Edinburgh Data-Intensive Research - FlyBrain

Flybrain Neuron Database, a comprehensive online database of the Drosophila brain neurons

Jano.van.Hemert — Thu, 14 Jan 2010 12:13:12 +0000

ANC Seminar Series

Speaker:

Pro Kei Ito

Morphological and functional knowledge of the neurons of the Drosophila melanogaster brain has been accumulated drastically, thanks to the recent improvements in visualization techniques. Identified neurons, however, have been reported in diverse publications with inconsistent formats, making it very difficult to acquire comprehensive overview about what is known and what remains uninvestigated. To address this problem, we developed an online database, called Flybrain Neuron Database, which aims to collect information about all the Drosophila brain neurons reported so far.

Images and verbal descriptions about the neuron names, projection sites, etc., are provided. The database currently carry the records of about 360 types of neurons, which may already cover most of the known neurons in the fly brain.

In addition, the database also provides information about the three-dimensional labeling patterns of useful molecular markers that label specific subsets of neurons, such as antibodies as well as GAL4 and LexAV enhancer-trap strains. Unlike previous databases of other brains, we also implemented an interactive browsing system of the brain structures. The tool provides volume-rendered images of the brains generated from raw confocal section image stack upon users'
request. Users can rotate, magnify, and cut the brain at any angles so that relative positions and three-dimensional morphologies of the brain structures can easily be figured out.

To inherit our knowledge to our descendants, such database digital atlases should be maintained for a very long period, well over 100 years, like printed atlases. Long term maintenance of databases, however, is not easy. Technical and organizational measures to enable such long-term archive should be considered seriously. Some of the topics concerning this problem will be discussed.

Date and time:

Tuesday, 19 January, 2010 - 11:00

Length:

60 minutes

Location:

IF431

Projects:

FlyBrain

Research topics:

Collaborative environments

New conceptual models for systems

Towards a Virtual Fly Brain

Jano.van.Hemert — Wed, 10 Jun 2009 14:32:42 +0000

Neuroinformatics and Grid Techniques to Build a Virtual Fly Brain

Jano.van.Hemert — Thu, 20 Nov 2008 20:22:49 +0000

The world of healthcare could be transformed by realistic models that capture the processes and disorders of the human brain – but creating these involves overcoming immense scientific and technological challenges. The aim of this Theme is to begin with a simpler, more tractable problem: simulating the brain of a fly.

With only 100,000 neurons, compared to a human’s 100 billion, the fruit fly Drosophila has the simplest brain capable of complex behaviour. Modelling this brain promises insights into animal and human cognition. Drosophila is also an excellent candidate for this study due to the well-established data that already exists for this organism. Its genome was sequenced in 2000, and efforts to improve the sequence and its functional annotation are highly integrated and span the entire community. Further, the application of ontologies in biology was in part pioneered in Drosophila and is thus more mature here than in most other organisms. This is the key underpinning step in linking information about brain components and low-level functions to complex high-level outcomes.

This Theme will produce a road map for the construction of a virtual fly brain, based on grid technology. It will explore data standards and integration, data-warehousing, large scale simulation and visualisation, annotation and curation, and applications in research and industry. Establishing a point of focus for bioinformatics and neuroinformatics in Drosophila will enable gaps in the current databases, biological domain and modelling/simulation efforts to be identified and translated into new projects. The Theme also aims to engage communities of interest in animal and human healthcare research, in order to advance the development of e-Science infrastructure for biological modelling and create new applications for study of Drosophila in the pharmaceutical and biotechnology industries.

Acronym:

FlyBrain

Web site:

http://wiki.esi.ac.uk/Neuroinformatics_and_Grid_Techniques_to_Build_a_Virtual_Fl…

Value:

£75,000

Dates:

1 September 2007 to 31 December 2009

Project members:

Jano.van.Hemert

Partners:

Institute for Adaptive and Neural Computation, Informatics, University of Edinburgh

Projects:

FlyBrain

Publications:

Towards a Virtual Fly Brain

Project Status:

Finished

Towards a Virtual Fly Brain

Jano.van.Hemert — Fri, 15 Aug 2008 13:36:46 +0000

Speaker(s):

Jano.van.Hemert

Presentation Type:

talk

Research into human and animal health covers a vast array of biological components and functions. Yet strategies to simulate entire biological systems across multiple levels, by integrating many components and modelling their interactions, are largely undeveloped. Integration all the way from molecules to behaviour is a huge challenge. We will explore how this challenge can be approached by considering the components and interactions between these requited to build a virtual fly brain. This offers a new proving ground for collaboration between e-Scientists, biologists and neuroinformaticists.

Date and time:

Tuesday, 9 September, 2008 - 10:30

Location:

e-Science All Hands Meeting 2008, Edinburgh, UK

Web site:

http://www.allhands.org.uk/

Projects:

FlyBrain