In this case study, we hear from Jack (Wei-Chieh Tsai), a doctoral student from History of Art and Geography who examines how cultural intermediaries, including artists, curators, and cultural organisations, have contributed to urban development. My PhD research examines the role of artistic interventions in transforming post-industrial Birmingham between 1986 and 2016. The project examines how cultural … Continue reading “Modelling Birmingham’s Cultural Ecology and Urban Oral History Using BlueBEAR”
Category: Case study
Binary classification of lung tissue immunofluorescence images by deep learning
In this case study we hear from Ellen Jenkins, a postdoctoral student from the Institute of Inflammation and Ageing. Ellen is looking into developing a deep learning model to automatically differentiate the tissue from the air space. There is an ongoing project in the respiratory research group (CMH, IIA) which utilises samples of human lung … Continue reading “Binary classification of lung tissue immunofluorescence images by deep learning”
March BEAR Newsletter
Birmingham Environment for Academic Research (BEAR) Newsletter You may have noticed that there was no February newsletter and there was a good reason for this! We were awaiting the release of the exciting news that the University has won funding from UKRI to provide a National Compute Resource (NCR). There are several new posts to support … Continue reading “March BEAR Newsletter”
Modelling accelerator-based neutron sources using the BlueBEAR cluster
In this case study we hear from Louis Butt, a doctoral researcher from Metallurgy and Materials, who has been using BlueBEAR to research accelerator-based neutron sources. I am a PhD student researching accelerator-based neutron sources in the School of Metallurgy and Materials. My work involves taking measurements with our source at the University’s MC40 Cyclotron … Continue reading “Modelling accelerator-based neutron sources using the BlueBEAR cluster”
The value of version control
The Research Software Group’s mission is rooted in the observation that most current research requires software, often written by researchers themselves, and that the application of a few core software engineering principles leads to more effective research. This is neatly captured by the Software Sustainability Institute‘s tag line: “better software, better research”. A core technology … Continue reading “The value of version control”
Investigating the Alternative Lengthening of Telomeres (ALT)
In this case study we hear from Ronan and Anubrata, both research staff in Cancer and Genomic Sciences, who have been using BlueBEAR to find therapeutic targets and biomarkers for the diagnosis of ALT-reliant cancers such as high-grade glioma. Our lab is investigating the Alternative Lengthening of Telomeres (ALT) process; a molecular mechanism used by … Continue reading “Investigating the Alternative Lengthening of Telomeres (ALT)”
Molecular simulations of small peptides as a means to interpreting mass spectra
In this case study we hear from Edwin, a PhD student in Biochemistry,who has been using BlueBEAR to evaluate the effectiveness of different Molecular Dynamics (MD) simulation protocols at assigning structural information to Ion Mobility data Ion Mobility Spectrometry (IMS), Traveling Wave Ion Mobility Spectrometry (TWIMS) and High-Field Asymmetric Wave Ion Mobility Spectrometry (FAIMS) are … Continue reading “Molecular simulations of small peptides as a means to interpreting mass spectra”
Energy Data Landscape – Challenges and Opportunities
Edward Barbour and Grant Wilson, Associate Professors in Chemical Engineering, explored detailed domestic heat pump demand data and became interested in their operational costs under different energy tariffs. They quickly discovered that tariff data was difficult to obtain and compare across different suppliers. With help from Mingxue (Jean) Du, a Research Software Engineer, they identified … Continue reading “Energy Data Landscape – Challenges and Opportunities”
SMLM Data Exploration with Nano-org and BlueBEAR
This case study highlights the ongoing collaboration between the Research Software Group, Professor Dylan Owen, and Dr Sandeep Shirgill in the development of Nano-org. Nano-org has recently been published in Nature Communications. Nano-org uses ultra-precise coordinate data to represent the nanoscale distributions of individual proteins within cells. The unique functionality provided by Nano-org supports a … Continue reading “SMLM Data Exploration with Nano-org and BlueBEAR”
Bayesian Modelling of Rising Decision Thresholds in DDMs using BlueBEAR
In this case study we hear from Sophie Wetz, a Masters student in Psychology, who has been using BlueBEAR to investigate whether a dynamic, rising boundary improved the fit of the full Drift Diffusion Model (DDM) to Random Dot Kinematogram (RDK) task data. I’m a Master’s student on the Computational Neuroscience stream in the School … Continue reading “Bayesian Modelling of Rising Decision Thresholds in DDMs using BlueBEAR”