building an informatics platform for research integrated biobanks
Klingström, Tomas
(2017).
Data integration and handling.
Diss. (sammanfattning/summary)
Uppsala :
Sveriges lantbruksuniv.,
Acta Universitatis Agriculturae Sueciae, 1652-6880
; 2017:99
ISBN 978-91-7760-088-6
eISBN 978-91-7760-089-3
[Doctoral thesis]
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PDF
7MB |
Abstract
Modern technology allows researchers to generate data at an ever increasing rate,
outpacing the capacity of researchers to analyse it. Developing automated support
systems for the collection, management and distribution of information is therefore an
important step to reduce error rates and accelerate progress to enable high-quality
research based on big data volumes. This thesis encompasses five articles, describing
strategies for the creation of technical research platforms, as well as descriptions of the
technical platforms themselves.
The key conclusion of the thesis is that technical solutions for many issues have been
available for a long time. These technical solutions are however overlooked, or simply
ignored, if they fail to recognise the social dimensions of the issues they try to solve.
The Molecular Methods database is an example of a technically sound but only
partially successful solution in regards to social viability. Thousands of researchers
have used the website to access protocols, but only a handful have shared their own
work on MolMeth. Experiences from the Molecular Methods database and other
projects have provided a foundation for studies supporting the development of the
eB3Kit
The eB3Kit is a portable, robust and scalable informatics platform for structured data
management. Deploying the platform enables research groups to carry out advanced
research projects with very limited means. With the eB3Kit researchers can integrate
data from a wide variety of sources, including the local laboratory information
management system and analyse it using the Galaksio interface. Galaksio provides user
friendly access to the Galaxy workflow management system and provides eB3Kit users
with access to tools developed by a far larger user community than the one actively
developing the eB3Kit. Using a workflow management system improves
reproducibility and enables bioinformaticians to prepare workflows without directly
accessing ethically or commercially sensitive data. Therefore, it is especially well-
suited for applications where researchers are worried about privacy and during disease
outbreaks where persistent storage and analysis capacity must be established quickly.
Authors/Creators: | Klingström, Tomas | ||||||||||||
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Title: | Data integration and handling | ||||||||||||
Subtitle: | building an informatics platform for research integrated biobanks | ||||||||||||
Alternative abstract: |
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Series/Journal: | Acta Universitatis Agriculturae Sueciae (1652-6880) | ||||||||||||
Year of publishing : | 27 October 2017 | ||||||||||||
Depositing date: | 30 October 2017 | ||||||||||||
Number: | 2017:99 | ||||||||||||
Number of Pages: | 111 | ||||||||||||
Papers/manuscripts: |
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Place of Publication: | Uppsala | ||||||||||||
Publisher: | Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences | ||||||||||||
ISBN for printed version: | 978-91-7760-088-6 | ||||||||||||
ISBN for electronic version: | 978-91-7760-089-3 | ||||||||||||
ISSN: | 1652-6880 | ||||||||||||
Language: | English | ||||||||||||
Additional Information: | The former published thesis has been replaced by edition where even the five papers are included with permissions from the publishers on the condition that the papers are not published separately in a repository such as Epsilon Open Archive. | ||||||||||||
Publication Type: | Doctoral thesis | ||||||||||||
Full Text Status: | Public | ||||||||||||
Subjects: | (A) Swedish standard research categories 2011 > 1 Natural sciences > 102 Computer and Information Science > 10203 Bioinformatics (Computational Biology) (applications to be 10610) (A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Bioinformatics and Systems Biology (methods development to be 10203) (A) Swedish standard research categories 2011 > 3 Medical and Health Sciences > 304 Medical Biotechnology > Biomedical Laboratory Science/Technology (A) Swedish standard research categories 2011 > 4 Agricultural Sciences > 403 Veterinary Science > Medical Bioscience | ||||||||||||
Agrovoc terms: | bioinformatics, genetics, ethics | ||||||||||||
Keywords: | bioinformatics, biobank, scholarly communication, ethics, genetics, galaxy, galaksio, the Molecular Methods database | ||||||||||||
URN:NBN: | urn:nbn:se:slu:epsilon-e-4443 | ||||||||||||
Permanent URL: | http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-e-4443 | ||||||||||||
ID Code: | 14669 | ||||||||||||
Faculty: | V - Veterinärmedicinsk fakultet (t.o.m. 2003) | ||||||||||||
Department: | (VH) > Dept. of Animal Breeding and Genetics | ||||||||||||
Deposited By: | Tomas Klingström | ||||||||||||
Deposited On: | 30 Oct 2017 12:45 | ||||||||||||
Metadata Last Modified: | 09 Sep 2020 14:17 |
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