openBIS from CISD

About the group

openBIS is being developed at the Center for Information Sciences and Databases (CISD) at the Department of Biosystems (D-BSSE) of ETH Zurich.
 
Extensions and integration solutions for biological research projects in SystemsX.ch and beyond are increasingly developed in the SyBIT community, an umbrella project initiated by SystemsX.ch to coordinate Systems Biology IT solutions.

 

Specific Contribution to Research in InfectX

CISD, supported by SyBIT, provides the InfectX community with "openBIS for HCS" - software for storing, organizing, browsing, searching and sharing all flavours of HCS data.
openBIS is integrated with iBrain2, which allows all the data to be imported automatically immediately after its acquisition. The system is being extended to satisfy specific needs of the InfectX project.
 
This is done in close collaboration with Mario Emmenlauer and Pauli Rämö, who gather user requirements and provide user training. The Research IT team, lead by Michael Podvinec, ensures that openBIS is running smoothly and is correctly configured.
 
Thanks to having all the data in openBIS, many tasks can be accomplished 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 heatmaps 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

 

Users

Besides InfectX, project solutions based on openBIS are currently used by several research projects of SystemsX.ch, several research consortia funded by the European Union and some pharmaceutical companies. e.g.:
  • openBIS in the HCS data pipeline runs productively at the LMC since early 2010.
  • at Vital-IT, Lausanne, an instance is running since the end of 2008, used by the SystemsX.ch RTD project LipidX.
  • a successful pilot project of openBIS as HCS image management solution has been run for Sanofi-Aventis (multinational pharmaceutical company, the world's fourth-largest by prescription sales).
  • a special "Publication Portal" extension is currently being developed for L. Pelkmans lab. The plan is to use openBIS to publish the final results of the screens, as an addition to the published papers.
  • SystemsX.ch RTD project DynamiX lead by Sebastian Maerkl uses openBIS to publish the projects results (data are not yet public)
 
openBIS is also used in many projects not related to HCS or Imaging.

CISD Members Involved in InfectX

Dr Bernd RinnDr Bernd Rinn, Head of CISD

 Contact

 

 

 

 


Software Development team:

Piotr Buczek, Franz-Josef Elmer, Kaloyan Enimanev, Pawel Glyzewski, Tomasz Pylak, Chandrasekhar Ramakrishnan