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

Related tags

Data Visualizationvisualizationpythoninteractivemetabolomicsmass-spectrometrymintextracts-data
Overview

CII Best Practices Github All Releases

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

Mint Jupyter 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:

  1. fork the repository
  2. implement the new feature or bug-fix
  3. add corresponding tests
  4. run flake8
  5. 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.

You might also like...
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

null 5 Oct 7, 2021
A visualization tool made in Pygame for various pathfinding algorithms.
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

Aysha sana 7 Jul 9, 2022
A command line tool for visualizing CSV/spreadsheet-like data
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

Gino Mempin 0 Jun 25, 2022
simple tool to paint axis x and y
simple tool to paint axis x and y

simple tool to paint axis x and y

G705 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
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

Dipto Chakrabarty 7 Sep 6, 2022
Bioinformatics tool for exploring RNA-Protein interactions
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)

Nahin Khan 3 Jan 27, 2022
A Scheil-Gulliver simulation tool using pycalphad.
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

pycalphad 6 Dec 10, 2021
A tool for automatically generating 3D printable STLs from freely available lidar scan data.
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

Mike Abbott 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 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.

Mabel 3 Oct 10, 2022
Comments
  • error

    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
Releases(0.0.56)
Owner
Sören Wacker
Research Associate in the Lewis Research Group at the University of Calgary.
Sören Wacker
GitHub Repository
Plot toolbox based on Matplotlib, simple and elegant.

Elegant-Plot Plot toolbox based on Matplotlib, simple and elegant. 绘制效果 绘制过程 数据准备 每种图标类型的目录下有data.csv文件，依据样例数据填入自己的数据。

3 Jul 15, 2022
Matplotlib tutorial for beginner

matplotlib is probably the single most used Python package for 2D-graphics. It provides both a very quick way to visualize data from Python and publication-quality figures in many formats. We are goi

Nicolas P. Rougier 2.6k Dec 28, 2022
Data aggregated from the reports found at the MCPS COVID Dashboard into a set of visualizations.

Montgomery County Public Schools COVID-19 Visualizer Contents About this project Data Support this project About this project Data All data we use can

James 3 Jan 19, 2022
Show Data: Show your dataset in web browser!

Show Data is to generate html tables for large scale image dataset, especially for the dataset in remote server. It provides some useful commond line tools and fully customizeble API reference to gen

Dechao Meng 83 Nov 26, 2022
An XLSX spreadsheet renderer for Django REST Framework.

drf-renderer-xlsx provides an XLSX renderer for Django REST Framework. It uses OpenPyXL to create the spreadsheet and returns the data.

The Wharton School 166 Dec 01, 2022
Tidy data structures, summaries, and visualisations for missing data

naniar naniar provides principled, tidy ways to summarise, visualise, and manipulate missing data with minimal deviations from the workflows in ggplot

Nicholas Tierney 611 Dec 22, 2022
Some method of processing point cloud

Point-Cloud Some method of processing point cloud inversion the completion pointcloud to incomplete point cloud Some model of encoding point cloud to

Tan 1 Nov 19, 2021
Python package for hypergraph analysis and visualization.

The HyperNetX library provides classes and methods for the analysis and visualization of complex network data. HyperNetX uses data structures designed to represent set systems containing nested data

Pacific Northwest National Laboratory 304 Dec 27, 2022
A python script to visualise explain plans as a graph using graphviz

README Needs to be improved Prerequisites Need to have graphiz installed on the machine. Refer to https://graphviz.readthedocs.io/en/stable/manual.htm

Edward Mallia 1 Sep 28, 2021
A python visualization of the A* path finding algorithm

A python visualization of the A* path finding algorithm. It allows you to pick your start, end location and make obstacles and then view the process of finding the shortest path. You can also choose

Kimeon 4 Aug 02, 2022
Color maps for POV-Ray v3.7 from the Plasma, Inferno, Magma and Viridis color maps in Python's Matplotlib

POV-Ray-color-maps Color maps for POV-Ray v3.7 from the Plasma, Inferno, Magma and Viridis color maps in Python's Matplotlib. The include file Color_M

Tor Olav Kristensen 1 Apr 05, 2022
又一个云探针

ServerStatus-Murasame 感谢ServerStatus-Hotaru，又一个云探针诞生了（大雾 本项目在ServerStatus-Hotaru的基础上使用fastapi重构了服务端，部分修改了客户端与前端 项目还在非常原始的阶段，可能存在严重的问题 演示站：https://stat

6 Oct 19, 2021
Visualization of numerical optimization algorithms

Visualization of numerical optimization algorithms

Zhengxia Zou 46 Dec 01, 2022
Glue is a python project to link visualizations of scientific datasets across many files.

Glue Glue is a python project to link visualizations of scientific datasets across many files. Click on the image for a quick demo: Features Interacti

675 Dec 09, 2022
A Python Library for Self Organizing Map (SOM)

SOMPY A Python Library for Self Organizing Map (SOM) As much as possible, the structure of SOM is similar to somtoolbox in Matlab. It has the followin

Vahid Moosavi 497 Dec 29, 2022
Extract and visualize information from Gurobi log files

GRBlogtools Extract information from Gurobi log files and generate pandas DataFrames or Excel worksheets for further processing. Also includes a wrapp

Gurobi Optimization 56 Nov 17, 2022
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

ae_attendances_modelling This repository contains the raw data and a python notebook to ingest historical A&E attendance data and then use a simple Pr

Mattia Ficarelli 2 Mar 29, 2022
AB-test-analyzer - Python class to perform AB test analysis

AB-test-analyzer Python class to perform AB test analysis Overview This repo con

13 Jul 16, 2022
Monochromatic colorscheme for matplotlib with opinionated sensible default

Monochromatic colorscheme for matplotlib with opinionated sensible default If you need a simple monochromatic colorscheme for your matplotlib figures,

Aria Ghora Prabono 2 May 06, 2022
Streaming pivot visualization via WebAssembly

Perspective is an interactive visualization component for large, real-time datasets. Originally developed for J.P. Morgan's trading business, Perspect

The Fintech Open Source Foundation (www.finos.org) 5.1k Dec 27, 2022