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README.md

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-BrainTrap
-=========
+# 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)