Locally Developed Software and Resources

Good computer programs have always been vitally important to the work of the LMB.
Many of the groups here write, or contribute to scientific software, and wherever possible this work is released to the open source software community.

RELION

RELION (for REgularised LIkelihood OptimisatioN) is a stand-alone computer program for Maximum A Posteriori (MAP) refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM). It is developed in the group of Sjors Scheres. Briefly, the ill-posed problem of 3D-reconstruction is regularised by incorporating prior knowledge: the fact that macromolecular structures are smooth, i.e. they have limited power in the Fourier domain. In the corresponding Bayesian framework, many parameters of a statistical model are learned from the data, which leads to objective and high-quality results without the need for user expertise. The underlying theory of MAP refinement is given in Scheres (2012) JMB. A more detailed description of its implementation is given in Scheres (2012) JSB.

MRC Image Processing Software

The MRC image processing package is a collection of around 80 computer programs for processing 2D crystal and helical electron microscope images. The programs have been written by members of the LMB over the last 40 years in FORTRAN or C. The visualization and manipulation program Ximdisp is based on a home-written library of X-Windows subroutines. File reading/writing requirements for all the programs are provided by a subset of CCP4 subroutines in order to maintain compatibility with CCP4 MAPFORMAT.

The package is distributed freely to academic users worldwide and further information can be found here. Please contact Richard Henderson for more information.

Members of Greg Jefferis' group have contributed the following:

Plugins for the NIH’s image analysis software ImageJ, see http://rsbweb.nih.gov/ij/plugins/file-handler.html

Fiji, an image processing package based on NIH’s ImageJ – Contributions to this package made by Greg Jefferis’ group, targeting the tools towards 3D analysis of biological images.

CMTK, a software toolkit for computational morphometry of biomedical images, CMTK comprises a selection of command line tools and a general-purpose library for processing and I/O. Contributions to this package made by the group, include the development of a simple front end for CMTK.

NeuronAnatomy Toolbox, a suite of packages written in R for analysis of neuronal branching patterns, 3D density data describing neuronal projections and deformation based morphometry (shape analysis of groups of co-registered brains). Includes I/O functions to allow import (and in some cases export) for:

  • SWC, Neurolucida and Amiramesh neuronal tracing formats
  • Biorad PIC, Nrrd, Amiramesh 2D/3D image data

Crystallography Software

CCP4: the CCP4 package is a large collection of crystallographic software distributed by STFC. A number of parts of this system have been contributed by LMB scientists, notably in the data processing of diffraction images.

The main programs in producing a list of reflection intensities from diffraction images are:-

  • MOSFLM (Andrew Leslie, Harry Powell): indexes the diffraction pattern and produces integrated reflection intensities. An interactive graphical interface iMosflm makes this easy for the user.
  • POINTLESS (Phil Evans): determines the point group & space group symmetry from the list of intensities from Mosflm.
  • AIMLESS (Phil Evans): scales symmetry-related intensities together to correct for differences in their measurement methods, averages them and produces a large variety of statistics indicating the data quality.

Semi-Automated Routines for Functional Image Analysis (SARFIA)

SARFIA was developed by Mario Dorostkar for the analysis of functional fluorescence data, for instance recordings from cells labeled with fluorescent calcium indicators. However, it allows access to a variety of inbuilt and custom-written image processing functions.

Key features are image-based detection of structures of interest using the Laplace operator, determining the positions of units in a layered network, clustering algorithms to classify units with similar functional responses, and a database to store, exchange and analyse results across experiments. GUI access to a wide range of analysis functions for image stacks.

The custom image processing functions include thresholding based on the Laplace operator, filtering of 3D waves using principal component analysis (PCA), rotating functions, images/image stacks without interpolation, line scan analysis; Automated baseline detection, hierarchical clustering and bleach subtraction from fluorescence traces.

The package includes a manual describing the control panels and a help file that describes all functions in detail.

SARFIA is available for Igor Pro on the Igor Exchange. The core thresholding and data extraction functions are also available for Matlab on Matlab Central.

Worm Tracker

Worm Tracker 2.0 suite was written by Ev Yemini, Tadas Jucikas, & Chris Cronin to perform high-throughput analysis of individual worm behaviour. We describe inexpensive hardware & plans to build a single worm tracker, and provide two software programs. The first program is the tracking software, which automatically follows a single worm, creating videos of its behaviour. The second program provides the analysis, automatically analyzing videos and quantifying the worms’ behaviour & morphology.

TiltStats

An open-source software package for robust evaluation of biological electron microscopy data and validation of cryo-EM structures using tilt-pairs. The algorithms and code were developed by Chris Russo and Lori Passmore. The software is available free to all here.

cryoEF

An open-source software package for analysis of the orientation distribution of cryo-electron microscopy data, developed by Chris Russo and Katerina Naydenova.

