The Metabolomics Integrator (MINT) is a post-processing tool for liquid chromatography-mass spectrometry (LCMS) based metabolomics.

Last update: May 04, 2022

Overview

MINT (Metabolomics Integrator)

The Metabolomics Integrator (MINT) is a post-processing tool for liquid chromatography-mass spectrometry (LCMS) based metabolomics. Metabolomics is the study of all metabolites (small chemical compounds) in a biological sample e.g. from bacteria or a human blood sample. The metabolites can be used to define biomarkers used in medicine to find treatments for diseases or for the development of diagnostic tests or for the identification of pathogens such as methicillin resistant Staphylococcus aureus (MRSA). More information on how to install and run the program can be found in the Documentation or check out the Quickstart to jump right into it.

Browser based as standalone application or server based

A demo server is available here. Be mindful, you share the server with others.

Metabolomics with Python

MINT originally started as Python project. The core of MINT is a Python class for targeted metabolomics that can be used independent of the graphical application.

from ms_mint.notebook import Mint
mint.ms_files = glob('/path/to/files/*mzML')
mint.peaklist_files = '/path/to/peaklist/file/peaklist.csv'
mint.run()
mint.results

Contributions are welcome

MINT integrates open-source software and packages into a Python library for metabolomics with a browser based GUI. It is programmed by scientists for scientists to contribute to better and faster science integrating best practices of data management and computer science. Contributions are welcome that improve the efficiency of the code, bug fixes, feature implementations, security enhancements among others. If you want to contribute to MINT please send me a notification.

How to contribute

Errors, Feedback, Feature Requests

If you encounter an error, if you have a request for a new feature, or for general feedback, please open a new ticket at the issue tracker.

Code contributions

If your are up to enhance the codebase yourself, we ask you to followowing steps:

fork the repository
implement the new feature or bug-fix
add corresponding tests
run flake8
submit a pull request

Code standards

Before submitting a pull request please run flake8.

Get in touch

Open an issue or join the slack channel.

Acknowledgements

This project would not be possible without the help of the open-source community. The tools and resources provided by GitHub, Docker-Hub, the Python Package Index, as well the answers from dedicated users on Stackoverflow and the Plotly community, as well as the free open-source packages used are the foundation of this project. Several people have made direct contributions to the codebase and we are extremely grateful for that.

@rokm refactored the specfile for Pyinstaller to create a windows package.
@bucknerns helped with the configuration of the versioneer file.

Last but not least, we want to thank all the users and early adopters that drive the development with feature requests and bug reports.

Simple spectra visualization tool for astronomers

SpecViewer A simple visualization tool for astronomers. Dependencies Python = 3.7.4 PyQt5 = 5.15.4 pyqtgraph == 0.10.0 numpy = 1.19.4 How to use py

5 Oct 7, 2021

A visualization tool made in Pygame for various pathfinding algorithms.

Pathfinding-Visualizer 🚀 A visualization tool made in Pygame for various pathfinding algorithms. Pathfinding is closely related to the shortest path

7 Jul 9, 2022

A command line tool for visualizing CSV/spreadsheet-like data

PerfPlotter Read data from CSV files using pandas and generate interactive plots using bokeh, which can then be embedded into HTML pages and served by

0 Jun 25, 2022

simple tool to paint axis x and y

1 Oct 21, 2021

A System Metrics Monitoring Tool Built using Python3 , rabbitmq,Grafana and InfluxDB. Setup using docker compose. Use to monitor system performance with graphical interface of grafana , storage of influxdb and message queuing of rabbitmq

SystemMonitoringRabbitMQGrafanaInflux This repository has code to setup a system monitoring tool The tools used are the follows Python3.6 Docker Rabbi

7 Sep 6, 2022

Bioinformatics tool for exploring RNA-Protein interactions

Explore RNA-Protein interactions. RNPFind is a bioinformatics tool. It takes an RNA transcript as input and gives a list of RNA binding protein (RBP)

