Wf4Ever publications

Structuring research methods and data with the research object model: genomics workflows as a case study. Kristina M 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, and Marco RoosJ Biomed Semantics. 2014; 5: 41
The Research Object Suite of Ontologies: Sharing and Exchanging Research Data and Methods on the Open Web. Belhajjame K, Zhao J, Garijo D, Hettne K, Palma R, Corcho O, Gómez-Pérez JM, Bechhofer S, Klyne G, Goble C.(ArXiv 2014)
When History Matters: Assessing Reliability for the Reuse of Scientific Workflows. Gómez-Pérez J.M., García-Cuesta E., Garrido Oberink A., Ruiz J.E. (The Semantic Web-ISWC 2013)
Workflow-Centric Research Objects: A First Class Citizen in the Scholarly Discourse. Belhajjame K, Corcho O, Garijo D, Zhao J, Missier P, Newman DR, Palma R, Bechhofer S, Garcia-Cuesta E, Gómez-Pérez JM, Klyne G, Page K, Roos M, Ruiz JE, Soiland-Reyes S, Verdes-Montenegro L, De Roure D, Goble CA. In proceedings of the ESWC2012 Workshop on the Future of Scholarly Communication in the Semantic Web (SePublica2012), Heraklion, Greece, May 2012
Best practices for workflow design: how to prevent workflow decay. Hettne K, Wolstencroft K, Belhajjame K, Goble CA, Mina E, Dharuri H, Verdes-Montenegro L, Garrido J, de Roure D, Roos M. SWAT4LS, 2012.
Why Workflows Break - Understanding and Combating Decay in Taverna Workflows.  Zhao J, Gómez-Pérez JM, Belhajjame K, Klyne G, García-Cuesta E, Garrido A, Hettne K, Roos M, De Roure D, Goble CA. 8th IEEE International Conference on e-Science (e-Science 2012).
Common Motifs in Scientific Workflows: An Empirical Analysis. Garijo D, Alper P, Belhajjame K, Corcho O, Gil Y, Goble CA. 8th IEEE International Conference on e-Science (e-Science 2012).
MIM: A Minimum Information Model Vocabulary and Framework for Scientific Linked Data. Gamble M, Goble CA, Klyne G, Zhao J. 8th IEEE International Conference on e-Science (e-Science 2012).  
Detecting Duplicate Records in Scientific Workflow Results. Belhajjame K, Missier P, Goble CA. Proceedings of IPAW, Springer, 2012.
A PROV encoding for provenance analysis using deductive rules. Missier P, Belhajjame K. Proceedings of IPAW, Springer, 2012.
Towards Open Publication of Reusable Scientific Workflows: Abstractions, Standards and Linked Data. Garijo D, Gil Y. (Submitted to JWS)
From workflows to Research Objects: an architecture for preserving the semantics of science. Page K, Palma R, Holubowicz P, Klyne G, Soiland-Reyes S, Cruickshank D, González-Cabero R et al. Linked Science, 2012.
RO-Manager: A Tool for Creating and Manipulating Research Objects to Support Reproducibility and Reuse in Sciences. Zhao J, Klyne G. Linked Science 2012.
Research Object Management: Opportunities and Challenges. Belhajjame K, De Roure D, Goble CA. Data Intensive Collaboration in Science and Engineering (DISCOSE) workshop, collocated with CSCW. 2012
A new approach for publishing workflows: Abstractions, standards, and linked data. Garijo D, Gil Y. Proceedings of the 6th workshop on Workflows in support of large-scale science, 2011.
Towards the preservation of scientific workflows. De Roure D, Belhajjame K, Missier P, Gómez-Pérez JM, Palma R, Ruíz JE, Hettne K, Roos M, Klyne G, Goble CA. Proceedings of the 8th International Conference on Preservation of Digital Objects (iPRES 2011).
Fostering scientific workflow preservation through discovery of substitute services. Belhajjame K, Goble CA, Soiland-Reyes S, De Roure D. 7th IEEE International Conference on e-Science (e-Science 2011).
Fostering Scientific Workflow Preservation through Discovery of Substitute Services. Belhajjme K, Goble CA, Soyland-Reyes S, De Roure D. 7th IEEE International Conference on e-Science (e-Science 2011).
Semantic Web Applications and Tools for Preserving Computational Experiments. Hettne K, Belhajjame K, Soiland-Reyes S, Gamble M, Corcho O, Klyne G, Bechhofer S, Roos M. Poster at SWAT4LS, 2011.

