3/21/2014 - Gerard's comments
  • BlastP gives blank page for result
  • Kinbase search page should be condensed, to get everything on one screen. No need for so many boxes, and can do two columns. Replace "The Kinase Database and Manning's Gropu" with "The Kinase Database". If we can get all of the search in one page (which we should), then I would put the search box at the bottom rather than the top. See here.
  • The Kinbase search gives a 404 if nothing is found - the old website had a semi-helpful way to suggest alternatives and bring the user back to a search page. Try here
  • Gene Page could also be condensed (see here):
    • - put most outside links on one line, omit the accession numbers (make the database name the hyperlink)
    • - the gene name needs to be more prominent, and the black header at the top can be shrunk substntially
    • - remove the "Basic Information" header and box, use the name of the gene as an overall header instead.
    • For classification, if no subfamily, then don't print the header. Can use the "i" link on the classification header but no need to spell out the two links.
    • - protein domains: Consider a simple initial view and less text at the top.
    • - not sure if it makes sense to have blast on the same page as the search, even if we can blast a found sequence, I'd rather first find the sequence and then offer to let it be blasted.
    • Suggestions if no hit.
  • The View Domains page (of multiple proteins) is pretty ugly, though I like how it has a single domain for each region. I think the box for 'full sequence' is confusing. Could we do something like the old one where the protein was a narrow bar, and the domains were fatter bars centered on that? Allowing rounded edges rather than the boxy current look would also be very helpful, I think.
  • Static pages under "About" are non-functional
  • Pages under "Projects" also non-functional

Static page to add

  • http://kinase.com/kinbase/
  • http://kinase.com/human/kinome/phylogeny.html
  • http://localhost:8000/blast/blast.html
  • http://kinase.com/kinbase/FastaFiles
  • http://kinase.com/tools/HyperTree.html
  • http://kinase.com/human/psu/
  • http://kinase.com/cgi-bin/KinCatMam/tools/logo.cgi.pl (colt:logo_aligner)
  • http://kinase.com/classification/ (colt:classification)
  • http://kinase.com/monosiga/convergent.html
  • http://kinase.com/monosiga/mapk.html
  • http://kinase.com/monosiga/pincus_comparison.html
  • http://kinase.com/celegans/worm_kinase.htm
  • http://kinase.com/celegans/worm_ptp_112399.htm
  • http://kinase.com/celegans/Worm_ppbd_112399.htm
  • http://kinase.com/celegans/worm_sum_112399.htm

Other

  • scrollable dropdown menu: http://stackoverflow.com/questions/19227496/scrollable-menu-with-bootstrap-3-menu-expanding-its-container-when-it-should-n
  • Custom scrollable dropdown menu. http://jscrollpane.kelvinluck.com/#download
  • Citation for update on http://kinase.com/tetrahymena/
  • How to deal with checkbox in JavaScript
  • Species checkbox
  • Gene checkbox in gene-list.html
  • Get gene sequences, alignments, and etc.
  • Group, family, subfamily page
  • Toggle pseudogenes
  • Add links to sequence in alignment
  • Web analysis
  • Help for kinbase index
  • Debug pviz for domain views of multiple sequences. They individual figure are striped.