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Freire, Juliana
Publications (6 of 6) Show all publications
Strömbäck, L. & Freire, J. (2011). XML Management for Bioinformatics Applications. Computing in science & engineering (Print), 13(5), 12-22
Open this publication in new window or tab >>XML Management for Bioinformatics Applications
2011 (English)In: Computing in science & engineering (Print), ISSN 1521-9615, E-ISSN 1558-366X, Vol. 13, no 5, p. 12-22Article in journal (Refereed) Published
Abstract [en]

Scientific exploration has become a data-intensive process, and increasing amounts of data need to be stored, analyzed, and shared. XML can help address these needs. As concrete examples from systems biology show, native XML storage can be combined with traditional relational databases to offer an effective, usable solution for storing scientific data.

Place, publisher, year, edition, pages
Institute of Electrical and Electronics Engineers (IEEE), 2011
National Category
Engineering and Technology
Identifiers
urn:nbn:se:liu:diva-70524 (URN)10.1109/MCSE.2010.100 (DOI)000294096200003 ()
Available from: 2011-09-12 Created: 2011-09-12 Last updated: 2017-12-08
Freire, J. (2010). Provenance management for data exploration. In: Patrick Lambrix and Graham Kemp (Ed.), Proceedings of the Seventh International Conference on Data Integration in the Life Sciences: . Paper presented at DILS 2010 (pp. 1-2). Springer Verlag
Open this publication in new window or tab >>Provenance management for data exploration
2010 (English)In: Proceedings of the Seventh International Conference on Data Integration in the Life Sciences / [ed] Patrick Lambrix and Graham Kemp, Springer Verlag , 2010, p. 1-2Conference paper, Published paper (Refereed)
Abstract [en]

Computing has been an enormous accelerator to science and industry alike and it has led to an information explosion in many different fields. The unprecedented volume of data acquired by sensors, derived by simulations and analysis processes, and shared on the Web opens up new opportunities, but it also creates many challenges when it comes to managing and analyzing these data.

Place, publisher, year, edition, pages
Springer Verlag, 2010
Series
Lecture Notes in Computer Science, ISSN 0302-9743 ; 6254
National Category
Engineering and Technology
Identifiers
urn:nbn:se:liu:diva-58846 (URN)10.1007/978-3-642-15120-0_1 (DOI)
Conference
DILS 2010
Available from: 2010-08-30 Created: 2010-08-30 Last updated: 2014-06-24
Ellkvist, T., Strömbäck, L., Didier Linz, L. & Freire, J. (2009). A First Study on Strategies for Generating Workflow Snippets. In: The first International Workshop on Keyword Search ob structured data KEYS 2009, Collocated with ACM SIGMOD/PODS: . Paper presented at The first International Workshop on Keyword Search ob structured data KEYS 2009, Collocated with ACM SIGMOD/PODS (pp. 15-20). Association for Computing Machinery (ACM)
Open this publication in new window or tab >>A First Study on Strategies for Generating Workflow Snippets
2009 (English)In: The first International Workshop on Keyword Search ob structured data KEYS 2009, Collocated with ACM SIGMOD/PODS, Association for Computing Machinery (ACM), 2009, p. 15-20Conference paper, Published paper (Refereed)
Abstract [en]

Workflows are increasingly being used to specify computational tasks, from simulations and data analysis to the creation of Web mashups. Recently, a number of public workflow repositories have become available, for example, myExperiment for scientific workflows, and Yahoo! Pipes. Workflow collections are also commonplace in many scientific projects. Having such collections opens up new opportunities for knowledge sharing and re-use. But for this to become a reality, mechanisms are needed that help users explore these collections and locate useful workflows. Although there has been work on querying workflows, not much attention has been given to presenting query results. In this paper, we take a first look at the requirements for workflow snippets and study alternative techniques for deriving concise, yet informative snippets.

Place, publisher, year, edition, pages
Association for Computing Machinery (ACM), 2009
National Category
Engineering and Technology
Identifiers
urn:nbn:se:liu:diva-60209 (URN)10.1145/1557670.1557678 (DOI)978-1-60558-570-3 (ISBN)
Conference
The first International Workshop on Keyword Search ob structured data KEYS 2009, Collocated with ACM SIGMOD/PODS
Available from: 2010-10-07 Created: 2010-10-07 Last updated: 2015-05-28
Ellkvist, T., Koop, D., Freire, J., Silvia, C. & Strömbäck, L. (2009). Using Mediation to Achieve Provenance Interoperability. In: 2009 Congress on Services - I: . Paper presented at In IEEE International Workshop on Scientific Workflows (pp. 291-298). IEEE Press
Open this publication in new window or tab >>Using Mediation to Achieve Provenance Interoperability
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2009 (English)In: 2009 Congress on Services - I, IEEE Press, 2009, p. 291-298Conference paper, Published paper (Refereed)
Abstract [en]

