WFRF:(Hinsen Konrad Researcher)
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| Fältnamn | Indikatorer | Metadata |
|---|---|---|
| 000 | 04945nam a2200637 4500 | |
| 001 | oai:DiVA.org:uu-358353 | |
| 003 | SwePub | |
| 008 | 180828s2018 | |||||||||||000 ||eng| | |
| 020 | a 9789151304274q print | |
| 024 | 7 | a https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-3583532 URI |
| 040 | a (SwePub)uu | |
| 041 | a engb eng | |
| 042 | 9 SwePub | |
| 072 | 7 | a vet2 swepub-contenttype |
| 072 | 7 | a dok2 swepub-publicationtype |
| 100 | 1 | a Lampa, Samuel,d 1983-u Uppsala universitet,Institutionen för farmaceutisk biovetenskap,Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Stockholm, Sweden,Pharmaceutical Bioinformatics4 aut0 (Swepub:uu)samla868 |
| 245 | 1 0 | a Reproducible Data Analysis in Drug Discovery with Scientific Workflows and the Semantic Web |
| 264 | 1 | a Uppsala :b Acta Universitatis Upsaliensis,c 2018 |
| 300 | a 68 s. | |
| 338 | a electronic2 rdacarrier | |
| 520 | a The pharmaceutical industry is facing a research and development productivity crisis. At the same time we have access to more biological data than ever from recent advancements in high-throughput experimental methods. One suggested explanation for this apparent paradox has been that a crisis in reproducibility has affected also the reliability of datasets providing the basis for drug development. Advanced computing infrastructures can to some extent aid in this situation but also come with their own challenges, including increased technical debt and opaqueness from the many layers of technology required to perform computations and manage data. In this thesis, a number of approaches and methods for dealing with data and computations in early drug discovery in a reproducible way are developed. This has been done while striving for a high level of simplicity in their implementations, to improve understandability of the research done using them. Based on identified problems with existing tools, two workflow tools have been developed with the aim to make writing complex workflows particularly in predictive modelling more agile and flexible. One of the tools is based on the Luigi workflow framework, while the other is written from scratch in the Go language. We have applied these tools on predictive modelling problems in early drug discovery to create reproducible workflows for building predictive models, including for prediction of off-target binding in drug discovery. We have also developed a set of practical tools for working with linked data in a collaborative way, and publishing large-scale datasets in a semantic, machine-readable format on the web. These tools were applied on demonstrator use cases, and used for publishing large-scale chemical data. It is our hope that the developed tools and approaches will contribute towards practical, reproducible and understandable handling of data and computations in early drug discovery. | |
| 650 | 7 | a MEDICIN OCH HÄLSOVETENSKAPx Medicinska och farmaceutiska grundvetenskaperx Farmakologi och toxikologi0 (SwePub)301022 hsv//swe |
| 650 | 7 | a MEDICAL AND HEALTH SCIENCESx Basic Medicinex Pharmacology and Toxicology0 (SwePub)301022 hsv//eng |
| 650 | 7 | a NATURVETENSKAPx Data- och informationsvetenskapx Bioinformatik0 (SwePub)102032 hsv//swe |
| 650 | 7 | a NATURAL SCIENCESx Computer and Information Sciencesx Bioinformatics0 (SwePub)102032 hsv//eng |
| 653 | a Reproducibility | |
| 653 | a Scientific Workflow Management Systems | |
| 653 | a Workflows | |
| 653 | a Pipelines | |
| 653 | a Flow-based programming | |
| 653 | a Predictive modelling | |
| 653 | a Semantic Web | |
| 653 | a Linked Data | |
| 653 | a Semantic MediaWiki | |
| 653 | a MediaWiki | |
| 653 | a RDF | |
| 653 | a SPARQL | |
| 653 | a Golang | |
| 653 | a Reproducerbarhet | |
| 653 | a Arbetsflödeshanteringssystem | |
| 653 | a Flödesbaserad programmering | |
| 653 | a Prediktiv modellering | |
| 653 | a Semantiska webben | |
| 653 | a Länkade data | |
| 653 | a Go | |
| 653 | a Bioinformatics | |
| 653 | a Bioinformatik | |
| 653 | a Pharmacology | |
| 653 | a Farmakologi | |
| 700 | 1 | a Spjuth, Ola,c Docent,d 1977-u Uppsala universitet,Institutionen för farmaceutisk biovetenskap,Science for Life Laboratory, SciLifeLab4 ths0 (Swepub:uu)olspj499 |
| 700 | 1 | a Grafström, Roland,c Professoru Institute of Environmental Medicine, Karolinska Institutet4 ths |
| 700 | 1 | a Hinsen, Konrad,c Researcheru Centre de Biophysique Moléculaire (CNRS), Orléans, France4 opn |
| 710 | 2 | a Uppsala universitetb Institutionen för farmaceutisk biovetenskap4 org |
| 856 | 4 | u https://uu.diva-portal.org/smash/get/diva2:1242336/FULLTEXT01.pdfx primaryx Raw objecty fulltext |
| 856 | 4 | u https://uu.diva-portal.org/smash/get/diva2:1242336/PREVIEW01.jpgx Previewy preview image |
| 856 | 4 8 | u https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-358353 |
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