29th-30th March 2011, Cambridge UK
The EUIndiaGrid project with support from the Cambridge Systems Biology Centre, the Cambridge Computational Biology Institute and the UK e-Science Engineering Taskforce invites applications to attend this free workshop highlighting state-of-the-art developments in computational biology on the Grid and the Cloud. With the increased computational needs of modern biology for data analysis, searches and simulations, and a deceleration in the development of faster processors, linking computers in a virtual network of a Grid or Cloud provides a much-needed solution. The alternative solution of parallel computing on Graphics Processing Units (GPUs) will also be covered. Our line-up of speakers includes experts on the technologies themselves, and those that have applied them to computational cell biology, neurobiology and gene regulation.
The workshop will start at 9am and end at 17:00, followed by a drinks reception.
Abstracts for the talks are now available
| 9:00 | Karen Lipkow (CSBC, Cambridge) | Introduction |
| 9:10 | Steve Andrews (FHCRC, Seattle) | Modelling cell biology with spatial and stochastic detail |
| 10:00 | Upi Bhalla (NCBS, Bangalore) | Multiscale modelling with MOOSE |
| 10:30 | Coffee | |
| 11:00 | Nick Luscombe (EBI, Hinxton) | A classification model to predict enhancer functions in the early Drosophila embryo |
| 11:30 | Lorenzo Dematté (CoSBI, Trento) | Scaling up Systems Biology: Model construction, simulation and visualization |
| 12:00 | Aswin Seshasayee (NCBS, Bangalore) | Functional and comparative genomics of DNA transactions in bacteria |
| 12:30 | Lunch | |
| 13:30 | Stefano Cozzini (CNR/IOM Democritos National Simulation Center, Trieste) | EUIndiaGrid infrastructures for computational biology |
| 14:00 | Robert Cannon (Textensor, Edinburgh) | Algorithms and architecture for cloud based stochastic simulation |
| 14:30 | Karim Chine (Cloud Era Ltd.) | Elastic-R: A Virtual Collaborative Environment for Scientific Computing and Data Analysis in the Cloud |
| 15:00 | Coffee | |
| 15:30 | Shahid Khan (MBC, Chicago & LUMS-SSE, Lahore) | Sequestration of CaMKII in dendritic spines in silico |
| 16:00 | Nicolas Le Novere (EBI, Hinxton) | Decoding calcium signals involved in synaptic plasticity |
| 16:30 | Robert Grossman (IGSB, Chicago) | Bionimbus: A Cloud-Based Infrastructure for Managing, Analyzing and Sharing Genomics Data |
| 17:00 | Drinks reception |
Location: MR3, Centre for Mathematical Sciences, Wilberforce Road, Cambridge CB3 0WA, UK
Directions to the Centre for Mathematical Sciences
30th March 2011: Smoldyn Tutorial
On the morning of 30th March, we will run a tutorial on an algorithm which has demonstrated the power of Grid computing. Smoldyn (www.smoldyn.org) is a stochastic simulator of cell-scale biochemical reactions at high spatial and temporal resolution. Smoldyn has been proven to be a powerful tool to reproduce a variety biological systems, make quantitative predictions, test novel hypotheses and quantify experimental data. The tutorial will be given by Smoldyn's developer, Steve Andrews, and some of its most experienced users, Karen Lipkow, Shahid Khan and Hugo Schmidt.
The tutorial will start at 9am and end at 12:30pm.
This EUIndiaGrid/CSBC tutorial is free and includes refreshments and lunch but not accommodation or travel.
Location: Bioinformatics Teaching Facility, Department of Genetics, Downing Site, Cambridge CB2 3EH, UK
Directions to the Department of Genetics
For all enquiries for either event, please contact Michael Simmons by email: mps48@cam.ac.uk in the first instance.
The tutorial will be followed by collaborative coding sessions to take Smoldyn to the next level, integrate it into the MOOSE environment, port it to run on GPUs, etc. Participation is by invitation only, but if you think you could contribute, please contact Karen Lipkow.
Organising committee: Karen Lipkow (chair), Mark Hayes, Gos Micklem, Michael Simmons.
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