Open source software

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

2020-

Title	Citation
Evaluation of an open-source pipeline to create patient-specific left atrial models: A reproducibility study	Solís-Lemus, J.A., Baptiste, T., Barrows, R., Sillett, C., Gharaviri, A., Raffaele, G., Razeghi, O., Strocchi, M., Sim, I., Kotadia, I., Bodagh, N., O’Hare, D., O’Neill, M., Williams, S.E., Roney, C. and Niederer, S. (2023) ‘Evaluation of an open-source pipeline to create patient-specific left atrial models: A reproducibility study’, Computers in Biology and Medicine, 162, p. 107009. Available at: https://doi.org/10.1016/j.compbiomed.2023.107009.
Visiomode: An open-source platform for building rodent touchscreen-based behavioral assays	Eleftheriou, C., Clarke, T., Poon, V., Zechner, M. and Duguid, I. (2023) ‘Visiomode: An open-source platform for building rodent touchscreen-based behavioral assays’, Journal of Neuroscience Methods, 386, p. 109779. Available at: https://doi.org/10.1016/j.jneumeth.2022.109779.
Assessment of perivascular space filtering methods using a three-dimensional computational model	Bernal, J., Valdés-Hernández, M.D.C., Escudero, J., Duarte, R., Ballerini, L., Bastin, M.E., Deary, I.J., Thrippleton, M.J., Touyz, R.M. and Wardlaw, J.M. (2022) ‘Assessment of perivascular space filtering methods using a three-dimensional computational model’, Magnetic Resonance Imaging, 93, pp. 33–51. Available at: https://doi.org/10.1016/j.mri.2022.07.016.
OpenSAFELY NHS Service Restoration Observatory 1: primary care clinical activity in England during the first wave of COVID-19	Curtis, H.J., MacKenna, B., Croker, R., Inglesby, P., Walker, A.J., Morley, J., Mehrkar, A., Morton, C.E., Bacon, S., Hickman, G., Bates, C., Evans, D., Ward, T., Cockburn, J., Davy, S., Bhaskaran, K., Schultze, A., Rentsch, C.T., Williamson, E.J., Hulme, W.J., McDonald, H.I., Tomlinson, L., Mathur, R., Drysdale, H., Eggo, R.M., Wing, K., Wong, A.Y., Forbes, H., Parry, J., Hester, F., Harper, S., Evans, S.J., Douglas, I.J., Smeeth, L., Goldacre, B., and (The OpenSAFELY Collaborative) (2022) ‘OpenSAFELY NHS Service Restoration Observatory 1: primary care clinical activity in England during the first wave of COVID-19’, British Journal of General Practice, 72(714), pp. e63–e74. Available at: https://doi.org/10.3399/BJGP.2021.0380.
Development of a semi-automated method for tumour budding assessment in colorectal cancer and comparison with manual methods	Fisher, N.C., Loughrey, M.B., Coleman, H.G., Gelbard, M.D., Bankhead, P. and Dunne, P.D. (2022) ‘Development of a semi‐automated method for tumour budding assessment in colorectal cancer and comparison with manual methods’, Histopathology, 80(3), pp. 485–500. Available at: https://doi.org/10.1111/his.14574.
Developing digital contact tracing tailored to haulage in East Africa to support COVID-19 surveillance: a protocol	Muwonge, A., Mpyangu, C.M., Nsangi, A., Mugerwa, I., Bronsvoort, B.M. deC, Porphyre, T., Ssebaggala, E.R., Kiayias, A., Mwaka, E.S. and Joloba, M. (2022) ‘Developing digital contact tracing tailored to haulage in East Africa to support COVID-19 surveillance: a protocol’, BMJ Open, 12(9), p. e058457. Available at: https://doi.org/10.1136/bmjopen-2021-058457.
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	Kaufmann, J., Biscio, C.A.N., Bankhead, P., Zimmer, S., Schmidberger, H., Rubak, E. and Mayer, A. (2021) ‘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’, Cancers, 13(8), p. 1924. Available at: https://doi.org/10.3390/cancers13081924.
Developing open-source software for bioimage analysis: opportunities and challenges	Levet, F., Carpenter, A.E., Eliceiri, K.W., Kreshuk, A., Bankhead, P. and Haase, R. (2021) ‘Developing open-source software for bioimage analysis: opportunities and challenges’, F1000Research, 10, p. 302. Available at: https://doi.org/10.12688/f1000research.52531.1.

