Conference proceedings, journals and other articles on the work of the Institute or projects we have collaborated with.
Papers with the Institute as an author or co-author
Sufi SA, Jay C. (2018) Raising the status of software in research: A survey-based evaluation of the Software Sustainability Institute Fellowship Programme. PeerJ Preprints 6:e26849v1 https://doi.org/10.7287/peerj.preprints.26849v1
Venters, Colin C.; Capilla, R.; Betz, S.; Penzenstadler, B.; Crick, T.; Crouch, S.; Nakagawa, E.Y.; Becker, C.; Carillo, C. (2017): "Software sustainability: Research and practice from a software architecture viewpoint", Journal of Systems and Software, Vol. 138, pp.174-188, December 2017. DOI: 10.1016/j.jss.2017.12.026.
Jimenez, R.C.; Kuzak, M.; Alhamdoosh, M.; Barker, M.; Batut, B.; Borg, M.; Capella-Gutierrez, S.; Chue Hong, N.; Cook, M.; Corpas, M.; Flannery, M.; Garcia, L.; Gelpí, J.L.; Gladman, S.; Goble, C.; Ferreiro, M.G.; Gonzalez-Beltran, A.; Griffin, P.C.; Grüning, B.; Hagberg, J.; Holub, P.; Hooft, R.; Ison, J.; Katz, D.S.; Leskošek, B.; Gómez, F.L.; Oliveira, L.J.; Mellor, D.; Mosbergen, R.; Mulder, N.; Perez-Riverol, Y.; Pergl, R.; Pichler, H.; Pope, B.; Sanz, F.; Schneider, M.V.; Stodden, V.; Suchecki, R.; Vařeková, R.S.; Talvik, H.; Todorov, I.; Treloar, A.; Tyagi, S.; Gompel, M.v.; Vaughan, D.; Via, A.; Wang, X.; Watson-Haigh, N.S.; Crouch, S. (2017): "Four simple recommendations to encourage best practices in research software", F1000Research, 6, ELIXIR-876, June 2017. DOI: 10.12688/f1000research.11407.1.
Lane, Simon I.R.; Crouch, Stephen; Jones, Keith T. (2017): "Imaging Chromosome Separation in Mouse Oocytes by Responsive 3D Confocal Timelapse Microscopy", Methods in Molecular Biology, Vol. 1471, pp.245-254, March 2017. DOI: 10.1007/978-1-4939-6340-9_13.
Pawlik A, van Gelder CWG, Nenadic A et al. "Developing a strategy for computational lab skills training through Software and Data Carpentry: Experiences from the ELIXIR Pilot action" [version 1; referees: 3 approved]. F1000Research 2017, 6:1040, DOI: 10.12688/f1000research.11718.1.
Yachdav, Guy; Goldberg, Tatyana; Wilzbach, Sebastian; Dao, David; Shih, Iris; Choudhary, Saket; Crouch, Steve; Franz, Max; García, Alexander; García, Leyla J; Grüning, Björn A; Inupakutika, Devasena; Sillitoe, Ian; Thanki, Anil S; Vieira, Bruno; Villaveces, José M; Schneider, Maria V; Lewis, Suzanna; Pettifer, Steve; Rost, Burkhard; Corpas, Manuel (2015): "Cutting edge: Anatomy of BioJS, an open source community for the life sciences", eLife;4;e07009, July 2015. DOI: 10.7554/eLife.07009.001.
Pawlik, Aleksandra; Petrie, Marian; Segal, Judith; Sharp, Helen (2015): "Crowdsourcing Scientific Software Documentation: A Case Study of the NumPy", Computing in Science & Engineering, Vol. 17, No. 1, pp.28,36, January/February 2015. DOI: 10.1109/MCSE.2014.93.
Budd, A, Corpas, M., Brazas, M.D., Fuller, J.C., Goecks, J., Mulder, N.J., Michaut, M., Ouellette, B.F.F., Pawlik, A., Blomberg, N. "A Quick Guide for Building a Successful Bioinformatics Community", PLOS Computational Biology, Vol.11., No.2, February 2015. DOI: 10.1371/journal.pcbi.1003972.
