The zip file below contains an example data set, executables for Windows, Mac, and Linux, and the source code for Pathline. Pathline was developed using the Processing programming language, and it has been tested for Processing 2.0b7.

You will need to download and install the free pixel font PF Tempesta Seven -- note that you need both the pf_tempesta_seven.ttf AND pf_tempesta_seven_bold.ttf.

pathline.zip

An example dataset is included with the executables below. This dataset is not a real-world example, but rather an arbitrary set of expression values and pathways. We plan to release the actual data that our collaborators are currently using with Pathline as soon as their data becomes public.

You can get a description of the file formation here: file_formats.rtf

The window is resizable, with the length of the pathway view, and the number of columns shown in in the curvemap view, updated on the fly. Pressing shift+p will take a screen shot of Pathline, and save the shot as a vector-graphics pdf file in the same directory as the executable.

Linearized Pathway Overview:

1. -pressing keys 1-3 switch between three different similarity metrics
   

2. -pressing key 4 displays two metrics together
   

3. -pressing key 5 displays all three metrics together
   

1. -rollover any pathway element to see the name and similarity value
   

2. -select a pathway element using the left mouse button, or, with the up and down arrow keys
   

3. -selected elements appear to the right in the curvemap view
   

4. -select multiple elements by using the left mouse button plus the CTRL key
   

5. -a scrollbar appears to the right of the pathway when the window resolution cannot accommodate the entire set of pathways
   

Curvemap Detail View:

1. -rollover any species name, phylogenetic tree node, or gene/metabolite name for highlighting in the overlay plots