Software Updates

SPIDER

(System for Processing Image Data from Electron microscopy and Related fields) a large image processing suite for electron microscopy.

XDrawChem

a two-dimensional molecule drawing program for Unix operating systems that can read and write MDL Molfiles, and read ChemDraw text and binary files, to allow sharing between XDrawChem and other chemistry applications, and it can create images in popular formats like PNG and EPS.

XDP

used for processing electron diffraction data. Previously available only on DEC Alpha.

TimeScapes

a Python-based program package that can be used to efficiently detect and characterize significant conformational changes in simulated biomolecular systems.

SHARP/autoSHARP

an automated structure solution pipeline built around the heavy-atom refinement and phasing program SHARP, the substructure determination program SHELXD, the density modification program SOLOMON and the model building programs BUCCANEER and ARP/wARP. It allows fully automated structure solution by experimental phasing, from merged reflection data to an initial model, without any user intervention.

ScÅtter

a JAVA-based application for basic analysis of SAXS datasets. Scatter is developed by Robert Rambo at the Diamond Light Source (Didcot, UK). The program was previously developed at the SIBYLS beamline (12.3.1) of the Advanced Light Source, Berkeley, CA.

RStudio

an integrated development environment (IDE) for R that includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management.

Python

a general-purpose, interpreted, object oriented, high-level dynamic programming language that emphasizes code readability. Its syntax allows programmers to express concepts in fewer lines of code than in C++ or Java, thus allowing programmers to work more quickly and integrate their systems more effectively.

PyRosetta

an interactive Python-based interface to the powerful Rosetta molecular modeling suite that enables users to design their own custom molecular modeling algorithms using Rosetta sampling methods and energy functions.

Priism/IVE

the graphical interface to a collection of applications for the analysis and visualization of multidimensional data, with a focus on data from 3D optical microscopy and electron tomography. IVE (Image Visualization environment) is the core set of software libraries that are the foundation for the tools in Priism.

NAMD

a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.

MAFFT

a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <200 sequences), FFT-NS-2 (fast; for alignment of <30,000 sequences).

Dynamo

a software environment for subtomogram averaging of cryo-EM data.

DSSR

(Dissecting the Spatial Structure of RNA) a software tool for dissecting the spatial structure of RNA.

Qt

a cross-platform application framework that is used for developing application software that can be run on various software and hardware platforms with little or no change in the underlying codebase, while still being a native application with native capabilities and speed.

mono

an open source implementation of Microsoft's .NET Framework based on the ECMA standards for C# and the Common Language Runtime.

OpenJDK

(Open Java Development Kit) is a free and open source implementation of the Java Platform, Standard Edition (Java SE).

Qt

a cross-platform application framework that is used for developing application software that can be run on various software and hardware platforms with little or no change in the underlying codebase, while still being a native application with native capabilities and speed.

mono

an open source implementation of Microsoft's .NET Framework based on the ECMA standards for C# and the Common Language Runtime.

vtk

(Visualization Tool Kit)f a C++ class library and several interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization algorithms including scalar, vector, tensor, texture, and volumetric methods, as well as advanced modeling techniques such as implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation.

3DNA

a versatile, integrated software system for the analysis, rebuilding, and visualization of 3-dimensional nucleic acid structures.

CUDA

redistributable software libraries to support CUDA applications for Linux.

EMAN2

a scientific image processing suite with a particular focus on single particle reconstruction from cryoEM images. EMAN2 is a complete refactoring of the original EMAN1 library and contains the SPARX applications.

BLAST+

a suite of BLAST (Basic Local Alignment Search Tool) tools that utilizes the NCBI C++ Toolkit with a number of performance and feature improvements over the legacy BLAST applications.

XRayView

uses interactive computer graphics to introduce basic concepts of X-ray diffraction by crystals, including the reciprocal lattice, the Ewald sphere construction, Laue cones, the wavelength dependence of the reciprocal lattice, primitive and centered lattices and systematic extinctions, rotation photography, Laue photography, space group determination and Laue group symmetry, and the alignment of crystals by examination of reciprocal space.

EPMR

a program that finds crystallographic molecular replacement solutions using an evolutionary search algorithm. The program directly optimizes three rotational and three positional parameters for the search model with respect to the correlation coefficient between Fo and Fc.