Mr Stian Soiland-Reyes

Technical Architect

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Publications

  1. 2020
  2. Published

    The role of metadata in reproducible computational research

    Leipzig, J., Nüst, D., Hoyt, C. T., Soiland-Reyes, S., Ram, K. & Greenberg, J., 15 Jun 2020, 59 p.

    Research output: Working paper

  3. Published

    ISO 23494: Biotechnology - Provenance Information Model for Biological Specimen and Data: Provenance Week 2020 Poster

    Wittner, R., Holub, P., Geiger, J., Müller, H., Goble, C., Soiland-Reyes, S., Fairweather, E., Pirredu, L., Frexia, F., Mascia, C., Zanetti, G., Nakae, H., Strambio, C., Moore, J., Grunwald, D. & Swedlow, J., 1 Jun 2020. 3 p.

    Research output: Contribution to conferencePoster

  4. 2019
  5. Published

    FAIR Computational Workflows

    Goble, C., Cohen-Boulakia, S., Soiland-Reyes, S., Garijo, D., Gil, Y., Crusoe, M. R., Peters, K. & Schober, D., 1 Nov 2019, In : Data Intelligence. 2, 1, p. 108–121 14 p.

    Research output: Contribution to journalArticle

  6. Published

    Sharing interoperable workflow provenance: A review of best practices and their practical application in CWLProv

    Khan, F. Z., Soiland-Reyes, S., Sinnott, R. O., Lonie, A., Goble, C. & Crusoe, M. R., 1 Nov 2019, In : GigaScience. 8, 11, 27 p., giz095.

    Research output: Contribution to journalArticle

  7. Published

    Unique, Persistent, Resolvable: Identifiers as the foundation of FAIR

    Juty, N., Wimalaratne, S. M., Soiland-Reyes, S., Kunze, J., Goble, C. A. & Clark, T., 1 Nov 2019, In : Data Intelligence. 2, 1, p. 30–39 10 p.

    Research output: Contribution to journalArticle

  8. Published

    BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows

    Andrio, P., Hospital, A., Conejero, J., Jordá, L., Del Pino, M., Codo, L., Soiland-reyes, S., Goble, C., Lezzi, D., Badia, R. M., Orozco, M. & Gelpi, J. L., 10 Sep 2019, In : Scientific Data. 6, 1, 8 p., 169.

    Research output: Contribution to journalArticle

  9. E-pub ahead of print

    A lightweight approach to research object data packaging

    Ó Carragáin, E., Goble, C., Sefton, P. & Soiland-Reyes, S., 20 Jun 2019.

    Research output: Contribution to conferenceAbstract

  10. Published

    Bioexcel building blocks test cases

    Andrio, P., Hospital, A., Conejero, J., Jordá, L., Del Pino, M., Codo, L., Soiland-Reyes, S., Goble, C., Lezzi, D., Badia, R., Orozco, M. & Gelpi, J. L., 18 Feb 2019

    Research output: Non-textual formData set/Database

  11. 2018
  12. Published

    Enabling precision medicine via standard communication of HTS provenance, analysis, and results

    Alterovitz, G., Dean, D., Goble, C., Crusoe, M. R., Soiland-Reyes, S., Bell, A., Hayes, A., Suresh, A., Purkayastha, A., King, C. H. S., Taylor, D., Johanson, E., Thompson, E. E., Donaldson, E., Morizono, H., Tsang, H., Vora, J. K., Goecks, J., Yao, J., Almeida, J. S. & 17 others, Keeney, J., Addepalli, K., Krampis, K., Smith, K. M., Guo, L., Walderhaug, M., Schito, M., Ezewudo, M., Guimera, N., Walsh, P., Kahsay, R., Gottipati, S., Rodwell, T. C., Bloom, T., Lai, Y., Simonyan, V. & Mazumder, R., 31 Dec 2018, In : PLoS Biology. 16, 12, 18 p., e3000099.

