Skip to content

Machine Learning APIs and apps based upon masskit

License

Notifications You must be signed in to change notification settings

usnistgov/masskit_ai

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

Repository files navigation

Masskit logo


Masskit AI is a Python package that uses the Masskit Python module and PyTorch to do machine learning on mass spectra, small molecules and peptides. Masskit AI includes:

  • AI models for predicting the HCD spectra of peptides.
  • AI models for computing the retention index of small molecules.

Table of Contents

Installation

Requirements

  • Masskit is installed using the package managers conda and mamba. If you do not have either installed we recommend installing mambaforge. Detailed installation instructions for macOS and Linux can be found here.

Windows

  • Download the latest Masskit Windows zip file from the Releases page.
  • Extract the contents of the file to a directory on your computer by navigating explorer to the Downloads folder, right clicking on the zip file, and selecting Extract all....
  • Run Miniforge Prompt or Anaconda Prompt from the Start menu depending on whether you installed mambaforge or a conda distribution.
  • In the prompt window, use cd masskit* to change to the directory starting with masskit in the directory you extracted the downloads to.
  • Run call init_masskit.bat /cpu to create the masskit_ai_cpu package environment.
    • Alternatively, if you know you have an Nvidia GPU of sufficient power run call init_masskit.bat /ml to create the masskit_ai package environment.
  • Run pip install --find-links=. masskit masskit_ai.

Whenever using the programs in Masskit, please make sure you initialize the appropriate package environment:

  • If you installed mambaforge run Miniforge Prompt from the Start menu otherwise run Anaconda Prompt from the Start menu.
  • If you installed the CPU only version package environment run conda activate masskit_ai_cpu.
  • If you installed the GPU version package environment run conda activate masskit_ai

Linux or macOS

  • first install Masskit using these instructions.
  • Change to a directory that will hold the masskit_ai directory.
  • Run git clone https://github.com/usnistgov/masskit_ai.git.
  • Run cd masskit_ai.
  • Run pip install ..

Whenever using the programs in Masskit, please make sure you have initialized the appropriate package environment:

  • If you installed the CPU only version package environment run conda activate masskit_ai_cpu.
  • If you installed the GPU only version package environment run conda activate masskit_ai.