Mura Lab

at the University of Virginia

The following software packages, libraries, utilities, patches, benchmarks, etc. have been developed in our lab or in collaboration with others, and are freely available:

Software Description

Contemporary biology has largely become computational biology, whether it involves applying physical principles to simulate the motion of each atom in a piece of DNA or using machine learning algorithms to integrate 'omics' data across whole cells. Programming for Bioscientists (P4B) is an educational project that introduces computer programming to newcomers from the biosciences. As with human languages, fluency in a computer language is developed actively, not passively. Developed by Charles McAnany in our lab, P4B is a self-contained pedagogical resource that is structured as a hybrid primer/tutorial of roughly 20 Chapters of Python code. The Chapters introduce any biologist—from high-school student to established scientist—to basic computing principles (control-flow, recursion, regular expressions, etc.), as well as the practicalities of programming and software design. Python is the language of choice because it now pervades the biosciences, from sequence-based bioinformatics and molecular evolution to phylogenomics, systems biology, structural biology, and beyond. To introduce both coding (in general) and Python (in particular), concrete examples and exercises are used to guide the student via a few thousand lines of heavily-annotated, freely distributed source code at http://p4b.muralab.org.

Project-related pages

Main project site → http://p4b.muralab.org

Software Description

PaPy is a framework to construct and execute bioinformatic pipelines (flow-charts) of arbitrary tasks in parallel, either locally, using multi-processing or multi-threading, or remotely, using remote procedure calls (as implemented in the Python library RPyC). The goal is to enable users to efficiently and reproducibly create clean, modular workflows for the execution of ad hoc computing grids consisting of local workstations, remote desktops/servers, clusters, or any aribitrary mixture of the above compute resources.

Project-related pages

Main project site → http://muralab.org/PaPy
Downloads → http://muralab.org/PaPy
Develop → Mercurial repos (bleeding-edge; intranet only)

ZenCogent — Macromolecular 3D structural analysis in PyCogent

Software Description

This software has been integrated into the PyCogent suite. See the code-base and our article in the Journal of Applied Crystallography for a description of the development, implementation, and feature-set of this code.

Project-related pages

Main project site → http://pycogent.org
Download locally → Download website
Latest → Mercurial repos

PBCTools — Unwrapping MD trajectories computed under periodic boundary conditions on oblique lattices

Software Description

PBCTools is a utility, developed in collaboration with Olaf Lenz, Jerome Henin and Jan Saam, for unwrapping MD trajectories computed under periodic boundary conditions (PBCs). Particular care was taken to ensure proper geometric handling for trajectories on oblique lattices (e.g., for truncated octahedral PBCs). The code is provided both as a standalone utility and as an integrated plugin in the VMD software package. See the User's Guide for further information.

Project-related pages

Main project site (maintained) → http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools
Locally → user-guide/whitepaper