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for on-going GenMAPP development projects. Contribute
to the process by giving us your feedback or contributing
code. |
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We
are developing a newly redesigned version of GenMAPP
to meet current challenges for integrating, visualizing,
and analyzing pathway data. This new version, called
GenMAPP-CS, is being developed as an open-source, Java-based
program in collaboration with the Cytoscape
Consortium and BiGCaT
Bioinformatics. GenMAPP-CS will incorporate core
capabilities of Cytoscape, while adding GenMAPP-specific
functionality. Complementary to this effort is the open
source development of PathVisio as an extended and rapidly
advancing Java version of GenMAPP (see below). The specific
aims of the GenMAPP-CS project are:
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To
build a client-server version of GenMAPP-CS, to
provide a dynamic environment for visualizing and
analyzing genomic data on biological pathways. |
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To
dynamically integrate GenMAPP-CS with major gene
and pathway databases for over 20 major model organisms. |
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To
enable GenMAPP-CS to visualize and analyze genome-wide
splicing, polymorphism, and interaction datasets. |
How
to Participate
You can contribute to GenMAPP-CS development in a number
of ways. The project and its products are 100% open
souce, public and freely available. We have applied
to mentor students through the 2007 Google
Summer of Code program. So if you are a student
(anywhere in the world), check out our GenMAPP
Ideas Page. We also have a open forum on Google
Groups to discuss GenMAPP-related issues and ideas.
Visit our GenMAPP
Google Group. You can also keep up-to-date on GenMAPP
news via our News Page, or by
registering on our
website and selecting 'Yes' to 'Get Updates By Email.
Resource
Links
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BioPAX
and GPML
A major challenge to effective pathway analysis is the
collection and maintenance of pathway knowledge in a robust,
computationally accessible format. The XML-based format,
BioPAX, is emerging
as the community standard. We are developing the GenMAPP
Pathway Meta Language (GPML) as the new GenMAPP pathway
exchange format capable of translating between our current
.mapp format and BioPAX.
GPML can store object coordinates and annotations, in
addition to node and edge network interactions, thus supporting
curated layouts and illustrated, human-readable pathways.
PathVisio
The work on GPML is being carried out in close collaboration
with BiGCaT Bioinformatics
who is also producing the Java-based, open source pathway
tool called PathVisio.
Modeled after GenMAPP, PathVisio
already provides much of the same functionality, and as
we shift our focus to the Java platform PathVisio
development will quickly advance. In fact, PathVisio
v.1 already surpasses GenMAPP as a pathway drawing
and editing tool, capable of reading/writing GPML and
.mapp as well as properly storing node-defined edges,
all in a cross-platform environment.
WikiPathways
In addition to supporting curation efforts by various
organizations, such as NetPath, we are applying PathVisio
to a more general, public curation resource. We are hosting
WikiPathways as
a public wiki for pathway editing. The idea is analogous
to Wikipedia, except for biological pathways. PathVisio
will be at the heart of WikiPathways,
allowing immediate, online editing and feedback. Our hope
is that the open, easy-to-use nature of a wiki site combined
with an embedded pathway editing tool will encourage more
active contribution and review by the pathway community.
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We
are collaborating with the Center
for Knowledge Managementat UCSF to produce ID mapping
services built on top of our GenMAPP-style gene databases.
We are generating MySQL, MSAccess and Apache
Derby versions of our databases using a semi-automated
protocol that takes advantage of the API provided by
Ensembl. This
will enable us to support GenMAPP analysis for any species
in the Ensembl database, with reliable and up-to-date
databases.
GenMAPP 2 also allows for the creation of custom species
databases. The process of creating a custom database
is a collaborative effort, where the GenMAPP group creates
a template database that you can add to. Using common
spreadsheet programs and GenMAPP, you can create a GenMAPP
database for any species you are interested in without
the need for database software or expertise. A set of
tutorials providing step-by-step instructions for how
to implement GenMAPP for a custom species are available
here:
Tutorial
for Implementing GenMAPP 2.0 for non supported species
(PDF)
Tutorial for Converting MAPPs between species (PDF)
Custom GenMAPP databases for E.coli and S.pombe have
already been created. For more information on database
and pathway contributions, click here.
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