Provenance is essential in scientific experiments. It contains information that is key to preserving the data, to determining their quality and authorship, and to reproduce as well as validate the results. In complex experiments and analyses, where multiple tools are used to derive data products, provenance captured by these tools must be combined in order to determine the complete lineage of the derived products. In this paper we describe a mediator-based architecture for integrating provenance information from multiple sources. This architecture contains two key components: a global mediated schema that is general and capable of representing provenance information represented in different model; and describe a new system-independent query API that is general and able to express complex queries over provenance information from different sources. We also present a case study where we show how this model was applied to integrate provenance from three provenance-enabled systems and discuss the issues involved in this integration process.

Place, publisher, year, edition, pages
IEEE Press, 2009
National Category
Engineering and Technology
Identifiers
urn:nbn:se:liu:diva-60210 (URN)10.1109/SERVICES-I.2009.68 (DOI)000274634100039 ()9781424449309 (ISBN)
Conference
In IEEE International Workshop on Scientific Workflows
Available from: 2010-10-07 Created: 2010-10-07 Last updated: 2016-08-22
Ellqvist, T., Koop, D., Freire, J., Silva, C. & Strömbäck, L. (2008). Using Mediation to Achieve Provenance Interoperability. In: 2009 World Conference on Services - I: . Paper presented at 4th IEEE Congress on Services, 6-10 July 2009, Los Angeles, CA, USA (pp. 398-399). IEEE
Open this publication in new window or tab >>Using Mediation to Achieve Provenance Interoperability
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2008 (English)In: 2009 World Conference on Services - I, IEEE , 2008, p. 398-399Conference paper, Published paper (Refereed)
Abstract [en]

Provenance is essential in scientific experiments. It contains information that is key to preserving the data and to determine its quality and uthorship. In complex experiments and analyses, where multiple tools are used to derive data products, provenance captured by these tools must be combined in order to determine the complete lineage of the derived products. We propose a mediator-based architecture to integrate provenance information from multiple sources, which contains two key components: a global mediated schema that is general and capable of representing provenance information represented in different models; and an expressive query interface that supports complex queries over provenance information spread over multiple different sources. We also present a case study where we show how this model was applied to integrate provenance from three provenance-enabled systems.

Place, publisher, year, edition, pages
IEEE, 2008
Keywords
provenanve, scientific workflow, data integration
National Category
Computer Sciences
Identifiers
urn:nbn:se:liu:diva-43763 (URN)10.1109/eScience.2008.100 (DOI)74678 (Local ID)978-0-7695-3535-7 (ISBN)978-1-4244-3380-3 (ISBN)74678 (Archive number)74678 (OAI)
Conference
4th IEEE Congress on Services, 6-10 July 2009, Los Angeles, CA, USA
Available from: 2009-10-10 Created: 2009-10-10 Last updated: 2018-01-12
Ellqvist, T., Koop, D., Anderson, E. W., Freire, J. & Silva, C. (2008). Using Provenance to Support Real-Time Collaborative Design of Workflows. In: Second International Provenance and Annotation Workshop,2008: . Paper presented at Second International Provenance and Annotation Workshop,2008 (pp. 266). New York: Springer, 5272
Open this publication in new window or tab >>Using Provenance to Support Real-Time Collaborative Design of Workflows
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2008 (English)In: Second International Provenance and Annotation Workshop,2008, New York: Springer , 2008, Vol. 5272, p. 266-Conference paper, Published paper (Refereed)
Abstract [en]

Because designing workflows is a notoriously difficult task, it often requires multiple users to collaborate. In such scenarios, sharing workflow evolution provenance in a timely manner is critical. We present an environment where collaborating users can see each other’s changes in real-time. The synchronization of workflow evolution provenance is automatic, immediate, and unobtrusive, allowing users to see collaborators’ changes as they are made. This enables a richer and fuller method of collaboration. We present the interface and algorithm for the synchronization and discuss common scenarios where this mechanism has been utilized.

Place, publisher, year, edition, pages
New York: Springer, 2008
Keywords
Scientific workflow, provenance, collaboration
National Category
Computer Sciences
Identifiers
urn:nbn:se:liu:diva-43760 (URN)10.1007/978-3-540-89965-5_27 (DOI)74674 (Local ID)978-3-540-89964-8 (ISBN)74674 (Archive number)74674 (OAI)
Conference
Second International Provenance and Annotation Workshop,2008
Available from: 2009-10-10 Created: 2009-10-10 Last updated: 2018-01-12
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