RNA centric research is of growing importance for medicine and molecular biology. Increasing amounts of data from deep sequencing experiments create a demand for automatic analysis and interpretation solutions. The RNA-Workbench offers a wide range of tools covering classic RNA-bioinformatics as well as RNA-seq fields. Predefined workflows for the annotation of non-coding RNAs or identification of differentially expressed genes are subsets of over 50 included tools from the categories RNA structure analysis, RNA alignment, RNA annotation, RNA-protein interaction, ribosome profiling, RNA-seq analysis and RNA target prediction. RNA specific visualisation solutions for dot-bracket plots and secondary structures are part of the workbench. In contrast to pre-existing solutions, our community driven approach allowes us to include classic RNA-bioinformatics tools often with the direct support of the tool-authors. These contributions enable us to provide excellent documentation, training material and interactive tours demonstrating the functionality of the workbench. Building on the Galaxy framework the workbench offers sophisticated analyses to users without command line knowledge, while emphasising reproducibility, customization and effortless scale up to larger infrastructures. The workbench is implemented as Galaxy Docker flavour and therefore easily extendable by additional tools, workflows, tours or training data, that can be installed from the Galaxy ToolShed. The workbench will be further improved and maintained in an ongoing community effort.

1. The RNA Workbench - reproducible,
transparent, and accessible RNA research
Florian Eggenhofer, Bj¨orn Gr¨uning, B´er´enice Batut, J¨org
Fallmann, Andrea Bagnacani, Peter F. Stadler, Rolf Backofen
and the RNA Workbench Team
Lehrstuhl Bioinformatik
University of Freiburg
16.03.2018

2. Goals of the RNA Workbench
Comprehensive set of RNA-bioinformatics tools

3. Goals of the RNA Workbench
Comprehensive set of RNA-bioinformatics tools
Community - authors and users

4. Goals of the RNA Workbench
Comprehensive set of RNA-bioinformatics tools
Community - authors and users
Set of predefined workflows and associated
descriptions/training material

5. Goals of the RNA Workbench
Comprehensive set of RNA-bioinformatics tools
Community - authors and users
Set of predefined workflows and associated
descriptions/training material
Easy and stable dissemination via Galaxy in Docker

6. Tools
More than 50 RNA bioinformatics tools

7. Tools Categories
More than 50 RNA bioinformatics tools

8. Workflows
Standardized analysis procedures

9. Workflows
Standardized analysis procedures
Based on tools as building blocks

10. Workflows
Standardized analysis procedures
Based on tools as building blocks
Can be developed, adapted and shared
(ToolShed/myexperiment.org)

11. Workflows
Currently six workflows in the RNA workbench
RNA
HTS analysisncRNA analysis
Structured RNA
RNA family model
C/D box scan
RNA-seq
PARCLIP
AREsite2-CLIP

12. Workflow - Analysis of non-coding RNAs
Test for functional structure via conservation

13. Workflow - Analysis of non-coding RNAs
Test for functional structure via conservation

14. Workflow - Analysis of non-coding RNAs
Test for functional structure via conservation

15. Workflow - Analysis of non-coding RNAs
Test for functional structure via conservation

16. Workflow - Analysis of non-coding RNAs
Test for functional structure via conservation

17. Workflow - Analysis of non-coding RNAs
Test for functional structure via conservation

18. Workflow - RNA family model construction
RNA family model construction

19. Workflow - RNA family model construction
RNA family model construction

20. Workflow - RNA family model construction
RNA family model construction

21. Workflow - RNA family model construction
RNA family model construction

22. Workflow - RNA-seq analysis
RNA-seq analysis

23. Workflow - RNA-seq analysis
RNA-seq analysis

24. Workflow - RNA-seq analysis
RNA-seq analysis

25. Workflow - RNA-seq analysis
RNA-seq analysis

26. Workflow - RNA-seq analysis
RNA-seq analysis

27. Workflows - CLIP analysis
PAR-CLIP analyse interaction sites of RNA-binding proteins

28. Workflows - CLIP analysis
PAR-CLIP analyse interaction sites of RNA-binding proteins
AREsite2 analyse CLIP data for AU-rich binding motifs

29. Visualisation
General purpose bar chart scatter plot
Connection to IGV, UCSC genome browsers
Specific RNA visualisation Dot plot, dot-bracket, tertiary
structure (3D)

30. Training & Usage

31. Training & Usage
Training

32. Training & Usage
Training
Training sessions (Introduction, HTS data and RNA-seq
analyses)

33. Training & Usage
Training
Training sessions (Introduction, HTS data and RNA-seq
analyses)
http://training.galaxyproject.org

34. Training & Usage
Training
Training sessions (Introduction, HTS data and RNA-seq
analyses)
http://training.galaxyproject.org
Galaxy Interactive Tours

35. Training & Usage
Training
Training sessions (Introduction, HTS data and RNA-seq
analyses)
http://training.galaxyproject.org
Galaxy Interactive Tours
Using the workbench

36. Training & Usage
Training
Training sessions (Introduction, HTS data and RNA-seq
analyses)
http://training.galaxyproject.org
Galaxy Interactive Tours
Using the workbench
docker run galaxy-rna-workbench

37. Training & Usage
Training
Training sessions (Introduction, HTS data and RNA-seq
analyses)
http://training.galaxyproject.org
Galaxy Interactive Tours
Using the workbench
docker run galaxy-rna-workbench
OSX and Windows using the graphical tool Kitematic

38. Acknowledgements & Thanks