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
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
- medaka research community
Medaka Genome Project (NIG DNA Sequencing Center)
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
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.
Genomic data of medaka is integrated in the Ensembl page:
- BLAST search, link to UT Genome Browser
- view of the karyotype
UCSC Genome Browser
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
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)
Descriptions and distribution information of transgenic strains provided as bioresources.
MEPD: Medaka Expression Pattern Database
Provides medaka EST search and gene expression data examined through whole mount in situ hybridization (WISH).
Medaka EST Database
Provides search by keyword, sequence, and expression.
MBase (Medaka Genome Database)
In addition to EST database search, the linkage map database and BAC database are accessible.
DFCI Medaka Gene Index
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
List of inbred strains, data on ESTs, genomic sequences, mitotic maps.
ZFIN The Zebrafish Database Project
The integrated database for zebrafish.
OECD Online Bookshop
Protocols for toxicity tests.
Cell dynamisms in formation of neural subdivisions
A movie showing cell movement during neurogenesis.
Development of the Japanese Medaka (Still Images and QuickTime Movies)
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.
Carolina Biological Supply Company (medaka supplier)
Tetra (fish feed supplier)
Medaka Honpo (medaka fish and feed supplier; only in Japanese)
Kyorin (fish feed supplier; only in Japanese)
Aquatic Habitats (fish keeping systems supplier)
Erecta (rack supplier)
Hirschmann Laborgeraete (glassware supplier)
Red sea (sea salt supplier)
Other websites introduced in the text
Coat Color Genes at ESPCR
ImageJ (Image processing and analysis in JAVA)
The Cartagena Protocol on Biosafety
American Fisheries Society
Canadian Council on Animal Care (Guidelines on use of animals)