SIMPLE

What SIMPLE does

SIMPLE is a high performance, end to end cryo-EM image processing and reconstruction platform. The README states it transforms raw electron microscopy data, meaning movies, micrographs, and particle images, into scientifically meaningful outputs. Those outputs are two dimensional class averages, high resolution three dimensional reconstructions, symmetry analysis, and atomic level structural models. In practice this is the software pipeline a structural biologist uses to go from the raw output of an electron microscope to a model of a molecule.

The platform supports both interactive batch workflows and fully automated streaming pipelines. The README says it scales from single workstations to distributed high performance computing environments, which matters because cryo-EM datasets can be large and compute heavy. A user can run a single machine for a small job or spread the work across a cluster for production scale processing. The framing of SIMPLE as end to end means the same tool covers the stages a reconstruction needs rather than stopping at one step. The README presents this as a platform built for real experimental workflows, so the intended audience is research labs that process microscopy data routinely. The version discussed on the page is 3.0.0, and the project links a stable release tag and public unit tests hosted on Zenodo, which signals an intention to be reproducible and citable.

Features and system requirements

The feature list is short and focused. SIMPLE offers an end to end cryo-EM workflow, streaming data processing, HPC scalability, a modular architecture, test driven development, and a production ready scientific computing environment. These points repeat the themes from the overview: the tool covers the whole pipeline, can process data as it arrives, runs on clusters, is built from separable parts, is developed with tests, and is meant for real use rather than only prototyping.

The system requirements are detailed because the build is from source. Linux is supported with Ubuntu 16.04 or newer recommended, and macOS 10.10 or newer is also supported. The build uses CMake 3.5 or newer and the GNU compiler collection with gfortran, both at version 14.2 or newer. Numerical libraries are needed: BLAS and LAPACK, and ARPACK or ARPACK-NG. FFTW version 3.3 or newer must be built with double, single, and threaded variants. libcurl 7 or newer and libTIFF 4 or newer are required, with jbigkit 2 or newer listed as optional. Python 3.10 or newer is also needed. The README lays these out as a checklist before building, which tells a new user exactly what must be installed on the host. Because SIMPLE is a scientific Fortran and C codebase with heavy numerical dependence, this explicit requirement list is the practical entry point to getting it running.

Building and philosophy

Building SIMPLE follows a standard CMake flow. After obtaining the source by unpacking the stable tarball or cloning the repository, the user makes a build directory, runs cmake from it, and runs make with install. Environment setup appends the project's shell snippet to the user's rc file, or sets PATH to the build bin and scripts directories and defines SIMPLE_PATH manually. Advanced configuration allows a custom install prefix and custom compiler or FFTW paths passed to cmake. Updating pulls the latest source and rebuilds, and a GUI build enables the NICE interface through a cmake flag.

Documentation lives at hael.github.io/SIMPLE, and the license is the GNU General Public License version 3 or later, with the software provided without warranty. The philosophy section says SIMPLE combines high performance numerical kernels, cryo-EM domain abstractions, workflow orchestration, and engineering discipline into a scalable scientific application suite. That summary explains the design intent: fast math at the bottom, domain specific concepts in the middle, orchestration to tie steps together, and engineering practice to keep it maintainable. For a research group, the combination means a tool that is both scientifically capable and operable as production software rather than a one off script. The presence of public unit tests and a documented build also lowers the barrier for a new lab to adopt SIMPLE without needing an in house engineer to port it.

Editorial conclusion

SIMPLE is distributed under the GNU General Public License version 3 and is written in Fortran and C, with source at github.com/hael/SIMPLE.