Links to other on-line resources

Principle sources of Drosophila information

• The World-Wide Web Virtual Library: Drosophila
• FlyBase - Indiana University
• Drosophila Labs and References
• Anatomical Atlas of Flies
• Berkeley Drosophila Genome Project
• BioGRID: A curated set of physical and genetic interaction
• Bloomington Drosophila Stock Center at Indiana University
• cis-Decoder: Search for Drosophila enhancers
• Developmental Studies Hybridoma Bank - at the University of Iowa
• DFCI Drosophila Gene Index
• DrosDel: An isogenic deficiency kit for Drosophila melanogaster
• Drosophila DNase I Footprint Database
• DEDB: Drosophila melanogaster Exon Database
• Drosophila at NCBI
• Drosophila Genetic Resource Center: Kyoto Institute of Technology
• Drosophila Genomics Resource Center: Indiana University
• Drosophila Information Service
• Drosophila Heterochromatin Genome Project
• Drosophila melanogaster genes: KEGG metabolic and regulatory pathways
• Drosophila Phylogeny
• EvoPrinter: In silico identification of evolutionarily resilient dna sequences
• Exelixis collection at Harvard Medical School
• FLIGHT: Integration of data from high-throughput experiments carried out in Drosophila
• Flybrain: An atlas of the Drosophila nervous system
• FlyC31: An integrase-based tools for Drosophila researchers
• Fly-FISH, an in situ hybridization database
• FlyMine: An integrated database for Drosophila and Anopheles genomics
• FlyEx: Computational analysis of transcriptional signals in Drosophila
• FlyExpress: An image-matching search engine for finding biologically similar gene expression patterns
• FlyMove - an internet resource to study the development of the fruit fly: University of Münster
• FlyNome: A database of Drosophila nomenclature
• FlyTrap: GFP protein trap database
• FlyView
• Gene Disruption Project Database of the Bellen/Hoskins/Spradling labs
• Homophila: Human Disease to Drosophila Gene Database
• Patterns of gene expression in Drosophila embryogenesis - From the BDGP
• Berkeley Drosophila Transcription Network Project: gene expression and embryo morphology in 3D at cellular resolution
• In Vivo DNA Binding: Use of whole genome tiling arrays to measure binding of transcription factors to DNA elements
• REDfly: Regulatory element database for Drosophila
• TaxoDros: The database on Taxonomy of Drosophilidae
• Trans-NIH Fly Initiative
• UC San Diego Drosophila Stock Center
• The twelve Drosophila genomes
• VDRC: The Vienna Drosophila RNAi Center

Insect resources

• Iowa State - Entomology Index
• Entomology Department - American Museum of Natural History
• Featured Creatures - University of Florida's Department of Entomology and Nematology

Developmental biology resources

• The Society for Developmental Biology
• The Virtual Library - Developmental Biology
• The Virtual Embryo
• Sive Lab - General Developmental Biology Links
• Cold Spring Harbor Meetings and Conferences
• Society for Developmental Biology Meetings

Drosophila laboratories

• Gerard Mannings List of Drosophila Research Labs on the Web
• Rubin Lab Methods Book - at Nicholas Baker lab, Albert Einstein University
• Gene Disruption Project Database - Bellen Lab Baylor College of Medicine
• EvoPrinter - Odenwald lab, NINDS, NIH
• GenePalette - A desktop application for genome sequence visualization and navigation - Posakony lab, UCSD
• The Drosophila melanogaster Malpighian tubule - Julian Dow's lab
• P elements in Drosophila - William R. Engels, University of Wisconsin
• Hyper-Neuroblast Map - Chris Doe's Lab
• Synapse formation in Drosophila - Andreas Prokof's Lab
• Andrea Brand laboratory - Includes images and movies of CNS development
• Motor Axon guidance primer - Zinn lab
• P Elements in Drosophila - Engels lab
• Drosophila visual receptors - Stark lab
• Microbial infection of Drosophila : a model for dissecting host-pathogen interactions - Bruno Lemaitre's lab
• Tracheal Database - Markus Affolter's lab
• The Polycomb and Trithorax Page - Giacomo Cavalli's Lab
• Pattern Formation - Bob Holmgren's Lab
• Drosophila Glutamate Pages - David Featherstone

