• Pathway Projector overview

• Zoomable User Interface

» Google Maps API

» Ext JS 2.0

• Pathway map

» KEGG Atlas

» Re-creation

• Search

• Meta word search

• Molecular mass search

» Results

• Route search

» Results

• Sequence-based search (BLAST)

» Results

• Pathway prediction (GEM System)

• Output

• Annotation

• Data mapping

• Mapping format

» Organism

» Genes

» Proteins

» Metabolites

» Time series data

» Pathway

» Organism comparison

• SOAP service

» Perl

» Python

» Ruby

• Manual editing

» XML data export

» XML data import

• Data

• Information window

» Click mode

» Mouse over mode

• Organism

• Databases

• Installation

Installation

Here we describe the instructions for setting up local copy of the limited version of Pathway Projector, which only includes working a reference pathway map and keyword search only. This process requires a web server supporting the execution of Perl-based CGI. Following examples are based on MacOS X 10.5. And require Perl module Image::Size.pm

• License

Pathway Projector is available under GNU General Public License v.3.

According the KEGG license, the Pathway Projector download version does not include KEGG data (e.g. svg file and image file)

Important Notice: The software automatically utilizes KEGG data on the server side. Academic users may freely download the KEGG data as provided at the GenomeNet ftp site at ftp://ftp.genome.ad.jp/pub/kegg/, but non-academic users are requested to obtain a license agreement through the licensor, Pathway Solutions Inc., for installation of KEGG at their sites, for distribution or reselling of KEGG data, for software development and any other commercial activities that make use of KEGG, and also as end users of the third-party programs that access the KEGG ftp site.

• Download

Download version available at: PathwayProjector.tar.gz (68Mb)

% wget "http://www.g-language.org/PathwayProjector/PathwayProjector-1.0.tar.gz"
% tar -xzf PathwayProjector-1.0.tar.gz
% mv PathwayProjector-1.0 /Library/WebServer/Documents/

• KEGG images

This package does not include KEGG images. Therefore, users have to download. This program get_img.pl download KEGG images in these directory "compound_gif" and "reaction_gif".

% cd PathwayProjector-1.0/lib/
% perl get_img.pl

• .htaccess

PathwayProjector directory must be CGI-executable. Since the directory contains its own .htaccess file which defines these settings, you only need to allow the override setting for your document root. In MacOS X 10.6, edit /etc/httpd/httpd.conf with your favorite text editor, locate the following and change the last line to AllowOverride All.

#
# This should be changed to whatever you set DocumentRoot to.
#

#
# Possible values for the Options directive are "None", "All",
# or any combination of:
# Indexes Includes FollowSymLinks SymLinksifOwnerMatch ExecCGI MultiViews
#
# Note that "MultiViews" must be named *explicitly* --- "Options All"
# doesn't give it to you.
#
# The Options directive is both complicated and important. Please see
# http://httpd.apache.org/docs/2.2/mod/core.html#options
# for more information.
#
Options Indexes FollowSymLinks MultiViews

#
# AllowOverride controls what directives may be placed in .htaccess files.
# It can be "All", "None", or any combination of the keywords:
# Options FileInfo AuthConfig Limit
#
AllowOverride All

Then type the following to restart your web server.

sudo apachectl restart

• Changing the Google Maps Key

First, go to Google Code Website for Google Maps API and obtain a Google Map Key for your website. Then, open the main.pl within the PathwayProjector directory, and locate the "script" tag where it reads "YOUR_GOOGLE_MAP_KEY_HERE", replacing it with the obtained key.

• Finish

Accessing your Pathway Projector Set up is now finished! Simply access
http://localhost/PathwayProjector-1.0/ to see it in action.