Project Rationale
Biological Network Comparison Toolkit (BNCT) is designed to
provide a set of tools on biological network reconstruction,
biological network alignment/comparison as well as their application, for
example, network-based phylogenetic analyses.
Considering network reconstruction, we currently work on the
organism-specific multi-level metabolism in
KEGG, where two easy-to-use
tools, MetaGen and MetAtlas, are developed on this
purpose. MetaGen is a console application, intentionally
designed for reconstructing metabolisms into different graphs in
batch processing, which saves researchers from the elaboration
on preparing metabolic networks for computation. MetAtlas
is developed to be a Cytoscape plug-in, to take advantages of
Cytoscape for the quick and friendly visualization and to
collaborate with the other plug-ins for more extensive
researches on metabolisms. Later we plan to expand the enzyme
graph model to the more general PPI network model by considering
biological processes other than metabolism inside
KEGG.
Besides, the data of
unipathway
will be integrated for annotation and curation soon.
The tools for network alignment/comparison are coming soon.
The tool for network-based phylogenetic analyses is coming soon.
MetaGen is a user-friendly utility for modeling metabolic networks from KEGG
in batch processing. It provides several options for modeling
metabolic networks into different graphs or on different levels.
MetaGen takes advantages of KEGG web service to update data
in
time and of a local SQL database to accelerate the model
process. Currently MetaGen exports the modeled graphs as
the Pajek format. More output file formats will be
available soon. MetaGen is implemented and tested on windows vista, but can work on
any platform, for example, Unix, Linux and MAC.
Know more about MetaGen
or download it.
MetAtlas is a cytoscape plug-in for the reconstruction and
exploration of metabolic networks from KEGG.
MetAtlas shares the same method and advantages from MetaGen
on the metabolic network modeling, but also takes
advantages of Cytoscape for more friendly and flexible
visualization and editing. Furthermore, as a plug-in to generate
metabolic network data, MetAtlas can work with the other
plug-ins together to make the research on metabolic networks
easy.
Know more about MetAtlas
or download it.
Other Tools
Coming soon!
People
The whole project is started by Tingting Zhou spontaneously. Now it's
partly funded by National Natural Science Foundation of China
(6077 3021 and 6060 3054).
At the current stage, MetaGen and MetAtlas have been developed primarily by Tingting Zhou and
Samuel K.F. Yung. More other tools are under development. With a
farsighted view, Samuel set up this Java project using
Spring and Maven, and made his way to host it on
Sourceforge in the true open
source spirit. This encourages more contributors to join us,
including (your name here!).
For any question, please do not hesitate to contact us.
| Tingting Zhou: |
grace dot tingting dot zhou at gmail dot com |
| Samuel Kin Fung Yung: |
cskfyung at comp dot polyu dot edu dot hk |