SOFTWARE FOR
Computational Biology
Software for Computational Biology implements computational methods for understanding the molecular basis of life. Software distributed to the scientific community covers processing of experimental data, modelling and simulation of biological systems, interpretation of 2D and 3D imaging data, and data management for projects.
CCP-EM software suite – programs for solving macromolecular structures from cryoEM data
CAPABILITIES
The CCP-EM software suite provides programs for solving macromolecular structures from cryoEM data, covering all stages from raw 2D images, via 3D volumes, to atomic models.
TRAINING INFORMATION
The CCP-EM support team organise and host regular training workshops and contribute to external courses. See the website or @ccp_em on X for details.
ACCESS
The suite is free for academic users and there is an annual fee for commercial users. See here for details.
CCP4 software suite – programs for solving macromolecular structures from X-ray diffraction data
CAPABILITIES
The CCP4 software suite provides programs for solving macromolecular structures from X-ray diffraction data, covering all stages from diffraction images to built atomic models.
TRAINING INFORMATION
The CCP4 support team organise and host regular training workshops and contribute to external courses. See the website.
ACCESS
The suite is licensed for free to non-profit users, and for an annual fee to for-profit users. See here for details.
CCPi Core Imaging Library (CIL) – open-source Python framework for tomographic imaging for cone and parallel beam geometries
CAPABILITIES
CIL is an open-source mainly Python framework for tomographic imaging for cone and parallel beam geometries. It comes with tools for loading, preprocessing, reconstructing and visualising tomographic data.
TRAINING INFORMATION
The CIL team run a range of online and in-person training courses. See the website for details.
ACCESS
The software is available with open-source license Apache-v2 via GitHub.
Code Entropy – set of tools for computing entropy of macromolecular systems
CAPABILITIES
CodeEntropy is a Python-based software package designed for the computation of configurational entropy in macromolecular systems. It leverages forces sampled from molecular dynamics (MD) simulations and implements the multiscale cell correlation method to deliver accurate, scalable, and generalizable entropy estimates.
CodeEntropy provides a unified and extensible framework for entropy analysis, supporting a broad range of molecular systems and simulation workflows. Key features include:
– Configurational entropy estimation using force-based multiscale cell correlation.
– Applicability to a wide variety of molecular systems, ranging from simple biomolecules to complex macromolecular assemblies.
– Integration with standard MD formats and pipelines for seamless workflow compatibility.
– Scalable performance suitable for high-throughput and large-scale simulations.
– Modular architecture enabling customization and extension for advanced use cases.
TRAINING INFORMATION
Comprehensive documentation is available at CodeEntropy Documentation
Training opportunities and workshops are regularly hosted by CCPBioSim: Upcoming Events
ACCESS
CodeEntropy is distributed under the MIT License, promoting open and collaborative development.
To install and begin using CodeEntropy, refer to the official Getting Started guide
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DIALS Package – data processing tools for single crystal diffraction experiments
CAPABILITIES
The DIALS Package provides data processing tools for single crystal diffraction experiments. The package provides a suite of programs for processing single-crystal diffraction image data sets from X-ray, electron and neutron sources.
TRAINING INFORMATION
The DIALS package is taught at macromolecular crystallography training workshops, including those organised by CCP4. See the website or @ccp4_mx on X for details.
ACCESS
DIALS is freely available to all users, under the terms of the BSD 3-Clause license.
Synergistic Image Reconstruction Framework (SIRF) – Open Source software for image reconstruction of biomedical imaging
CAPABILITIES
The Synergistic Image Reconstruction Framework (SIRF) is an Open Source software for image reconstruction of biomedical imaging (currently PET, SPECT and MR) data in a research context.
TRAINING INFORMATION
Documentation is available on the CCP-SyneRBI wiki. There are also regular training courses based on the SIRF-Exercises jupyter notebooks.
ACCESS
SIRF is available as a Virtual Machine, a Docker image, or as code to be built. The underlying code is licensed as GPL v2 and Apache 2.0.
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