Earlier this year the RSE team in Sheffield put a call out for proposals for researchers in the University of Sheffield to collaborate with the RSE team. The successful applicants would receive dedicated support from an RSE Team member at 50% FTE for a period of six months.
A total of 26 applications were received from across the faculties of the University and the review panel which consisted of nine RSEs had robust discussions about which to fund as the quality and proposed work was of a high standard.
In the end the RSE team was able to fund support for three proposals and team members Dr Robert Chisholm and Neil Shephard are about to start work on two of the projects with the third postponed, with agreement, until a new RSE who has been recruited starts later in the year.
All work undertaken will be done with a view to adhering to the FAIR for Research Software Principles
The SubLab, which is lead by Dr Ian Subery, have developed software to analyse the output of SLAMSeq experiments which performs sequence alignment of variably spliced RNA sequences to assess degradation rates. Despite wide adoption of the technique the current software is limited to only being run on a per-gene basis rather than per isoform basis and statistical comparison of differences in decay rates are limited. The Sudlab have addressed this deficiency by developing an analysis pipeline with pre-processing performed in Python and statistical analysis undertaken in R.
RSE support will be used to refactor the code into formal packages with a modular code structure and formal tests which facilitate long-term maintenance and make extension easier and will make it straight-forward for users to install. Translation of code into a single language will be considered as this would lower the barrier to uptake by external users and documentation will be developed and deployed covering the API and the practical side of using the software.
HYBIRD is software developed by Dr Alessandro Leonardi and his research group with the Geo-Technical Engineering group and is written using C++. It combines the Discrete Element Method (DEM) and the Lattice Boltzmann Method (LBM) to simulate complex particle-fluid interactions. These fluid-structure interactions have allowed the investigation of the formation of granular fronts in free-surface flows, enhancing understanding of particle-laden flow dynamics which have been successfully applied to key areas in environmental and geo-technical engineering.
Work will be undertaken by Dr Robert Chisholm, a performance optimisation and GPU parallelisation specialist from our team, to modernise HYBIRD’s build system, address the limiting factors of its performance and enable it to take advantage of GPU parallelisation. The broad objectives of this project are to reduce barriers to entry for new users and to increase the performance to enable faster and larger research experiments.
Polychron is prototype software developed by Dr Bryony Moody of the School of Mathematical and Physical Sciences that facilitates the analysis and archiving of archaeological dating evidence. Written in Python the prototype consists of a statistical algorithm (backend) and a GUI frontend to facilitate usage.
Work will be undertaken by a new RSE who will be starting later in the year. The exact remit of the work to be undertaken has not yet been finalised but the code base will benefit from restructuring into a Python package with refactoring of the GUI to make it easier to maintain and extend and improved error detection.
As the number of applications demonstrated, the demand for RSE support across all faculties within the University is high and it was interesting to find out about the broad range of software projects being undertaken by different research groups. We wish we could have supported more of these teams.
If you are considering putting in a funding application that involves writing/developing/maintaining software having dedicated RSE support can strengthen your proposal. If you would like to speak to the RSE team about support please don’t hesitate to get in touch by emailing rse@sheffield.ac.uk.
For queries relating to collaborating with the RSE team on projects: rse@sheffield.ac.uk
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