3 Jan 27, 2022

A Scheil-Gulliver simulation tool using pycalphad.

scheil A Scheil-Gulliver simulation tool using pycalphad. import matplotlib.pyplot as plt from pycalphad import Database, variables as v from scheil i

6 Dec 10, 2021

A tool for automatically generating 3D printable STLs from freely available lidar scan data.

mini-map-maker A tool for automatically generating 3D printable STLs from freely available lidar scan data. Screenshots Tutorial To use this script, g

51 Nov 6, 2022

The Spectral Diagram (SD) is a new tool for the comparison of time series in the frequency domain

The Spectral Diagram (SD) is a new tool for the comparison of time series in the frequency domain. The SD provides a novel way to display the coherence function, power, amplitude, phase, and skill score of discrete frequencies of two time series. Each SD summarises these quantities in a single plot for multiple targeted frequencies.

3 Oct 10, 2022

Comments

error

Hello, first of all congratulations for the application. I tried to run the application but got an error. First of all, the application is constantly updating itself in the part with dash. Secondly, when it comes to the upload data part, the following calback error appears.

Callback error updating {"index": "ms-uploader-output", "type": "output"}, "children" TypeError: expected str, bytes or os.PathLike object, not list fn_new = P(ms_dir) / P(fn).name I couldn't run it, it seems to load the data, but it doesn't, giving these errors.

(I guess P(fn).name doesn't see it as path.)

opened by hilaluzunoglu 0

The Metabolomics Integrator (MINT) is a post-processing tool for liquid chromatography-mass spectrometry (LCMS) based metabolomics.

Related tags

Overview

MINT (Metabolomics Integrator)

Browser based as standalone application or server based

Metabolomics with Python

Contributions are welcome

How to contribute

Errors, Feedback, Feature Requests

Code contributions

Code standards

Get in touch

Acknowledgements

You might also like...

Simple spectra visualization tool for astronomers

A visualization tool made in Pygame for various pathfinding algorithms.

A command line tool for visualizing CSV/spreadsheet-like data

simple tool to paint axis x and y

A System Metrics Monitoring Tool Built using Python3 , rabbitmq,Grafana and InfluxDB. Setup using docker compose. Use to monitor system performance with graphical interface of grafana , storage of influxdb and message queuing of rabbitmq

Bioinformatics tool for exploring RNA-Protein interactions

A Scheil-Gulliver simulation tool using pycalphad.

A tool for automatically generating 3D printable STLs from freely available lidar scan data.

The Spectral Diagram (SD) is a new tool for the comparison of time series in the frequency domain

Comments

error

Releases(0.0.56)

Owner

Sören Wacker

matplotlib: plotting with Python

trade bot connected to binance API/ websocket.,, include dashboard in plotly dash to visualize trades and balances

Because trello only have payed options to generate a RunUp chart, this solves that!

Create HTML profiling reports from pandas DataFrame objects

Functions for easily making publication-quality figures with matplotlib.

This is a learning tool and exploration app made using the Dash interactive Python framework developed by Plotly

Visualization Data Drug in thailand during 2014 to 2020

Pretty Confusion Matrix

Generate visualizations of GitHub user and repository statistics using GitHub Actions.

This repository contains the raw data and a python notebook to ingest historical A&E attendance data and then use a simple Prophet model to predict the number of A&E attendances in England if the COVID-19 pandemic had not happened

Squidpy is a tool for the analysis and visualization of spatial molecular data.

This package creates clean and beautiful matplotlib plots that work on light and dark backgrounds

Datapane is the easiest way to create data science reports from Python.

Some useful extensions for Matplotlib.

A Jupyter - Three.js bridge

Numerical methods for ordinary differential equations: Euler, Improved Euler, Runge-Kutta.

Generate visualizations of GitHub user and repository statistics using GitHub Actions.

This is a place where I'm playing around with pandas to analyze data in a csv/excel file.

Insert SVGs into matplotlib

A Bokeh project developed for learning and teaching Bokeh interactive plotting!