Software
ATSAS
ATSAS is a program suite for small-angle scattering data analysis from biological macromolecules. It includes multiplatform data manipulation and displays tools, programs for automated data processing and calculation of overall parameters, usage of high- and low-resolution models from other structural methods, algorithms to build three-dimensional models from weakly interacting oligomeric systems and complexes, and enhanced tools to analyse data from mixtures and flexible systems.
AUTOPROC
autoPROC is a set of tools and programs to automate the whole range of steps involved in data processing: analysis of collections of images and image headers, indexing of diffraction images, determination of accurate cell parameters, integration of a series of images, processing of multi-sweep datasets, production of files of intensities and amplitudes in various formats (MTZ, Scalepack), analysis of anomalous signal, automatic determination of most likely space group symmetry.
Avizo
3D analysis software for scientific and industrial data. Different application areas: Materials Science, Quality Assurance in Industrial Environments, Electronics, Digital Rock Analysis etc. It enables users to perform interactive visualization and computation on 3D data sets. The Avizo interface is modelled on the visual programming. Users manipulate data and module components, organized in an interactive graph representation (called Pool), or in a Tree view. Data and modules can be interactively connected together, and controlled with several parameters, creating a visual processing network whose output is displayed in a 3D viewer. With this interface, complex data can be interactively explored and analyzed by applying a controlled sequence of computation and display processes resulting in a meaningful visual representation and associated derived data.
BINoculars
BINoculars is a tool for data reduction and analysis of large sets of surface diffraction data that have been acquired with a 2D X-ray detector. The intensity of each pixel of a 2D-detector is projected onto a 3-dimensional grid in reciprocal lattice coordinates using a binning algorithm. This allows for fast acquisition and processing of high-resolution datasets and results in a significant reduction of the size of the dataset. The subsequent analysis then proceeds in reciprocal space. It has evolved from the specific needs of the ID03 beamline at the ESRF, but it has a modular design and can be easily adjusted and extended to work with data from other beamlines or from other measurement techniques.
BornAgain
BornAgain is a software package to simulate and fit small-angle scattering at grazing incidence. It supports analysis of both X-ray (GISAXS) and neutron (GISANS) data. Its name, BornAgain, indicates the central role of the distorted wave Born approximation in the physical description of the scattering process. The software provides a generic framework for modeling multilayer samples with smooth or rough interfaces and with various types of embedded nanoparticles.
BUSTER
BUSTER is a framework for automatic refinement of macromolecules. It uses maximum-likelihood (ML) and maximum-entropy (ME) techniques to overcome two major shortcomings encountered by classical methods (least-squares (LS) + difference maps) when dealing with the refinement and completion of partial structures:
CONUSS
The CONUSS software package provides evaluation methods for data obtained by nuclear resonant scattering techniques. It is used for the interpretation of time or energy spectra from coherent elastic nuclear resonant scattering, i.e., forward scattering and Bragg/Laue scattering,
CrysAlis Pro
Data collection and data processing software for small molecule and protein crystallography. Main features: automatic crystal screening, data collection and strategy modules. It provides the user with information regarding the unit cell, intensity estimation by resolution range and suggested frame exposure times for the full data collection.
CRYSTAL
Computational tool for solid state physics and chemistry. The CRYSTAL package performs ab initio calculations of the ground state energy, energy gradient, electronic wave function and properties of periodic systems. Hartree-Fock or Kohn- Sham Hamiltonians (adopting an Exchange-Correlation potential following the DFT postulates of ) can be used. Systems periodic in 0 (molecules, 0D), 1 (polymers, 1D), 2 (slabs, 2D), and 3 dimensions (crystals, 3D) are treated on an equal footing. In each case the fundamental approximation made is the expansion of the single particle wave functions ('Crystalline Orbital', CO) as a linear combination of Bloch functions (BF) defined in terms of local functions, i.e. Atomic Orbitals.
CrystFEL
CrystFEL is a suite of programs for processing diffraction data acquired "serially" in a "snapshot" manner, such as when using the technique of Serial Femtosecond Crystallography (SFX) with a free-electron laser source. CrystFEL comprises programs for indexing and integrating diffraction patterns, scaling and merging intensities, simulating patterns, calculating figures of merit for the data and visualising the results. Supporting scripts are provided to help at all stages, including importing data into CCP4 for further processing. [From: the Website]
DaFy
DaFy, short for Data Analysis Factory, is a software package that contains a bunch of PyQt5 based GUI applications for processing synchrotron X-ray data.
dahu
Data Analysis RPC server over Tango Dahu is a lightweight plugin based framework... ... technically a JSON-RPC server over Tango * plugin can be class or can be generated from state-less function * a plugin is executed within a job, each job lives in its own thread. * plugins have empty constructors plus 4 methods (or more) - setup allows to set the input parameters. It performs sanitization if needed - process does the taff - teardown sets the output and the logging and cleans up if needed - abort can be used to stop the processing if a plugin is a daemon. * the job is responsible for serializing on disk the plugin input and output * jobs can be launched using the tango interface (or other ...) * plugins have a single input and output, they are simple JSON-serializable dictionaries.
DARTS on-demand computing
The Data Analysis Remote Treatment Service (DARTS) [1] is a remote desktop service that launches virtual machines in the cloud, and displays them in your browser. These machines can be used for e.g. scientific data treatment. A user indicates how many CPU cores and how much memory he wishes, can optionally request a GPU for heavy-duty computations, and can be customized at start-up. The sessions typically start in about 10 seconds, and can be shared with colleagues within their life-time (typically 4 days). Each user can manage all his active sessions (connect, stop, share). This service can be installed and configured within a few minutes (sudo apt install qemu-web-desktop), and it requires minimal maintenance. It can also run on a set of servers without any underlying complex infrastructure. The source code is fully open-source, and relies on very simple elements (Apache web-server and QEMU). Give it a try ! The source code is at https://gitlab.com/soleil-data-treatment/soleil-software-projects/remote-desktop
DAWN
DAWN, the Data Analysis WorkbeNch, is an Eclipse based application for scientific data analysis. It comes with a range of tools for visualization (1D, 2D and 3D), code development environments (for Python, Jython and Eclipse plug-ins) as well as processing workflows with visual algorithms for analyzing scientific datasets. It is primarily developed at Diamond Light Source, but external contributions are most welcome! DAWN is distributed freely and is released under the Eclipse Public License.
Demeter
Demeter is a comprehensive system for processing and analyzing X-ray Absorption Spectroscopy data. It contains several packages such as Athena, Artemis and Hephaestus, which are widely used in the XAFS community.
