Rank: 2431 based on 58 downloads (last 30 days) and 3 files submitted
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Arsen Arakelyan

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24 Mar 2014 Screenshot KEGGParser: parsing and editing KEGG pathway maps in Matlab Matlab graph based tool for KEGG pathway parsing, editing, visualization and analysis Author: Arsen Arakelyan bioinformatics, pathway visualization, graph manipulation an..., gene expression 22 5
  • 5.0
5.0 | 3 ratings
31 Jan 2013 Screenshot Geometric Gaussian-Kernel Bolstered Error Estimation for Linear Classification This is fast implementation of bolstered error estimation algorithm for linear SVM classification. Author: Arsen Arakelyan linear classification, feature selection, bolstered error estim..., bioinformatics, omics data analysis 16 0
13 Jul 2012 Graph manipulation These four files are intended for adding/deleting nodes and edges in biograph object Author: Arsen Arakelyan graphs, graph theory, graph manipulation, bioinformatics 20 1
  • 5.0
5.0 | 1 rating
Comments and Ratings by Arsen View all
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09 Aug 2013 Mason.m Mason.m uses mason's rule to simplify signal flow graphs. Author: Rob Walton

Hi, thanks for this submission. It's really great job.

Yet, I have a question. I'm using it to calculate gains for the graphs with positive feedback loops. at the calculation step I feed network with numeric coefficients (via num2str) and the call eval(Num)/eval(Den) to obtain numerical gain. But with positive feedback loops I always get negative denumerator. Is there a way how to handle positive feedback loop properly using Masons formula?

Thanks,

Arsen

24 Mar 2013 KEGGParser: parsing and editing KEGG pathway maps in Matlab Matlab graph based tool for KEGG pathway parsing, editing, visualization and analysis Author: Arsen Arakelyan

Dear Lee, thanks for your comments and suggestions. I'll have a look to the code to find out the problem. Plus will add adjacency matrix. I'd like to know your opinion on the matrix format. It can be n-by-n (n - number of vertices) matrix with 1 indicating edge and 0 otherwise, or N-by-2 matrix, first element of the row defining source and second element in the row defining sink.

Regards,

Arsen

06 Aug 2012 spheresegmentvolume Volume of a (hyper)sphere, sphere cap, or any band through a sphere defined by two parallel planes Author: John D'Errico

Dear John,

Thanks for posting the code.

06 Aug 2012 spheresegmentvolume Volume of a (hyper)sphere, sphere cap, or any band through a sphere defined by two parallel planes Author: John D'Errico

02 Aug 2012 KEGGParser: parsing and editing KEGG pathway maps in Matlab Matlab graph based tool for KEGG pathway parsing, editing, visualization and analysis Author: Arsen Arakelyan

Hello,

Your comments on functionality or improvement suggestions are very important for me. Feedback is highly appreciated.

Thanks,

Arsen

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08 Nov 2013 Graph manipulation These four files are intended for adding/deleting nodes and edges in biograph object Author: Arsen Arakelyan Sven

Excellent submission. I was surprised that there's nothing already in biograph to manipulate an already-computed graph. I'm making a few small additions such as the ability to remove a set of nodes by sticking this loop at the top of node_del()

if isnumeric(NodeID) && numel(NodeID)>1
for i = 1:length(NodeID)
thisNID = NodeID(i);
bg = node_del(bg,thisNID);
NodeID(NodeID>thisNID) = NodeID(NodeID>thisNID)-1;
end
return;
end

19 Apr 2013 KEGGParser: parsing and editing KEGG pathway maps in Matlab Matlab graph based tool for KEGG pathway parsing, editing, visualization and analysis Author: Arsen Arakelyan Yuping

I have little knowledge about bioinformatics and been looking for tools to edit pathways. This tool helps me out. I still have a problem to export xml after editing the pathways. By the way, if a pathway is not from Homo sapiens (hsa), the corresponding static image cannot be loaded. This might due to the citation of url in load_image.m file.

19 Apr 2013 KEGGParser: parsing and editing KEGG pathway maps in Matlab Matlab graph based tool for KEGG pathway parsing, editing, visualization and analysis Author: Arsen Arakelyan Yuping

24 Mar 2013 KEGGParser: parsing and editing KEGG pathway maps in Matlab Matlab graph based tool for KEGG pathway parsing, editing, visualization and analysis Author: Arsen Arakelyan Arakelyan, Arsen

Dear Lee, thanks for your comments and suggestions. I'll have a look to the code to find out the problem. Plus will add adjacency matrix. I'd like to know your opinion on the matrix format. It can be n-by-n (n - number of vertices) matrix with 1 indicating edge and 0 otherwise, or N-by-2 matrix, first element of the row defining source and second element in the row defining sink.

Regards,

Arsen

24 Mar 2013 KEGGParser: parsing and editing KEGG pathway maps in Matlab Matlab graph based tool for KEGG pathway parsing, editing, visualization and analysis Author: Arsen Arakelyan Lee

There may be a problem with the code - when I parse hsa04010.txt, it seems that ELK4 should be pointing to ELK1. When I check the biograph matrix, it seems that the opposite is recorded. Other binding/association interactions seem to be pointing in the correct direction, but not this one.

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