README

Standalone software: magnapp_gui_osx64

Data set to demo: see folder "toy" (made available by Vijayan et al at https://www3.nd.edu/~cone/MAGNA++/documentation.html)



1. System requirements:
MAGNA++ runs on Linux, Mac OS X, and Windows (Further information can be found here: https://www3.nd.edu/~cone/MAGNA++/documentation.html, also see Magna Documentation.pdf).

There is only 1 version available.

No special hardware is needed. 



2. Installation Guide:
MAGNA++ is available in the format of Statically compiled executables, which are provided for all three operating systems, so the aligner is ready to run immediately after downloading.

The installation is negligible as the file is ready for use upon decompression. 



3. Demo:
Instructions provided by the authors can be found: https://www3.nd.edu/~cone/MAGNA++/documentation.html

Key steps:
Choose two networks to align. Network 1 must have fewer nodes than Network 2. MAGNA++ accepts networks in either LEDA network format (.gw) (see an example), edge list format (.txt) (see an example) or Simple Interaction Format (.sif) (see an example). Various real-world, synthetic, testing, and toy networks (LEDA formatted) can be found here.


Choose the output directory and a prefix for each output file name. For example, if "ex_" is entered, then "ex_" will appear at the beginning of the name of each file that MAGNA++ outputs. MAGNA++ will output files for the resulting alignments, the parameters used to create the alignments, and some statistics of the alignments. See Section 3 for a more detailed description of output files.


Choose an edge-based measure to optimize. S3 is the recommended optimization measure since it avoids biases due to network sizes.

Expected output:

Upon beginning an execution (and supposing the prefix defined in 2.II is "ex_"), MAGNA++ generates three output files by default. The final alignment file "ex_final_alignment.txt" consists of the aligned pairs of nodes calculated by MAGNA++. The alignment statistics file "ex_final_stats.txt" contains the EC, ICS, S3, node similarity, and the overall score of the final alignment. The common conserved subgraph file, "ex_final_visualize.sif", contains the common conserved subgraph of the alignment of the two networks. It provides an intuitive visualization of the final alignment, and can be viewed using a program such as Cytoscape.

If the frequency of output option is set to k, then MAGNA++ outputs the details of the best alignment every n/k generations (where n is the total number of generations, asdefined in 2.XI). Each alignment is written to a file, containing a list of node pairs. Nodes in the left column are from Network 1 and the nodes on the right are from Network 2. Also according to the frequency of output, MAGNA++ will append statistics of the best alignment to the file "ex_stats.txt".

The format of the output alignment file names is "ex_M_p_n_i.aln", where M is the edge conservation measure (one of EC, ICS, S3), p is the population size, n is the total number of generations, and i is the generation that the alignment was written. The alignment from the last generation (ex_M_p_n_n.aln) is the final alignment produced by MAGNA++.

MAGNA++ will also create a file "ex_params.txt", which contains a summary of the initial parameters given.

Expected run time: It depends on the network sizes. For the food web data we have used, it took about 15 mins on average. 


4. Instructions for use:
TO run Magna++ on a given pair of control and drought webs, use the drought web as Network 1 and the control web as Network 2. Set Edge-Node Weight to zero. 

 

