Nov 30 2022
|
SBGrid Installer
The SBGrid installation manager is the primary application for managing an SBGrid software installation. Users can choose a subset of applications for installation on their laptops or desktops or configure site installations for clusters, servers or cloud resources. This version is the command-line interface. A graphical version is available for download on the SBGrid wiki : https://sbgrid.org/wiki/client_downloads .
Updated versions:
2.8.5-beta | OS X INTEL
2.8.5-beta | Linux 64
|
Nov 30 2022
|
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.
Updated versions:
0.2.1 | Linux 64
0.2.1 | OS X INTEL
|
Nov 30 2022
|
ESMFold
harnesses the ESM-2 language model to generate accurate structure predictions end to end directly from the sequence of a protein.
Updated versions:
1.0.3 | Linux 64
|
Nov 29 2022
|
Julia
is a flexible dynamic language appropriate for scientific and numerical computing with performance comparable to traditional statically-typed languages.
Updated versions:
1.8.3 | Linux 64
1.8.3 | OS X INTEL
|
Nov 27 2022
|
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.
Updated versions:
20221123 | Linux 64
20221123 | OS X INTEL
|
Nov 23 2022
|
RDKit
a collection of cheminformatics and machine-learning software written in C++ and Python.
Updated versions:
2022.09.1 | Linux 64
2022.09.1 | OS X INTEL
|
Nov 23 2022
|
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.
Updated versions:
3.4.1 | Linux 64
3.4.1 | OS X INTEL
|
Nov 22 2022
|
Geneious
a powerful and comprehensive suite of molecular biology and NGS analysis tools.
Updated versions:
2022.2.2 | Linux 64
2022.2.2 | OS X INTEL
|
Nov 22 2022
|
Vina-GPU
a heterogeneous OpenCL implementation of AutoDock Vina.
Updated versions:
20220525_f314354 | Linux 64
|
Nov 22 2022
|
ProDy
a protein structural dynamics analysis software package.
ProDy is installed as a module within python.
Updated versions:
2.3.1 | OS X INTEL
|
Nov 22 2022
|
ATSAS
a program suite for small-angle scattering (SAXS) data analysis from biological macromolecules.
Updated versions:
3.1.3 | Linux 64
3.1.3 | OS X INTEL
|
Nov 22 2022
|
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.
Updated versions:
0.4.11 | OS X INTEL
0.4.11 | Linux 64
|
Nov 22 2022
|
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.
Updated versions:
1.3.3 | Linux 64
|
Nov 21 2022
|
AWS CLI
(Amazon Web Services Command Line Interface) a command line interface tool to manage multiple Amazon Web Services and automate them through scripts.
Updated versions:
1.27.13 | Linux 64
1.27.13 | OS X INTEL
|
Nov 21 2022
|
FASTA
a DNA and protein sequence alignment software package that searches for matching sequence patterns or words, called k-tuples.
Updated versions:
36.3.8i | Linux 64
36.3.8i | OS X INTEL
|
Nov 21 2022
|
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.
Updated versions:
2.13.0 | Linux 64
2.12.0 | Linux 64
2.13.0 | OS X INTEL
2.12.0 | OS X INTEL
|
Nov 21 2022
|
Anaconda
a Python distribution that includes more than 400 of the most popular Python packages for science, math, engineering, and data analysis.
Updated versions:
2022.10 | Linux 64
2022.10 | OS X INTEL
|
Nov 17 2022
|
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.
Updated versions:
20220816_7ee5f50 | Linux 64
|
Nov 17 2022
|
RFDesign
protein hallucination and inpainting with RoseTTAFold.
Updated versions:
c882ab0 | Linux 64
|
Nov 16 2022
|
SIDESPLITTER
a tool for mitigating local over-fitting during single particle reconstruction.
Updated versions:
1.2 | OS X INTEL
|
Nov 16 2022
|
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.
Updated versions:
4.11.21 | OS X INTEL
4.11.21 | Linux 64
|
Nov 16 2022
|
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/
Updated versions:
20220530_cu11 | Linux 64
|
Nov 15 2022
|
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.
Updated versions:
3.7.0 | Linux 64
|
Nov 15 2022
|
SIDESPLITTER
a tool for mitigating local over-fitting during single particle reconstruction.
Updated versions:
1.2 | Linux 64
|
Nov 14 2022
|
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.
Updated versions:
1.2.0 | OS X INTEL
1.2.0 | Linux 64
|
Nov 14 2022
|
ModelAngelo
an automatic atomic model building program for cryo-EM maps.
Updated versions:
0.2.2 | Linux 64
|
Nov 14 2022
|
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.
Updated versions:
3.7.0 | OS X INTEL
|
Nov 10 2022
|
AlphaFold
an implementation of the inference pipeline of AlphaFold v2.0 using a completely new model that was entered in CASP14.
Updated versions:
2.2.3 | Linux 64
2.2.4 | Linux 64
|
Nov 09 2022
|
TomoTwin-cryoet
a deep metric learning based particle picking procedure for cryo-ET
Updated versions:
0.2.0 | Linux 64
|
Nov 07 2022
|
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.
Updated versions:
1.5.0 | Linux 64
1.6.1 | Linux 64
|
Nov 04 2022
|
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.
Updated versions:
3.12.0 | Linux 64
3.12.0 | OS X INTEL
|
Nov 04 2022
|
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/
Updated versions:
20220530_cu10 | Linux 64
|
Nov 04 2022
|
intel
Redistributable Libraries for IntelĀ® C++ and Fortran 2020 Compilers.
Updated versions:
2016.4.258 | Linux 64
|
Nov 01 2022
|
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.
Updated versions:
4.2.1 | Linux 64
|