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Archived sites hosted by Virtual Fly Brain

By maintaining these archives, VFB ensures that valuable scientific resources remain accessible to researchers often after the original hosting sites become unavailable.

1 - BrainTrap

BrainTrap is a database of 3D protein expression patterns in the Drosophila brain, providing interactive visualization and exploration of confocal datasets showing reporter gene expression and protein localization.

BrainTrap

BrainTrap is a database of 3D protein expression patterns in the Drosophila brain, providing interactive visualization and exploration of confocal datasets showing reporter gene expression and protein localization.

Overview

BrainTrap was developed as part of a large-scale collaborative research project to collect protein expression location information from protein-trap lines generated by the Cambridge Protein Trap (CPT) project. The database provides detailed 3D confocal datasets showing protein expression patterns throughout the adult Drosophila brain.

Features

  • Interactive web-based viewer for exploring 3D confocal datasets
  • Full-size images throughout the brain volume can be viewed interactively
  • Secondary immunohistochemical label (anti-brp) aids navigation and helps identify brain structures
  • Searchable annotations linked to the FlyBase Drosophila anatomy ontology
  • Anatomical search criteria can be specified using:
    • Automatic term completion
    • Hierarchical browser for the ontology
  • Annotation provenance tracking with highlighted expression locations
  • Downloadable confocal dataset files in original format
  • XML format annotation data export
  • Gene comparison tables for selected genes

Original Publication

Knowles-Barley S, Longair M and Armstrong JD (2010). BrainTrap: a database of 3D protein expression patterns in the Drosophila brain. Database, Vol. 2010, Article ID baq005, doi:10.1093/database/baq005 (https://doi.org/10.1093/database/baq005)

Funding

Original development was funded by:

  • Engineering and Physical Sciences Research Council (EPSRC)
  • Medical Research Council
  • Biotechnology and Biological Sciences Research Council (BBSRC)
  • British Society for Developmental Biology
  • Society for Experimental Biology
  • Virtual Fly Brain e-Science Institute (ESI) Theme

The fly lines were generated by the Cambridge Protein Trap Project, supported by a Wellcome Trust grant to Kathryn Lilley, Steve Russell and Daniel St. Johnson.

Current Maintenance

This resource is currently archived and maintained by Virtual Fly Brain (VFB).

Current website: https://braintrap.virtualflybrain.org/

Source code repository: https://github.com/VirtualFlyBrain/BrainTrap

Original Development

School of Informatics
The University of Edinburgh
Edinburgh, EH8 9AB, UK

Citation

If you use BrainTrap in your research, please cite:

Knowles-Barley S, Longair M and Armstrong JD (2010). BrainTrap: a database of 3D protein expression patterns in the Drosophila brain. Database, Vol. 2010, Article ID baq005, doi:10.1093/database/baq005 (https://doi.org/10.1093/database/baq005)

2 - FLYBRAIN Neuron Database (NDB)

FLYBRAIN NDB is an extension to the Flybrain, an Online Atlas of the Drosophila Nervous System. It collected images and descriptions of single identified neurons in the Drosophila brain, providing morphological information of all fly brain neurons identified at the time.

FLYBRAIN Neuron Database (NDB)

FLYBRAIN NDB is an extension to the Flybrain, an Online Atlas of the Drosophila Nervous System. It collects images and descriptions of single identified neurons in the Drosophila brain, providing morphological information of all fly brain neurons identified to date.

Current website: https://flybrain-ndb.virtualflybrain.org/

Database Structure

FLYBRAIN NDB is a relational database searchable by two main criteria:

Search neurons by:

  • Name (full or partial)
  • Areas of arborizations
  • Distribution of pre- or postsynaptic sites (where known)
  • Keywords in documentation

Search molecular markers including:

  • Antibodies
  • Drosophila strains (e.g., GAL4 enhancer-trap lines)
  • Specific neural pathways

Data Categories

  • Visual Neurons
  • Olfactory Neurons
  • Auditory Neurons
  • Gustatory Neurons
  • Central Complex Neurons
  • Clonal Units
  • Brain Region Definitions
  • GAL4 and LexAV Strain Collections

Brain Explorer Features

The online brain browsing system allows users to:

  • Rotate volume-rendered images
  • Create sections
  • Adjust magnification
  • Browse confocal data

Terms of Use

Access

  • FLYBRAIN NDB is freely available
  • No login or registration required
  • All contents © 2008 FLYBRAIN NDB or their original publication
  • Copyright is noted in respective images

Usage Rights

  • Free use for non-profit, educational, and scientific purposes with proper citation
  • Republication or commercial use requires consent from the FLYBRAIN NDB manager

Citation Guidelines

Citing the Database

When citing the database as a whole, use: “Flybrain Neuron Database (https://flybrain-ndb.VirtualFlyBrain.org)”

Citing Specific Records

Format: [Neuron type], [Author(s)], ([Year]) Flybrain Neuron Database (https://flybrain-ndb.VirtualFlyBrain.org), acc. [number]

Example: “LC10 neuron, Otsuna, H., and Ito, K. (2007) Flybrain Neuron Database (https://flybrain-ndb.VirtualFlyBrain.org), acc. 10010”

Important Notes:

  • Include accession numbers when citing specific neurons
  • Cite original publications where applicable
  • Multiple contributors may exist for each record

Current Maintenance

This resource is currently archived and maintained by Virtual Fly Brain (VFB).

Original Development

© 2010 FLYBRAIN Neuron Database
Original Contact: Kazunori Shinomiya