Bioinformatics

Using prototyping to select software for a research software project

Author: Mike Jackson
Posted: 1 Mar 2021 | 14:03

A selection of macaronsChoosing the right software for use in a research software project can be challenging. How do we know which software is both fit for purpose and provides a sound basis for our project for the foreseeable future? And, how do we make such a choice given that the time and effort to explore what could be myriad alternatives may be limited?

This was a challenge we faced in the RiboViz project, a multi-disciplinary team of biologists, bioinformaticians and research software engineers based at EPCC and The Wallace Lab at University of Edinburgh, The Shah Lab at Rutgers University, and The Lareau Lab at University of California, Berkeley. RiboViz is an open source package to help us develop our understanding of protein synthesis via analysis of ribosome profiling data. At the heart of RiboViz is an analysis workflow, implemented in a Python script. To conform to best practices for scientific computing, which recommend the use of build tools to automate workflows and to reuse code instead of rewriting it, we sought to reimplement this workflow within a bioinformatics workflow management system.

Understanding protein synthesis via analysis of ribosome profiling data

Author: Mike Jackson
Posted: 8 Aug 2019 | 10:51

The molecular structure of a yeast ribosome, composed of 79 proteins

A multi-disciplinary team of biologists, bioinformaticians and research software engineers based at EPCC and The Wallace Lab at University of Edinburgh, The Shah Lab at Rutgers University, and The Lareau Lab at University of California, Berkeley, will enhance and extend a software suite called RiboViz to extract biological insight from "ribosome profiling" data and drive forward understanding of protein synthesis.

Rocket surgery for PickCells

Author: Mike Jackson
Posted: 14 Dec 2018 | 17:33

PickCells usability evaluation PickCells is image analysis software developed by the Centre for Regenerative Medicine (CRM) at The University of Edinburgh. PickCells allows biologists to explore multidimensional biological images of stem cell niches, organoids, and embryos. In late October, with the assistance of six researchers, we evaluated the usability of PickCells to help guide its future development.

To run our usability evaluation, we followed Steve Krug's highly-recommended and very readable book "Rocket Surgery Made Easy: The Do-It-Yourself Guide to Finding and Fixing Usability Problems". This book describes a practical way to carry out usability evaluations with minimal overhead.

PickCells and exploratory image analysis in cell biology

Author: Mike Jackson
Posted: 11 Sep 2018 | 16:09

Cells being analysed within PickCells

PickCells is an image analysis platform developed by the Centre for Regenerative Medicine (CRM) at The University of Edinburgh. It combines generic image analysis algorithms, visualisation modules and data mining functionality within a stand-alone Java application.

Bootstrapping with R and SPRINT

Author: Terry Sloan
Posted: 24 Feb 2014 | 12:10

EPCC and the Division of Pathway Medicine at the University of Edinburgh have made public the report from their recent study into the performance of bootstrapping within their SPRINT R software package.

R users can calculate Hamming distance faster

Author: Terry Sloan
Posted: 10 Jan 2014 | 14:09
 
EPCC and the Division of Pathway Medicine at the University of Edinburgh have released version 1.0.5 of the SPRINT R software package. This includes a new faster parallel implementation of the Hamming distance function.

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