Stian Soiland-Reyes orcid.org/0000-0001-9842-9718
stian@soiland-reyes.com Kilburn building, Oxford Road, Manchester, M13 9PL, UK.
Education
- 2003 - 2006: MSc Computer Science, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.
- 2005 - 2006: Visiting Researcher at School of Computer Science, University of Birmingham
- Thesis: Sequence learning in a model of the basal ganglia
- 1998 - 2003: BSc Computer Science, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.
Professional experience
- 2010 - current: Technical Software Architect. eScience Lab at School of Computer Science, The University of Manchester. Software architect developing and researching open source projects like BioExcel (biomolecular modeling workflows on HPC/HTC), Wf4Ever (workflow preservability), Open PHACTS (pharmacology workflows), BioVel (biodiversity workflows) and Apache Taverna (scientific workflow system). Focus on scientific workflow systems, distributed systems, linked data, provenance, reproducibility, open science, open source communities.
- 2006 - 2010: Software Engineer/Research Associate. School of Computer Science, The University of Manchester. Software development for the myGrid project, working on the open source scientific workflow system Taverna. Java, distrituted computing, web services, REST, semantic web, ontologies, XML.
- 2002 - 2005: System developer. NTNU IT Department, Trondheim, Norway. Software development for NAV (network administration tool), Cerebrum (user management, SSO). System administrator in a team managing ~70 Linux/Solaris servers (email, web and SSO for 30k staff and students). DNS host master for
ntnu.no. IT hardware and network administration. - 2000 - 2002: Software Consultant. Linpro AS, Trondheim, Norway. Web applications, databases, security, mobile, Linux.
- 1997 - 2000: IT Assistant. Sandviks AS, Stavanger, Norway. System administration, IT support, CRM development.
Professional engagement
- 2016 - current: Project THOR Ambassador promoting use of ORCID.
- 2014 - current: Foundation Member at Apache Software Foundation (since 2017-03), Committer on (Apache Taverna incubating, Apache Commons RDF incubating). PMC (Project Management Committe) member at Apache Commons, Apache Incubator .
- 2011 - current: W3C: PROV Working Group, Open Annotation Community group, JSON-LD community group, Big Data Community Group
Skills
Software Engineering: Production-grade software development, testing, and releases. Open source development and community building. Data modelling and representation. System architecture and API design. Specifications and standards. Java, Clojure, Python, Ruby, JavaScript, Docker, virtualization, cloud, Web, REST, SOAP, XML.
Computer Science: Knowledge representation, ontologies, artificial intelligence, databases, computational science, concurrency, distributed computing, scientific workflows.
Sciences: Bioinformatics, cheminformatics, pharmacology, biodiversity, molecular dynamics.
Languages: English, Norwegian, Spanish
Selected presentations
- 2016-07: Big Data Europe (BDE) webinar: Open PHACTS Architecture and Docker install. Slides and video available.
- 2016-05: ELIXIR Technical Hackathon: Tools, Workflows and Workbenches, Institut Pasteur, Paris, France: Make research reproducible again.
- 2015-07: Bioinformatics Open Source Conference (BOSC) 2015, Dublin, Ireland: Sustaining research software at the Apache Software Foundation.
- 2013-03: Metagenomics, metagenetics and Pylogenetic workflows for Ocean Sampling Day Workshop, Max Planck Institute for Marine Microbiology, Bremen, German: What can provenance do for me?
- 2012-02: EGI/SHIWA Workshops on eScience Workflows, Budapest, Hungary: myExperiment 2.0 – Preserving digital Research Objects using the Wf4Ever architecture.
- 2011-07: Bioinformatics Open Source Conference (BOSC) 2011, Vienna, Austria. SCUFL2 - because a workflow is more than its definition.
- 2011-06: ITER Integrated Modelling Expert Group Workshop, Cadarache, France: Taverna workflow system.
Selected publications
- Paolo Ciccarese*, Stian Soiland-Reyes*, Khalid Belhajjame, Alasdair J G Gray, Carole Goble, Tim Clark (2013): PAV ontology: Provenance, Authoring and Versioning. Journal of Biomedical Semantics 4 (37). doi:10.1186/2041-1480-4-37 (* joint first author)
- Kyle Chard, Mike D' Arcy, Ben Heavner, Ian Foster, Carl Kesselman, Ravi Madduri, Alexis Rodriguez, Stian Soiland-Reyes, Carole Goble, Kristi Clark, Eric W. Deutsch, Ivo Dinov, Nathan Price, Arthur Toga (2016): I'll Take That to Go: Big Data Bags and Minimal Identifiers for Exchange of Large, Complex Datasets. 2016 IEEE International Conference on Big Data. doi:10.1109/BigData.2016.7840618 [pdf]
- Kristina Hettne, Harish Dharuri, Jun Zhao, Katherine Wolstencroft, Khalid Belhajjame, Stian Soiland-Reyes, Eleni Mina, Mark Thompson, Don Cruickshank, Lourdes Verdes-Montenegro, Julian Garrido, David de Roure, Oscar Corcho, Graham Klyne, Reinout van Schouwen, Peter A C 't Hoen, Sean Bechhofer, Carole Goble, Marco Roos (2014): Structuring research methods and data with the research object model: genomics workflows as a case study. Journal of Biomedical Semantics 5(1). doi:10.1186/2041-1480-5-41
- Katherine Wolstencroft, Robert Haines, Donal Fellows, Alan Williams, David Withers, Stuart Owen, Stian Soiland-Reyes, Ian Dunlop, Aleksandra Nenadic, Paul Fisher, Jiten Bhagat, Khalid Belhajjame, Finn Bacall, Alex Hardisty, Abraham Nieva de la Hidalga, Maria P. Balcazar Vargas, Shoaib Sufi, Carole Goble (2013): The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud. Nucleic acids research 41(W1). doi:10.1093/nar/gkt328
- Wei Tan, Ravi Madduri, Alexandra Nenadic, Stian Soiland-Reyes, Dinanath Sulakhe, Ian Foster and Carole A Goble (2010): CaGrid Workflow Toolkit: A Taverna based workflow tool for Cancer Grid. BMC Bioinformatics 11:542. doi:10.1186/1471-2105-11-542
- Paolo Missier, Stian Soiland-Reyes, Stuart Owen, Wei Tan, Alexandra Nenadic, Ian Dunlop, Alan Williams, Tom Oinn, Carole Goble (2010):
Taverna, Reloaded. Proceedings of Scientific and Statistical Database Management: 22nd International Conference, SSDBM 2010. doi:10.1007/978-3-642-13818-8_33
Reviewing
- 2016: ISWC 2016 Resources Track, including open reviews 48, 59 and 88
- 2016 -: The Journal of Open Source Software including open review 107
- 2016 -: Linked Research (on panel)
- 2015: GigaScience including open review of doi:10.1186/s13742-015-0080-7 (acknowledged in paper)
- 2015: IEEE Internet Computing
- 2013: BMC Bioinformatics review of doi:10.1186/1471-2105-14-201