Publications

Note: This page is generated from www.research.manchester.ac.uk which usually is more up to date and includes preprints.

2020

Leipzig J, Nüst D, Hoyt CT, Soiland-Reyes S, Ram K, Greenberg J. The role of metadata in reproducible computational research. 2020 Jun 15.
arXiv:2006.08589 [pdf]

Wittner R, Holub P, Geiger J, Müller H, Goble C, Soiland-Reyes S et al. ISO 23494: Biotechnology - Provenance Information Model for Biological Specimen and Data: Provenance Week 2020 Poster. 2020. Poster session presented at 4th Provenance Week 2020, Virtual, United States. https://doi.org/10.5281/zenodo.3901011

2019

Goble C, Cohen-Boulakia S, Soiland-Reyes S, Garijo D, Gil Y, Crusoe MR et al. FAIR Computational Workflows. Data Intelligence. 2019 Nov 1;2(1):108–121. https://doi.org/10.5281/zenodo.3268653, https://doi.org/10.1162/dint_a_00033

Khan FZ, Soiland-Reyes S, Sinnott RO, Lonie A, Goble C, Crusoe MR. Sharing interoperable workflow provenance: A review of best practices and their practical application in CWLProv. GigaScience. 2019 Nov 1;8(11). giz095. https://doi.org/10.5281/zenodo.1966881, https://doi.org/10.5281/zenodo.3196309, https://doi.org/10.1093/gigascience/giz095

Juty N, Wimalaratne SM, Soiland-Reyes S, Kunze J, Goble CA, Clark T. Unique, Persistent, Resolvable: Identifiers as the foundation of FAIR. Data Intelligence. 2019 Nov 1;2(1):30–39. https://doi.org/10.5281/zenodo.3267434, https://doi.org/10.1162/dint_a_00025

Andrio P, Hospital A, Conejero J, Jordá L, Del Pino M, Codo L et al. BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows. Scientific Data. 2019 Sep 10;6(1). 169. https://doi.org/10.1038/s41597-019-0177-4

Ó Carragáin E, Goble C, Sefton P, Soiland-Reyes S. A lightweight approach to research object data packaging. 2019. Abstract from Bioinformatics Open Source Conference (BOSC) 2019, Basel, Switzerland. https://doi.org/10.5281/zenodo.3250687

Andrio P (Author), Hospital A (Author), Conejero J (Author), Jordá L (Author), Del Pino M (Author), Codo L (Author) et al. Bioexcel building blocks test cases Zenodo. 2019. https://doi.org/10.5281/zenodo.2581362

2018

Alterovitz G, Dean D, Goble C, Crusoe MR, Soiland-Reyes S, Bell A et al. Enabling precision medicine via standard communication of HTS provenance, analysis, and results. PLoS Biology. 2018 Dec 31;16(12). e3000099. https://doi.org/10.1371/journal.pbio.3000099

Soiland-Reyes S, Cáceres M. The Archive and Package (arcp) URI scheme. In 2018 IEEE 14th International Conference on e-Science (e-Science). IEEE. 2018. 18 https://doi.org/10.5281/zenodo.1320264, https://doi.org/10.1109/eScience.2018.00018

Khan FZ (Author), Soiland-Reyes S (Curator). CWL run of Alignment Workflow: CWLProv 0.6.0 Research Object Mendeley Data. 2018. https://doi.org/10.17632/6wtpgr3kbj.1

Khan FZ (Author), Soiland-Reyes S (Curator). CWL run of RNA-seq Analysis Workflow: CWLProv 0.5.0 Research Object Mendeley Data. 2018. https://doi.org/10.17632/xnwncxpw42.1

Khan FZ (Author), Soiland-Reyes S (Curator). CWL run of Somatic Variant Calling Workflow: CWLProv 0.5.0 Research Object Mendeley Data. 2018. https://doi.org/10.17632/97hj93mkfd.3

Soiland-Reyes S, Khan FZ, Sinnott R, Lonie A, Crusoe MR, Goble C. Capturing interoperable reproducible workflows. 2018. Abstract from Workshop on Research Objects, Amsterdam, Netherlands. https://doi.org/10.5281/zenodo.1312623

Stanford N, Bacall F, Zamanzad Ghavidel F, Golebiewski M, Jonassen I, Kleppe R et al. FAIR Bioinformatics computation and data management: FAIRDOM and the Norwegian Digital Life initiative. 2018. Abstract from NETTAB 2018 Network Tools and Applications in Biology , Genova, Italy.

