Welcome to Protter — the open-source tool for interactive integration and visualization of annotated and predicted protein sequence features together with experimental proteomic evidence!
The code for the final version 1.0 has just been released, check it out at GitHub (https://github.com/ulo/Protter). A public instance of the Protter Server can be found at http://wlab.ethz.ch/protter/
- make sur you have an up-to-date Java runtime enivronment
- download MiKTeX from http://miktex.org/download
- install MiKTeX using default settings and make sure to select "Yes" for the "Install missing packages on-the-fly" option during setup.
- download the complete Protter package from http://ulo.github.io/Protter/ and extract the archive to your local drive (e.g. "C:\Protter")
- take a look at the "protter.config" file to configure the server to your enivronment
- double-click the extracted "protterServer.jar" file and open your browser at http://localhost:81/
Note #1: The very first time your Protter server is asked to generate a protein visualization, a MiKTeX window will pop-up where you have to confirm installation of tex\latex\textopo\textopo.sty. Note #2: The API to UniProt is changing every second month or so. If Protter gives you error messages regarding UniProt, shut down the Protter server, get the latest uniprotjapi.jar and copy it to the protterServer_lib subfolder (e.g. C:\Protter\protterServer_lib). Note #3: To access you Protter server from other machines in your network, make sure to open the used port (81 per default) in the Windows Firewall.
A manuscript on Protter has been published in Bioinformatics, 2013: http://bioinformatics.oxfordjournals.org/content/early/2013/11/21/bioinformatics.btt607.long
If you have questions, encounter any error or bug, or have suggestions on how to improve Protter, please contribute to the Protter discussion group: https://groups.google.com/d/forum/protter
This projected is licensed under the terms of the GNU General Public License v3.0.