2010-2019

Title	Citation
MAGpy: a reproducible pipeline for the downstream analysis of metagenome-assembled genomes (MAGs)	Stewart, R.D., Auffret, M.D., Snelling, T.J., Roehe, R. and Watson, M. (2019) ‘MAGpy: a reproducible pipeline for the downstream analysis of metagenome-assembled genomes (MAGs)’, Bioinformatics. Edited by I. Birol, 35(12), pp. 2150–2152. Available at: https://doi.org/10.1093/bioinformatics/bty905.
Integrated tumor identification and automated scoring minimizes pathologist involvement and provides new insights to key biomarkers in breast cancer	Bankhead, P., Fernández, J.A., McArt, D.G., Boyle, D.P., Li, G., Loughrey, M.B., Irwin, G.W., Harkin, D.P., James, J.A., McQuaid, S., Salto-Tellez, M. and Hamilton, P.W. (2018) ‘Integrated tumor identification and automated scoring minimizes pathologist involvement and provides new insights to key biomarkers in breast cancer’, Laboratory Investigation, 98(1), pp. 15–26. Available at: https://doi.org/10.1038/labinvest.2017.131.
PolNet: A Tool to Quantify Network-Level Cell Polarity and Blood Flow in Vascular Remodeling	Bernabeu, M.O., Jones, M.L., Nash, R.W., Pezzarossa, A., Coveney, P.V., Gerhardt, H. and Franco, C.A. (2018) ‘PolNet: a tool to quantify network-level cell polarity and blood flow in vascular remodeling’, Biophysical Journal, 114(9), pp. 2052–2058. Available at: https://doi.org/10.1016/j.bpj.2018.03.032.
FISSA: A neuropil decontamination toolbox for calcium imaging signals	Keemink, S.W., Lowe, S.C., Pakan, J.M.P., Dylda, E., Van Rossum, M.C.W. and Rochefort, N.L. (2018) ‘FISSA: A neuropil decontamination toolbox for calcium imaging signals’, Scientific Reports, 8(1), p. 3493. Available at: https://doi.org/10.1038/s41598-018-21640-2.
Validation of the systematic scoring of immunohistochemically stained tumour tissue microarrays using QuPath digital image analysis	Loughrey, M.B., Bankhead, P., Coleman, H.G., Hagan, R.S., Craig, S., McCorry, A.M.B., Gray, R.T., McQuaid, S., Dunne, P.D., Hamilton, P.W., James, J.A. and Salto-Tellez, M. (2018) ‘Validation of the systematic scoring of immunohistochemically stained tumour tissue microarrays using QuPath digital image analysis’, Histopathology, 73(2), pp. 327–338. Available at: https://doi.org/10.1111/his.13516.
QuPath: Open source software for digital pathology image analysis	Bankhead, P., Loughrey, M.B., Fernández, J.A., Dombrowski, Y., McArt, D.G., Dunne, P.D., McQuaid, S., Gray, R.T., Murray, L.J., Coleman, H.G., James, J.A., Salto-Tellez, M. and Hamilton, P.W. (2017) ‘QuPath: Open source software for digital pathology image analysis’, Scientific Reports, 7(1), p. 16878. Available at: https://doi.org/10.1038/s41598-017-17204-5.
Automated detection and measurement of isolated retinal arterioles by a combination of edge enhancement and cost analysis	Fernández, J.A., Bankhead, P., Zhou, H., McGeown, J.G. and Curtis, T.M. (2014) ‘Automated detection and measurement of isolated retinal arterioles by a combination of edge enhancement and cost analysis’, PLoS ONE. Edited by J. Chen, 9(3), p. e91791. Available at: https://doi.org/10.1371/journal.pone.0091791.
cudaMap: a GPU accelerated program for gene expression connectivity mapping	McArt, D.G., Bankhead, P., Dunne, P.D., Salto-Tellez, M., Hamilton, P. and Zhang, S.-D. (2013) ‘cudaMap: a GPU accelerated program for gene expression connectivity mapping’, BMC Bioinformatics, 14(1), p. 305. Available at: https://doi.org/10.1186/1471-2105-14-305.
Chaste: An Open Source C++ Library for Computational Physiology and Biology	Mirams, G.R., Arthurs, C.J., Bernabeu, M.O., Bordas, R., Cooper, J., Corrias, A., Davit, Y., Dunn, S.-J., Fletcher, A.G., Harvey, D.G., Marsh, M.E., Osborne, J.M., Pathmanathan, P., Pitt-Francis, J., Southern, J., Zemzemi, N. and Gavaghan, D.J. (2013) ‘Chaste: an open source c++ library for computational physiology and biology’, PLoS Computational Biology. Edited by A. Prlic, 9(3), p. e1002970. Available at: https://doi.org/10.1371/journal.pcbi.1002970.
Meta4: a web application for sharing and annotating metagenomic gene predictions using web services	Richardson, E.J., Escalettes, F., Fotheringham, I., Wallace, R.J. and Watson, M. (2013) ‘Meta4: a web application for sharing and annotating metagenomic gene predictions using web services’, Frontiers in Genetics, 4. Available at: https://doi.org/10.3389/fgene.2013.00168.
viRome: an R package for the visualization and analysis of viral small RNA sequence datasets	Watson, M., Schnettler, E. and Kohl, A. (2013) ‘viRome: an R package for the visualization and analysis of viral small RNA sequence datasets’, Bioinformatics, 29(15), pp. 1902–1903. Available at: https://doi.org/10.1093/bioinformatics/btt297.