Genome and bioinformatics links

• General Sites
  • PubMed/Medline Query - National Library of Medicine
       As of 2004 this resource includes over 14 million citations for biomedical articles back to the 1950's.
  • SRS - European Bioinformatics Institute
       A powerful data integration platform providing rapid access to life science data stored in more than 400 databases.      Use this resource to recover almost any information, including structure, evolution and literature about any gene      or protein of interest.
  • Biocarta: Observe how genes interact
       Dynamic graphical models of gene interaction
  • STRING - EMBL Biocomputing
       Search Tool for the Retrieval of Interacting Genes/Proteins     STRING uses the genes summaries from The Interactive Fly for text-mining
  • GenMAPP: UCSF      Human, mouse, yeast and rat gene expression datasets visualized using the GenMAPP application program
  • American Association for Laboratory Animal Science
       The "Links" page consists of the following subcategories: Associations, comparative medicine departments,      diagnostic labs and testing alternatives. See for example University of California Center for Animal Alternatives       and The Animal Welfare Information Center of U.S. Department of Agriculture
• Multiple Resource Sites
  • Database resources of NCBI
       Major databases include PubMed, nucleotide and protein sequences, protein structures, complete genomes and taxonomy.
  • ExPASy Molecular Biology Server - proteomics server of the Swiss Institute of Bioinformatics
       Databases include Swiss-Prot and TrEMBL, PROSITE, SWISS-2DPAGE and SWISS-3DIMAGE.
  • Database Resources of the Sanger Institute
       Database resources include (1) Pfam, a protein families database, (2) Rfam, an RNA families database of alignments,       (3) Wormbase, a C. elegans genome database browser, and (4) SRS, a sequence retrieval system.
  • Ensembl Genome Browser - Sanger Center
       BLAST server and sequence retrieval for several species, including human, chimp, mouse, rat, zebrafish, fugu, mosquito,      fruitfly, C. elegans and C. Briggsae
  • Canadian Bioinformatics.ca Links Directory
       A compendium of tools and resources for molecular biology
• Molecular Analysis Sites
  • Entrez Gene - National Library of Medicine
        a searchable database of genes
  • Entrez Protein - National Library of Medicine
       Along with Entrez Nucleotide, a redundant database of sequences providing citations and other relevant links
  • SwissProt - Swiss Institute of Bioinformatics
       A curated protein sequence database, which strives to provide a high level of annotation (such as the description of the       function of a protein, its domains structure, post-translational modifications, variants, etc.), a minimal level      of redundancy and high level of integration with other database.
  • iProClass - Georgetown University
       Protein Information Resources
  • NCBI BLAST server
       Tools for recovery of protein and nucleic acid alignments
  • Genomic resourcs - Sanger Institute
  • Protein Data Bank: RCSB
       Worldwide repository for the processing and distribution of 3-D biological macromolecular structure data
  • IHOP (Information Hyperlinked over Proteins): Protein Design Group National Center of Biotechnology in Madrid      A gene network for navigating the literature

• Human Bioinformatics Sites
  • UCSC Genome Bioinformatics - Genome Bioinformatics Group of UC Santa Cruz
       Human Genome and Human Gene Family Browsers
  • Online Mendelian Inheritance in Man - NCBI
       Catalog of human genes and genetic disorders
  • GeneCards - Weizmann Institute of Science
       A database of human genes, their products and their involvement in diseases
  • Harvester - EMBL Heidelberg
       Harvester caches and cross-links public bioinformatic databases and prediction servers to provide fast access      to protein specific bioinformatic information. Contains information on human proteins only
  • OMIM Locus-specific mutation database links - NCBI
       Links to two dozen human genetic disease databases
  • Variation Databases and Related Sites - complied by the Human Genome Variation Society
       Includes locus specific mutation databases, disease centered mutation databases, and central mutation & snp databases
  • MEDLINEplus Health Information: Brain and Nervous System Topics - National Library of Medicine, NIH
       Links to dozens of sites related to human neural diseases
  • Database List of the Human Genome Variation Society

Gene family and gene specific sites

• ATPases Associated with diverse cellular Activities (AAA) server
• The World Wide Web Wnt Window
• Chromatin Structure & Function
• Cytokines Online Pathfinder Encyclopaedia
• Myosin Home Page
• Web links to Pc-G and trx-G material
• The Protein Kinase Resource
• Transcription factor classification from The Transcription Factor Database

Model Organsims

• Caenorhabditis elegans
  • WormBase      Accurate, current, accessible information concerning the genetics, genomics and biology of C. elegans     and some related nematodes
  • WormAtlas

• Zebrafish
  • ZFIN - Zebrafish Information Network - University of Oregon      Search for wild-type stocks, mutant/transgenic lines, genes/markers clones or gene expression

• Xenopus
  • The Xenopus Molecular Marker Resource - University of Calgary      Includes a BLAST tool, gene expression patterns, and compilation of literature

• Mice
  • Mouse Genome Informatics - The Jackson Laboratory           Integrated access to data on the genetics, genomics, and biology of the laboratory mouse (UL)
  • Gene Ontology Browser - The Jackson Laboratory
    • Links to molecular function including cell adhesion molecule activity, motor activity. signal transducer activity, transcription regulator activity, and
    • Links to biological process including behavior, cellular process, and development
    • Links to cellular component including extracellular, cell projection, cell surface, cytoplasm and nucleus
  • Gene Expression Data - The Jackson Laboratory      Search by gene symbol, gene ontology classification, chromosomal location, developmental stage      and anatomical structure       ES cell lines for the purpose of producing knockout mouse

• Mosquito Genome
  • Mosquito at Ensembl

• Pufferfish
  • Fugu Blast Server - DOE Joint Genome Institute      The current Fugu data is unassembled. The compact nature of the genome is largely due      to scarcity of dispersed repetitive sequences (<10%). Fugu has been proposed as a model vertebrate genome      to understand the more complex human genome and other vertebrate genomes.

• Sea Squirt
  • Ciona intestinalis - At the DOE Joint Genome Institute      Included is a Ciona BLAST server - The Ciona intestinalis genome is the smallest of any experimentally      manipulable chordate. This organism provides a good system for exploring the evolutionary origins      of the chordate lineage, from which all vertebrates evolved.

• Honey Bee
  • Honey Bee Brain EST Project - The W. M. Keck Center for Comparative and Functional Genomics at University of Illinois at Urbana-Champaign      Brain library ESTs were assigned molecular function and biological process using the Gene Ontology classification system. The site includes a BLAST tool.