EOL/seabase

%h3 Export to Gephi

%p 
  At this stage we use cosine similarity to find similar expression 
  patterns and then we export similarity data to the network visualization 
  and analysis application 
  %a{ href: 'http://gephi.org' } Gephi.
  The process takes two stages.

%h4 Stage 1: Similarity calculations

This stage has to be performed only once. As soon as similarity is calculated 
the date can be reused. 

%form#cosine{ method: :post, action: '/cosine_calculate' }
  .item
  .item
    %input#cosine_submit{ type: :submit, value: 'Calculate similarity', disabled: true }

%p Calculation is finished and button is disabled

%h4 Stage 2: Download files to open in Gephi

%p 
  These file represent undirectional graph where nodes are transcripts and
  edges represent existance of a strong similarity. Offset in one hour 
  represents similarity calculated with shift (for example 5 hour data point 
  in one transcript was matchres with 4 and 6 hours of all other matches

.item
  %a{ href: '/nematostella_0h.csv' } 
    Nematostella, 0h offset, 99.5% similarity 

.item
  %a{ href: '/nematostella_1h.csv' } 
    Nematostella, 1h offset, 99% similarity