Algorithms for Single Particle Reconstruction
ASPIRE - Algorithms for Single Particle Reconstruction
This is the Python version to supersede the Matlab ASPIRE.
ASPIRE is an open-source software package for processing single-particle cryo-EM data to determine three-dimensional structures of biological macromolecules. The package includes advanced algorithms based on rigorous mathematics and recent developments in statistics and machine learning. It provides unique and improved solutions to important computational challenges of the cryo-EM processing pipeline, including 3-D ab-initio modeling, 2-D class averaging, automatic particle picking, and 3-D heterogeneity analysis.
ASPIRE is a pip-installable package that works on Linux/Mac/Windows, and requires Python 3.6. The simplest option is to use Anaconda 64-bit for your platform with a minimum of Python 3.6 and pip, and then use
pip to install
aspire in that environment.
conda create -n aspire_env python=3.6 pip conda activate aspire_env pip install aspire
The final step above should install any dependent packages from
Note that this step installs the base
aspire package for you to work with, but not the unit tests/scripts/documentation. If you need to install ASPIRE for development purposes, read on.
After cloning this repo, the simplest option is to use Anaconda 64-bit for your platform, and use the provided
environment.yml file to build a Conda environment to run ASPIRE.
cd /path/to/git/clone/folder conda env create -f environment.yml conda activate aspire
Make sure everything works
Once ASPIRE is installed, make sure the unit tests run correctly on your platform by doing:
cd /path/to/git/clone/folder python setup.py test
Tests currently take around 2 minutes to run. If some tests fail, you may realize that
python setup.py test produces too much information.
You may want to re-run tests using:
cd /path/to/git/clone/folder PYTHONPATH=./src pytest tests
This provides a cleaner output to analyze.
If the tests pass, install the ASPIRE package for the currently active Conda environment:
cd /path/to/git/clone/folder python setup.py install
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
|Filename, size||File type||Python version||Upload date||Hashes|
|Filename, size aspire-0.5.3.tar.gz (128.2 kB)||File type Source||Python version None||Upload date||Hashes View hashes|