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http://www.complex.iastate.edu/download/Picky/
A software tool for selecting optimal oligonucleotides (oligos) that allows the rapid and efficient determination of gene-specific oligos based on given gene sets, and can be used for large, complex genomes such as human, mouse, or maize.
Proper citation: Picky (RRID:SCR_010963) Copy
http://stockcenter.vdrc.at/control/main
Biomaterial supply resource which collects, maintains, and distributes independent transgenic fly lines. Most of the 38,000 fly lines are RNAi lines, but VDRC also maintains a collection of enhancer-GAL4 driver lines. Nearly all lines are in duplicate. Users can search for the stocks or DNA constructs for the gene of interest by entering CG number, synonym, or Transformant ID.
Proper citation: Vienna Drosophila Resource Center (RRID:SCR_013805) Copy
https://www.mcdb.ucla.edu/Research/Hartenstein/dbla/index.html
Atlas providing structure and development of Drosophila brain lineages. Used to learn about projection pattern of lineages as first step towards reconstructing and understanding all neurons.
Proper citation: Drosphila Brain Lineage Atlas (RRID:SCR_017507) Copy
An on-going atlas project of the Virtual Insect Brain Project with the goal of reconstructing and standardizing Gal4 expression patterns in Drosophila brains. Neurofly will be a web-based tool that will enable the online comparison of mutations and Gal4 expression patterns in the Drosophila brain. To this end, a database of reconstructed and standardized Gal4 expression patterns - on the basis of the existing Drosophila StandardBrain - was developed along with tools for 3D image data set processing. Users will be able to evaluate the expression patterns intersections of various Gal4 driver lines and/or mutations.
Proper citation: Neurofly (RRID:SCR_013833) Copy
http://insitu.fruitfly.org/cgi-bin/ex/insitu.pl
Database of embryonic expression patterns using a high throughput RNA in situ hybridization of the protein-coding genes identified in the Drosophila melanogaster genome with images and controlled vocabulary annotations. At the end of production pipeline gene expression patterns are documented by taking a large number of digital images of individual embryos. The quality and identity of the captured image data are verified by independently derived microarray time-course analysis of gene expression using Affymetrix GeneChip technology. Gene expression patterns are annotated with controlled vocabulary for developmental anatomy of Drosophila embryogenesis. Image, microarray and annotation data are stored in a modified version of Gene Ontology database and the entire dataset is available on the web in browsable and searchable form or MySQL dump can be downloaded. So far, they have examined expression of 7507 genes and documented them with 111184 digital photographs.
Proper citation: Patterns of Gene Expression in Drosophila Embryogenesis (RRID:SCR_002868) Copy
Flytrap is an interactive database for displaying gene expression patterns, in particular P(GAL4) patterns, via an intuitive WWW based interface. This development consists of two components, the first being the HTML interface to the database and the second, a tool-kit for constructing and maintaining the database. The browser component of the project is entirely platform independent; based on javascript and HTML and therefore only requires a "standard" browser. This is to facilitate CD-ROM distribution and off-line browsing. Whether on-line or on CD, the basic browser structure does not reply on any server based scripts. Basic searching is now available. The search page uses javascript and will work off-line (i.e. from a CD-ROM copy). The construction tool-kit is UNIX based and requires an on-line web server. The tool-kit is used to compile the HTML browser interface from a simple database. The tool-kit part comprises a forms based HTML interface to the datasets allowing new information to b e added and updated very simply. We are also developing a java interface for the tool-kit that will enable us to edit and annotate images on-line. The basic browser interface is complete and a demonstration version can be accessed via the website. The first working version of the tool-kit is now on-line and is available for use.