The orientation distribution of a single-particle electron cryo-microscopy specimen can limit the resolution of the reconstructed density map if the particles are not randomly oriented on the support surface. This method describes the quality of an orientation distribution in terms of providing uniform resolution in all directions, by a single number – the efficiency. The cryoEF program will assist you in determining to what extent this affects the resolution of your 3D reconstruction.

More information and the software package are available here.

Computational Structural Biology Group Software

Garib Murshudov’s group’s research is centred on the development of efficient mathematical, statistical, computational algorithms for macromolecular X-ray crystallography (MX) and electron cryo-microscopy (cryo-EM) structure analysis. Software developed in the group includes the following:

REFMAC5 (Garib Murshudov) – REFinement of MACromolecular Structures. Use the Maximum Likelihood method and some elements of Bayesian Statistics to perform full model refinement and map calculation. Originally designed for use with data from MX, REFMAC5 has been adapted and extended to support data from other sources including cryo-EM.

Coot (Paul Emsley) – Crystallographic Object-Oriented Toolkit. For macromolecular model building, model completion and validation, particularly suitable for protein modelling using MX and cryo-EM data. Coot displays maps and models and allows model manipulations such as idealization, real space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers, Ramachandran plots, skeletonization, non-crystallographic symmetry and more.

AceDRG (Fei Long) – stereo-chemical description generator for monomers/ligands. Encapsulates information about local chemical and topological environments derived from a small molecule database (the Crystallography Open Database), and uses this information to derive ideal bond lengths, angles, etc. for an unknown monomer/ligand. AceDRG can also generate link information to encapsulate a covalent bond between two monomers.

ProSMART (Rob Nicholls) – PROcrustes Structural Matching Alignment and Restraints Tool. Designed for the conformation-independent comparison of macromolecular structural models, and the generation of external restraints for use during macromolecular refinement at low resolution. Restraints to reference structures, hydrogen bonding patterns, and generic self-restraints may be generated. Supports models corresponding to protein and nucleic acids, from MX and cryo-EM.

LibG (Fei Long) – Generates restraints to stabilise refinement of DNA/RNA models during refinement. Restraints are generated for base-pairs, stacking planes, sugar puckers, and other torsion angles.

LORESTR (Oleg Kovalevskiy) – LOw RESolution STRucture refinement pipeline. Executes multiple model refinement instances using different parameters in order to find the best protocol. Generates restraints using ProSMART and LibG, and refines models using REFMAC5. The pipeline performs auto-detection of twinning and selects the optimal scaling method and solvent parameters. Can either use user-supplied homologous structures, or run an automated BLAST search and download homologues from the PDB

ProSHADE (Michal Tykac) – PROtein SHApe DEscription and symmetry detection. Library and associated tool providing functionalities for computing shape-wise structural distances between pairs of molecules, detecting symmetry over the centre of mass of a single structure, map re-sizing, as well as matching density maps and coordinate models.

BALBES (Fei Long) – automatic molecular replacement pipeline. A system for solving protein structures using x-ray crystallographic data, which aims to integrate all components necessary for finding a solution structure by molecular replacement. It comprises a database, scientific programs and a python pipeline. The system is automated so that it needs no user intervention when running a complicated combination of jobs such as model searching, molecular replacement and refinement.

More information about this software can be found on the Computational Structural Biology Group website.

This software is distributed by CCP4 and/or CCP-EM, and can be executed as standalone programs or via a number of graphical interfaces including Coot, CCP4i, CCP4i2, CCP4 Cloud, CCP-EM and CCP4mg.

Computational Genomics Group

Julian Gough’s group has produced a range of software and resources that span the scales of biology from DNA, proteins, interactions, networks, and cells, up to whole organism phenotypes. These include the following:

SCOP – Structural Classification of Proteins. Nearly all proteins have structural similarities with other proteins and, in some of these cases, share a common evolutionary origin. The SCOP database, created by manual inspection and abetted by a battery of automated methods, aims to provide a detailed and comprehensive description of the structural and evolutionary relationships between all proteins whose structure is known.

SUPERFAMILY  – A database of structural and functional annotation for all proteins and genomes.

Mogrify – A directory of defined factors for direct cell reprogramming. The Mogrify resource predicts how to trans-differentiate from any human cell-type to any other human cell-type by perturbing the transcriptional network. Mogrify includes all cell-types from the FANTOM5 project and uses a network-based algorithm designed to find transcription factors that impart the most influence on changes in cellular state.

The full list of software and resources managed by the Computational Genomics Group can be found on their group page.