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RNAcommender

RNAcommender is a tool for genome-wide recommendation of RNA-protein interactions. It is a recommender system capable of suggesting RNA targets to unexplored RNA binding proteins, by propagating the available interaction information, taking into account the protein domain composition and the RNA predicted secondary structure.

Installing RNAcommender

RNAcommender can be installed from:

1. Docker (Kinematic)

2. Docker (standard)

3. Galaxy tool shed

4. Source code


1. Docker (Kinematic)

Docker containers wrap up a piece of software in a complete filesystem that contains everything it needs to run: code, runtime, system tools, system libraries - anything you can install on a server. This guarantees that it will always run the same, regardless of the environment it is running in.

RNAcommender can be run using Kinematic, which is part of the Docker Toolbox and can be installed on Mac OSX and Windows.

After installing Kinematic, RNAcommender can be run by following few easy steps:
  1. Search 'galaxy-rnacommender'
  2. Click on 'CREATE'
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  4. Wait for the Docker to be downloaded and started
  5. Then click on the a icon (next to 'WEB PREVIEW') to go to the Galaxy home page
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  7. RNAcommeder is available under the RNA subsection in the left menu
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2. Docker (standard)

Docker containers wrap up a piece of software in a complete filesystem that contains everything it needs to run: code, runtime, system tools, system libraries - anything you can install on a server. This guarantees that it will always run the same, regardless of the environment it is running in.

Docker can be installed on Linux, Mac, and Windows.

The Docker container for RNAcommender can be downloaded from Docker Hub:

docker pull gianlucacorrado/galaxy-rnacommender

or from Quay:

docker pull quay.io/gianlucacorrado/galaxy-rnacommender

The Docker container delivers a Galaxy instance with only RNAcommender pre-installed.


3. Galaxy tool shed

Galaxy is an open, web-based platform for data intensive biomedical research. Whether on the free public server or your own instance, you can perform, reproduce, and share complete analyses.

RNAcommender can be added as a tool to an existing Galaxy instance. RNAcommender can be installed from the tool shed.


4. Source code

Complete functionalities of RNAcommender are provided only in the command line based application. RNAcommender is implemented in Python and it is freely available.

Source code and documentation are available under MIT licence on github.





Please cite:
Gianluca Corrado, Toma Tebaldi, Fabrizio Costa, Paolo Frasconi, and Andrea Passerini. "RNAcommender: genome-wide recommendation of RNA-protein interactions." Bioinformatics (2016): btw517.


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