The openBIS Importer Toolset is a tightly integrated collection of tools that allows for the semi- automated, semi-unsupervised registration of annotated datasets into openBIS directly from the acquisition stations.

1. Aaron Ponti
Single CellFacility,D-BSSE ETHZ(Basel) aaron.ponti@bsse.ethz.ch

2. Saturday, January 2, 2016 2Single Cell Unit / D-BSSE
Raw data
centralized storage
HRM
backed upannotated

3. openBIS – open Biology Information System
openBIS is an extensible, open source software framework for constructing user-
friendly, scalable and powerful information systems for data and metadata
acquired in biological experiments.
It enables users to collect, integrate, share, publish data and to connect to data
processing pipelines.
http://www.cisd.ethz.ch/software/openBIS
3Saturday, January 2, 2016 Single Cell Unit / D-BSSE

4. § Separate metadata (application server) and data (data store server)
§ Clean and flexible hierarchical metadata structure:
§ Space > Project > Experiment > Sample > Dataset > File
§ Authorization at space level
§ Samples and datasets: entities have parent/child or container/contained relationships
§ Datasets belong to samples orexperiments
§ All entities have user defined types, propertiesand vocabularies
§ Attachments can be associated to most entities
§ Information indexing and searching by metadata
§ Rich set of APIs and plug-in interfaces
§ Java, Python (Jython), RESTful web services
openBIS core
Saturday, January 2, 2016 4Single Cell Unit / D-BSSE

5. § Core plug-ins
§ Dropboxes(dataset ingestion)
§ Master data (import/export/updateuser types, properties,assignments)
§ Data sources (additional databases)
§ Aggregation (reporting)plug-ins (metadata collection)
§ Processing plug-ins (on datasets)
§ Ingestion plug-ins (create/update entities)
§ Maintenance tasks (update/fix)
§ Web applications / RESTful web services (custom openBIS views)
§ An organized set of core plug-ins can become a “core technology”
§ Core plug-ins extend openBIS APIs to interface with custom client apps
openBIS extensions
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6. openBIS “vanilla”
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7. Current technologies
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8. Screening core technology
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9. Custom web apps
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10. Custom web apps
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11. Custom web apps
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12. Embedded openBIS
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13. Embedded openBIS
Saturday, January 2, 2016 13Single Cell Unit / D-BSSE

14. Saturday, January 2, 2016 14Single Cell Unit / D-BSSE
Raw data
centralized storage
HRM
backed upannotated

15. oBIT – openBIS Importer Toolset
The openBIS Importer Toolset is a tightly integrated collection of tools that allows
for the semi-automated, semi-unsupervised registration of annotated datasets
into openBIS directly from the acquisitionstations.
It also extends openBIS with custom data viewers and server-side core plug-ins
packaged into two new official core technologies (flow cytometry and microscopy).
15Saturday, January 2, 2016 Single Cell Unit / D-BSSE

16. openBIS
Data storeopenBIS
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Export
or save
as aWindows service
Acquisitionstation
dropbox
Example: BD LSRFortessa cell analyzer
Scan
Annotate
Incoming
User
folder
Annotation Tool

17. [Admin] Annotation Tool Admin
Saturday, January 2, 2016 17Single Cell Unit / D-BSSE
An administratormust set up the acquisitionmachine before the first use

18. Saturday, January 2, 2016 18Single Cell Unit / D-BSSE
Set the openBIS URL(s)
[Admin] Annotation Tool Admin

19. [Admin] Annotation Tool Admin
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Select the acquisitionstationor type

20. [Admin] Annotation Tool Admin
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Set the local working directories

21. Light microscopes
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bio-formats

22. Saturday, January 2, 2016 22Single Cell Unit / D-BSSE

23. Saturday, January 2, 2016 23Single Cell Unit / D-BSSE
pontia
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pontia
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pontia
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26. Incoming
User
folder
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1
2
3
4
5
67

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28. Saturday, January 2, 2016 28Single Cell Unit / D-BSSE

29. Saturday, January 2, 2016 29Single Cell Unit / D-BSSE

33. Experiment/dataset actions
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34. Deconvolution (Huygens Remote Manager)
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35. Huygens Remote Manager
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http://huygens-rm.org http://svi.nl
https://github.com/aarpon/hrm
https://github.com/aarpon/hrm_ng

36. Installation instructions and user manuals
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openBIS http://www.cisd.ethz.ch/software/openBIS
The openBIS Importer Toolset requires openBIS 15.xx that will be released soon.
oBIT https://wiki-bsse.ethz.ch/display/oBIT
User manuals and detailed installation instructions.
https://github.com/aarpon
openBIS Importer Toolset repositories, packages and installer.

37. openBIS – new technologies
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http://www.cisd.ethz.ch/software/openBIS

38. openBIS Importer Toolset Installer
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https://github.com/aarpon/obit_installer/releases

39. Saturday, January 2, 2016 39Single Cell Unit / D-BSSE
https://wiki-bsse.ethz.ch/display/oBIT

40. Summary
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§ The openBIS/openBIS Importer Toolset synergy aims to:
§ offer a powerful and scalable data and metadata management
system
§ streamline data registration directly from the acquisition machines
§ support multiple acquisition hardware classes
§ offer a reasonably simple way for third parties to add support for
new hardware classes

41. Acknowledgments
Saturday, January 2, 2016 41Single Cell Unit / D-BSSE
SIS
Bernd Rinn
Chandrasekhar Ramakrishnan
Piotr Kupczyk
Antti Luomi
Jakub Straszewski
Franz-Josef Elmer
Juan Fuentes Serna
Caterina Barillari
Manuel Kohler
ITSC
VernonBailey
Simon Paul Diethelm
JohnRyan
AndreasJecklin
https://wiki-bsse.ethz.ch/display/oBIT