Software Updates

PHENIX

(Python-based Hierarchical Environment for INtegrated Xtallography) a software suite for the automated determination of molecular structures using X-ray crystallography and other methods.

FFmpeg

a complete, cross-platform solution to record, convert and stream audio and video.

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.

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.

deepTools

a suite of python tools particularly developed for the efficient analysis of high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq. deepTools contains useful modules to process the mapped reads data for multiple quality checks, creating normalized coverage files in standard bedGraph and bigWig file formats, that allow comparison between different files (for example, treatment and control). Finally, using such normalized and standardized files, deepTools can create many publication-ready visualizations to identify enrichments and for functional annotations of the genome.

Rosetta

a software suite for modeling macromolecular structures and for predicting and designing protein structures, protein folding mechanisms, and protein-protein interactions.

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.

Schrodinger

a suite of tools for small molecule drug discovery. The Schrodinger Suite runs on Linux and Mac workstations, but due to its size, it is not included in our default installation.

Topaz

Topaz is a pipeline for particle detection in cryo-electron microscopy images using convolutional neural networks trained from positive and unlabeled examples.  Topaz includes methods for micrograph denoising using deep denoising models.

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.

PDB_REDO

refines any structural model you are working on, by optimising REFMAC refinement and by partial model rebuilding. The process is fully automated so you only need to provide an initial structure model and your reflection data.

FASTA

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

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.

NMRFAM-Sparky

is a new version of Sparky renamed because NMRFAM, through the generous allowance of Tom Ferrin and Tom Goddard of UCSF, has taken over the original Sparky for continuous development to support advances in the biomolecular NMR field.

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.

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.

Slingshot

an R package that provides functions for inferring continuous, branching lineage structures in low-dimensional data. Designed to model developmental trajectories in single-cell RNA sequencing data and serve as a component in an analysis pipeline after dimensionality reduction and clustering, Slingshot is flexible enough to handle arbitrarily many branching events and allows for the incorporation of prior knowledge through supervised graph construction.

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.

O

a model building application for X-ray crystallography.

xdsme

a collection of python scripts made to simplify the processing of crystal diffraction images with the XDS Program Package. Provided that the diffraction parameters are well recorded in the diffraction image headers, XDS data processing can be started with a simple command lines (see manual for details).

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.

Coot

(Crystallographic Object-Oriented Toolkit) supports model building and real space refinement. This application interfaces with refmac, Phenix, and several other applications. Coot was recognized as the best structural biology application in 2008 by SBGrid.

SPHIRE

(SParx for HIgh Resolution Electron microscopy) for cryoEM using statistical resampling to attain quality assessment and result reproducibility. Includes movie frame alignments (movie), CTF estimation of raw electron micrographs (cter), picking/stack creation (window), reproducible 2-D classification (isac), reproducible initial model generation (viper), automatic gold-standard 3-D refinement (meridien), local resolution estimation and filtering (localres), and up to the 3-D sorting of different conformational states based on the statistical 3-D variability of the data (sort3D).

iMosflm

a data processing application for macromolecular crystallography. iMosflm (Graphical User Interface) and Mosflm (data processing application) are distributed with this package.

CCP4mg

offers a quick and easy way to create beautiful publication quality images and movies and to superpose and analyze structures.

anvi'o

an open-source, community-driven analysis and visualization platform for ‘omics data. Its interactive interface facilitates the management of metagenomic contigs and associated data for automatic or human-guided identification of genome bins and their curation.