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ApicoAPCS / ApicoAP-CS Client Software User Manual

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Introduction

ApicoAP-CS Client Software is a program that is capable of training classifiers for predicting Apicoplast targeted proteins that use bipartite signaling mechanism (ApicoTPs).

Instructions for running ApicoAP-CS

Requirements: Python version 2.7x is needed to launch the software, which can be downloaded from http://www.python.org/download/releases/2.7.3/ . First, unpack the archive ApicoAPCSxx.zip on your path of choice. Please note some files in this directory are essential and any damage to them would cause ApicoAP-CS Client Software stop working.

ApicoAP-CS Client Software depends on two external libraries:

We recommend you to download the source codes of these libraries (with the extension .tar.gz) and unzip them in in the location where python.exe exist (In Windows, it is under C:/Python 27/). This way you don't have to worry about adding the paths of these libraries to PYTHONPATH. Once they are unzipped to folders named setuptools-0.6c11 and suds-0.4, here is what you have to do to install them:

  • Open a command window and change directories to the location of setuptools-0.6c11, and type: python setup.py install
  • Then, change directories to the location of suds-0.4, and type: python setup.py install

Running these commands should install these libraries in your system. Please note that having installed Python version 2.7x in your system is crucial for these libraries to work.

NOTE: Sometimes, run-time messages (mostly warnings) will occur due to different versions of some of the supporting software. These messages should be ignored since they are benign.

Launching ApicoAP-CS Client Software with Graphical User Interface (GUI):

  • For Mac OS X, simply double-clicking ApicoAPCS_Client_GUI.py would launch the software if the default program to open ".py" files is set to be the terminal. If instead of the program, an editor opens the source code, and you don't know how to change the default program to open a file, then, open the Terminal app, change directories to the location of ApicoAP-CS Client Software, and type: python ApicoAPCS_Client_GUI.py

  • NOTE on MAC OS X: Splash screen of the program may not appear when above instructions were followed. Instructions will be included as a separate wiki page for you to convert .py file to an .app file at the end of this document. When app file is launched splash screen will be visible.

  • For Windows, simply double click on ApicoAPCS_Client_GUI.py or open a command prompt, change directories to the location of ApicoAP-CS Client Software, and type:
    python ApicoAPCS_Client_GUI.py

Instructions for using ApicoAP-CS Client Software GUI

Check out the Supplementary User Manual for the instructions to use this software. This manual can be found under the downloads link. Also you can watch the manual video.

Please cite the following paper if you are using this tool: Cilingir, Gokcen, and Shira L. Broschat. "Automated Training for Algorithms That Learn from Genomic Data." BioMed research international 2015 (2015).

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