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b-schubert edited this page Oct 29, 2015 · 2 revisions

FRED2 - A Framework for Epitope Detection and Vaccine Design

Copyright 2014 by Benjamin Schuber, Mathias Walzer, Philipp Brachvogel, Andras Szolek, Christopher Mohr, and Oliver Kohlbacher

FRED is a framework for T-cell epitope detection, and vaccine design. It offers consistent, easy, and simultaneous access to well established prediction methods for MHC binding and antigen processing. FRED can handle polymorphic proteins and offers analysis tools to select, assemble, and design linker sequences for string-of-beads epitope-based vaccines. It is implemented in Python in a modular way and can easily be extended by user defined methods.

For Users

Getting started

The current stable version can be found in the master branch and can be directly install via pip with:

pip install git+https://github.com/FRED-2/Fred2

You should start by reading the Ipython tutorials and documentation.

Getting in Contact

For general usage problems, bug reports and questions, please contact the authors schubert@informatik.uni-tuebingen.de or walzer@informatik.uni-tuebingen.de.

Reporting Bugs/Issues

In order to report a new bug, please use either our GitHub issues system or contact us directly.

Please include the following information into your bug report:

  • the source snippet
  • the complete trace back
  • operating system (e.g. "Windows XP 32bit", "Win 7 64bit", "Fedora 8 32bit", "MacOS 10.6 64bit")
  • Python version and module versions (e.g. Biopython, Pandas, Pyomo)

Please provide files that we need to reproduce the bug via a download link, via the mailing list or by directly contacting one of the developers.

For Developers

Developing with FRED2

If you would like to contribute to FRED2, this is how to best get started:

Any questions can be directed at the mailing list.

Development model

FRED2 follows the Gitflow development workflow which is excellently described here. Additionally we encourage every developer (even if he/she is eligible to push directly to FRED2) to create his own fork (e.g. @username). The GitHub people provide superb documentation on forking and how to keep your fork up-to-date. With your own fork you can follow the Gitflow development model directly, but instead of merging into "develop" in your own fork you can open a pull request. Before opening the pull request, please check the checklist

Some more details and tips are collected here.

Coding Convention

FRED2 follows the PEP8 style guide and uses Sphinx for documentation.

Commit Messages

In order to ease the creation of a CHANGELOG we use a defined format for our commit messages.

See the manual for proper commit messages: How to write commit messages

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