Resources
Genome Projector
Genome Projector, a searchable database browser with zoomable user interface using Google Map API. Genome Projector currently contains 4 views: Genome map, Plasmid map, Pathway map, and DNA walk.
-How to use
Visit this web site
http://www.g-language.org/g3/-Project web site
http://www.g-language.org/GenomeProjector/
-Contact
E-Cell Simulation Environment
E-Cell Project is an international research project aiming to model and reconstruct biological phenomena in silico, and developing necessary theoretical supports, technologies and software platforms to allow precise whole cell simulation.
-How to use
Download from web site
-Project web site
-Reference
A multi-algorithm, multi-timescale method for cell simulation.
Takahashi K., Kaizu K., Hu B. and Tomita M.
Bioinformatics20:18-26. (2004)
-Contact
G-language Genome Analysis Environment
The G-language Genome Analysis Environment is a generic genome analysis environment aiming to:
- Construct an integrated environment for the development of analysis software.
- Systematically accumulate existing analysis software methodologies for analysis and their results.
- Construct generic analysis packages that allow users to avoid redundancy in the process of analysis.
-How to use
Download from web site
-Project web site
-Reference
G-language Genome analysis Environment: a workbench for nucleotide sequence data mining.
Arakawa K., Mori K., Ikeda K., Matsuzaki T., Kobayashi Y. and Tomita, M.
Bioinformatics 19: 305-6. (2003)
-Contact
Keio Collection
Systematic construction of single gene knock out mutants of all genes/ORFs including putative ones has been performed (Baba et al., 2003) by using the Wanner's method (Datsewnko and Wanner, 1997). The mutants are expected to be useful resources not only for the functional analysis of y-genes (genes of unknown functions) but also for the analysis of gene expression profiles based on DNA microarray and other methods. The collection will be termed the "Keio Collection" and will be freely distributed upon request when the construction is completed.
-How to use
Register from web site
-Project web site
http://ecoli.naist.jp/gb6/Resources/deletion/deletion.html
-Reference
Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection.
Baba, T., Ara, T., Hasegawa, M., Takai, Y., Okumura, Y., Baba, M., Datsenko, K.A., Tomita, M, Wanner, B.L. and Mori, H.
Molecular Systems Biology 2:2006.0008. (2006)
MathDAMP
MathDAMP facilitates the visualization of differences between metabolite profiles acquired by hyphenated mass spectrometry techniques. Differences are highlighted by applying arithmetic operations to all corresponding signal intensities from whole raw (automatically preprocessed and normalized) datasets on a datapoint-by-datapoint basis. The results are visualized using density plots.
-How to use
Download from web site
-Project web site
http://mathdamp.iab.keio.ac.jp
-Reference
MathDAMP: a package for differential analysis of metabolite profiles.
Baran, R., Kochi, H., Saito, N., Suematsu, M., Soga, T., Nishioka, T., Robert, M. and Tomita, M.
BMC Bioinformatics7: 530. (2006)
-Contact
MassBank.jp
This site presents the database of comprehensive, high-resolution mass spectra of metabolites. Supported by the JST-BIRD project, it offers various query methods for standard spectra from Keio Univ., RIKEN PSC, and others.
-Project web page
http://www.massbank.jp/index-e.html
-Contact
eXpanda
eXpanda enables an analysis of a very broad range of biological networks , with a special focus on the extraction of characteristic topologies which potentially function as units in the networks.
-Project web page
https://github.com/expanda/expanda
-Contact
E-Cell Simulation Environment 3D
E-Cell 3D is a visualization environment for complex systems biology simulation data with sophisticated 3D graphics.
-Project web page
http://ecell3d.iab.keio.ac.jp/
Pathway Projector
Pathway Projector provides integrated pathway maps that are based upon the KEGG Atlas, with the addition of nodes for genes and enzymes, and is implemented as a scalable, zoomable map utilizing the Google Maps API. Users can search pathway-related data using keywords, molecular weights, nucleotide sequences, and amino acid sequences, or as possible routes between compounds. In addition, experimental data from transcriptomic, proteomic, and metabolomic analyses can be readily mapped. Pathway Projector is freely available for academic users at http://www.g-language.org/PathwayProjector/
-Project web page
http://www.g-language.org/PathwayProjector/
-Contact
Multi-omics database of Escherichia coli
This database lists all data obtained and reported in Ishii et al. (2005) Science, including transcriptomome, proteome, metabolome, and fluxome data of E.coli.