An open source data pipeline for (non-) expert users
Open source data pipeline for HCS
The aim of this project is to provide an open source data mining platform - based on the integrative software platform KNIME - for integrating, sharing and processing HCS data using a workflow-oriented architecture which can be used by (non-) experts. Our intention is to develop a platform that covers the entire data pipeline of a high-throughput / high-content screen consisting of
- Basic compound / instrument / user management
- Data acquisition using automated microscopy
- Automated image processing
- Normalization together with quality control
- Data storage and archiving using relational databases
- Data analysis including data modeling and visualization for hit definition
- Bioinformatics
Thus, the entire software package will enable to (i) store and annotate HCS data; (ii) handle libraries (e.g. siRNAs); (iii) process images; (iv) define hits using multiparamteric classification methods; (v) browse through the data via visualization kits and (vi) answer quality control suits (see Screening pipeline below).
For data processing and analysis a large number of integrations is available. For a simplified overview, see
KNIME integrations
The overview also specifies integrations which are provided by BioQuant / RNAi Screening Facility - they can be downloaded as additional internal plugins
BioQuant
CellProfiler
in the Workflow Repository.