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.
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
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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
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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
Saturday, January 2, 2016 5Single 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).
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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
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An administratormust set up the acquisitionmachine before the first use
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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
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
Saturday, January 2, 2016 36Single Cell Unit / D-BSSE
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