2000-2009

Title	Citation
Chaste: incorporating a novel multi-scale spatial and temporal algorithm into a large-scale open source library	Bernabeu, M.O., Bordas, R., Pathmanathan, P., Pitt-Francis, J., Cooper, J., Garny, A., Gavaghan, D.J., Rodriguez, B., Southern, J.A. and Whiteley, J.P. (2009) ‘Chaste : incorporating a novel multi-scale spatial and temporal algorithm into a large-scale open source library’, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 367(1895), pp. 1907–1930. Available at: https://doi.org/10.1098/rsta.2008.0309.
Chaste: using agile programming techniques to develop computational biology software	Pitt-Francis, J., Bernabeu, M.O., Cooper, J., Garny, A., Momtahan, L., Osborne, J., Pathmanathan, P., Rodriguez, B., Whiteley, J.P. and Gavaghan, D.J. (2008) ‘Chaste: using agile programming techniques to develop computational biology software’, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 366(1878), pp. 3111–3136. Available at: https://doi.org/10.1098/rsta.2008.0096.

Title

Citation

Chaste: incorporating a novel multi-scale spatial and temporal algorithm into a large-scale open source library

Bernabeu, M.O., Bordas, R., Pathmanathan, P., Pitt-Francis, J., Cooper, J., Garny, A., Gavaghan, D.J., Rodriguez, B., Southern, J.A. and Whiteley, J.P. (2009) ‘Chaste : incorporating a novel multi-scale spatial and temporal algorithm into a large-scale open source library’, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 367(1895), pp. 1907–1930. Available at: https://doi.org/10.1098/rsta.2008.0309.

Chaste: using agile programming techniques to develop computational biology software

Pitt-Francis, J., Bernabeu, M.O., Cooper, J., Garny, A., Momtahan, L., Osborne, J., Pathmanathan, P., Rodriguez, B., Whiteley, J.P. and Gavaghan, D.J. (2008) ‘Chaste: using agile programming techniques to develop computational biology software’, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 366(1878), pp. 3111–3136. Available at: https://doi.org/10.1098/rsta.2008.0096.

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This article was published on 10 Aug, 2023