Proper citation: flytrap (RRID:SCR_003075) Copy
http://openconnectomeproject.org/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9, 2023. Connectomes repository to facilitate the analysis of connectome data by providing a unified front for connectomics research. With a focus on Electron Microscopy (EM) data and various forms of Magnetic Resonance (MR) data, the project aims to make state-of-the-art neuroscience open to anybody with computer access, regardless of knowledge, training, background, etc. Open science means open to view, play, analyze, contribute, anything. Access to high resolution neuroanatomical images that can be used to explore connectomes and programmatic access to this data for human and machine annotation are provided, with a long-term goal of reconstructing the neural circuits comprising an entire brain. This project aims to bring the most state-of-the-art scientific data in the world to the hands of anybody with internet access, so collectively, we can begin to unravel connectomes. Services: * Data Hosting - Their Bruster (brain-cluster) is large enough to store nearly any modern connectome data set. Contact them to make your data available to others for any purpose, including gaining access to state-of-the-art analysis and machine vision pipelines. * Web Viewing - Collaborative Annotation Toolkit for Massive Amounts of Image Data (CATMAID) is designed to navigate, share and collaboratively annotate massive image data sets of biological specimens. The interface is inspired by Google Maps, enhanced to allow the exploration of 3D image data. View the fork of the code or go directly to view the data. * Volume Cutout Service - RESTful API that enables you to select any arbitrary volume of the 3d database (3ddb), and receive a link to download an HDF5 file (for matlab, C, C++, or C#) or a NumPy pickle (for python). Use some other programming language? Just let them know. * Annotation Database - Spatially co-registered volumetric annotations are compactly stored for efficient queries such as: find all synapses, or which neurons synapse onto this one. Create your own annotations or browse others. *Sample Downloads - In addition to being able to select arbitrary downloads from the datasets, they have also collected a few choice volumes of interest. * Volume Viewer - A web and GPU enabled stand-alone app for viewing volumes at arbitrary cutting planes and zoom levels. The code and program can be downloaded. * Machine Vision Pipeline - They are building a machine vision pipeline that pulls volumes from the 3ddb and outputs neural circuits. - a work in progress. As soon as we have a stable version, it will be released. * Mr. Cap - The Magnetic Resonance Connectome Automated Pipeline (Mr. Cap) is built on JIST/MIPAV for high-throughput estimation of connectomes from diffusion and structural imaging data. * Graph Invariant Computation - Upload your graphs or streamlines, and download some invariants. * iPad App - WholeSlide is an iPad app that accesses utilizes our open data and API to serve images on the go.
Proper citation: Open Connectome Project (RRID:SCR_004232) Copy
A cross-database search service for Drosophila gene expression data, including microarray data from FlyAtlas and in situ images from BDGP and Fly-TED. The applications provide different ways to search for and compare gene expression data for the fruit fly Drosophila melanogaster. You may Search Gene Expression Data by Gene, Gene Batch, and by Tissue Expression Profile. A number of Web services (SPARQL endpoints) are provided from this site which may be queried programmatically for data.
Proper citation: OpenFlyData.org (RRID:SCR_004807) Copy
http://buridan.sourceforge.net/
Open source software written in R that tracks a single animal walking in a homogenous environment (Buritrack) and analyzes its trajectory. It extracts eleven metrics and includes correlation analyses and a Principal Components Analysis (PCA). It was designed to be easily customized to personal requirements. In combination with inexpensive hardware, these tools can readily be used for teaching and research purposes. Buritrack is a program to track individual Drosophila fruit flies online with any camera as they walk in Buridan's paradigm. The program extracts the coordinate locations of the fly and stores them in a text file.
Proper citation: Centroid Trajectory Analysis (RRID:SCR_006331) Copy
Curated collection of known Drosophila transcriptional cis-regulatory modules (CRMs) and transcription factor binding sites (TFBSs). Includes experimentally verified fly regulatory elements along with their DNA sequence, associated genes, and expression patterns they direct. Submission of experimentally verified cis-regulatory elements that are not included in REDfly database are welcome.
Proper citation: REDfly Regulatory Element Database for Drosophilia (RRID:SCR_006790) Copy
We provide high quality Drosophila transgenic service to both research institutions and companies. We offer you partial to full service ranging from DNA preparation, embryo microinjection, screening for white+, yellow+, and/or GFP/RFP phenotypes, to balancing crosses. Most importantly, the cost of our Drosophila embryo injection services is more reasonable compared to that of others. With a large number of facilities and the highly experienced staff, we are able to initiate the process immediately upon receiving your sample. Our friendly web-based database allows you to track your sample status, service history and more.
Proper citation: BestGene (RRID:SCR_012605) Copy
http://csb.pitt.edu/erc_analysis/Methods.php
Web-based statistical application that measures correlated rates across a phylogeny, allowing for extraction of genes with similar evolutionary histories. It can identify new functional connections between genes.
