Merge pull request #819 from RSE-Sheffield/ns-rse/blog-funded-proposals

_posts/2024-09-24-funded-proposals.md

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+---
+layout: post
+title: "RSE Supported Projects"
+author: Neil Shephard
+slug: 2024-09-24-funded-proposals
+date: 2024-09-24 12:00:00 UTC
+tags: rse "call for proposals" support
+category:
+link:
+description:
+social_image:
+type: text
+excerpt_separator: <!--more-->
+---
+
+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][originalproposal] team. The successful applicants would receive dedicated support from an RSE
+Team member at 50% FTE for a period of six months.
+
+<!--more-->
+
+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.
+
+![Distribution of applications by faculty](/assets/images/2024-09-24-funded-proposals-faculty.png)
+
+In the end the RSE team was able to fund support for three proposals and team members [Dr Robert Chisholm][rob] and [Neil
+Shephard][neil] 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][fair4rs]
+
+## SLAMSeq
+
+The [SubLab][sudlab], which is lead by [Dr Ian Subery][ian], 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][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
+
+[HYBIRD][hybrid] is software developed by [Dr Alessandro Leonardi][alessandro] 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][rob], 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
+
+[Polychron][polychron] is prototype software developed by [Dr Bryony Moody][bryony] 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.
+
+## Summary
+
+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 [[email protected]](mailto:[email protected]).
+
+[alessandro]: https://www.sheffield.ac.uk/mac/people/civil-academic-staff/alessandro-leonardi
+[bryony]: https://www.sheffield.ac.uk/mps/people/all-academic-staff/bryony-moody
+[fair4rs]: https://rse.shef.ac.uk/training/fair4rs/
+[hybrid]: https://github.com/gnomeCreative/HYBIRD
+[ian]: https://www.sheffield.ac.uk/biosciences/academic-staff/people/ian-sudbery
+[neil]: https://rse.shef.ac.uk/contact/neil-shephard/
+[originalproposal]: originalproposal
+[polychron]: https://github.com/bryonymoody/PolyChron
+[rob]: https://rse.shef.ac.uk/contact/robert-chisholm/
+[sudlab]: https://www.sudlab.co.uk/team-1/ian-sudbery