Software Updates

SBGrid Installer

cryoCARE

PIP package memory efficient implementation of cryoCARE (Content-Aware Image Restoration for Cryo-Transmission Electron Microscopy Data), is a restoration method that dramatically increases contrast in cryo-TEM images, improving the interpretability of the acquired data.

ESMFold

harnesses the ESM-2 language model to generate accurate structure predictions end to end directly from the sequence of a protein.

Julia

is a flexible dynamic language appropriate for scientific and numerical computing with performance comparable to traditional statically-typed languages.

NMRPipe

a set of comprehensive facilities for Fourier processing of spectra in one to four dimensions, as well as a variety of facilities for spectral display and analysis. This is the official NMRScience version of NMRPipe.

RDKit

a collection of cheminformatics and machine-learning software written in C++ and Python.

APBS

(Adaptive Poisson-Boltzmann Solver) a software package designed for the numerical solution of the Poisson-Boltzmann equation (PBE), solves the equations of continuum electrostatics for large biomolecular assemblages.

Geneious

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

Vina-GPU

a heterogeneous OpenCL implementation of AutoDock Vina.

ProDy

a protein structural dynamics analysis software package.

ProDy is installed as a module within python.

ATSAS

a program suite for small-angle scattering (SAXS) data analysis from biological macromolecules.

starfile

a Python implementation of the STAR file format designed principally for compatibility with RELION format STAR files. It allows STAR files to be created and opened easily using a very simple API, exposing data blocks as pandas DataFrame objects.

AreTomo

(Alignment and Reconstruction for Electron Tomography) is a GPU-accelerated software package that provides an integrated solution to both fiducial-free alignment and reconstruction for cryoEM tomography.

AWS CLI

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

FASTA

a DNA and protein sequence alignment software package that searches for matching sequence patterns or words, called k-tuples.

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.

Anaconda

a Python distribution that includes more than 400 of the most popular Python packages for science, math, engineering, and data analysis.

DAQ Score

a computational tool using deep learning that can estimate the residue-wise local quality for protein models from cryo-Electron Microscopy (EM) maps.

RFDesign

protein hallucination and inpainting with RoseTTAFold.

SIDESPLITTER

a tool for mitigating local over-fitting during single particle reconstruction.

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.

DeepEMhancer

(Deep cryo-EM Map Enhancer) a python package designed to perform non-linear post-processing of cryo-EM maps for local sharpening, automatic masking and denoising. Systems using cuda 11+ should use the 20210511 version of deepEMhancer, and the modified models distributed in /programs/share/deepemhancer/20210511/deepEMhancerModels/production_checkpoints/

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.

SIDESPLITTER

a tool for mitigating local over-fitting during single particle reconstruction.

Neggia

an HDF5 read plugin for XDS. Neggia presents HDF5 data to XDS in a fully parallelized way, directly and without interconversion and speeds up the processing of HDF5 data.

ModelAngelo

an automatic atomic model building program for cryo-EM maps.

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.

AlphaFold

an implementation of the inference pipeline of AlphaFold v2.0 using a completely new model that was entered in CASP14.

TomoTwin-cryoet

a deep metric learning based particle picking procedure for cryo-ET

emClarity

(enhanced macromolecular classification and alignment for high-resolution in situ tomography) a GPU-accelerated image processing software for high-resolution cryo-electron tomography and subtomogram averaging and classification.

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.

DeepEMhancer

(Deep cryo-EM Map Enhancer) a python package designed to perform non-linear post-processing of cryo-EM maps for local sharpening, automatic masking and denoising. Systems using cuda 11+ should use the 20210511 version of deepEMhancer, and the modified models distributed in /programs/share/deepemhancer/20210511/deepEMhancerModels/production_checkpoints/

intel

Redistributable Libraries for Intel® C++ and Fortran 2020 Compilers.

CellProfiler

is a cell image analysis software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically.