Tools for Understanding miRNA–mRNA Interactions for Reproducible RNA Analysis

  • Andrea BagnacaniEmail author
  • Markus Wolfien
  • Olaf Wolkenhauer
Part of the Methods in Molecular Biology book series (MIMB, volume 1912)


MicroRNAs (miRNAs) are an integral part of gene regulation at the post-transcriptional level. The use of RNA data in gene expression analysis has become increasingly important to gain insights into the regulatory mechanisms behind miRNA–mRNA interactions. As a result, we are confronted with a growing landscape of tools, while standards for reproducibility and benchmarking lag behind. This work identifies the challenges for reproducible RNA analysis, and highlights best practices on the processing and dissemination of scientific results. We found that the success of a tool does not solely depend on its performances: equally important is how a tool is received, and then supported within a community. This leads us to a detailed presentation of the RNA workbench, a community effort for sharing workflows and processing tools, built on top of the Galaxy framework. Here, we follow the community guidelines to extend its portfolio of RNA tools with the integration of the TriplexRNA ( Our findings provide the basis for the development of a recommendation system, to guide users in the choice of tools and workflows.

Key words

miRNA–mRNA interactions Gene regulation RNA workbench Galaxy Database 



The authors would like to thank the de.NBI and ELIXIR initiatives, for their support in the bioinformatics infrastructure. Thanks also to the Galaxy community, for developing, maintaining, and providing guidance on the use of this comprehensive framework. A warm thank you goes to the RBC Freiburg group, in particular to Anup Kumar, Björn Grüning, and Rolf Backofen for their efforts and commitment in improving the Galaxy framework.


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Andrea Bagnacani
    • 1
    Email author
  • Markus Wolfien
    • 1
  • Olaf Wolkenhauer
    • 1
    • 2
  1. 1.Department of Systems Biology and Bioinformatics, Institute of Computer ScienceUniversity of RostockRostockGermany
  2. 2.Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research CentreStellenbosch UniversityStellenboschSouth Africa

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