Photo Jo Jorem Aarseth Lars Ailo Bongo larsabcsuitno Center for Bioinformatics SfB Interdisciplinary research and services Computer science Biotechnology Bioinformatics Special focus on marine metagenomics ID: 598591
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Slide1
Our cloud usage - and not
Photo: Jo
Jorem
Aarseth
Lars Ailo Bongo
(
larsab@cs.uit.no
)Slide2
Center for Bioinformatics (
SfB)
Interdisciplinary research and services
Computer science
Biotechnology
Bioinformatics
Special focus on marine metagenomics
~15 people
6
from computer science
http://sfb.cs.uit.noSlide3
Bioinformatics services for Norwegian users
ToolsPipelinesCompute resourcesStorage resources (project & archive)UiT, UiB, UiO, NTNU, NMBUUiT participating in all work packagesFinanced by NFR
Infrastruktur grantNew grant submitted
https://nels.bioinfo.no/Slide4
NeLS architectureSlide5
ELIXIR: An international distributed infrastructure for biological data
Data
Standards
Tools
Compute
Training
Technical platforms
User communities
Marine
metagenomics
Human data
Crop and forest plants
Rare diseasesSlide6
Technical ArchitectureSlide7
Backend ArchitectureSlide8
Cloud DeploymentSlide9
Norwegian Woman and Cancer (NOWAC)
Large and unique
biobank
of blood samples
Understand development of cancer (and how to avoid it)
Develop diagnosis approaches
Develop or improve treatment
http://site.uit.no/nowac/Slide10
Lung sounds
1000s of recordings (
Tromsøundersøkelsen
)
Machine learning based classification
Air pollution
Mobile air pollution measurements
Orchestrate crowd sourcingSlide11
inf-2202Slide12
OutreachSlide13
Cloud use in our research
Focus: build cloud technologiesTechnologies: Hadoop, HBase, Spark, Pachyderm, …AWS: Scalability evaluation(Uninett) Kubernetes (or Azure, GCP): Scalable pipelines with built-in data versioningAWS (or Azure, Tensorflow): Deep learningHeroku: Data management for air pollution
Github: open source repositoriesGoogle docs: paper writing
Slack: chat…Slide14
Cloud NOT used in our research
Data analyses on data we cannot move out of StalloGitlab for not (yet) open sourced softwareSharePoint for paper writingDeveloper clusterBut testing a virtual machine based clusterVirtual realitySlide15
Cloud use in infrastructure development
Focus: deliver data analysis servicesTechnologies: Spark, OpenStack, AppImage, JenkinsOpenStack: portable Spark based backend for research cloudsELIXIR cloud platform: run anlysesAWS (or Azure, GCP): scalability evaluationJenkins: application deployment
Jira: project coordinationBitbucket: private repositories
Github, slack, Google docs, ….Slide16
Cloud NOT used in infrastructure development
Stallo backendServersData storageDe-novo assemblySlide17
Cloud use in teaching
Focus: computer science educationTechnologies: Spark, Docker, Tensorflow, …GitHub and GitHub Classroom: course materialsAWS Education: big data analysis in an undergraduate course Slide18
Cloud NOT used in teaching
“In person” activitiesDeveloper machinesAll but one courseDigital exam?Mailing listsSlide19
Cloud use in outreach
We just created a Twitter accountWebinars in youtubeLær kidsa å kode activitiesSlide20
Cloud NOT used in outreach
“In person” activitiesWebpage hosted locallySlide21
Summary
Cloud in research:Must in computer scienceNeed in life scienceCloud in life science analysis services:Must to provide a good serviceEasier to develop and maintain servicesCloud in teaching:Should for computer scienceShould for other courses
Cloud in outreachMust and shouldSlide22
Summary - Issues
Who can develop the services?Who pays for the use of services?How to overcome cloud skepticism?Research vs. other usage?Ethical, legal, and political problemsSlide23
The Team
NOWAC
Einar
Holsbø
(PhD student)
Bjørn
Fjukstad (PhD student)
Morten
Grønnesby,
(PhD student)
Lung sounds,
and others
Johan
Ravn
(master student)
Frode
Opdahl
(master student)
Nina
Angelvik
(master student)
Center for Bioinformatics (
SfB
)
Edvard
Pedersen
(PhD student)
Espen
Robertsen
(PhD student)
Inge
Alexander
Raknes
(engineer)
Giacomo Tartari (engineer)
Aleksandr
Agafonov
(engineer)
Jon Ivar Kristiansen (system administrator)