[Pipet Devel] glossary

[J.W. Bizzaro]

Attached is a glossary of the terms we've been using to describe Loci.

Please let me know if there is any confusion, changes, or additions.

You will find some names that you haven't seen before.  For example, I'd like to
call our XML, "BICML", as in "The BIC Group", instead of LociML.


Jeff
-- 
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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Glossary of Terms for The Loci Project
Version 0.1; 01 Mar 1999


analytical tool
    A small Python module, or program with a Python interface,
    with the ability to work on biological data of type
    sequence or structure.  This in non-graphical.  See
    also Library.

Benchtop
    Part of the Workspace.  A highly graphical client that
    is the primary user interface for managing data and the
    Work Flow System

BICML
    (formerly LociML or LocusML) The Biomolecular Informatics
    and Computation Markup Language.  The XML describing
    the biological data.

client
    Any tool that runs under its own process, usually
    a graphical tool or the Workspace.

collaboratory
    The system by which multiple users, on separate computers,
    can collaborate on a research project.

command/command-line
    The characters typed to start a program that would normally
    run in a console.

Gatekeeper
    The application broker that resides on a remote computer
    and translates Loci data streams and files into commands
    (input) for remote algorithms and queries for remote
    databases.  Output from the algorithms and databases
    is translated back into Loci data streams and files.

Graphical Command Language (GCL)
    (now deprecated) A representation of piped commands and
    files using pictures.  See Work Flow Diagram.

graphical/gui tool
    A type of client and type of tool.  What is actually
    seen and used by the user to work on the biological
    data.  This doesn't include the Workspace, which is not
    a "tool".

hub
    A remote computer that connects Loci to registered
    Gatekeepers on the Internet.

library
    Used in the common sense.  Loci can be considered a
    library of tools, both graphical and analytical.

Notebook
    Part of the Workspace.  Keeps a running log, written in
    HTML of all work perfomed using Loci.  The notebook can
    take inserted text from the user but no deletions.  This
    is an electronic version of a laboratory notebook.

object
    Used in the common sense.  Objects are data that can be
    streamed or stored.  BICML files are not considered
    objects.

tool
    A Python module or program wrapped in Python.  Can be
    either graphical or analytical, but is used for work
    on biological data.

local
    On the user's very own computer or NFS.

loci
    Plural for locus.

locus
    Any real part of Loci: modules, tools, clients, and
    libraries, including hubs and remote programs.  Usually
    doesn't include data.  "Locus" can in fact appear before
    every other name in this glossary beginning with a capital
    letter. The loci are represented on the Work Flow
    Diagram as boxes.

Locus AA1DV
    Amino Acid 1-Dimensional Viewer.  A graphical tool.

Locus AA1DE
    Amino Acid 1-Dimensional Editor.  A graphical tool.

Locus AA2DV
    Amino Acid 2-Dimensional Viewer.  A graphical tool.

Locus AA3DV
    Amino Acid 3-Dimensional Viewer.  A graphical tool.

Locus NA1DE
    Nucleic Acid 1-Dimensional Editor.  A graphical tool.

Locus NA1DV-L
    Nucleic Acid 1-Dimensional Viewer for linear strands.
    A graphical tool.

Locus NA1DV-Ci
    Nucleic Acid 1-Dimensional Viewer for cicular strands.
    A graphical tool.

Locus NA1DV-Ch
    Nucleic Acid 1-Dimensional Viewer for chromosomes.
    A graphical tool.

Locus NA3DV
    Nucleic Acid 3-Dimensional Viewer.  A graphical tool.

path/pathway
    The progress of work performed by the user, manually
    or automatically, that results in one locus calling on
    another and another, so that the progress can be traced.  
    The path is represented on the Work Flow Diagram as
    a line connecting boxes (loci).

Paos
    The "active object server" written by Carlos Maltzahn.
    Paos acts as the communication backbone for the Loci
    system and a guide through the work path.

porta
    Any connection between the local Loci system and another
    system, be it the Gatekeeper, CORBA system, or whatever.
    Porta can be local or remote.

Porta Internet
    The connection between the local Loci system and the
    Gatekeeper.

Porta CORBA
    The connection between the local Loci system and a
    CORBA system.

Python
    The de-facto programming/scripting language of Loci.

query
    A database query sent to the remote database via
    data stream.

remote
    Not on the user's very own computer or NFS.  Across a
    network or the Internet.

remote algorithm
    A command-line program for complex biological analyses,
    which resides on a remote computer.

remote database
    A biological database that resides on a remote computer.

remote program
    A remote algorithm or database that resides on a remote
    computer.

server
    Used in the common sense.  Any program serving or
    contolling a client.

stream
    Active passing of objects from one locus to another,
    without writing to disk.  Usually done via Paos.

Translator
    Client that converts common formats for biological
    data (such as PDB or GenBank) into BICML, and visa
    versa.

transfer
    Passing files across a porta.

workflow
    The flow of all work being performed on the Loci system.

Work Flow Diagram (WFD)
    The representation or choreography of work.  Part of
    the Workspace.  The WFD is a dynamic flow chart where
    loci are represented as boxes and paths are represented
    as lines between boxes.

Work Flow System (WFS)
    Paos control and monitoring of workflow.

Workspace or Locus Primus
    The client(s) that provide user control and monitoring
    of workflow.  This includes the Benchtop and Notebook.
    The Workspace is not considered a "tool".