workshop_2019

Processing of proteomics data in KNIME (November 2019)

On the 20th of November 2019 we organized the first workshop on processing of proteomics data using the KNIME software .

In the theoretical part the software container was introduced along with the general description of KNIME environment itself and its components and features. We also introduced the pipeline we use for the processing of label-free bottom-up mass spectrometry data and the wide variety of tools we are using in this process (e.g. normalization and imputation techniques, visualizations, etc.)

In the practical part the participants had hands-on experience with the KNIME environment (we were using version 3.7.2a), they tried to build their own workflow and then to process the model data using workflow for initial processing of label-free quantitative proteomics data.

Materials related to the workshop:

• Presentations for the workshop
  • Software container running KNIME
  • Introduction to KNIME
  • Practical applications, our KNIME metanodes
• KNIME manual (describing step-by-step everything which was done in the practical part)
• Model workflow (used for the practical part, processed; compressed exported workflow; please extract the exported workflow (knwf file) into your KNIME workspace, import it into KNIME and open it)

Organizers

The workshop was organized by people from several laboratories (in alphabetical order):

• Kristína Gömöryová
  • Laboratory of cellular communication, Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
• David Potěšil
  • Proteomics Research group, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
• Zbyněk Zdráhal
  • Proteomics Research group, Central European Institute of Technology, Masaryk University, Brno, Czech Republic

Assistants

• Proteomics Research group, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
  • Ranjani Ganji
  • Pavel Hruška
  • Anna Schneiderová

Acknowledgement

We would like to acknowledge work of all people from events office of CEITEC-MU that help us to make the workshop happen.

Access to the CERIT-SC computing and storage facilities provided by the CERIT-SC Center, under the programme "Projects of Large Research, Development, and Innovations Infrastructures" (CERIT Scientific Cloud LM2015085), is greatly appreciated.