Other related publications

Why linked data is not enough for scientists. S.Bechhofer et.al. Future Generation Computer Systems, 2011.
Workflows to Open Provenance Graphs, round-trip. Missier, P., and Goble, C. Future Generation Computer Systems (FGCS), Volume 27, Issue 6, June 2011, pp: 812-819
Extending Semantic Provenance into the Web of Data. Zhao, Jun; Sahoo, Satya S.; Missier, Paolo; Sheth, Amit; Goble, Carole., IEEE Internet Computing, vol.15, no.1, pp.40-48, Jan.-Feb
Scientific Social Objects: The Social Objects and Multidimensional Network of the myExperiment Website. De Roure, D., Bechhofer, S., Goble, C. and Newman, D. Proc 1st International Workshop on Social Object Networks (SocialObjects 2011), 2011.
W3C, PROV-O: The PROV Ontology.

Wf4Ever presentations and invited talks

2010-12-08 Nara 2010 IVOA Fall Interop; Nara, Japan

Jose Enrique Ruiz: Wf4Ever: Advanced Workflow Preservation Technologies for Enhanced ScienceNara 2010 IVOA Fall Interop

  • Presentation as PDF

2011-03-16 National Centre for BioMedical Ontologies Webinar

Carole Goble: Social Computing for Scientists: Building collaborative e-Laboratories

2011-04-04 2011 dotAstronomy Conference; Oxford, UK

Jose Enrique Ruiz: Wf4Ever: Collaborative digital experiments2011 dotAstronomy Conference

  • Presentation as PDF

2011-05-19 Naples 2011 IVOA Spring Interop; Naples, Italy

Jose Enrique Ruiz: Wf4Ever: Curating and preserving collaborative digital experimentsNaples 2011 IVOA Spring Interop

  • Presentation as PDF

2011-05-25 The Growing Demands on Connectivity and Information Processing in Radio Astronomy - From VLBI to the SKA, Aveiro, Portugal

Jose Enrique Ruiz: Web services based workflows to deal with 3D dataThe Growing Demands on Connectivity and Information Processing in Radio Astronomy - From VLBI to the SKA

  • Presentation as PDF

2011-06-08 ITER IMAS workshop on workflow systems, Cadarache

Stian Soiland-Reyes: Taverna workflow system. http://www.iter.org/

  • Presentation as pdf

2011-06-22 CERN Workshop on Innovations in Scholarly Communication (OAI7); Geneva, Switzerland

Sean Bechhofer: Research Objects: Towards Exchange and Reuse of Digital KnowledgeOAI7

2011-07-08 The 7th IEEE 2011 World Congress on Services (SERVICES 2011), Washington DC, USA, 4-9 July 2011

Carole Goble Web Services in the Scientific Wilds

2011-07-13 Seminar IMG Group at School of Computer Science; Manchester, UK

Jose Enrique Ruiz: VO web-services-based astronomy workflows, Seminar for the Information Management Group - School of Computer Sciences - Univ. Manchester

  • Presentation as PDF

2011-07-16 BOSC 2011 / ISMB; Vienna, Austria

  • Stian Soiland-Reyes: SCUFL2, because a worklow is more than its definition.BOSC 2011
  • Abstract by Stian Soiland-Reyes, Alan R Williams, Stuart Owen, David Withers and Carole Goble
  • Presentation as SlidesharePDFpptx
  • Poster as PDFpptxSlideshare

2011-08-03 Live-link Seminar to Monash University Australia

Carole Goble: The Long Tail Scientist

2011-09-29 The 1st Nordic e-Science Conference, Helsinki, Finland

Carole Goble Opening Keynote: e-Science: Changes in Research Process, Being a Scientist today

2011-10-09 1st International Workshop on Social Object Networks, Boston, USA

David De Roure, Sean Bechhofer, Carole Goble, David Newman, Scientific Social Objects

2011-10-24  3rd International Conference on Knowledge Discovery, Knowledge Engineering and Knowledge Management (ICK3) Paris, France

Carole Goble Keynote: Accelerating Scientists' Knowledge Turns

Carole Goble Panel Position

2011-10-17 Pune 2011 IVOA Fall Interop; Pune, India

Jose Enrique Ruiz: Workflows PreservationPune 2011 IVOA Fall Interop

  • Presentation as PDF

Jose Enrique Ruiz: Workflows in the VOPune 2011 IVOA Fall Interop

  • Presentation as PDF

2011-11-09 Paris, Astronomical Data Analysis Software and Systems conference (ADASS XXI)

Juande Santander-Vela, José Enrique Ruiz, Lourdes Verdes-Montenegro, Susana Sánchez Expósito: Wf4Ever: Workflows for Methodology and Science PreservationADASS XXI, Birds of a Feather (BoF) session on Scientific Workflows in Astronomy, Paris, 2011

2011-12-07 London, Semantic Web Applications and Tools for Life Sciences Workshop (SWAT4LS)

Kristina Hettne, Khalid Belhajjame, Stian Soiland-Reyes, Matthew Gamble, Oscar Corcho, Graham Klyne, Sean Bechhofer, Marco Roos: Workflow forever: Semantic Web Semantic models and tools for preserving and digitally publishing computational experiments, SWAT4LS, London, 2011

