12th Herbstseminar der Bioinformatik

Hosted Workshop

FRTW@HS14 --- Freiburg RNA Tools Workshop

by Sebastian Will

+++ Need to find targets for your non-coding RNAs like miRNAs or sRNAs?

+++ Want to find motifs, structures and alignments of your RNAs?

+++ Have RNAs with pseudoknots or more than one conserved structure?

+++ Using these or similar tools, but want to improve your results?

+++ Wonder about the hidden advanced features of these tools?

+++ Want to see the future of RNA bioinformatics today?


In this workshop, you will learn to practically apply the online tools that help you out: IntaRNA, LocARNA, ExpaRNA, and CARNA. In two sessions, you will have time to follow examples and explore the tools live on your notebook and pick up the essential background.

To provide a short overview, IntaRNA performs fast and accurate prediction of interactions between two RNA molecules; LocARNA computes multiple alignment of RNA molecules -- at the same time predicting RNA structures and taking structure similarities into account; ExpaRNA determines exactly matching local sequence-structure motifs in RNAs; and CARNA finds optimal RNA alignments considering pseudoknotted structure, multiple structures, or entire RNA ensembles.

As a special bonus you will witness a miracle: life access to the Freiburg RNA Webserver without Internet!


The workshop will be held in the conference room of hotel JEF. It is planned that we have two days, 7th and 8th of October, with a session of 90 minutes each day. We will give you an update when there is new information available.


None, but all these tools (and some more) are accessible online at rna.informatik.uni-freiburg.de including documentation and more detailed background information; you are invited.


Be the first of your peers to run the Freiburg RNA Tools HS14-Edition on your own notebook!
Bringing your own installation to the workshop is HIGHLY APPRECIATED, since it helps to save valuable computational ressources and bandwidth. Of course, you will most directly profit from the exclusive access to your own webserver instance.

To install the software, first of all you need a recent Linux installation; the rest is fairly simple:
  1. Install docker

    For most common Linuces, specific installation information is provided at https://docs.docker.com/

    It is very important to install a recent docker (>=version 1.2); some systems still offer older versions by default.

  2. Run the web server (as root/using sudo)

    >docker run -d -p 9999:8080 -h frtwebserver bgruening/freiburger-rna-tools

    The first time you call this you need fast internet and probably still have to wait for some time. The second time, this will be started from your local disk. So, DON'T wait until you are in Doubice (or on your way).

  3. Test it!

    browse to localhost:9999

  4. optionally, kill the webserver again

    ask for the docker module name:

    >docker ps

    and then run

    >docker stop <name>


Active participants will be officially authorized to bear the title "Certified Freiburg RNA Tools user (HS14)" in personal communications with the Freiburg RNA Tools team and receive preferential attention at the team's discretion.