NetR is a Python script that allows users to integrate diverse lists of genes or proteins (from a series of experimental model organisms) into a network file that contains information about their interactions. With NetR, users also have the option of integrating curated information about genetic and protein-protein interactions stored in the Intermine database. The output network files generated by NetR are ready to be uploaded and visualized with Cytoscape, an open-source network mapping and visualization software.
AttR is a companion Python script that allows users to assign attributes to all the nodes present in a NetR network file. The AttR output file can also be directly uploaded into Cytoscape as an attributes table for a network. Both programs automatically update the gene or protein identifiers uploaded by the user to their most current identification.
NetR and AttR were conceived primarily to help experimental researchers in their efforts to integrate poorly structured published datasets that are highly valuable for the information that they contain but largely inaccessible to other network mapping programs.
Both NetR and AttR run on Python3, so users need to make sure that they have Python3 installed in their machines. Both programs also require the one-time installation of two dependencies: the Intermine API and the Pandas package for data structure and analysis in Python (see below for details). Once both dependencies have been locally installed, the NetR.py and AttR.py scripts can be started from command line in both Mac OS and Windows, and they will operate through a standard graphic user interface (GUI) with a familiar look and operability. Windows users can also download the corresponding standalone executable files, which will allow them to start the current version of both programs by double-clicking on the corresponding file/icon. NB: users will have to work around the usual warnings about opening programs from an unverifiable/untrusted source.
Users need to download and install the following:
- [Python3] (https://www.python.org/). Python3 can be downloaded and installed from the Python website through a standard download/install. To determine if Python was properly installed, open a command window (Windows)/terminal (Mac) and type
python
If you get an error message, Python will need to be (re-)installed. If Python is properly installed, you should see information about the version and location of the program (such as...)
Python 3.7.0 (v3.7.0:1bf9cc5093, Jan 25 2019, 07:44:31) [MSC v.1914 64 bit (AMD64)] on win32
Type “help”, “copyright”, “credits” or “license” for more information.
- [pip] Pip is a package-management system used to install and manage software packages written in Python, and is used to install the Intermine and Pandas packages mentioned below. The following information was obtained from the Raspberry.org website (Thank you!).
While pip is included in Python, it wouldn't hurt to check that it was properly installed. In a command/terminal window, type
pip --version
If pip is installed and working, you will see a version number and a directory path to the relevant files. If not, you may need to update it, by typing
Windows users
python -m pip install -U pip
MacOS users
$ sudo pip install --upgrade pip
- [Pandas] (https://pandas.pydata.org). The Pandas package needs to be installed only once via command line, as follows:
Windows users
C:\>pip install pandas
Mac users
C:\>pip3 install pandas
- [Intermine] (https://www.programmableweb.com/api/intermine). The Intermine API needs to be installed only once via command line, as follows:
Windows users
C:\>pip install intermine
Mac users
C:\>pip3 install intermine
If the intermine and Pandas packages are already locally installed, users will see a message indicating that the "Requirement is already satisfied" and a path to the installation. Users may also get a warning message about updating the pip installer. They may disregard this message - it will not affect their installation of the needed APIs.
Once Python3 and the Intermine and Pandas packages have been installed, users need to download the NetR.py and AttR.py files to a folder. We recommend that users create a folder in the Desktop, called "NetR_AttR".
To initiate NetR or AttR from terminal, users need to first navigate to the folder where both .py files where saved. For example, if they were saved in a folder called "NetR_AttR" in their desktop, they can first move to the desktop by typing the following in a terminal:
cd desktop
and then move to the NetR_AttR folder by typing
cd NetR_AttR
Once positioned in the folder containing the NetR.py and AttR.py files, both programs can be started by correspondingly typing in terminal...
Windows users
py NetR.py (or AttR.py)
Mac users
python3 NetR.py (or AttR.py)
Once started, both programs will operated through a graphic user interface (GUI) with a rather standard appearance and operability.
Windows users also have the option of downloading the two executable files (NetR.exe and AttR.exe) saved in this repository. Once downloaded, both programs can be started by double-clicking on the executable files, or double-clicking on the icons (if the files were copied to Desktop). Notice that you will likely get a typical warning about opening a program from an unverifiable/untrusted source.