Khan FZ, Soiland-Reyes S, Crusoe MR, Lonie A, Sinnott R. CWLProv - Interoperable Retrospective Provenance capture and its challenges. 2018. Paper presented at International Provenance and Annotation Workshop (IPAW) 2018, London, United Kingdom. https://doi.org/10.5281/zenodo.1208478

Soiland-Reyes S (Author). stain/arcp-py: arcp 0.2.0: Create/parse arcp (Archive and Package) URIs in Python Zenodo. 2018. https://doi.org/10.5281/zenodo.1165986

Soiland-Reyes S, Cáceres M. The Archive and Package (arcp) URI scheme: Internet-Draft. Internet Engineering Task Force. 2018 Jan 17.

2017

Möller S, Prescott SW, Wirzenius L, Reinholdtsen P, Chapman B, Prins P et al. Robust cross-platform workflows: How technical and scientific communities collaborate to develop, test and share best practices for data analysis. Data Science and Engineering. 2017 Nov 16. https://doi.org/10.1007/s41019-017-0050-4

Robinson M (Developer), Soiland-Reyes S (Developer), Crusoe MR (Other), Goble C (Other). CWL Viewer v.1.1.0: common-workflow-language/cwlviewer Zenodo. 2017. https://doi.org/10.5281/zenodo.841692

Robinson M, Soiland-Reyes S, Crusoe MR, Goble C. Common Workflow Language Viewer: (Talk). 2017. Abstract from Bioinformatics Open Source Conference (BOSC) 2017, Prague, Czech Republic. https://doi.org/10.7490/f1000research.1114453.1

Robinson M, Soiland-Reyes S, Crusoe MR, Goble C. CWL Viewer: The Common Workflow Language Viewer. 2017. Poster session presented at Bioinformatics Open Source Conference (BOSC) 2017, Prague, Czech Republic. https://doi.org/10.7490/f1000research.1114375.1

Robinson M (Developer), Soiland-Reyes S (Developer), Crusoe MR (Other), Goble C (Other). CWL Viewer v1.0: common-workflow-language/cwlviewer Zenodo. 2017. https://doi.org/10.5281/zenodo.823535

McMurry JA, Juty N, Blomberg N, Burdett T, Conlin T, Conte N et al. Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data. PLoS Biology. 2017 Jun 29;15(6). e2001414. https://doi.org/10.1371/journal.pbio.2001414

Khan FZ, Soiland-Reyes S, Lonie A, Sinnott R. CWL+Research Object == Complete Provenance. 2017. Poster session presented at Bioinformatics Open Source Conference (BOSC) 2017, Prague, Czech Republic. https://doi.org/10.7490/f1000research.1114781.1

Matser V, Apostolov R, Carter A, De Groot BL, Harrow I, Hospital A et al. Building biomolecular modelling communities through BioExcel Interest Groups. 2017. Poster session presented at ISMB/ECCB 2017, Prague, Czech Republic.

Troumpoukis A, Charalambidis A, Mouchakis G, Konstantopoulos S, Digles D, Siebes R et al. A Benchmark Suite for Federated SPARQL Query Processing from Existing Workflows. 2017.

Amstutz P (Author), Crusoe MR (Author), Singh M (Author), Kumar K (Author), Chilton J (Author), [Unknown] B (Author) et al. common-workflow-language/cwltool GitHub: GitHub. 2017.

Robinson M (Author), Soiland-Reyes S (Author), Crusoe MR (Author). common-workflow-language/cwlviewer: CWL Viewer 2017. https://doi.org/10.5281/zenodo.848163

2016

Chard K, D' Arcy M, Heavner B, Foster I, Kesselman C, Madduri R et al. I'll take that to go: Big data bags and minimal identifiers for exchange of large, complex datasets. 2016. Paper presented at 2016 IEEE International Conference on Big Data, Washington, DC, United States. https://doi.org/10.1109/BigData.2016.7840618

