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Reproducible bioinformatics

using pipelines and cloud -

in depth view

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Nikita Shvetsov

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Scientific developer / Senior engineer at UiT

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Challenges

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  • Data and processing platform

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  • Pipeline framework for pre-processing

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  • Reproducibility and documentation

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Infrastructural

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NOWAC (Norwegian women and cancer)

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Id-lung

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Tromsø Lung Study (i.c.w. Medsens.io)

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NOWAC lab scheme

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Lab interaction scheme (TLS - Medsens.io)

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Pipeline platform

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Core features

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  • git-like

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  • Incrementality

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  • k8s and cloud by design

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  • Reproducibility

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  • Language-agnostic

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  • Data provenance

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Omics explanations and pipelines

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mRNA preprocessing

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miRNA preprocessing

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DNAm processing

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Microarray data

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Data engineer

Researcher

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nikita.shvetsov@uit.no

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  • Infrastructure in place

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  • Support many omics types

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  • Already in use

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