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.

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.

I am currently developing the openBIS Importer Toolset at the Single Cell Unit of the D-BSSE as part of my appointment as a data management engineer.

The Single Cell Unit (SCU) is a centralized scientific facility that provides equipment in the areas of flow cytometry, advanced automated microscopy and laboratory automation.

In collaboration with the IT Services and Consulting group (ITSC) and the Center for Information Sciences and Databases (CISD), the SCU provides centralized, secured storage for all the raw data acquired in the facility. The associated metadata is stored in a department-wide installation of openBIS.

Data registered in openBIS will be easily accessible for further analysis and processing work either on high-end workstations and dedicated processing servers (e. g. the Huygens Remote Manager) provided by the SCU, or from end-user machines.

Group instances of openBIS can access data in the SCU openBIS instance via linked datasets. This allows groups to organize their openBIS instance as desired and without data duplication.

Toolset composition

The openBIS Importer Toolset is composed of several tools (Annotation Tool, Datamover as Windows service, Dropbox scripts, server-side plug-ins, custom HTML5 views) described in detail in the following poster, presented at the OME Meeting 2013 in Paris.

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

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

User and administrator instructions

Documentation is hosted externally; it is still incomplete.