Can't see any interactions

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caufi...@mymail.vcu.edu

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May 12, 2014, 10:20:46 AM5/12/14
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Hello - I tried out PINV after seeing the recent paper in BMC Bioinformatics. Unfortunately, I haven't been able to visualize any interactions with any of the example data sets.

The documentation suggests using an M. leprae data set (http://biosual.cbio.uct.ac.za/pinViewer.html?core=PINV_leprae). When I try this URL, the filter window pops up first and tells me there are 1412 with 27566 interactions. That's great, but whether I execute a filter or just close the window, I don't see any nodes or network graphics at all. The Table tab just provides an empty data table (complete with the label, "No data available in table").

I expect that this is the result of something specific about my system or my browser version. I'm using Chromium Version 33.0.1750.152 on Ubuntu 12.04. I tried PINV in Chrome Version 34.0.1847.131 on Win 7 and got the same result. The issue renders PINV unusable so I hope there's a quick fix! Thanks!

Gustavo Adolfo Salazar Orejuela

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May 12, 2014, 10:36:45 AM5/12/14
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Hello there,

The default option for the filter window(bottom) is to Apply on future queries,  that means that if you press execute with that setting, no proteins are been queried on PINV. I am guessing you haven't change that option.
Then you have 2 options, either keep this configuration and then use the text area at the top left of the main screen to input a list of ids or to change the setting to Execute filters over the full network, if you go for the latter make sure the filter reduce the number of interactions to display to less than 1000 because around this number the performance on the browser starts been affected.
Please let us know if this solve your issue or if you are still having problems.

Thanks for Using PINV.
 

caufi...@mymail.vcu.edu

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May 12, 2014, 10:48:05 AM5/12/14
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Thanks for the quick response! Filtering by ID does solve the problem. Please add this to the example documentation - I'm completely familiar with why users wouldn't want to render the whole network by default (as in other network visualizations i.e. Cytoscape) but it's not immediately intuitive as the current documentation implies that a random subset of interactions is rendered by default.

Thanks again!

Gustavo Adolfo Salazar Orejuela

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May 12, 2014, 10:57:54 AM5/12/14
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You are welcome, 
We need to update the documentation because we have implemented quite a few changes since the docs were written.
One of those changes was to removed the random subset visualization, because we got to the conclusion that it was misleading. 

Thanks for making us notice the problem in our documentation. 
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