    Research output: Contribution to journalArticle

  13. Published

    The Archive and Package (arcp) URI scheme

    Soiland-Reyes, S. & Cáceres, M., 27 Dec 2018, 2018 IEEE 14th International Conference on e-Science (e-Science). IEEE, 5 p. 18

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  14. Published

    CWL run of Alignment Workflow: CWLProv 0.6.0 Research Object

    Khan, F. Z. & Soiland-Reyes, S., 4 Dec 2018

    Research output: Non-textual formData set/Database

  15. Published

    CWL run of RNA-seq Analysis Workflow: CWLProv 0.5.0 Research Object

    Khan, F. Z. & Soiland-Reyes, S., 4 Dec 2018

    Research output: Non-textual formData set/Database

  16. Published

    CWL run of Somatic Variant Calling Workflow: CWLProv 0.5.0 Research Object

    Khan, F. Z. & Soiland-Reyes, S., 4 Dec 2018

    Research output: Non-textual formData set/Database

  17. Published

    Capturing interoperable reproducible workflows

    Soiland-Reyes, S., Khan, F. Z., Sinnott, R., Lonie, A., Crusoe, M. R. & Goble, C., 29 Oct 2018.

    Research output: Contribution to conferenceAbstract

  18. Accepted/In press

    FAIR Bioinformatics computation and data management: FAIRDOM and the Norwegian Digital Life initiative

    Stanford, N., Bacall, F., Zamanzad Ghavidel, F., Golebiewski, M., Jonassen, I., Kleppe, R., Krebs, O., Leonov, H., Owen, S., Peterson, K., Rey, M., Soiland-Reyes, S., Tekle, K., Weiderman, A., Williams, A., Wittig, U., Wolstencroft, K., Goksøyr, A., Snoep, J., Vik, J. O. & 2 others, Müller, W. & Goble, C., 4 Sep 2018, (Accepted/In press). 4 p.

    Research output: Contribution to conferenceAbstract

  19. Published
  20. Published

    The Archive and Package (arcp) URI scheme: Internet-Draft

    Soiland-Reyes, S. & Cáceres, M., 17 Jan 2018, Internet Engineering Task Force, 21 p.

    Research output: Working paperDiscussion paper

  21. 2017
  22. Published

    Robust cross-platform workflows: How technical and scientific communities collaborate to develop, test and share best practices for data analysis

    Möller, S., Prescott, S. W., Wirzenius, L., Reinholdtsen, P., Chapman, B., Prins, P., Soiland-Reyes, S., Klötzl, F., Bagnacani, A., Kalaš, M., Tille, A. & Crusoe, M. R., 16 Nov 2017, In : Data Science and Engineering.

    Research output: Contribution to journalArticle

  23. Published

    CWL Viewer v.1.1.0: common-workflow-language/cwlviewer

    Robinson, M., Soiland-Reyes, S., Crusoe, M. R. & Goble, C., 11 Aug 2017

    Research output: Non-textual formSoftware

  24. Published

    Common Workflow Language Viewer: (Talk)

    Robinson, M., Soiland-Reyes, S., Crusoe, M. R. & Goble, C., 22 Jul 2017.

    Research output: Contribution to conferenceAbstract

  25. Published

    CWL Viewer: The Common Workflow Language Viewer

    Robinson, M., Soiland-Reyes, S., Crusoe, M. R. & Goble, C., 6 Jul 2017. 1 p.

    Research output: Contribution to conferencePoster

  26. Published

    CWL Viewer v1.0: common-workflow-language/cwlviewer

    Robinson, M., Soiland-Reyes, S., Crusoe, M. R. & Goble, C., 6 Jul 2017

    Research output: Non-textual formSoftware

  27. Published

    Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data.

