[Pipet Devel] to do list

J.W. Bizzaro bizzaro at bc.edu
Mon Jan 4 14:59:13 EST 1999


Here is a copy of the to do list I recently sent to the others:

The next step is to build a list, not of analysis tools, but of dynamic
client-side interfaces.  EMBOSS will take care of the big analysis tools for
us.  For now, here is a brief list of some dynamic "loci" I've been thinking
of.  Please feel free to add to this:

  (1)  Benchtop/workspace.  GUI representation of all data objects
       (files, documents, graphs) and possibly various loci.  Also
       may be used for automation of analyses (recall GCL?).

  (2)  File translation interface:  to read in various DNA/protein
       document formats and convert them to XML.  Also may be used
       to query databases and sort/compile documents.

  (3)  Sequence visualization/editing tool:  to manipulate DNA/protein

  (4)  Sequence comparison tool:  to show multiple sequences aligned
       or translated.  May also perform some functions of (6)

  (5)  3D visualization tool:  to display molecules as 3D structures, with
       emphasis on a schematic/cartoon representation.

  (6)  Graphing tool:  to display plots against sequences and to make simple
       graphs.  Some may argue this isn't needed, but I need it for my
       programs, so others may too ;-)

  (7)  HTML browser implementation:  separate from the other tools, this
       would be a way for anyone with a browser to access analysis loci.

The best approach may be for each of us to pick a single tool to concentrate
on.  And remember, most of these tools will be XML browsers of a sort.

We should also make a list of "trivial" analysis/conversion tools for the

J.W. Bizzaro                  Phone: 617-552-3905
Boston College                mailto:bizzaro at bc.edu
Department of Chemistry       http://www.uml.edu/Dept/Chem/Bizzaro/

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