Recent Discussions - PHISTO Forum

BAM! You’ve got a sweet forum

System — Sun, 11 Nov 2018 20:25:30 +0000

There’s nothing sweeter than a fresh new forum, ready to welcome your community. A Vanilla Forum has all the bits and pieces you need to build an awesome discussion platform customized to your needs. Here’s a few tips:

Use the Getting Started list in the Dashboard to configure your site.
Don’t use too many categories. We recommend 3-8. Keep it simple!
“Announce” a discussion (click the gear) to stick to the top of the list, and “Close” it to stop further comments.
Use “Sink” to take attention away from a discussion. New comments will no longer bring it back to the top of the list.
Bookmark a discussion (click the star) to get notifications for new comments. You can edit notification settings from your profile.

Go ahead and edit or delete this discussion, then spread the word to get this place cooking. Cheers!

How can I perform “BLAST search”?

nskarakoc — Tue, 19 Aug 2014 07:48:23 +0000

Make the pathogen protein sequence ready in FASTA format. Paste it into the box in BLAST page, or upload the FASTA file. Remember to select a database (Uniprot-kb is default).

It may take some seconds to do BLAST search. The results give matched pathogen proteins (E-score < 0.05) with links to UniProt IDs.

How can I visualize my searches /my browses via a bipartite graph?

nskarakoc — Tue, 19 Aug 2014 07:44:23 +0000

Make a quick or advanced search, or make a browsing. Then, use “Graph JS” button in the results page under “PHI Analysis Tools” Menu.

As you have noted, there are two tools for graph visualization. Graph JS is based on java-script, and it is really fast. It is the option to visualize PHI networks which have at most 800 nodes. Graph Java option is available for larger networks. In that case, you should give necessary permissions to let JAVA work in your computer.

A new window will be opened with the bipartite graph. Both nodes (proteins) and edges (interactions) in the graph. In the graph, blue nodes show human proteins, and red nodes show pathogen proteins.

You can optimize the graph view by using the “Optimize Graph” button. This option will minimize the edge intersections in the graph.

It is very easy to zoom into the graph by using your mouse scroll wheel.

Also, automatic resizing functionality is available when you increase the size of the window by using the right-bottom corner of the visualization window.

The Layout option “Circle” lets the users see the bipartite graph in circular view.

- You can change the position of the nodes easily by using your mouse to make the visual look clearer.
Visualisation option provides two different filtering functionalities:
In the Human PPI based filtering; the user can filter the human proteins which have a degree score (or any of the other scores: closeness, betweenness, eigenvector or Katz centrality, or clustering coefficient) lower than a selected threshold. In this way, for example, the user can remove human proteins with low intra-PPI connectivity from the graph.
- In the PHI-based filtering; the user can filter the pathogen or human proteins with low interspecies connectivity.