    McMurry, J. A., Juty, N., Blomberg, N., Burdett, T., Conlin, T., Conte, N., Courtot, M., Deck, J., Dumontier, M., Fellows, D., Gonzalez-Beltran, A., Gormanns, P., Grethe, J., Hastings, J., Hériché, J-K., Hermjakob, H., Ison, J. C., Jimenez, R. C., Jupp, S., Kunze, J. & 24 others, Laibe, C., Le Novère, N., Malone, J., Martin, M. J., McEntyre, J. R., Morris, C., Muilu, J., Müller, W., Rocca-Serra, P., Sansone, S. A., Sariyar, M., Snoep, J. L., Soiland-Reyes, S., Stanford, N. J., Swainston, N., Washington, N., Williams, A. R., Wimalaratne, S. M., Winfree, L. M., Wolstencroft, K., Goble, C., Mungall, C. J., Haendel, M. A. & Parkinson, H., 29 Jun 2017, In : PLoS Biology. 15, 6, 18 p., e2001414.

    Research output: Contribution to journalArticle

  28. Accepted/In press

    CWL+Research Object == Complete Provenance

    Khan, F. Z., Soiland-Reyes, S., Lonie, A. & Sinnott, R., 14 Jun 2017, (Accepted/In press). 1 p.

    Research output: Contribution to conferencePoster

  29. Accepted/In press

    Building biomolecular modelling communities through BioExcel Interest Groups

    Matser, V., Apostolov, R., Carter, A., De Groot, B. L., Harrow, I., Hospital, A., Ippoliti, E., Melquiond, A., Soiland-Reyes, S. & Trellet, M., 26 May 2017, (Accepted/In press).

    Research output: Contribution to conferencePoster

  30. Published

    common-workflow-language/cwltool

    Amstutz, P., Crusoe, M. R., Singh, M., Kumar, K., Chilton, J., [Unknown], B., Soiland-Reyes, S., Chapman, B., Kotliar, M., Leehr, D., Carrasco, G., Kartashov, A., Tijanic, N., Ménager, H., Safont, P. R., Porter, J. J., Molenaar, G., Yuen, D., Barrera, A., Ivkovic, S. & 10 others, Spangler, R., [Unknown], P., Tanjo, T., Vandewege, W., Randall, J. C., Kern, J., Bradley, J., Li, J., der Zwaan, J. V. & Connelly, A., 2017

    Research output: Non-textual formSoftware

  31. Published

    common-workflow-language/cwlviewer: CWL Viewer

    Robinson, M., Soiland-Reyes, S. & Crusoe, M. R., 2017

    Research output: Non-textual formSoftware

  32. 2016
  33. Published

    I'll take that to go: Big data bags and minimal identifiers for exchange of large, complex datasets

    Chard, K., D' Arcy, M., Heavner, B., Foster, I., Kesselman, C., Madduri, R., Rodriguez, A., Soiland-Reyes, S., Goble, C., Clark, K., Deutsch, E. W., Dinov, I., Price, N. & Toga, A., 8 Dec 2016. 10 p.

    Research output: Contribution to conferencePaper

  34. Published

    Developing a Benchmark Suite for Semantic Web Data from Existing Workflows

    Troumpoukis, A., Charalambidis, A., Mouchakis, G., Konstantopoulos, S., Siebes, R., de Boer, V., Soiland-Reyes, S. & Digles, D., 6 Oct 2016. 12 p.

    Research output: Contribution to conferencePaper

  35. Published

    The Open PHACTS Discovery Platform from a network biology perspective

    Evelo, C., Willighagen, E. L., Lynch, N., Williams-Jones, B., Loizou, A., Soiland-Reyes, S., Miller, R., Gaulton, A., Papadatos, G., Harland, L., Goble, C., Woollard, P., Ecker, G., Digles, D. & Senger, S., 22 Jul 2016.

