New version

We updated the Erl Wood nodes yesterday and the new version is available on the nightlybuilds update site. Beside some bugfixes, the main novelty is a new similarity network viewer in the GPL plugin. It is very similar to the activity cliffs viewer that is contained in the BSD licensed collection of our nodes, but does not require proprietary licenses. Moreover, it is designed to work on arbitrary data type, whereas the activity cliff viewer is restricted to molecular data to offer its full functionality.

Nikolas

dear nikolas

I think that similarity network viewer is a good tools expanded not only for compounds. the problem is to obtain a NxN pairwaise distances matrix. Not in knime do that , is it possible to add as calculation node in erl wood group a pairwaise ditance matrix calculator with tanimoto, ecluidean and other metrics?

regards  

Hi Fab,

we also don't have a dedicated node for that. The "Distance Matrix Calculate" node from the Knime Distance Matrix extension does exactly this. It definitely works with RDKit and MOE fingerprints and Tanimoto similarities.

Best,

Nikolas

dear nikolas,

I have asked you this for the reason that i found this type of error

ERROR Similarity network viewer View instantiation failed: org.rdkit.knime.types.RDKitMolCell2 cannot be cast to org.knime.core.data.def.StringCell

this i think is due to the format !? i used RDKIT

ERROR Similarity network viewer View instantiation failed: -1

If I use rowid i found this type of error , but this ?

can you help me to better understand the node functionality?

thanks

The ID column has to be a string type, which indeed should made clearer in the node dialog, the data column should allow arbitrary celltypes.

 

I hope that helps,

Nikolas

dear nikolas

I attach a simple workflow to view the network (with data) but in my hands i found the same error.

tell what i do of wrong

Hi Fab,

you just have to connect the table containing the similarity matrix to the second input port. We will try to make that clearer in the node description.

I hope that it works then,

Nikolas

Dear nikolas,

 

I did every combinations, inverting the imput port miss distances matrix and dosen't work. I don't know wich is the problem ...maybe my java version. Could you post a simple workflow as mine that in your hands works? in this case if i receive some error post you the message...and the intere debug.

thanks

I modifed to workflow you sent earlier and attached a working version. The top input ports expects a table containing a string id column and an arbitrary data column, the second input port expects a distance matrix column.

I hope that helps

Nikolas

 

ear Nikolas,

thank you very much for you modified workflow!

My impression is that the provided data set gives a very good first start to get familiar with the principles of the similarity network viewer.

Is there any scientific background to animate the network?

Does the coloring correspond to the activity data - can this be modified?

In order to draw an edge between two similar cpds (e.g. 0 & 14) - what is the tanimoto cutoff to do so?

 

Cheers & Thanks,

Paul

 

P.S.: I do not recall all details from your KOS presentation and therefore I have to ask these silly questions.. ;)

dear nikolas

 

thank you, sorry for my errors. This seems as SARANEA software , i use to use the landscape_gui in R as plugin for this , and that are able to do a surface with color coded by activity/property. I think thant your job is great for start to focus on continuos/discontinous omo/etergeneous SAR inside a platform as Knime.

thanks a lot

  

Dear Paul,

The animation is done using the prefuse library and is motivated by particle dynamics. The reason for that is mainly to layout and spread the network graph, because it is a non-trivial task to draw a complex graph such that is it usable by humans. We usually stop the animation after a certain graph relaxation has occured.

The nodes are coloured using a green -> red heatmap scheme, the edge colouring only highlights activity cliffs. The edge cutoff in the dialog defines the maximum distance in which points are regarded to be neighbors and connected by an edge. The edge colour is controlled by the cliff cutoff value, which is not very intuitive and probably has to be selected by trying out some values.

Generally, the node is designed to be a visualization and not a cliff detection/analyzation - this has to be done by the user.

 

I hope this clarifies it a bit.

Best,

Nikolas

Dear Nikolas,

I started using the network viewer on a data set of roughly about 2000 molecules. Which time period do you recommend for equilibration of the visualisation? It appears to me that I end up with different networks when running the viewer two times in a row - but I'm not sure if the time period was long enough to place the molecules accordingly.

Furthermore, in some cases, the view becomes blank when zooming in - even when the animation is stop. Restarting the animation does not give a new view.

Cheers & Thanks,

Paul

Dear Paul,

the relaxation is randomized and will lead to different network layout every run. The time until equilibrium depends strongly on the network (in some cases the network will start oscillating and never reach a stable configuration), thus I am afraid that I cannot provide any guidelines.

Regarding the blank visualization bug, I also noticed this behaviour, but struggled with reproducing it and therefore could not really figure the underlying problem. If you recognize a pattern in this behaviour it would be great if you could report it here.

Thanks a lot for the comments and the error reports!

Best,

Nikolas

Dear Nicolas,

I am late in this discussion, however I wanted to know whether SARANEA features like 

I. SAR index (SARI), II. SAR Tree viewer, III. Path builder can be implemented to  Activity clip viewer.

 

Thanks,

Sunil