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/

-Reference

-Contact

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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

   http://www.e-cell.org

-Reference

    A multi-algorithm, multi-timescale method for cell simulation.
    Takahashi K., Kaizu K., Hu B. and Tomita M.
    Bioinformatics20:18-26. (2004)

-Contact

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G-language

 
The G-language Genome Analysis Environment is a generic genome analysis environment aiming to:

1. Construct an integrated environment for the development of analysis software.
2. Systematically accumulate existing analysis software methodologies for analysis and their results.
3. 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

    http://www.g-language.org

    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

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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

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SPLITS

A program for predicting split and intron-containing tRNA genes at the genome level.

-How to use

    Download from web site

-Project web page

   http://splits.iab.keio.ac.jpあ

-Reference

    SPLITS: a new program for predicting split and intron-containing tRNA genes at the genome level.
    Sugahara, J., Yachie, N., Sekine, Y., Soma, A., Matsui, M., Tomita, M. and Kanai, A.
    In Silico Biology 6: 0039. (2006)

-Contact

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