Zebrafish Databases & Resource Centres

The Zebrafish Information Network (ZFIN)
is a web based community resource that serves as a centralized location for the curation and integration of Zebrafish genetic, genomic and developmental data. ZFIN provides an integrated representation of mutants, genes, genetic markers, mapping panels, publications and community contact data.

Zebrafish on Bionet
is a google group, online bulletin board system where regisered users can search the archives, or post messages to the forum that can be read (and responded to) by anyone who has access to the system.  Bionet is an excellent way of solving fishy problems.  By getting your troubles amoung the experts, you can get feed back on anything from problems with protocols to better breeding tips.  Bionet is a moderated forum.

ResearchGATE
offers tools tailored to researchers' need. Whether you are working with a co-researcher in a different country or even continent, or would like to find a forum to discuss your research ideas and results, ResearchGATE keeps you in touch with scientists all over the world. You can find new research contacts in people performing in the same field or in different fields using the same techniques as you do. ResearchGATE connects researchers and information.

The Zebrafish International Resource Center (ZIRC)
is housed on the University of Oregon campus in Eugene. Its mission is to provide a central repository for wild-type and mutant strains of Zebrafish and for materials and information about Zebrafish research.

The Tübingen Zebrafish Stockcentre
keeps about 400 mutant zebrafish lines, which are publicly available for scientific research.  The collection of mutants kept as live fish in the stock center is in some flux. Because of limited capacity, a portion of the current strains may be removed, particularly those that have not met with any interest from researches until now. Other strains carrying newly induced mutations may have be added instead.

Ensembl Zebrafish
is a website that features the zebrafish assembly (version 8 (Zv8)), with it you can explore the Danio rerio genome.  The assembly was produced by integrating finished clone sequence from the physical map with whole genome shotgun assembly sequence.  Aligned zebrafish cDNAs are used to add UTR regions. Genes are named based on the alignment of their coding regions to known entries in public databases; ZFIN genes have priority in this process.

FishNet
is a three dimensional database of Zebrafish development from the early embryo to adult. Models of Zebrafish development may be virtually sectioned, viewed as 3D renderings, or downloaded for your own manipulations.

Atlas of Zebrafish Anatomy
is a collection of sections through Zebrafish embryos at four different stages of development assisting the understanding of how the Zebrafish embryo looks inside.  Anatomy of the 24, 48, 72 and 120 hours Zebrafish Embryo.

ZF-MODELS
Zebrafish Models for Human Development and Disease is an Integrated Project funded by the European Commission as part of its Sixth Framework Programme (EC Contract LSHG-CT-2003-503496). The project started on January 1, 2004 and is scheduled to run over a period of five years. 
The aim of this project is to exploit the advantages of the Zebrafish to produce knowledge, technology and materials in the form of disease models, drug targets and insight into pathways of gene regulation applicable to human development and disease.

Znomics Inc
is a Portland, Oregon biotechnology company founded in 2001. The company works on the Zebrafish as a system to identify genes underlying human disease and as a system for high throughput in vivo drug discovery. Znomics is creating the ZeneMark® Library, a comprehensive library of mutations using retroviral insertional mutagenesis where every gene of the Zebrafish is mutated, allowing for analysis of gene function.

The Sanger Institute's Zebrafish Mutation Resource
is a tilling project that seeks to identify, phenotype and distribute a large number of mutant zebrafish lines.  Mutations are identified from populations of chemically mutagenised animals using PCR of specific exons followed by re-sequencing.  Mutants are analysed for morphological and molecular differences and distributed to the community.  This is an open resource.  The status of genes already in the pipeline.  If your gene is not already on the list go to their gene requests form to request a gene for targeting.  If your gene is already available you can request alleles for shipment.  All of the alleles are freely distributed under a minimal MTA.

Gene Tools
is the sole commercial manufacturer selling research quantities of Morpholino antisense oligos world-wide. Morpholino oligonucleotides (oligos) are an antisense technology used to block access of other molecules to specific sequences within nucleic acid. Gene Tools also hosts a useful forum where Morpholino users may freely share ideas as well as troubleshoot problems. This board is a dynamic Frequently Asked Questions for those who are researching the uses of Morpholinos.

Zinc Finger Protein Search
Reagents and resources relating to the use of Zinc Finger nucleases (ZFNs) to generate targeted mutations in zebrafish are now available to the wider Zf community.  These tools will enable you to perform bacterial 1-hybrid selections to make zinc finger proteins against a particular target site of interest.  The resources include the plasmids and the bacterial selection strains that are now available through addgene, along with tips for getting started with the bacterial 1-hybrid, and an on-line tool that will help identify good sites and generate libraries for screening.

SciClips Zebrafish Protocols
Sciclips has launched a unique database of bioprotocols for researchers.  Researchers have free access to bioprotocols which have been extracted from published journal articles and patents/patent applications. They are the first to list protocols from published US patents, US patent and WO (PCT) applications, with thousands of protocols on molecular biology, proteomics, biological imaging, virology, immunology, stem cells, drug Discovery, immunoassays, cell biology, epigenetics, genomics, neurosciecne, plant biology, microbiology, tissue microarrays and more.  In addition, they have also listed new sections on high throughput screening (HTS) and biopharmaceutical assay protocols. All the protocols are linked to the articles or patent/patent applications.

The Zebrafish Husbandry Association (ZHA)
is a professional organization dedicated to promoting the improvement of husbandry standards for usage of the Zebrafish in scientific research.

  UTHSCSA ImageTool (V3.0)
UTHSCSA ImageTool (IT) is a free image processing and analysis program for Microsoft Windows.  IT can acquire, display, edit, analyze, process, compress, save and print gray scale and color images.  Image analysis functions include dimensional (distance, angle, perimeter, area) and gray scale measurements (point, line and area histogram with statistics).  Spatial calibration is available to indicate real world dimensional measurements such as millimeters, microns, feet, miles, etc. for linear and area. Density or gray scale calibration can be done relative to radiation or optical density(OD) standards.  Accessories and plugins are also available for download.