Software Updates

CUDA

redistributable software libraries to support CUDA applications for Linux.

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.

MoRDa

a pipeline for molecular replacement protein structure solution using X-ray data. The software package includes a database and a set of programs for the structure solution.

CCP4

(Collaborative Computational Project, Number 4) a collection of programs and associated data and software libraries used for macromolecular structure determination by X-ray crystallography.

DIALS

(Diffraction Integration for Advanced Light Sources) a software project for the analysis of crystallographic diffraction images for many new methods from shutterless, fine-sliced rotation scans to randomly-oriented snapshots of serial crystallography. It uses multiple CPU and GPU machines to increase speed and accuracy based on a comprehensive physical model.

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.

Fast Data Transfer - FDT

FDT is an Application for Efficient Data Transfers which is capable of reading and writing at disk speed over wide area networks (with standard TCP). It is written in Java, runs an all major platforms and it is easy to use.

CryoAssess

an automatic pipeline for cryo-EM data preprocessing and assessment using a combination of deep learning and image analysis tools.

SAMtools

(Sequence Alignment/Map) a generic format for storing large nucleotide sequence alignments that provides various utilities for manipulating alignments, including sorting, merging, indexing and generating alignments in a per-position format.

Scipion

an image processing framework to obtain 3D models of macromolecular complexes using 3D EM that allows you to execute workflows combining different software tools, while taking care of formats and conversions.

R

a free software environment for statistical computing and graphics.

DivCon Discovery Suite

a linear-scaling, semiempirical quantum mechanics (SE-QM) program DivCon with the Phenix X-ray refinement engine. Phenix/DivCon does not utilize CIF(s), link restraints and other refinement parameters so there are fewer assumptions about the model. Accurate energy and density scoring tools also allow tautomer/protomer and “flip state” determination.

TensorFlow

an open source software library for high performance numerical computation. Its flexible architecture allows easy deployment of computation across a variety of platforms (CPUs, GPUs, TPUs), and from desktops to clusters of servers to mobile and edge devices. Originally developed by researchers and engineers from the Google Brain team within Google’s AI organization, it comes with strong support for machine learning and deep learning, and the flexible numerical computation core is used across many other scientific domains.

CCP4

(Collaborative Computational Project, Number 4) a collection of programs and associated data and software libraries used for macromolecular structure determination by X-ray crystallography.

RELION

(REgularised LIkelihood OptimisatioN) a stand-alone computer program for Maximum A Posteriori (MAP) refinement of (multiple) 3D reconstructions or 2D class averages in cryo-electron microscopy.

IGV

(Integrative Genomics Viewer) a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations.

NovaCTF

NovaCTF provides 3D-CTF correction for cryo-electron tomography

DIALS

(Diffraction Integration for Advanced Light Sources) a software project for the analysis of crystallographic diffraction images for many new methods from shutterless, fine-sliced rotation scans to randomly-oriented snapshots of serial crystallography. It uses multiple CPU and GPU machines to increase speed and accuracy based on a comprehensive physical model.

IMOD

a set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections.

VMD

a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.

xterm

a terminal emulator for the X Window System that provides DEC VT102 and Tektronix 4014 compatible terminals for programs that can't use the window system directly.