  • Poster as PDF

2012-01-18 Paris, VO France Meeting. Workflow Working Group

José Enrique Ruiz, Lourdes Verdes-Montenegro, Susana Sánchez Expósito, Juande Santander-Vela and the Wf4Ever Team. Wf4Ever: Workflows Preservation2012 VO France Meeting, Paris, 2012

  • Presentation as PDF

2012-02-10 SHIWA Workshops on eScience Workflows, Budapest

Stian Soiland-Reyes, David De Roure: myExperiment 2.0 - preserving digital research objects using the Wf4Ever ArchitectureEGI/SHIWA Workshops on e-Science Workflows 2012 - EGI workshop

2012-03-28 EGI Community Forum 2010, Munich

Stian Soiland-Reyes: Wf4Ever: Preserving workflows as digital Research Objects, EGI Community forum 2012Workflow Systems workshop

2012-04-11 2nd BCS Karen Spärck Jones Lecture Named Lecture, University of York, UK

Carole Goble Working with Scientists: Fun, Profit & the e in e-Science

  • Presentation as ppt

2012-04-24 e-Science in bioinformatics: enabling the reuse of methods while unravelling the epigenetic factors of Huntington's Disease (presentation), NBIC Conference, Lunteren, The Netherlands

Eleni Mina, Reinout van Schouwen, Kostas Karasavvas, Kristina Hettne, Peter-Bram 't Hoen, Pernette J. Verschure, Christine Chichester, Barend Mons, Willeke van Roon-Mom, Marco Roos

2012-04-24 Run Taverna on the web, NBIC Conference, Lunteren, The Netherlands (Application Showcase Award)

Kostas Karasavvas, Reinout van Schouwen, Eleni Mina, Barend Mons, Marco Roos

2012-04-25 Dagstuhl Seminar on Semantic Data management

José Manuel Gómez-Pérez: Scientific Data Management: From the Lab to the Web, Semantic Data Management SeminarDagstuhl

2012-05-03 2012 General Assembly of the International Internet Preservation Consortium, Washington DC

Sean Bechhofer. Panelist: Harvesting and Preserving the Future Web. No slides, but a rough mindmap of notes.

2012-05-11 10 Best Practices for Workflow Design presentation at the BioVeL workshop, Gothenburg, Sweden

Kristina Hettne: 10 Best Practices for Workflow Design

2012-05-23 Speeding up research with the Semantic Web, 6th European Conference on Rare Diseases and Orphan Products, Brussels, Belgium

Marco Roos, Erik A. Schultes, Barend Mons

2012-05-23 Opening new gateways to workflows for scientists, IWSG-Life 2012, Amsterdam, The Netherlands

Kostas Karasavvas (NBIC), Marco Roos

  • Presentation (pdf)

2012-05-28 RO model presentation at the Sepublica workshop, Crete, Heraklion

Khalid Belhajjame: Workflow-Centric Research Objects: First Class Citizens in Scholarly Discourse

2012-06-12 Carole keynote at the JCDL, Washington, USA

Carole Goble, The Reality of Reproducibility for in silico

  • Presentation as ppt, as pdf

2012-06-21 IPAW, Santa Barbara, CA

Khalid Belhajjame, Paolo Missier and Carole A. Goble: Detecting Duplicate Records in Scientific Workflow Results

2012-07-03 SHIWA Summer School, Budapest, Hungary

The Astronomy challenge: How can workflow preservation help?

Susana Sánchez, Jose Enrique Ruíz, Lourdes Verdes-Montenegro, Julian Garrido, Juan de Dios Santander-Vela and Wf4Ever team

  • Presentation as pptx

2012-07-14 The 13th Annual Bioinformatics Open Source Conference (BOSC 2012), Long Beach, CA, USA

Carole Goble, If We Build It Will They Come?

The 13th Annual Bioinformatics Open Source Conference (BOSC 2012) July 13-14, 2012 Long Beach, CA

  • Presentation as ppt

2012-07-14 SEA, Valencia, Spain

Digital Science Reproducibility and Visibility in Astronomy

José Enrique Ruiz, Lourdes Verdes-Montenegro, Susana Sánchez, Julian Garrido, Juan de Dios Santander and the Wf4Ever Team

2012-07-15 Enabling the reuse of methods while unraveling the epigenetic factors of Huntington's Disease, ISMB 2012, Long Beach, California, USA

Kostas Karasavvas (Netherlands Bioinformatics Centre) Christine Chichester (NBIC, BioAssist); Eleni Mina (LUMC, Human Genetics); Reinout van Schouwen (LUMC, BioSemantics); Kristina Hettne (LUMC, Human Genetics); Peter-Bram 't Hoen (LUMC, Human Genetics); Pernette Verschure (University of Amsterdam, Swammerdam Institute for Life Sciences); Barend Mons (NBIC, Research); Willeke van Roon-Mom (LUMC, Human Genetics); Marco Roos (LUMC / NBIC, BioSemantics Group, Human Genetics);

