todo.txt

Network_portal TODO
===================

Home page
---------
done  About in center, link to more detail on biological purpose
       * what are GRN's and what do we hope to learn from them?
       * brief explanation of cMonkey and Inferelator and links
       * links to papers: cMonkey, Inferelator, EGRIN, etc.
       * links to data sources and partner sites: microbes online, RegPrecise/RegPredict, kegg, etc.
done  Clean up statistics box
      Make news into RSS / Atom / or Twitter feed


Data
----
      functional enrichment for biclusters
done   * at subcategory level
       * use TopGO for GO annotations
      import betas
       * display activation/repression in networks
      import condition descriptions
       * see email from Dave Reiss
      import data for links to RegPrecise
      import VIMSS IDs for linking to Microbes Online (in genomeInfo tsv files)


Search
------
      Return genes, functions, biclusters, species
      Accepts as input: genes, functions, species, plus related terms from descriptions and synonyms,
      limit search to a specific organism or network
      
      gene names, symbols, keywords -> genes
      gene names, symbols, keywords -> biclusters
      functions names, native_ids, keywords -> functions
      functions -> genes
      functions -> biclusters
      species -> species


Gene tabs
---------
      what does this do when there is more than one network for a species?
      gene tab, circle thing?
      gene tab: either put stuff in tabs or all in one page, not both
      gene tab: gene neighborhood graphic?
done  gene | regulators: implement
      gene | motifs: implement
done  gene | functions: implement
      links to regulators and conditions


Bicluster tabs
--------------
      bicluster / regulon tab
       * either put stuff in tabs or all in one page, not both
      bicluster | conditions tab?
      bicluster | functions
done   * show number of genes
done   * show type of function (KEGG/GO/etc.)
       * let the user filter to a specific type of function?
done  bicluster | genes: link to gene


Documentation
-------------
      tutorial / examples
      screencast
      add snippets to networks detailing credits for data sources & collaborators


Cleanup
-------
      Remove Contact / Login until implemented?
      duplicate IDs in HTML elements
      ReSTful URLs
      move bicluster-tabs page and gene-tabs page into separate apps?
      identify biclusters by (network_id and k) or id consistently


Features to be added later
--------------------------
      Login through ISB gmail accts
      links into microbes online
      links into RegPrecise, RegPredict
      cMonkey/inferelator stats for a given network
      view network for a set of genes
      programmatic API
      gaggle microformats