NetPathMiner implements a flexible module-based process flow for network path mining and visualization, which can be fully inte-grated with user-customized functions. It supports construction of various types of genome scale networks from three different pathway file formats, enabling its utility to most common pathway databases. In addition, NetPathMiner provides different visualization techniques to facilitate the analysis of even thousands of output paths.
To report bugs and arising issues, please visit https://github.com/ahmohamed/NetPathMiner
NetPathMiner depends on libxml2 and libsbml to process pathway files. Installation or running certain functions MAY fail if these prerequisite libraries are not available. Please read through the following instructions.
Make sure your system has library libxml2 installed. In Mac OSX 10.6 or later, libxml2 are built in. For Linux users also, this is almost always the case, however, developing headers may be missing. To install libxml2 and the headers:
sudo apt-get install libxml2
sudo apt-get install libxml2-dev
Installing libSBML for Unix users is optional. However, NetPathMiner will not be able to process SBML files. If you will not use SBML functions, you can skip this part.
From the website of libSBML http://sbml.org/Software/libSBML, you can directly download the binaries suitable for your system from ``Download libSBML'' link. You can follow the installation instructions on the website.
If you are installing the package through Bioconductor, you don't have to install external libraries. However, currently the Bioconductor version for Windows doesn't support SBML processing. Alternatively, we have prepared all dependencies in a tar file, downloadable from https://github.com/ahmohamed/NPM_dependencies . Please download the file and place in in the home directory of R (type R RHOME in command prompt to locate it), before installation.
Unless you want to use customized libraries, you can skip the rest of this section.To use customized libraries, you have to compile them and provide them to R at the time of installation. This is not a trivial task, please be sure you really need these custom libraries.
NetPathMiner expects an enviroment variable LIB_XML or LIB_XML2 pointing to directory where
libxml2 is installed. This directory should have both the compiled library (DLL file) and the header files.
You can download libxml2.dll from http://sourceforge.net/projects/gnuwin32/files/libxml/ among other sources.
Please, place it in a bin folder under the installation directory.
You will need also the header files, which can be obtained from NPM_dependecies.tar file. After extracing it, copy the include directory to the installation directory.
Finally, set the LIB_XML2 variable to point to the installation directory, which should now contain dll files inder bin
and header files under include.
Since libSBML is a C++ libraries, it needs to be compiled using GCC compiler. Unforturantely, there is no binary version for Windows comipled with GCC. To use libSBML, you need to build it from source.
First, dowload source package from http://sourceforge.net/projects/sbml/files/libsbml/ , extract it. You will
need also MinGW http://www.mingw.org/ or the 64-bit version http://mingw-w64.sourceforge.net/ depending on your system.
Add mingw/bin to your PATH, by editing eviroment variables.
Second, you need CMake http://www.cmake.org/ . You can follow the instructions at http://sbml.org/Software/libSBML/docs/java-api/libsbml-installation.html#windows-configuring , however, choose "MinGW Makefiles" instead of "Visual Studio 10".
After finishing the CMake step, use the MinGW's make.exe to compile libSBML. Copy the dependencies you used
during the compilation to the bin directory. Set the enviroment variable LIB_SBML to point the installation
directory, which should now contain dll files inder bin and header files under include
NetPathMiner depends on package igraph to represent network objects. Installing igraph is required for the package to work. You will also need devtools package to install directly from github. NetPathMiner suggests package rBiopaxParser to process BioPAX files, RCurl to download annotations from the web, and RCytoscape to visualise networks in Cytoscape. NetPathMiner can still work without installing the suggested packages, but you will not be able to use the aforementioned functionalities.
Package igraph is available at CRAN. To install it call:
install.packages("igraph")
Package devtools is available at CRAN. For Windows, this seems to depend on having Rtools for Windows installed. You can download and install this from: http://cran.r-project.org/bin/windows/Rtools/
To install R package devtools call:
install.packages("devtools")
For Unix users, make sure your Linux has library libcurl installed. Check out:
locate libcurl
locate curl-config
If these are not found (usually the developer version is missing), most Linux
users will be able to fix this by running:
sudo apt-get install libcurl4-openssl-dev
You will now be able to install R package RCurl. In R console:
install.packages("RCurl")
If you encounter other problems check out http://www.omegahat.org/RCurl/FAQ.html
Package rBiopaxParser is available on Bioconductor. For installation instructions check out http://www.bioconductor.org/packages/release/bioc/html/rBiopaxParser.html or call:
source("http://bioconductor.org/biocLite.R")
biocLite("rBiopaxParser")
to install it right away.
Package RCytoscape is available on Bioconductor. For installation instructions check out http://www.bioconductor.org/packages/release/bioc/html/RCytoscape.html . Please note that RCytoscape requires Cytoscape 2.8 installed with XMLRPC plugin. Cytoscape 3 is not yet supported. After installing Cytoscape, call:
source("http://bioconductor.org/biocLite.R")
biocLite("RCytoscape")
to install RCytoscape.
If everything went well you will be able to install the NetPathMiner package.
In R console, type:
source("http://bioconductor.org/biocLite.R")
biocLite("NetPathMiner")
In R console, type:
library(devtools)
install_github(repo="NetPathMiner", username="ahmohamed")