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:
* KNIME >= 3.1: http://www.knime.org
* Docker >= 1.9: https://www.docker.com/
* Generic KNIME Node (with Docker support): (https://github.com/genericworkflownodes/GenericKnimeNodes)

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. 

3) 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```

4) 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