2012-07-18 BioVel, Bonn, Germany

BioVel Technical Workshop Summer 2012, Bonn

Alan R Williams (myGrid)

  • Presentation (not yet publicly available)

2012-08-29 International Astronomical Union. Special Simposium 15: Data Intensive Astronomy, Beijing, China

Juan de Santander-Vela: e-Science for the Square Kilometre Array

2012-09-21 EGI Technical Forum, Prague, Czech Republic

WF4Ever: Supporting Reuse and Reproducibility in Experimental Science

Susana Sánchez, Jose Enrique Ruíz, Lourdes Verdes-Montenegro, Julian Garrido, Juan de Dios Santander-Vela and Wf4Ever team

  • Presentation as pptx

2012-09-25 hubhub2012, Indianpolis, USA

David De Roure: myExperiment and the Rise of Social Machines

2012-10-10 8th IEEE eScience Conference, Chicago, USA

2012-10-11 8th IEEE eScience Conference, Chicago, USA

Carole Goble: The Reality of Reproducibility of Computational Science (Keynote), 

The 8th IEEE International Conference on eScience (eScience 2012) Chicago, Illinois, 8-12 October 2012

  • Presentation as ppt

2012-10-11 8th IEEE eScience Conference, Chicago, USA

Matthew Gamble:MIM: A Minimum Information Model Vocabulary and Framework for Scientific Linked Data (paper presentation)

The 8th IEEE International Conference on eScience (eScience 2012) Chicago, Illinois, 8-12 October 2012

  • Presentation as pdf

2012-10-23 Sao Paolo Fall Interop Meeting, Sao Paolo, Brazil

Curation and Characterization of Web Services in the VO

Jose Enrique Ruíz

  • Presentation as ppt

2012-10-25 Sao Paolo Fall Interop Meeting, Sao Paolo, Brazil

Julián Garrido: AstroTaverna

2012-10-25 Sao Paolo Fall Interop Meeting, Sao Paolo, Brazil

Julián Garrido: PDL services integration in Taverna

2012-10-25 Sao Paolo Fall Interop Meeting, Sao Paolo, Brazil

Research Objects in Wf4Ever

Jose Enrique Ruíz on behalf of the Wf4Ever Team

  • Presentation as ppt

2012-11-7 APA 2012 Conference, Rome, Italy

Cezary Mazurek: Wf4Ever Introduction

2012-11-15 RadioNet Advanced Radio Astronomy, Commissioning Skills and Preparation for the SKA

e-Science for SKA. WF4Ever: Supporting Reuse and Reproducibility in Experimental Science

WF4Ever: Supporting Reuse and Reproducibility in Experimental Science

Lourdes Verdes-Montenegro, AMIGA and  Wf4Ever Projects

  • Presentation as pptx

2012-11-28 Best Practices for workflow design: how to prevent workflow decay, SWAT4LS 2012, Paris, France

Kristina Hettne, Katherine Wolstencroft, Khalid Belhajjame, Carole Goble, Eleni Mina, Harish Dharuri, David De Roure, Lourdes Verdes-Montenegro, Julian Garrido and Marco Roos

  • Workshop proceedings in preparation, see here for SWAT4LS web site.

2012-11-29 8th VOFrance Workflow WG Meeting, Paris, France

AstroTaverna plugin : VO-services-based workflows in Taverna workbench

Julian Garrido

  • Live Tutorial  

2012-11-29 8th VOFrance Workflow WG Meeting, Paris, France

Wf4Ever : reflections on structured digital experiments and curation of VO services

Jose Enrique Ruiz

2012-12-09 ISCB-Asia/SCCG 2012, ShenZhen, China

Marco Roos: Now that Newton's work is well preserved: how about yours?

  • Presentation as pptx

2013-01-14 Scholarly Communication Workshop, Pittsburgh, USA

Carole Goble: The Reality of Reproducibility in Computational Science (invited talk)

  • Presentation as pdf
  • (PPT in Dropbox as it's >10 MB)

2013-01-17 Internal meeting with NIBHI, University of Manchester, UK

Stian Soiland-Reyes, Khalid Belhajjame: Research Objects - Preserving scientific data and methods

2013-01-18 ESAC Faculty Seminars, ESAC Madrid, Spain

Digital Science: Reproducibility and Visibility in Astronomy

Jose Enrique Ruiz

2013-03-19 Beyond the PDF2, Amsterdam,  The Netherlands

Aleix Garrido Oberink: Demoing Collaboration Spheres and RO Monitoring (Reliability)