[Pipet Devel] TODO!

[J.W. Bizzaro]

Locians,

We finally have a TODO list (attached).  There are many projects within Loci
and sub-projects within those.  So, I listed them all out in outline format
with a very brief description under each project.  Each project (and most
sub-projects) needs a 'project leader', and some leaders are named BY MY
ASSUMPTION (please confirm).  Where no leaders are identified, you will see a
'???'.  This is where we need YOUR help!  Any suggestions/additions for this
list are of course welcome.

Jeff
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THE LOCI PROJECT; TODO 19991216

LOCI PROJECT LEADER: J.W. Bizzaro <jeff at bioinformatics.org>
ASSISTANT: Gary Van Domselaar <gary at bioinformatics.org>




I.    CORE WORKSPACE

      PROJECT LEADER: J.W. Bizzaro <jeff at bioinformatics.org>

      Part of loci-core.  This project covers the entire GUI for Loci and
      the implementation of GUI extentions.


      A. GUI construction via XML


      B. Dynamic menu generation


      C. Themes


      D. CORBA integration


      E. Bonobo integration




II.   CORE SCRIPTING LANGUAGE (XML-based)

      PROJECT LEADER: ???

      Part of loci-core.  Once a graphical script is generated by the user,
      via the Workspace, it can be executed.  The graphical script will
      therefore need to be represented in text (XML) and executed by an
      interpreter.


      A. Language definition


      B. Interpreter




III.  CORE DATABASE CONNECTIVITY

      PROJECT LEADER: Brad Chapman? <chapmanb at arches.uga.edu>

      Part of loci-core.  The line is blurred between what is a 'real'
      database being used by Loci and just about everything else.


      A. Representation of filesystem as containers


      B. Representation of databases as containers




IV.   CORE DIRECTORY SERVICES (formerly called 'hub')

      PROJECT LEADER: ???

      Part of loci-core.  Akin to domain name serving, a world-wide registry
      needs to be made containing what loci are available where.  Each copy
      of Loci will in fact have the ability to contact others to find out
      what is _pulicly_ available there.  All copies of Loci should register
      their available loci with a central registry too.



V.    CORE UTILITIES

      PROJECT LEADER: ???

      Part of loci-core.  This includes helper applications that are
      external to Loci.  What would be interesting is finding a way to
      run these as loci.


      1. Installation Manager

         SUB-PROJECT LEADER: ???


      2. User Preferences Configuration

         SUB-PROJECT LEADER: ???




VI.   PYTHON BINDINGS

      PROJECT LEADER: Justin Bradford <justin at ukans.edu>

      Since most/all of Loci's core is written in Python and uses Gnome
      libraries, several bindings are needed.


      A. GTK/GNOME

         These already exist, thanks to James Henstridge.


      B. ORBit


      C. Bonobo




VII.  WEB INTERFACE (loci-web)

      PROJECT LEADER: David Lapointe? <david.lapointe at umassmed.edu>

      This would replace the Workspace and allow a limited number of
      loci to run via Web browser.




VIII. CORE WRAPPERS AND EXTENSIONS

      PROJECT LEADER: J.W. Bizzaro <jeff at bioinformatics.org>

      Part of loci-core.  These are basic loci that come with each copy
      of Loci.


      A. Locus output to command-line

         SUB-PROJECT LEADER: J.W. Bizzaro <jeff at bioinformatics.org>


      B. Locus input from command-line/stdout

         SUB-PROJECT LEADER: Thomas Junier? <thomas.junier at isrec.unil.ch>


      C. Generic XML database

         SUB-PROJECT LEADER: Brad Chapman? <chapmanb at arches.uga.edu>




IX.   BIOINFORMATICS WRAPPERS AND EXTENSIONS (loci-bio)

      PROJECT LEADER: ???

      These are loci for basic bioinformatics research.


      A. Bioinformatics XML and Converters
         ('internal format')

         SUB-PROJECT LEADER: Humberto Otiz Zuazaga? <hortiz at neurobio.upr.clu.edu>


      B. Misc. Converters

         SUB-PROJECT LEADER: ???

         1. GenBank to Raw Sequence




X.    EMBOSS WRAPPERS (loci-emboss)

      PROJECT LEADER: David Lapointe <david.lapointe at umassmed.edu>

      These are loci for running EMBOSS under Loci.




XI.   DOCUMENTATION

      PROJECT LEADER: Gary Van Domselaar <gary at bioinformatics.org>
      ASSISTANT: David Lapointe? <david.lapointe at umassmed.edu>