Proper citation: Evolutionary Rate Covariation (RRID:SCR_015669) Copy
Complete siRNA target database, complete Peptide-Antigen target database and a Kinase-Phosphatase database. They have also developed the largest database of illustrated signal transduction pathways, which are interconnected to their extensive protein database and online gene / protein analysis tools. The interactive web-based databases and software help life-scientists understand the complexity of systems biology. Systems biology efforts focus on understanding cellular networks, protein interactions involved in cell signaling, mechanisms of cell survival and apoptosis leading to development or identification of drug candidates against a variety of diseases. In the post-genomic era, one of the major concerns for life-science researchers is the organization of gene / protein data. Protein Lounge has met this concern by organizing all necessary data about genes / proteins into one portal.
Proper citation: Protein Lounge (RRID:SCR_002117) Copy
Web platform that provides access to data and tools to study complex networks of genes, molecules, and higher order gene function and phenotypes. Sequence data (SNPs) and transcriptome data sets (expression genetic or eQTL data sets). Quantitative trait locus (QTL) mapping module that is built into GN is optimized for fast on-line analysis of traits that are controlled by combinations of gene variants and environmental factors. Used to study humans, mice (BXD, AXB, LXS, etc.), rats (HXB), Drosophila, and plant species (barley and Arabidopsis). Users are welcome to enter their own private data.
Proper citation: GeneNetwork (RRID:SCR_002388) Copy
http://bioweb.ensam.inra.fr/esther
Database and tools for analysis of protein and nucleic acid sequences belonging to superfamily of alpha/beta hydrolases homologous to cholinesterases. Covers multiple species, including human, mouse caenorhabditis and drosophila., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: ESTHER (RRID:SCR_002621) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. Integrated database of genomic, expression and protein data for Drosophila, Anopheles, C. elegans and other organisms. You can run flexible queries, export results and analyze lists of data. FlyMine presents data in categories, with each providing information on a particular type of data (for example Gene Expression or Protein Interactions). Template queries, as well as the QueryBuilder itself, allow you to perform searches that span data from more than one category. Advanced users can use a flexible query interface to construct their own data mining queries across the multiple integrated data sources, to modify existing template queries or to create your own template queries. Access our FlyMine data via our Application Programming Interface (API). We provide client libraries in the following languages: Perl, Python, Ruby and & Java API
Proper citation: FlyMine (RRID:SCR_002694) Copy
http://cshprotocols.cshlp.org/cgi/collection/behavioral_assays
A bibliography of published Behavioral Assays by Cold Spring Harbor Protocols. Cold Spring Harbor Protocols is an interdisciplinary journal providing a definitive source of research methods in cell, developmental and molecular biology, genetics, bioinformatics, protein science, computational biology, immunology, neuroscience and imaging. Each monthly issue details multiple essential methods - a mix of cutting-edge and well-established techniques. Newly commissioned protocols and unsolicited submissions are supplemented with articles based on Cold Spring Harbor Laboratorys renowned courses and manuals. All protocols are up-to-date and presented in a consistent, easy-to-follow format.
Proper citation: Cold Spring Harbor Protocols: Collected Resources - Behavioral Assays (RRID:SCR_001697) Copy
http://www.stanford.edu/group/nusselab/cgi-bin/wnt/
A resource for members of the Wnt community, providing information on progress in the field, maps on signaling pathways, and methods. The page on reagents lists many resources generously made available to and by the Wnt community. Wnt signaling is discussed in many reviews and in a recent book. There are usually several Wnt meetings per year.
Proper citation: Wnt homepage (RRID:SCR_000662) Copy
http://www.virtualflybrain.org
An interactive tool for neurobiologists to explore the detailed neuroanatomy, neuron connectivity and gene expression of the adult Drosophila melanogaster brain.
Proper citation: Virtual Fly Brain (RRID:SCR_004229) Copy
https://www.janelia.org/confocal-imagery-management-and-analysis-tools
A discovery platform used to analyze and annotate imagery for individual projects, while assembling shared data resources. It was originally applied to Drosophila neuronal anatomy and neuroblast lineage analysis and is currently being extended to support mouse whole-brain projection tracing. The Workstation is both a pipeline management system that extracts entities from 3D imagery and a suite of tools that enable scientists to annotate large imagery datasets. A Entity-Attribute-Value (EAV) graph permits any element to be annotated by users with custom ontologies. By allowing any entity to have multiple parents, the graph can be re-arranged by each user without copying the underlying image data.
Proper citation: Janelia Workstation (RRID:SCR_014302) Copy
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