    Research output: Contribution to conferencePoster

  36. Published

    Common Workflow Language, v1.0

    Amstutz, P. (ed.), Crusoe, M. R. (ed.), Tijanić, N. (ed.), Chapman, B., Chilton, J., Heuer, M., Kartashov, A., Leehr, D., Ménager, H., Nedeljkovich, M., Scales, M., Soiland-Reyes, S. & Stojanovic, L., 8 Jul 2016, figshare .

    Research output: Book/ReportCommissioned report

  37. Published

    Tracking workflow execution with TavernaProv

    Soiland-Reyes, S., Alper, P. & Goble, C., 6 Jun 2016. 3 p.

    Research output: Contribution to conferencePaper

  38. Published

    Drug Discovery and Big Linked Data

    Siebes, R., de Boer, V., Williams-Jones, B. & Soiland-Reyes, S., 2016. 2 p.

    Research output: Contribution to conferencePoster

  39. Accepted/In press

    FAIRDOM: Reproducible Systems Biology through FAIR Asset Management

    Stanford, N., Bacall, F., Golebiewski, M., Krebs, O., Kuzyakiv, R., Nguyen, Q., Owen, S., Soiland-Reyes, S., Straszewski, J., van Niekerk, D., Williams, A., Wolstencroft, K., Malmström, L., Rinn, B., Snoep, J., Müller, W. & Goble, C., 2016, (Accepted/In press). 5 p.

    Research output: Contribution to conferencePaper

  40. Published

    FAIRDOMHub: a repository and collaboration environment for sharing systems biology research

    Wolstencroft, K., Krebs, O., Snoep, J., Stanford, N. J., Bacall, F., Golebiewski, M., Kuzyakiv, R., Nguyen, Q., Owen, S., Soiland-Reyes, S., Straszewski, J., van Niekerk, D. D., Williams, A., Malmström, L., Rinn, B., Müller, W. & Goble, C., 2016, In : Nucleic acids research. 45, D1, p. D404-D407 4 p.

    Research output: Contribution to journalArticle

  41. 2015
  42. Published

    Portable workflow and tool descriptions with the CWL

    Amstutz, P., Tijanić, N., Soiland-Reyes, S., Kern, J., Stojanovic, L., Pierce, T., Chilton, J., Mikheev, M., Lampa, S., Ménager, H., Frazer, S., Malladi, V. S. & Crusoe, M. R., 10 Jul 2015. 1 p.

    Research output: Contribution to conferenceAbstract

  43. Published

    Research shared: www.researchobject.org

    Gamble, M., Morrison, N., Soiland-Reyes, S. & Goble, C., 10 Jun 2015. 1 p.

    Research output: Contribution to conferenceAbstract

  44. Published

    Apache Taverna: Sustaining research software at the Apache Software Foundation

    Soiland-Reyes, S., Dunlop, I., Williams, A. R. & Apache Taverna Team, 2015.

    Research output: Contribution to conferenceAbstract

  45. Published

    Semantic-web access to patent annotations

    Gaulton, A., Harland, L., Davies, M., Papadatos, G., Loizou, A., Dedman, N., Digles, D., Soiland-Reyes, S., Tkachenko, V., Senger, S., Overington, J. P. & Lynch, N., 2015, p. 212-213. 2 p.

    Research output: Contribution to conferencePoster

  46. 2014
  47. Published

    Research Object Bundle 1.0: researchobject.org Specification 05 November 2014

    Soiland-Reyes, S., Gamble, M. & Haines, R., 1 Nov 2014, researchobject.org. 9 p.

