openBIS from SIS


About openBIS

openBIS was originally developed by the Center for Information Sciences and Databases (CISD) at the Department of Biosystems Science and Engineering (D-BSSE) of ETH Zurich. In 2013, CISD was incorporated into the Scientific IT Services division (SIS) of ETH Zurich, where development of openBIS continues in the SIS group Scientific Software and Data Management (SSDM).


Extensions and integration solutions for biological research projects in and beyond have been developed by the SyBIT community, which coordinates Systems Biology IT solutions within SIS has now taken over SyBIT project responsibilities for ETH Zurich.

Specific Contribution to Research in TargetInfectX


SIS provides the TargetInfectX community with "openBIS for HCS", which is a software for storing, organizing, browsing, searching and sharing all flavors of HCS data.

openBIS is integrated with the Bee Workflow Manager (BeeWM), which is used to control automatic import of the data, immediately after its acquisition, and its subsequent analysis on the cluster. Data can be analyzed multiple times using different algorithms and everything is tracked in openBIS via BeeWM.  

The system has been extended on demand to satisfy specific needs of the InfectX and TargetInfectX projects. This was done in close collaboration with Mario Emmenlauer and Pauli Rämö, who gathered user requirements and provided user training.

The sciCORE team –the scientific computing facility of the University of Basel- ensures that openBIS is running smoothly and is correctly configured.

openBIS allows users to accomplish many tasks quickly, e.g.:

•          finding all the images acquired for a specified gene, together with the results of image analysis

•          sharing data with collaborators

•          publishing results

•          archiving raw data without loosing the possibility of having an overview of the images

•          visualizing quality assurance data and analysis results on the heat maps with direct access to images

•          showing the images of the chosen well and plate, optionally with information about image segmentation

•          finding images in wells annotated with specified tags

•          calculating aggregated statistics and rankings for each gene


Besides TargetInfectX, project solutions based on openBIS are currently used by several research projects of, research facilities and labs at ETH Zurich and beyond, pharmaceutical companies, and will be used in the European FAIRDOM project for sharing data and models.

SIS Members Involved in TargetInfectX

Dr Bernd Rinn, Head of SIS.

Scientific Software and Data Management team

Chandrasekhar Ramakrishnan (Group Head), Franz-Josef Elmer, Juan Mariano Fuentes Serna, Sascha Fedorenko, Bela Hullar, Piotr Kupczyk, Antti Olavi Luomi, Emanuel Schmid, Uwe Schmitt, Jakub Straszewski.