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Internet websites related to medaka research

Currently there are many websites related to medaka research, and many sites are still under development. Some links may not always work, and new sites will probably appear. The following are the websites that we find to be useful at the time of publication.

Databases

Medakafish Homepage

http://biol1.bio.nagoya-u.ac.jp:8000/

A homepage that could be called “the” medakafish homepage for all. Not all contents are provided in English, but this site covers a large range of medaka research. Some of the information that can be obtained includes:

description of medaka in general
developmental stages
links to various medaka research projects and resources
literature
medaka research community

Medaka Genome Project (NIG DNA Sequencing Center)

http://dolphin.lab.nig.ac.jp/medaka/index.php

BLAST search of medaka genomic sequences. Whole genome shotgun reads can be downloaded. This site is provided by the National Institute of Genomics (NIG).

UT Genome Browser

http://medaka.utgenome.org/

The latest version of the assembled medaka genome can be browsed using the browser developed in the University of Tokyo. Keyword searches and online mapping (using the ALPS alignment server) are available. The browser presents results with various tracks, and downloading from the database is possible.

Ensemble Medaka

http://www.ensembl.org/Oryzias_latipes/index.html

Genomic data of medaka is integrated in the Ensembl page:

BLAST search, link to UT Genome Browser
view of the karyotype

UCSC Genome Browser

http://genome.ucsc.edu/cgi-bin/hgGateway

This site lets one browse the genome of many organisms as well as medaka. The browser was created by the Genome Bioinformatics Group of UC Santa Cruz. The dataset for medaka is the same as the latest genome assembly of the above-mentioned UT Genome Browser and Ensemble Medaka websites.

National BioResource Project Medaka

http://www.shigen.nig.ac.jp/medaka/

This site is provided by the National BioResource Project (NBRP) on medaka. Although it is currently still under construction adding many features, this site offers:

list of strains provided by the project and contact persons
online protocols for medaka research
rules on nomenclature of medaka strains
the medaka atlas
BLAST search to the NBRP sequence database

National BioResource Project (Medaka Transgenic)

http://park.itc.u-tokyo.ac.jp/K-medaka/Kashiwa-TGM.html

Descriptions and distribution information of transgenic strains provided as bioresources.

MEPD: Medaka Expression Pattern Database

http://ani.embl.de:8080/mepd/

Provides medaka EST search and gene expression data examined through whole mount in situ hybridization (WISH).

Medaka EST Database

http://medaka.lab.nig.ac.jp/est_index.html

Provides search by keyword, sequence, and expression.

MBase (Medaka Genome Database)

http://mbase.bioweb.ne.jp/~dclust/medaka_top.html

In addition to EST database search, the linkage map database and BAC database are accessible.

DFCI Medaka Gene Index

http://compbio.dfci.harvard.edu/tgi/cgi-bin/tgi/gimain.pl?gudb=o_latipes

Integration of EST projects, providing gene ontology of medaka genes. BLAST sequence search against databases, annotation of EST, and list of EST libraries are available.

Washington University Zebrafish Genome Resources

http://zfish.wustl.edu/

List of inbred strains, data on ESTs, genomic sequences, mitotic maps.

ZFIN The Zebrafish Database Project

http://zfin.org

The integrated database for zebrafish.

OECD Online Bookshop

http://www.oecdbookshop.org/

Protocols for toxicity tests.

Images

Cell dynamisms in formation of neural subdivisions

http://dev.biologists.org/content/vol131/issue11/images/data/2553/DC1/Movie1.mpg

A movie showing cell movement during neurogenesis.

Development of the Japanese Medaka (Still Images and QuickTime Movies)

http://biog-101-104.bio.cornell.edu/BioG101_104/tutorials/Medaka_stills.html
http://biog-101-104.bio.cornell.edu/BioG101_104/tutorials/Medaka_videos.html

Images of medaka embryos, from fertilization to hatching. Developing organs and other features of the embryos are indicated, which aids understanding. Movies show the heartbeat of embryos and moving larva.

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