GMOD demos at ISMB

Hello,

There are several GMOD-related demos at the ISMB meeting; if you are in
at the meeting, please feel come by and show your support and ask your
questions. The demos are:

SynBrowse: A Synteny Browser for Comparative Sequence Analysis
Sunday, June 26 - 9:30-10:30am, room: Nicolet
Author(s): Xiaokang Pan, et. al.
Short Description: We have developed SynBrowse, a synteny browser for
visualizing and analyzing microsynteny, macrosynteny, homologous genes
both within and between species. SynBrowse is a GBrowse family software
tool that runs on top of the open source Bioperl modules. It consists of
two components: a web-based front end and a set of relational database
back ends. Each database stores pre-computed comparative alignments from
a focus sequence to reference sequences and genome annotations of the
focus sequence. The user interface lets end users search for syntenic
blocks between two sequences and zoom in to view the detailed
comparisons.

Using GMOD Tools to Create, Edit, and Browse Genome Features
Sunday, June 26 - 3-4pm, room: Richard
Author(s): Scott Cain, et. al.
Short Description: The Generic Model Organism Database project has
created a suite of software for creating a MOD. This demo will focus on
the software to create, edit, and browse genome features using open
source tools, including GBrowse, Apollo, and CMap running on top of a
modular genomics schema, chado.

Apollo: A Genome Annotation Editing Tool
Sunday, June 26 - 4-5pm , room: Richard
Author(s): Suzanna Lewis, et. al.
Short Description: Apollo is an interactive genome browser and editor
written in Java and available as an Open Source tool under the BSD
license. It allows researchers to explore genomic annotations at many
levels of detail, and to perform expert annotation curation, all in a
graphical environment. We will demonstrate how to read data of various
formats into Apollo, view the computational evidence, create and edit
detailed annotations, and customize the visual display.

The Pathway Tools Software
Monday, June 27 - 9:30-10:30am, room: Cadillac
Author(s): Suzanne Paley, et. al.
Short Description: Pathway Tools is a software environment for creating,
querying, visualizing, and analyzing Pathway/Genome Databases (PGDBs).
PGDBs integrate information about the genes, proteins, metabolic
network, and genetic network of an organism. This demonstration will
cover two Pathway Tools modalities for interacting with a PGDB: a
graphical environment for visualizing the contents of a PGDB and
interactively updating a PGDB; and a sophisticated ontology and database
API that allows programs to perform complex queries, symbolic
computations, and data mining on the contents of a PGDB. Those APIs
allow users to query the 165 PGDBs within SRI's BioCyc database
collection.

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