NetSearch Help Page and FAQ   -   Back to Run NetSearch

General Notes

Picking starting and endpoints randomly will produce zero paths approximately half the time going from membrane protein to transcription factor, and most of the time when going from any protein to any other. If you just hit the submit button without changing any parameters you should obtain 3 paths from ERP2 to CCR4. 

If you don't find the protein you are looking for in the drop-down lists, it's because it didn't have any interactions in our dataset. The data files we used can be found here:  File Lists

Graphing

1) Download the graphing program. We use the freely available program PAJEK.

2) Create and save the input files. Pajek input files can be generated by checking the box at the bottom of the table. When you receive your output, there will be links to two files at the bottom of the page. Download these files to your computer by right-clicking on the link and choose (for Internet Explorer)  "Save Target As" , or (for Netscape) "Save Link As" and save them initially with the suggested names. Unfortunately, you can not rename them as you are saving them, as many browsers will proceed to handle the files incorrectly if they are not initially saved with the ".txt" extension. Once you have saved them to your hard disk, rename the files such that they have the extensions ".net" and ".vec". This may also be challenging if your windows explorer window hides file extensions. If you hide file extensions, then you must first go under the "Tools" menu to "Folder Options" then click the "View" tab and uncheck the box next to "Hide File Extensions of Known File Types".  

3) Load the network file: Go to the drop down menu "File" and select "Network" and "Read" and then enter the .net file.

4) Load the vector file: Go to the drop down menu "File" and select "Vector" and "Read" and then enter the .vec file.

5) Draw the vector: Go to the drop down menu "Draw" and select "Draw-Vector". The network with all nodes arranged on the perimeter of an ellipse should appear in a new window. Type "Ctrl+L" to make the names of the nodes appear. (Or, under the "Options" menu, select "Mark Vertices Using"  and then "Labels".)

6) You can arrange the nodes by clicking and dragging. You may also want to try one of the automated routines. Two that we've found useful are under the "Layout" menu on the graph window. Select "Energy", then "Kamada-Kawai" and "Free". Also try:   "Layout"  -  "Energy"   -   "Fruchterman Rheingold"  -   "2D".

7) Once you have arranged the network to your liking, you can export a bitmap image by going to the "Export" menu and selecting "bitmap". Figures in the paper were drawn using "Export" - "SVG" - "General" (Multiple colors were done manually.)

Questions? - email martin steffen