Troumpoukis A, Charalambidis A, Mouchakis G, Konstantopoulos S, Siebes R, de Boer V et al. Developing a Benchmark Suite for Semantic Web Data from Existing Workflows. 2016. Paper presented at Workshop on Benchmarking Linked Data, Kobe, Japan. https://doi.org/10.5281/zenodo.159568

Evelo C, Willighagen EL, Lynch N, Williams-Jones B, Loizou A, Soiland-Reyes S et al. The Open PHACTS Discovery Platform from a network biology perspective. 2016. Poster session presented at Network Biology SIG 2016, Orlando, United States. https://doi.org/10.7490/f1000research.1112676.1

Amstutz P, (ed.), Crusoe MR, (ed.), Tijanić N, (ed.), Chapman B, Chilton J, Heuer M et al. Common Workflow Language, v1.0. figshare , 2016. https://doi.org/10.6084/m9.figshare.3115156.v2

Soiland-Reyes S, Alper P, Goble C. Tracking workflow execution with TavernaProv. 2016. Paper presented at PROV: Three Tears Later, Washington DC, United States. https://doi.org/10.5281/zenodo.51314

Siebes R, de Boer V, Williams-Jones B, Soiland-Reyes S. Drug Discovery and Big Linked Data. 2016. Poster session presented at Semantic Web Applications and Tools for Life Sciences (SWAT4LS) 2016, Amsterdam, Netherlands.

Stanford N, Bacall F, Golebiewski M, Krebs O, Kuzyakiv R, Nguyen Q et al. FAIRDOM: Reproducible Systems Biology through FAIR Asset Management. 2016. Paper presented at Reproducibility, standards and SOP in bioinformatics, Rome, Italy.

Wolstencroft K, Krebs O, Snoep J, Stanford NJ, Bacall F, Golebiewski M et al. FAIRDOMHub: a repository and collaboration environment for sharing systems biology research. Nucleic acids research. 2016;45(D1):D404-D407. https://doi.org/10.1093/nar/gkw1032

2015

Amstutz P, Tijanić N, Soiland-Reyes S, Kern J, Stojanovic L, Pierce T et al. Portable workflow and tool descriptions with the CWL. 2015. Abstract from Bioinformatics Open Source Conference, Dublin, Ireland.

Gamble M, Morrison N, Soiland-Reyes S, Goble C. Research shared: www.researchobject.org. 2015. Abstract from Bioinformatics Open Source Conference, Dublin, Ireland.

Soiland-Reyes S, Dunlop I, Williams AR, Apache Taverna Team. Apache Taverna: Sustaining research software at the Apache Software Foundation. 2015. Abstract from Bioinformatics Open Source Conference, Dublin, Ireland.

Gaulton A, Harland L, Davies M, Papadatos G, Loizou A, Dedman N et al. Semantic-web access to patent annotations. 2015. Poster session presented at SWAT4LS International Conference: Semantic web applications and tools for life sciences, Riley Auditorium, Gillespie Center, Clare College, Cambridge, England, .

2014

Soiland-Reyes S, Gamble M, Haines R. Research Object Bundle 1.0: researchobject.org Specification 05 November 2014. researchobject.org, 2014. 9 p. https://doi.org/10.5281/zenodo.12586

Belhajjame K (Author), Zhao J (Author), Garijo D (Author), Garrido A (Author), Soiland-Reyes S (Author), Alper P (Author) et al. A workflow PROV-corpus based on Taverna and Wings (Datasets) 2014. https://doi.org/10.5281/zenodo.11607

Wolstencroft K, Pawlik A, Williams AR, Li P, Morrison N, Soiland-Reyes S et al. Taverna Tutorials 2014-09-01 (Bonn): Training material. 2014. https://doi.org/10.5281/ZENODO.11590

Soiland-Reyes S, Gamble M, Corcho O, Warner S. ORE User Guide - Resource Map Implementation in JSON-LD 0.9. Open Archives Initiative, 2014. (Open Archives Initiative Object Reuse and Exchange). https://doi.org/10.5281/zenodo.11293

Nies TD, Coppens S, Missier P, Moreau L, Cheney J, Lebo T et al. PROV-Dictionary: Modeling Provenance for Dictionary Data Structures. http://www.w3.org/TR/prov-dictionary/: World Wide Web Consortium, 2014.