Goble, Carole "Better Software, Better Research", IEEE Internet Computing, vol.18, no.5, pp.4,8, Sept/Oct 2014. DOI: 10.1109/MIC.2014.88.
Sufi, Shoaib; Chue Hong, Neil; Hettrick, Simon; Antonioletti, Mario; Crouch, Stephen; Hay, Alexander; Inupakutika, Devasena; Jackson, Mike; Pawlik, Aleksandra; Peru, Giacomo; Robinson, John; Carr, Les; De Roure, David; Goble, Carole; Parsons, Mark, "Software in Reproducible Research: Advice and Best Practice collected from experiences at the Collaborations Workshop", Proceedings of the 1st ACM SIGPLAN Workshop on Reproducible Research Methodologies and New Publication Models in Computer Engineering (TRUST'14), Article No. 2, ACM New York, NY, USA, 2014. ISBN: 978-1-4503-2951-4.
Crouch, Stephen; Chue Hong, Neil; Hettrick, Simon; Jackson, Mike; Pawlik, Aleksandra; Sufi, Shoaib; Carr, Les; De Roure, David; Goble, Carole; Parsons, Mark, "The Software Sustainability Institute: Changing Research Software Attitudes and Practices," Computing in Science & Engineering , vol.15, no.6, pp.74,80, Nov-Dec 2013. DOI: 10.1109/MCSE.2013.133. A copy of the text from this paper is also available on our website.
Crusoe, Michael R.; Brown, C. Titus (2013): "Walking the talk: adopting and adapting sustainable scientiﬁc software development processes in a small biology lab", figshare. DOI: 10.6084/m9.figshare.791567.
Hedges, M., Neuroth, Smith K.M., Blanke, T., Romary, L., Küster, M., Illingworth, M. "TextGrid, TEXTvre, and DARIAH: Sustainability of Infrastructures for Textual Scholarship", Journal of the Text Encoding Initiative [Online], Issue 5, June 2013. DOI: 10.4000/jtei.774.
Jackson, M. and Tunnell, C. "MAUS online data quality" Computing in High Energy and Nuclear Physics 2012 (CHEP 2012), New York, 21-25 May 2012. Open Access Journal of Physics: Conference Series 396 Part 1. 012025 DOI:10.1088/1742-6596/396/1/012025.
Cohen, J., Filippis, I., Woodbridge, M., Bauer, D., Chue Hong, N., Jackson, M., Butcher, S., Colling, D., Darlington, J., Fuchs, B. and Harvey, M. "RAPPORT: Running Scientific HPC Applications on the Cloud" (eds. Townend, P., Xu, J. and Austin, J.) Phil. Trans. R. Soc. A, 371, December 2012. DOI: 10.1098/rsta.2012.0073.
Walters, R.J., Crouch, S., Bennett, P. "Building computational grids using ubiquitous web technologies" In Proceedings of 13th IFIP Working Conference on Virtual Enterprises, Bournemouth, UK, October 1-3, 2012.
Wilson, G., Aruliah, D.A.,Titus Brown, C.T., Chue Hong, N. P., Davis, M., Guy, R. T., Haddock, S.H.D, Huff, K., Mitchell, I.M., Plumbley, M., Waugh, B., White, E. P. and Wilson, P. "Best Practices for Scientific Computing" CoRR, arXiv:1210.0530 [cs.MS], 2012.
Shaon, A., Woolf, A. Crompton, Boczek, R., Rogers, W. and Jackson, M. "An Open Source Linked Data Framework for Publishing Environmental Data under the UK Location Strategy. Proceedings of the Terra Cognita Workshop on Foundations, Technologies and Applications of the Geospatial Web" (eds. Grütter, R., Kolas, D., Koubarakis, M. and Pfoser, D.) In conjunction with the International Semantic Web Conference (ISWC2011), Bonn, October 23-27, 2011.
