openbis – an open resource for academic laboratories
TRANSCRIPT
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Caterina BarillariScientific IT Services, ETH Zurich
2018-09-13Caterina Barillari
openBIS – an open resource for academic laboratories
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Research workflow in experimental & computational labs
Sample preparation
Analysis Publication
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Measurement
Processing
Data collection
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What does it take to manage research data?
2018-09-13Caterina Barillari
Complex process that requires tracking and linking different types of information
Materials/samples
Protocols/ SOPs
Raw data
Processed data
Results
Code
Analysis notebooks
Model
TitleDate
MaterialsMethodsAnalysisResults
Experimental description/notes
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Results Analysis notebooks
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A very common scenario @ ETH
Experimental description/notes
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Materials/samples Code
Raw dataProcessed data
Protocols/ SOPs
Model
Local HD NAS CDS LTS
Cluster Cloud
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The ideal scenario
Central storage
TitleDate
Materials…..
A combined ELN/LIMS can provide such solution
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The ideal scenario
A combined ELN/LIMS can provide such solution
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Central storage
TitleDate
Materials…..
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openBIS facts
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Summer 2007• openBIS
development start (SystemsX)
April 2008• first openBIS
release (v08.04)
Summer 2009• SystemsX
projects start using openBIS
Summer 2013• openBIS ELN-
LIMS UI start
Spring 2014• first ELN-LIMS
beta version
May 2015• first
downloadable ELN-LIMS plugin
May 2016• first ELN-
LIMS official release
May 2017• BigDataLink
v.1
December 2017• JupyterHub
integration
Platform for managing scientific information and supporting research data workflows from “bench” to publication
Can be used in most quantitative science fields (e.g. life sciences, physics, env. sciences, etc)
Used by research groups and facilities @ ETH, Swiss & European Universities, a few companies
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openBIS in a nutshell
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openBIS is a solution for research labs
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openBIS in a nutshell
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openBIS is a solution for research labs
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openBIS in a nutshell
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openBIS is a solution for research labs
TitleDate
MaterialsMethodsAnalysisResults
ProjectsExperiments
Experimental steps
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openBIS in a nutshell
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openBIS is a solution for research labs
TitleDate
MaterialsMethodsAnalysisResults
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openBIS in a nutshell
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Workflow manager (e.g. Snakemake)
openBIS is a solution for research labs
TitleDate
MaterialsMethodsAnalysisResults
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Jupyter notebooks
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Application that combine documentation, code, input and output generated by the code, e.g. graphs, plots (Nature 515, 151–152)
Useful for exploratory data analysis and reproducibility >40 programming languages supported (Python, R, Scala, Julia, etc) Notebooks can be shared
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openBIS in a nutshell
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openBIS is a solution for research labs
Workflow manager (e.g. Snakemake)
TitleDate
MaterialsMethodsAnalysisResults
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openBIS solutionsopenBIS ELN-LIMS is available in two flavors:
For life sciences: customizable predefined types and fields suitable for most biological labs
Generic: only basic generic types predefined. To be fully customized by users.
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openBIS ELN-LIMS features
Relationships Import/Export
openBIS features
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Ordering
https://labnotebook.ch
User rights management
x
User rights management
Long term storage (tapes)
Audit trail
Data preservation
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Samples' storage manager
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openBIS ELN-LIMS features
Plasmid mapsBLAST search
openBIS features for life sciences
2018-09-13Caterina Barillarihttps://labnotebook.ch
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Best practices for openBIS introduction as ELN/LIMS in a biology lab
Create inventory of materials and samples
• Establish relationship between samples
Create inventory of standard lab protocols
• Link protocols to samples
Describe experiments
• Links to samples• Links to
protocols/copy protocols
• Upload data
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openRDM.swiss - National ARDM Service
Cloud-hosted openBIS ELN-LIMS• Virtual servers per research group, institute or institution• Generic or life-science ‘flavor’• Optionally with JupyterHub server for analytics• Automated deployment (Ansible)• Integration with Community Service Hub
Training & user support (‘best effort’)
Service Marketing & Business Model• Infrastructure & service charges for sustainable long-
term operation
Connection with repositories• Covering the entire data life cycle
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Acknowledgements
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Scientific Software and Data Management
• Matthew Baker (Group Head)• Franz-Josef Elmer• Juan Fuentes• Antti Luomi• Yves Noirjean• Althea Parker• Mikolaj Rybinski• Uwe Schmitt• Swen Vermeul• Cezary Czernecki
Research Informatics
• Thomas Wüst (Group Head)• Caterina Barillari• Vincenzo Capece• Tarun Chadha• Diana Coman Schmid• Henry Lütcke• Michal Okoniewski• Jarunan Panyasantisuk• Emanuel Schmid• Cristian Scurtescu
High-Performance Computing
• Olivier Byrde (Group Head)
• Steven Armstrong• Christian Bolliger• Urban Borstnik• Samuel Fux• Bruno Löpfe• Eric Müller• Allen Neeser• Christiane Pousa Ribeiro
Alex Upton (Community Project Manager)
Bernd Rinn (Section Head)The SIS team