Palma R, Hołubowicz P, Page K, Soiland-Reyes S, Klyne G, Mazurek C. A suite of APIs for the management of research objects. 2014. Paper presented at ISWC Developers Workshop 2014, Riva del Garda, Italy.

Bergmann FT, Adams R, Moodie S, Cooper J, Glont M, Golebiewski M et al. COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project. BMC Bioinformatics. 2014;15:369. https://doi.org/10.1186/s12859-014-0369-z

Möller S, Afgan E, Banck M, Bonnal RJP, Booth T, Chilton J et al. Community-driven development for computational biology at Sprints, Hackathons and Codefests. B M C Bioinformatics. 2014. https://doi.org/10.1186/1471-2105-15-S14-S7

Page KR, Palma R, Holubowicz P, Klyne G, Soiland-Reyes S, Garijo D et al. Research Objects for audio processing: Capturing semantics for reproducibility. In Proceedings of the AES International Conference|Proc. AES Int. Conf.. Audio Engineering Society. 2014. p. 149-156 http://www.aes.org/e-lib/browse.cfm?elib=17116

Hettne K, Dharuri H, Zhao J, Wolstencroft K, Belhajjame K, Soiland-Reyes S et al. Structuring research methods and data with the research object model: genomics workflows as a case study. Journal of Biomedical Semantics. 2014;5(1). https://doi.org/10.1186/2041-1480-5-41

2013

Ciccarese P, Soiland-Reyes S, Belhajjame K, Gray AJG, Goble C, Clark T et al. PAV ontology: Provenance, Authoring and Versioning. Journal of Biomedical Semantics. 2013 Nov;4(37). 37. https://doi.org/10.1186/2041-1480-4-37

Ciccarese P, Soiland-Reyes S, Clark T. Web annotation as a first-class object. IEEE Internet Computing. 2013 Nov;17(6):71-75. 6682930. https://doi.org/10.1109/MIC.2013.123

Zhang H, Soiland-Reyes S, Goble C. Taverna Mobile: Taverna workflows on Android. In Cannata N, Romano P, editors, NETTAB 2013 Workshop on “Semantic, Social, and Mobile Applications for Bioinformatics and Biomedical Laboratories” 16-18 October 2013, Lido of Venice, Italy http://www.nettab.org/2013/: EMBnet.journal. Vol. 19(suppl B). Netherlands: EMBnet Stichting. 2013 https://doi.org/10.14806/ej.19.B.727

Wolstencroft K, Haines R, Fellows D, Williams A, Withers D, Owen S et al. The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud. Nucleic acids research. 2013 Jul;41:W557-561. https://doi.org/10.1093/nar/gkt328

Gil Y, Miles S, Belhajjame K, Deus H, Garijo D, Klyne G et al. PROV Model Primer: W3C Working Group Note. Provenance Working Group. 2013 Apr 30. (W3C Working Group Note).

Klyne G, Groth P, Moreau L, Hartig O, Simmhan Y, Myers J et al. PROV-AQ: Provenance Access and Query. http://www.w3.org/TR/prov-aq/: World Wide Web Consortium, 2013. (W3C Working Group Note).

Moreau L, Missier P, Cheney J, Soiland-Reyes S. PROV-N: The Provenance Notation. http://www.w3.org/TR/prov-n/: World Wide Web Consortium, 2013. (W3C Recommendation).

Lebo T, Sahoo S, McGuinness D, Belhajjame K, Cheney J, Corsar D et al. PROV-O: The PROV Ontology. http://www.w3.org/TR/prov-o/: World Wide Web Consortium, 2013. (W3C Recommendation).

Belhajjam K, Zhao J, Garijo D, Garrido A, Soiland-Reyes S, Alper P et al. A workflow PROV-corpus based on Taverna and Wings. In Proceedings of the Joint EDBT/ICDT 2013 Workshops : New York, NY, USA. Association for Computing Machinery. 2013. p. 331-332 https://doi.org/10.1145/2457317.2457376

Soiland-Reyes S, Sanderson R, Ciccarese P, Van De Sompel H. Designing the W3C open annotation data model. http://www.openannotation.org/spec/core/: Association for Computing Machinery, 2013. 9 p. (W3C Community Draft). https://doi.org/10.1145/2464464.2464474

2012

Page K, Palma R, Hołubowicz P, Klyne G, Soiland-Reyes S, Cruickshank D et al. From workflows to Research Objects: an architecture for preserving the semantics of science. Proceedings of the 2nd International Workshop on Linked Science. 2012 Oct 22.