    Research output: Book/ReportOther report

  48. Published

    A workflow PROV-corpus based on Taverna and Wings (Datasets)

    Belhajjame, K., Zhao, J., Garijo, D., Garrido, A., Soiland-Reyes, S., Alper, P. & Corcho, Ó., 1 Sep 2014

    Research output: Non-textual formData set/Database

  49. Published

    Taverna Tutorials 2014-09-01 (Bonn): Training material

    Wolstencroft, K., Pawlik, A., Williams, A. R., Li, P., Morrison, N., Soiland-Reyes, S. & Brenninkmeijer, C., 1 Sep 2014

    Research output: Other contribution

  50. Published

    ORE User Guide - Resource Map Implementation in JSON-LD 0.9

    Soiland-Reyes, S., Gamble, M., Corcho, O. & Warner, S., 14 Aug 2014, Open Archives Initiative. (Open Archives Initiative Object Reuse and Exchange)

    Research output: Book/ReportCommissioned report

  51. Published

    PROV-Dictionary: Modeling Provenance for Dictionary Data Structures

    Nies, T. D., Coppens, S., Missier, P., Moreau, L., Cheney, J., Lebo, T. & Soiland-Reyes, S., 30 Apr 2014, http://www.w3.org/TR/prov-dictionary/: World Wide Web Consortium.

    Research output: Book/ReportCommissioned report

  52. Published

    A suite of APIs for the management of research objects

    Palma, R., Hołubowicz, P., Page, K., Soiland-Reyes, S., Klyne, G. & Mazurek, C., 2014, p. 43-48. 6 p.

    Research output: Contribution to conferencePaper

  53. Published

    COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project

    Bergmann, F. T., Adams, R., Moodie, S., Cooper, J., Glont, M., Golebiewski, M., Hucka, M., Laibe, C., Miller, A. K., Nickerson, D. P., Olivier, B. G., Rodriguez, N., Sauro, H. M., Scharm, M., Soiland-Reyes, S., Waltemath, D., Yvon, F. & Le Novère, N., 2014, In : BMC Bioinformatics. 15, p. 369

    Research output: Contribution to journalArticle

  54. Published

    Community-driven development for computational biology at Sprints, Hackathons and Codefests

    Möller, S., Afgan, E., Banck, M., Bonnal, R. J. P., Booth, T., Chilton, J., Cock, P. J. A., Gumbel, M., Harris, N., Holland, R., Kalaš, M., Kaján, L., Powell, D. R., Prins, P., Quinn, J., Sallou, O., Strozzi, F., Seemann, T., Sloggett, C., Soiland-Reyes, S. & 6 others, Steinbiss, S., Tille, A., Travis, A. J., Guimera, R. V., Katayama, T. & Chapman, B. A., 2014, In : B M C Bioinformatics.

    Research output: Contribution to journalArticle

  55. Published

    Research Objects for audio processing: Capturing semantics for reproducibility

    Page, K. R., Palma, R., Holubowicz, P., Klyne, G., Soiland-Reyes, S., Garijo, D., Belhajjame, K. & Mayer, R., 2014, Proceedings of the AES International Conference|Proc. AES Int. Conf.. http://www.aes.org/e-lib/browse.cfm?elib=17116: Audio Engineering Society, p. 149-156 7 p.

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  56. Published

    Structuring research methods and data with the research object model: genomics workflows as a case study

    Hettne, K., Dharuri, H., Zhao, J., Wolstencroft, K., Belhajjame, K., Soiland-Reyes, S., Mina, E., Thompson, M., Cruickshank, D., Verdes-Montenegro, L., Garrido, J., de Roure, D., Corcho, O., Klyne, G., van Schouwen, R., 't Hoen, P. A. C., Bechhofer, S., Goble, C. & Roos, M., 2014, In : Journal of Biomedical Semantics. 5, 1, 41 p.

    Research output: Contribution to journalArticle

  57. 2013
  58. Published

    PAV ontology: Provenance, Authoring and Versioning

    Ciccarese, P., Soiland-Reyes, S., Belhajjame, K., Gray, A. J. G., Goble, C., Clark, T., Ocana, M., Wong, G., Wu, E., Kinoshita, J. & Groth, P., Nov 2013, In : Journal of Biomedical Semantics. 4, 37, 22 p., 37.

    Research output: Contribution to journalArticle

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