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ImmunoNodes - Commandline tools and KNIME extension of FRED 2

What is ImmunoNodes:

ImmunoNodes is a collection of immunoinformatics command line tools and community KNIME nodes (http://www.knime.org), written in Python with FRED 2 (http://fred-2.github.io/). It offers unified interfaces to many popular immunoinformatics methods and covers a wide variety of standard applications, such as: (neo-)epitope, cleavage site, and TAP prediction, as well as HLA genotyping, and epitope-based vaccine design. Building onto of KNIME, ImmunoNodes is a powerful and intuitive toolbox to develop complex workflows, even without any programming experience.

Licensing:

The ImmunoNodes source code is published under a 3-clause BSD license. The licenses of the individual applications integrated into ImmunoNodes can be found in LICENSE.

  • DTU(CBS) Prediction tools (NetMHC etc): Academic use only (please contact the administration of CBS for non-academic use http://www.cbs.dtu.dk/)
  • LKH Solver: Academic use only (please contact the author of LKH for non-academic use http://www.akira.ruc.dk/~keld/research/LKH/)
  • CBC Solver: Eclipse Public License v1.0
  • Docker: Apache License v2.0
  • Generic KNIME Nodes: Apache License v2.0

Prerequisite:

ImmunNodes is platform independent using Docker images (https://www.docker.com/), the CPU must support VT-x or AMD-v.

For KNIME integration you need:

For commandline tool usage, you can either use the provided Docker image and call the command lines within the Docker container (see Installation).

Installation

To install ImmunoNodes, please make sure that you fulfill all prerequisites and that you have installed KNIME >= 3.1 and Docker >= 1.9.

  1. First, download ImmunoNodes' Docker image by typing the following command on the command line:
docker pull aperim/immunonodes

and executing it by hitting Enter. This will download the image from Docker Hub.

To install it, start KNIME and click Help->Install New Software and add the nightly build URL if you not have done so already:

http://update.knime.org/community-contributions/trunk
2) ImmunoNodes is, as of now, available in KNIME's nightly branch.

Once you have added and selected the nightly build, you are ready to install ImmunoNodes.

  1. ImmunoNodes is listed under KNIME Community Contributions (nightly build) - Bioinformatics & NGS, or simply type in the search field ImmunoNodes. Mark ImmunoNodes, hit Next, and follow the installation instructions on the screen. After a KNIME restart, ImmunoNodes should be listed under Community Nodes

  2. Lastly, you have to set KNIME's directory for temporary files to a folder beneath our user directory. Otherwise Docker wont function properly. To do so open KNIME and open the Perferences. Click on menu open KNIME and change the directory specified in the Directory for temprary files-option to a directory in your user-directory.

Citation

Please cite:

Schubert, B., De la Garza, L., Mohr, C., Walzer, M., and Kohlbacher O. (2017). ImmunoNodes – Graphical Development of Complex Immunoinformatics Workflows. BMC Bioinformatics (accepted).

and the original articles of the methods used in your workflow.

Contact

Benjamin Schubert
schubert@informatik.uni-tuebingen.de
University of Tübingen, Applied Bioinformatics,
Center for Bioinformatics, Quantitative Biology Center,
and Dept. of Computer Science,
Sand 14, 72076 Tübingen, Germany