Welcome to SimEx-Lite’s documentation!
Quickstart
SimEx-Lite is the core package of the SIMEX platform providing the calculator interfaces and data APIs.
Free software: GNU General Public License v3
Documentation: https://SimEx-Lite.readthedocs.io
Installing
SimEx-Lite can be installed with Python 3.6 or later:
$ pip install SimEx-Lite
To test the latest updates, install from sources as shown below.
Developing
We encourage everyone to contribute to SimEx. For a detailed guide, please visit https://simex-lite.readthedocs.io/en/latest/contributing.html
Clone this Github repository:
$ git clone --recursive git@github.com:PaNOSC-ViNYL/SimEx-Lite.git
Install the package locally:
$ cd SimEx-Lite
$ pip install -e .
Tests
Enable the testFiles submodule.
$ git submodule init
$ git submodule update
Run the test
$ pytest .
Features
SimEx-Lite provides
- python interfaces for SIMEX backengines (aka “Calculators”)
SourceCalculators
PropagationCalculators
PMICalculators (PhotonMattterInteractionCalculators)
DiffractionCalculators
DetectorCalculators
- data APIs for different data formats.
PMI (Photon matter interaction) data
Wavefront data
Diffraction data
Citation
Please cite the following paper if you use SimEx-Lite for your research:
E, J. et al. SimEx-Lite: easy access to start-to-end simulation for experiments at advanced light sources. in Advances in Computational Methods for X-Ray Optics VI (eds. Chubar, O. & Tanaka, T.) 22 (SPIE, San Diego, United States, 2023). doi.org/10.1117/12.2677299
Publications using SIMEX platform
E, J. et al. SimEx-Lite: easy access to start-to-end simulation for experiments at advanced light sources. in Advances in Computational Methods for X-Ray Optics VI (eds. Chubar, O. & Tanaka, T.) 22 (SPIE, San Diego, United States, 2023). doi:10.1117/12.2677299.
E, J. et al. Water layer and radiation damage effects on the orientation recovery of proteins in single-particle imaging at an X-ray free-electron laser. Sci Rep 13, 16359 (2023).
E, J. et al. Expected resolution limits of x-ray free-electron laser single-particle imaging for realistic source and detector properties. Structural Dynamics 9, 064101 (2022).
E, J. et al. Effects of radiation damage and inelastic scattering on single-particle imaging of hydrated proteins with an X-ray Free-Electron Laser. Sci Rep 11, 17976 (2021).
E, J. et al. VINYL: The VIrtual Neutron and x-raY Laboratory and its applications. in Advances in Computational Methods for X-Ray Optics V (eds. Sawhney, K. & Chubar, O.) 33 (SPIE, Online Only, United States, 2020). doi:10.1117/12.2570378.
Fortmann-Grote, C. et al. Start-to-end simulation of single-particle imaging using ultra-short pulses at the European X-ray Free-Electron Laser. IUCrJ 4, 560–568 (2017).
Fortmann-Grote, C. et al. Simulations of ultrafast x–ray laser experiments. in Advances in X-ray Free-Electron Lasers Instrumentation IV (eds. Tschentscher, T. & Patthey, L.) 102370S (Prague, Czech Republic, 2017). doi:10.1117/12.2270552.
Fortmann-Grote, C. et al. SIMEX: Simulation of Experiments at Advanced Light Sources. arXiv:1610.05980 [physics] (2016).
Yoon, C. H. et al. A comprehensive simulation framework for imaging single particles and biomolecules at the European X-ray Free-Electron Laser. Scientific Reports 6, 24791 (2016).
Acknowledgement
This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 823852.