-CSV-file-creator-and-SQL-appender- This creates a ohlc timeseries from downloaded CSV files from National Stock Exchange India (NS

PILLAI, Amal 1 Oct 02, 2022
University Challenge 2021 With Python

University Challenge 2021 This repository contains: The TeX file of the technical write-up describing the University / HYPER Challenge 2021 under late

2 Nov 27, 2021