Learn out about researchers' work on open source software. Open research software, or open-source research software, refers to the use and development of software for analysis, simulation, visualisation, etc. where the full source code is available. (...) open-source software must be distributed in source and/or compiled form (with the source code available in the latter case), and must be shared under a licence that allows modification, derivation and redistribution. FOSTER Open Science Training Handbook Discover CMVM researchers' publications on the topic of open source software. Names in bold denote CMVM authors. 2021- 2025Aziz Sheikh, co-author with Samuel Cox and others: Conversion of Sensitive Data to the Observational Medical Outcomes Partnership Common Data Model: Protocol for the Development and Use of Carrot - protocol in JMIR Research ProtocolsKathy Harrison, co-author with Chuang Gao and others: A pipeline for harmonising NHS Scotland laboratory data to enable national-level analyses - article in Journal of Biomedical InformaticsThemis N. Efthimiou & Catherine J. Crompton: duet: An R package for dyadic analysis of motion data generated by OpenPose - article in Behavior Research Methods2024Jamie Burke, Samuel Gibbon, Justin Engelmann, Adam Threlfall, Ylenia Giarratano, Charlene Hamid, Stuart King, Ian J. C. MacCormick & Thomas J. MacGillivray: SLOctolyzer: Fully Automatic Analysis Toolkit for Segmentation and Feature Extracting in Scanning Laser Ophthalmoscopy Images - article in Translational Vision Science & TechnologyCharlene Hamid, Megan Reid-Schachter, Neeraj Dhaun, Tom MacGillivray, Miguel O. Bernabeu and Ian J. C. MacCormick, co-authors with Justin Engelmann and others: Choroidalyzer: An Open-Source, End-to-End Pipeline for Choroidal Analysis in Optical Coherence Tomography - article in Investigative Ophthalmology & Visual ScienceAaron Yli-Hallila, Peter Bankhead, Mark J. Arends, Petri Lehenkari and Sanna Palosaari: QuPath Edu and OpenMicroanatomy: Open-source virtual microscopy tools for medical education - article in Journal of AnatomyAlan O’Callaghan, Fiona Inglis & Peter Bankhead, co-authors with Jakub R. Kaczmarzyk and others: Open and reusable deep learning for pathology with WSInfer and QuPath – brief communication in NPJ Precision OncologySteven E. Williams, co-author with Zhouyang Xu and others: CardioXplorer: An Open-Source Modular Teleoperative Robotic Catheter Ablation System - article in Robotics2023Lucy Kershaw and Michael J Thrippleton, co-authors with Petra J van Houdt and others: Contrast-agent-based perfusion MRI code repository and testing framework: ISMRM Open Science Initiative for Perfusion Imaging (OSIPI) – article in Magnetic Resonance in MedicineMichael J Thrippleton, co-author with Ben R. Dickie and others: A community-endorsed open-source lexicon for contrast agent–based perfusion MRI: A consensus guidelines report from the ISMRM Open Science Initiative for Perfusion Imaging (OSIPI) – article in Magnetic Resonance in MedicineSteven Williams, co-author with José Alonso Solís-Lemus and others: Evaluation of an open-source pipeline to create patient-specific left atrial models: A reproducibility study – article in Computers in Biology and MedicineConstantinos Eleftheriou, Thomas Clarke, V. Poon, Marie Zechner and Ian Duguid: Visiomode: An open-source platform for building rodent touchscreen-based behavioral assays – article in Journal of Neuroscience Methods2022Maria Valdés-Hermández, Roberto Duarte, Mark Bastin, Ian Deary, Michael Thrippleton and Joanna Wardlaw, co-authors with Jose Bernal and others: Assessment of perivascular space filtering methods using a three-dimensional computational model – article in Magnetic Resonance ImagingKevin Wing, co-author with Helen J. Curtis and others: OpenSAFELY NHS Service Restoration Observatory 1: primary care clinical activity in England during the first wave of COVID-19 – article in British Journal of General PracticePeter Bankhead, co-author with Natalie C. Fisher and others: Development of a semi-automated method for tumour budding assessment in colorectal cancer and comparison with manual methods – article in HistopathologyAdrian Muwonge and others: Developing digital contact tracing tailored to haulage in East Africa to support COVID-19 surveillance: a protocol – article in BMJ Open2021Peter Bankhead, co-author with Justus Kaufmann and others: Using the R Package Spatstat to Assess Inhibitory Effects of Microregional Hypoxia on the Infiltration of Cancers of the Head and Neck Region by Cytotoxic T Lymphocytes – article in CancersPeter Bankhead, co-author with Florian Levet and others: Developing open-source software for bioimage analysis: opportunities and challenges – paper in F1000Research 2010-2020 2019Mick Watson, co-author with Robert Stewart and others: MAGpy: a reproducible pipeline for the downstream analysis of metagenome-assembled genomes (MAGs) – article in Bioinformatics2018Peter Bankhead and others: Integrated tumor identification and automated scoring minimizes pathologist involvement and provides new insights to key biomarkers in breast cancer – article in Laboratory InvestigationMiguel Bernabeu and others: PolNet: A Tool to Quantify Network-Level Cell Polarity and Blood Flow in Vascular Remodeling – article in Biophysical JournalNathalie Rochefort, co-author with Sander W. Keemink and others: FISSA: A neuropil decontamination toolbox for calcium imaging signals – article in Scientific Reports2013Emily J. Richardson, Franck Escalettes, Ian Fotheringham, Robert J. Wallace and Mick Watson: Meta4: a web application for sharing and annotating metagenomic gene predictions using web services – article in Frontiers in GeneticsMick Watson, Esther Schnettler and Alain Kohl: viRome: an R package for the visualization and analysis of viral small RNA sequence datasets – article in Bioinformatics If you are a CMVM-affiliated author and would like your publication on open-source software featured on this page, please get in touch at CMVMopenaccess@ed.ac.uk. This article was published on 2024-09-09
