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Abstract

The openBIS Importer Toolset is a set of tools to streamline registration of acquired data and metadata into openBIS and extend openBIS via custom views and apps for working with data.

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openBIS

openBIS Importer Toolset

Description

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.

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.

The openBIS Importer Toolset is being developed at the Single Cell Unit (SCU) of the D-BSSE in collaboration with Scientific IT Services (SIS) of the ETH Zurich.

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The openBIS Importer Toolset will support a variety of hardware classes (flow cytometers, cell sorters, light microscopes, automation robots) and will provide an infrastructure for third-parties to support even more types of acquisition machines. Currently, oBIT supports the cell analyzers and sorters from BD (Becton Dickinson) BioSciences and all bio-formats compatible light microscopes.

openBIS Importer Toolset flow chart

The initial goal of the openBIS Importer Toolset was to offer optimized workflows for registering data into openBIS from shared acquisition stations. With time, it is also progressively extending openBIS itself with custom data viewers and server-side core plug-ins packaged into two official openBIS core technologies. Soon, two new official openBIS core technology for flow cytometry and microscopy will be released along with openBIS.

The openBIS Importer Toolset relies on two components that are installed and configured on the acquisition machine: the Annotation Tool and Datamover as a Windows Service; and on a third one: a hardware class-specific openBIS dropbox core plug-in that is on the remote data store server. 

Data to be registered is directly saved or exported into a specified user folder at the end of an acquisition round.

When the data is ready to be registered, the user launches the Annotation Tool that scans the data and allows the user to add custom and optional annotations. Data and metadata in the form of an XML file are then moved to a folder that is monitored by Datamover, a background service that checks for new data periodically and moves it to the dropbox folder on the data store server after a validation step.

On the data store server (one of the two server components of openBIS), a dropbox core-plugin registers the data to openBIS using the annotations provided in the XML file.

Most of this is transparent to the user, who only needs to interact with one tool: the Annotation Tool.

openBIS Importer Toolset talks and posters

oBIT was presented at various conferences. Here a selection of talks and posters.

 openBIS Importer Toolset talk at the 3rd OpenBIS user Group Meeting (2016) [10MB]

 openBIS Importer Toolset talk at the EuBIAS Meeting 2015 [10MB]

 openBIS Importer Toolset talk at the OME Meeting 2014 [12MB]

 openBIS Importer Toolset poster at the OME Meeting 2013 [18MB]

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