I have a data set of pairwise interactions (present / absent) among 50 bacteria and I want to visualize their interactions in a network. What can I do? What program or software do you think I can use?
Cytoscape would be the ideal choice. If you prepare your data as a tab-separated pairwise interaction table (each line containing a pair of interacting microbes) you can import this as a set of 'edges' easily.
Cytoscape would be the ideal choice. If you prepare your data as a tab-separated pairwise interaction table (each line containing a pair of interacting microbes) you can import this as a set of 'edges' easily.
+1 to Jonathan's comment - I've used cytoscape for exactly this purpose.
Nil bioinformatic skills then spotfire
Some bioinfo skills cytoscape
Good skills then R.
You can also try the MENA Pipeline http://ieg2.ou.edu/MENA/login.cgi; you have to register- afterwards it's straight forward to get an output file for the visualization in Cytoscape.
Cytoscape is a good choice and easy to interpret the results.....go ahead
Cytoscape iOS a good choice because NO scripting or any other skills are needed , and it has several plugins for you further analyze the network
I didn't really get your question or the design of your experiment. Could you explain it briefly? Since I am using an R script which even gives you the statistically significant interactions.
@ Holger, my input is a table (51 x 51) with one row and one column for bacterial ID. The value is 1 or 0 for whether there is interaction or not.
how did you define this interaction?? just let both strains grow together and checked OD or what did u do??
@ Holger, I used Burkholder agar diffusion assay to see whether the test bacteria can inhibit the lawn bacteria indicated by a inhibition halo.
- Badges
- Science topic
- Similar topics
- Computer Science and Engineering
- Bioinformatics
- Bioinformatic Tools