Baxter, R and Chue Hong, N. "Tracking community intelligence with Trac" Phil. Trans. R. Soc. A. August 28, 2011 369 1949 pp. 3372-3383; 1471-2962. DOI: 10.1098/rsta.2011.0141.
Meredith, D., Crouch, S., Galang, G., Jiang, M., Nguyen, H., Turner, P. "Towards a Scalable, Open Standards Service for Cross-Protocol Data Transfers across Multiple Sources and Sinks" Phil. Trans. R. Soc. A. September 13, 2010 368 1926 pp4115-4131. DOI: 10.1098/rsta.2010.0148.
Papers acknowledging the work of the Institute
Basham, M., Filik, J., Wharmby, M.T., Chang, P.C.Y., Kassaby, B.E., Gerring, M., Aishma, J., Levik, K., Pulford, B.C.A., Sikharudlidze, I., Sneddon, D., Webber, M., Dhesi, S.S., Maccherozzi, F., Svensson, O., Brockhauser, S., Naray, G., Ashtun, A. "Data Analysis WorkbeNch (DAWN)", Journal of Synchrotron Radiation, Vol.22, No.3, pp.853-858, May 2015. DOI: 10.1107/S1600577515002283.
Crusoe, M.R., Brown, C.T. "Walking the talk: adopting and adapting sustainable scientific software development processes in a small biology lab", Presented at the First Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE1), November 2013, Denver CO, USA, Technical Report 791567, figshare, 2013. DOI: 10.6084/m9.figshare.791567.
Tunnell, C., Adams, J. "MAUS:MICE Analysis User Software" in Proceedings of the 2nd International Particle Accelerator Conference (IPAC 2011), San Sebastian, Spain 4th-9th September 2011, pp. 850-852.
Other reports acknowledging the work of the Institute
Gompel, M.D., Valk, R.D., Noordzij, J., Scharnhorst, A.M. "Guidelines for Software Quality: CLARIAH Task 54.100", Data Archiving and Networked Services (DANS); ICT (HI), Working paper, August 2016.
"EPSRC in Numbers." EPSRC Pioneer, 15, Summer 2015.
Hettrick, Simon. "Why we need to create careers for research software engineers." Scientific Computing World, 11 November 2015.
"Oath market", The Economist, 6th February 2015.
Tessella. "Better software delivers better science.", Physics World, 4th February 2015.
"Campus close-up." Times Higher Education, 22nd January 2015.
Purcell, Andrew. "Survey finds research software is vital for most academic work." iSGTW, 14th January 2015.
Pearson, Jordan. "How Bad Software Leads to Bad Science." Motherboard, 4th December 2014.
Hettrick, Simon. "Speak up for software." Research Fortnight, 29th October 2014.
Smith, Adam. "Engineering a future for research software and its makers." Research Fortnight, 23rd July 2014.
Hettrick, Simon. "What's wrong with Britain's computer scientists?" The Register, 25th November 2013.
Parr, Chris. "Save your work – give software engineers a career track." Times Higher Education, 15th August 2013.
Chue Hong, Neil. "Cough up money for software or fall behind in science ranks." The Conversation, 14th June 2013.
Hay, Alexander. "Bits and Bugs - Making the most of Technology in Entomology." Antenna, Summer 2013 Volume 37 (3), pp. 111-115.
Chue Hong, Neil. "Software: the hidden infrastructure behind the world's largest scientific facilities." Innovation Into Success - The Quarterly Journal of UKSPA, Spring 2013 Issue no. 31, pp. 28-29.
"RSE State of the Nation 2017", a report by the RSE Network, April 2017.
"Research Software Sustainability", a report for Knowledge Exchange, February 2016
"Measuring the success of the Software Sustainability Institute", April 2014.
Institute overview and status report, September 2014.
Institute overview and status report, April 2014.
Institute overview and status report, September 2013.