Goble C, Zhao J, Klyne G, Hołubowicz P, Palma R, Soiland-Reyes S et al. RO-Manager: A Tool for Creating and Manipulating Research Objects to Support Reproducibility and Reuse in Sciences. Proc. 2nd Intl. Workshop on Linked Science. 2012 Oct 22.

Hettne K, Soiland-Reyes S, Klyne G, Belhajjame K, Gamble M, Bechhofer S et al. Workflow forever: Semantic Web Semantic models and tools for preserving and digitally publishing computational experiments. In ACM International Conference Proceeding Series|ACM Int. Conf. Proc. Ser.. Association for Computing Machinery. 2012. p. 36-37. (SWAT4LS '11). https://doi.org/10.1145/2166896.2166909

Belhajjame K, Corcho O, Garijo D, Zhao J, Missier P, Newman D et al. Workflow-centric research objects: First class citizens in scholarly discourse. CEUR Workshop Proceedings. 2012;903:1-12.

Belhajjame K, Corcho O, Garijo D, Zhao J, Missier P, Newman D et al. Workflow-centric research objects: First class citizens in scholarly discourse. CEUR Workshop Proceedings. 2012;903:1-12.

2011

Belhajjame K, Goble C, Soiland-Reyes S, De Roure D. Fostering scientific workflow preservation through discovery of substitute services. In Proceedings - 2011 7th IEEE International Conference on eScience, eScience 2011|Proc. - IEEE Int. Conf. eScience, eScience (5-8 Dec. 2011). IEEE. 2011. p. 97-104 https://doi.org/10.1109/eScience.2011.22

Soiland-Reyes S, Williams AR, Owen S, Withers D, Goble C. Scufl2 - because a workflow is more than its definition. In host publication. 2011. p. 37-37

Soiland-Reyes S, Williams A, Owen S, Withers D, Goble C. Scufl2 – because a workflow is more than its definition. 2011. Abstract from BOSC 2011, Vienna, Austria, .

2010

Tan W, Madduri R, Nenadic A, Soiland-Reyes S, Sulakhe D, Foster I et al. CaGrid workflow toolkit: A taverna based workflow tool for cancer grid. BMC Bioinformatics. 2010 Nov 2;11. 542. https://doi.org/10.1186/1471-2105-11-542

Goble C, Soiland-Reyes S, Missier P, Owen S, Nenadic A, Dunlop I et al. Taverna, reloaded. In Gertz M, Hey T, Ludaescher B, editors, SSDBM 2010. 2010. p. 471-481

Missier P, Soiland-Reyes S, Owen S, Tan W, Nenadic A, Dunlop I et al. Taverna, reloaded. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2010;6187:471-481. https://doi.org/10.1007/978-3-642-13818-8_33

2009

Nenadic A, Soiland-Reyes S, Goble C. Bringing caBIG services together using Taverna. Unknown Journal. 2009 Dec 7;3.

Tan W, Chard K, Sulakhe D, Madduri R, Foster I, Soiland-Reyes S et al. Scientific workflows as services in caGrid: A Taverna and gRAVI approach. In 2009 IEEE International Conference on Web Services, ICWS 2009|IEEE Int. Conf. Web Serv., ICWS. IEEE Press. 2009. p. 413-420 https://doi.org/10.1109/ICWS.2009.19

2008

Li P, Castrillo JI, Velarde G, Wassink I, Soiland-Reyes S, Owen S et al. Performing statistical analyses on quantitative data in Taverna workflows: An example using R and maxdBrowse to identify differentially-expressed genes from microarray data. BMC Bioinformatics. 2008 Aug 7;9. 334. https://doi.org/10.1186/1471-2105-9-334

Li P, Oinn T, Soiland S, Kell DB, Soiland-Reyes S. Automated manipulation of systems biology models using libSBML within Taverna workflows. Bioinformatics. 2008 Jan 15;24(2):287-289. https://doi.org/10.1093/bioinformatics/btm578

2006

Søiland S. Sequence learning in a model of the basal ganglia. 2006. 118 p. https://doi.org/11250/251073