Loci Project - for distributing bioinformatics programs and databases

Thu, 23 Sep 99 05:35:54 GMT

http://theopenlab.uml.edu/loci/

The Open Lab Presents...
The Loci Project

Introduction

Loci is an extremely modular and extensible system of clients and
servers for distributing bioinformatics programs and databases. We are
first of all concentrating on making GUI wrappers for command-line
programs and databases that run on UNIX-type systems, of which a
countless number exist. We are using the highly object-oriented
scripting language Python as the base language.

Despite the fact that we are using platform-independent tools such as
XML and Python, we are not concerned with making a
platform-independent application. This may bother people who have
traditionally developed on Windows systems, but we see an enormous
void that needs to be filled: There is no highly graphical,
comprehensive suite of bioinformatics tools native to UNIX. And there
certainly isn't one that is free. Programs like DNAStar and MacVector
are very nice commercial applications, but they are only for Windows
and Macs. We say, let's take advantage of the power of UNIX, the
status it has in Universities where so many command-line driven
bioinformatics tools are written, and let's provide something that
doesn't exist anywhere else.

Below is an early production screenshot from June 19, 1999.
Loci/locuses are represented by boxes connected with lines, forming a
"work flow diagram". Double-clicking on a box will show or hide the
actual GUI of each locus. A popup menu (from a right mouse button
click) can be seen over one of the loci (bottom right). A windowlet
(from a left mouse button double-click) can be seen below another (top
right). Everything can be dragged and dropped, and loci can be merged
to form higher level loci.

                                [Image]

Features

   * A system of servers and clients.
   * Communicates with other systems across an intra/Internet.
   * Allows for bioinformatics collaboratories across an
     intra/Internet.
   * Gives command-line programs and databases a consistent look and
     feel.
   * Has built-in support for sequence and structure analyses of
     macromolecules.
   * Provides native support for phylogenetics and systematics.
   * Includes a library of basic analysis tools.
   * Produces 2D vector-drawn schematics.
   * Treats biological data as scientific illustrations.
   * Provides drawing tools and a materials library for figure
     construction.
   * Tracks the system's work path with a flow chart.
   * Automatically logs activity to an electronic notebook.
   * Seamlessly integrates utilities for building applications and
     extending the system.
   * Free software!

As far as graphics are concerned, the idea is to define vector
graphics so that custom made schematics can be generated by the
plug-in, and the plug-in developer can choose some high-level
representations...sort of like graphical widgets.

How is Loci developed?

This project is under heavy development, and we are in need of
assistance.  If you are interested in contributing to Loci, please
visit the Development page for more information.

We are also collaborating with other free-software, bioinformatics
projects: AMMP and tacg(and EMBOSS more or less).  It is our desire
that all projects compatible with the GNU LGPL license will become at
least interoperable and hopefully combined.

<P><A HREF="http://theopenlab.uml.edu/loci/">The Loci Project</A> - 
a modular and extensible system of clients and servers for distributing
bioinformatics programs and databases; written in Python.  (10-Sep-99)

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