Software Updates

OpenMPI

an open source Message Passing Interface implementation that is developed and maintained by a consortium of academic, research, and industry partners. Open MPI is therefore able to combine the expertise, technologies, and resources from all across the High Performance Computing community in order to build the best MPI library available.

Geneious

a powerful and comprehensive suite of molecular biology and NGS analysis tools.

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.

Raddose-3D

RADDOSE‐3D, a software tool allowing the estimation of the dose absorbed in a macromolecular crystallography diffraction experiment.

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.

crYOLO

a novel automated particle picking software based on the deep learning object detection system 'You Only Look Once' (YOLO). CrYOLO is available as standalone program under http://sphire.mpg.de/ and will be part of the image processing workflow in SPHIRE.

DOCK

a molecular docking application used to a) predict binding modes of small molecule-protein complexes; b) search databases of ligands for compounds that inhibit enzyme activity, bind a particular protein, bind nucleic acid targets; c) examine possible binding orientations of protein-protein and protein-DNA complexes; d) help guide synthetic efforts by examining small molecules that are computationally derivatized. Dock is offered in the SBGrid collection in two iterations, Dock 3 and Dock 6.

SRA Toolkit

a collection of tools and libraries for using data in the INSDC Sequence Read Archives.

LigPlot+

a graphical front-end to the LIGPLOT (protein-ligand interactions) and DIMPLOT (protein-protein, domain-domain interactions) programs. The plots generated by these programs can be interactively edited on screen, superposed and printed.

OpenMPI

an open source Message Passing Interface implementation that is developed and maintained by a consortium of academic, research, and industry partners. Open MPI is therefore able to combine the expertise, technologies, and resources from all across the High Performance Computing community in order to build the best MPI library available.

AWS CLI

(Amazon Web Services Command Line Interface) a command line interface tool to manage multiple Amazon Web Services and automate them through scripts.

BCFtools

a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.

AWS CLI

(Amazon Web Services Command Line Interface) a command line interface tool to manage multiple Amazon Web Services and automate them through scripts.

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.

XDS

(X-ray Detector Software) a software tool for processing single-crystal monochromatic diffraction data recorded by the rotation method.

PyMOL

widely used molecular visualization package developed by Warren DeLano, now maintained by Schödinger, LLC. This installation includes official incentive builds of PyMOL.

CUDA

redistributable software libraries to support CUDA applications for Linux.

OpenMPI

an open source Message Passing Interface implementation that is developed and maintained by a consortium of academic, research, and industry partners. Open MPI is therefore able to combine the expertise, technologies, and resources from all across the High Performance Computing community in order to build the best MPI library available.

CUDA

redistributable software libraries to support CUDA applications for Linux.

BioXTAS RAW

a program for analysis of SAXS data that enables creation of 1D scattering profiles from 2D detector images, standard data operations such as averaging and subtraction, analysis of radius of gyration (Rg) and molecular weight, and advanced processing using GNOM, DAMMIF, and AMBIMETER. It also allows easy processing of inline SEC-SAXS data.

ARIA

(Ambiguous Restraints for Iterative Assignment) a software that automates NOE assignment and NMR structure calculation.

OpenBabel

a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas.

BUSTER

a software system containing crystallographic structure refinement using Bayesian statistical methods (BUSTER), ligand fitting (rhofit) and a fully automated pipeline (Pipedream) to drive a structure based fragment/ligand screening pathway.

Perl

is a highly capable, feature-rich programming language with over 30 years of development. Perl runs on over 100 platforms from portables to mainframes and is suitable for both rapid prototyping and large scale development projects.

ChimeraX

a next-generation molecular visualization program, following UCSF Chimera. Compared to Chimera, ChimeraX has improved graphics (e.g. interactive ambient shadows); faster handling of large structures (millions of atoms); and a more modern, single-window user interface. ChimeraX will have documented programming interfaces and an easy-to-use “Tool Shed” web repository of extensions.

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.

Bsoft

a collection of programs and a platform for the development of software for image processing of electron micrographs, interpretation of reconstructions, molecular modeling, and general image and molecular processing.

SBGrid Installer

a graphical installation client used to install the SBGrid software collection on Apple OSX computers running MacOSX v10.11 - 10.15. Users can cherrypick a subset of applications for installation on their laptops or desktops. Software updates are highlighted, but users trigger the software update manually at their convenience.