Neuroinformatics and Grid Techniques to Build a Virtual Fly Brain

From ESIWiki

The main website page for this theme is at http://www.nesc.ac.uk/esi/themes/theme_07/

Introduction

This theme runs from 01 September 2007 until 31 September 2009.

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.

Update (November 2009)

The funding obtained for the theme has contributed to a number of direct scientific outputs including publications, new collaborations (some of which require funding to take further and have grant applications submitted) but more importantly have clarified a route forward for the main challenge itself. In brief, a major conclusion to date is that a virtual fly model might want to focus on the strengths of the model (behaviour and anatomy) rather than follow the physiological precedent set by the mouse blue brain project. Immediate goals include a better anatomical framework and more standardised behaviour and these have formed the core recent activities

Update (November 2011)

The activities of this eSI theme have been continued in the BBSRC sponsored Virtual Fly Brain project.

Theme Events

Mapping Behaviour onto Anatomical Framework Workshop

We have identified that mapping behaviour onto anatomical framework could form a good basis for a virtual brain model for Drosophila. We aim to explore the behavioural side of this in a workshop. We have expressions of interest from the key people in the field but are yet to set a date – there has been a flood of workshops and meetings in recent months (May-September) that mean that Summer/Autumn 2009 may be more appropriate. Deliverable: Meeting report manuscript.

Virtual Fly Brain Behaviour Workshop, Oxford, Sept 2009

A small workshop looking at methods for the systematic analysis and measuring of behaviour in Drosophila than can in future be applied to structure/function models to be held at Magdalen College, Oxford September, 2009 see details

We have identified that mapping behaviour onto anatomical framework could form a good basis for a virtual brain model for Drosophila. We explored the behavioural side of this in a theme-hosted workshop at Oxford. A number of potential grant applications have been initiated as a result of the workshop (to be submitted in the new year) and two manuscripts are in preparation.

Virtual fly brain workshop

at e-Science Institute, 15 South College Street, Edinburgh 9-11 June, 2008

The Theme held its first official workshop in July 2008 at the e-Science Institute. The event was attended by leading researchers in the field and had a first public day of talks followed by a second discussion day looking at the challenge itself and routes forward. A summary of the talks and discussions was written up and is in press pending minor revisions (Phil Soc Trans A). The workshop attracted the attention of national press with an article in the Sunday Herald and a radio interview with Armstrong during the workshop.

Collaborative Knowledge Extraction (CoKE): Sequencing Animal Behaviour

at e-Science Institute, 15 South College Street, Edinburgh 30 July, 2007 12:30 - 31 July, 2007 14:00

Associated eSI Events

Theme leaders have participated in the following eSI events.

TBC (October 2008) Learning in model organisms workshop at Janelia Farm

15-16 May, 2008 NIH meeting on Drosophila and neural data meeting

11-14 May, 2008 Central complex meeting

10-11 May, 2008 Drosophila brain anatomy group meeting at Janelia Farm

19 November, 2007 November SAB Workshop

Papers

van Hemert and Armstrong. Report from Virtual Fly Brain Workshop. TBC.

Armstrong JD and van Hemert JI. Towards a virtual fly brain. Phil. Trans. R. Soc. A June 13, 2009 367:2387-2397. http://rsta.royalsocietypublishing.org/content/367/1896/2387.abstract

Presentations

Oxford Virtual Fly Brain workshop

Sepember 2009, e-Science Research (by van Hemert) http://www.slideshare.net/jvhemert/escience-research

Edinburgh/Riken Bioinformatics Conference, Tokyo

May 2009 (Armstrong)

Society for Neuroscience

November 2008 (Armstrong)

Neurofly, Wurzburg

September 2008 (by Armstrong)

UK e-Science All Hands Meeting: A Virtual Fly Brain

8-11 September 2008 (by van Hemert)

Neurofly 2008 Conference, Wurzburg, Germany: A Virtual Fly Brain

8-11 September 2008, http://neurofly2008.biozentrum.uni-wuerzburg.de/ (by Armstrong)

SBRN Text Mining - Combining text mining with the 'omics': Between the Devil and the Deep Blue Sea

at [Finding Hidden Knowledge: Text mining for biology and medicine, SBRN Text mining workshop, Glasgow

21-22 February, 2008 1330-1400

Invited Lecture: iBehave, Behaviour in Drosophila

at GlaxoSmithKline, Harlow

29 October, 2007

The e-Science Institute Public Lecture: "Building a better (fly) brain..."

at e-Science Institute, 15 South College Street, Edinburgh

02 November, 2007 16:00-17:00

Microsoft eScience: A Virtual Fly Brain

at The 2007 Microsoft eScience Workshop at RENCI

22 October 2007, 15:00-15:30 in the e-Neuroscience track

Funding awards

BBSRC Research Grant: Structured and graphical queries for Drosophila neuroscience data. 07/09-06/12 with Prof Michael Ashburner FRS, Cambridge

Collaborations

Activities

November 2008, Armstrong had discussions with E. Kravitz (Harvard), B. Brembs (Journal of Visualised Experiments, JOVE; Berlin) and M Mahoney (Vitruvean Inc, MA, USA) to promote theme activities and establish new theme-related collaborations

Visitors

11 Nov 2009, David Osumi-Sutherland (FlyBase).

March 2009, Bjoern Brembs.

10-11 March 2008, Gero Meisenbock

31 March-2 April 2008, Eugene Myers

October 2008, David Sutherland (Cambridge) to discuss refining the anatomy ontology used by FlyBase. We have developed a series of proposed changes for handing neuroscience specific anatomy that extends beyond existing databases (in any species). These proposals have contributed to a BBSRC grant proposal (submitted) and a new collaboration with Michael Ashburner (Cambridge) and FlyBase.

Planned, Ashburner, Strausfeld, Ito: Aiming to host a meeting of the core anatomical framework group. Ideally in Edinburgh but may need to be elsewhere. Aims are to finalise the revised anatomical ontology for the fly brain. Deliverable: Revised FlyBase ontology and manuscript.

Planned early 2009, Brembs: to discuss and ideally establish the first standardised behaviour tests. This may be done in conjunction with JOVE. Deliverable: manuscript.

Theme Leaders

Douglas Armstrong (Institute for Adaptive and Neural Computation, School of Informatics, University of Edinburgh)

Jano van Hemert (National e-Science Centre, School of Informatics, University of Edinburgh)