Events

The EUIndiaGrid project with support from the Cambridge Systems Biology Centre and the Cambridge Computational Biology Institute invites applications to attend this free workshop highlighting state-of-the-art developments in computational biology on the Grid and the Cloud.

EUIndiaGrid2 Biology Grid and Cloud Workshop - 29 March

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 is the perfect opportunity for experts, developers and end-users in the Biotechnology space to learn more about the benefits and practical usage of Grid and Cloud computing as well as highlighting EU-Indian collaboration in this field.

Event speakers are as follows

• Steve Andrews, FHCRC, Seattle  - "Modelling cell biology with spatial and stochastic detail"
• Upi Bhalla, NCBS, Bangalore - "Multiscale modelling with MOOSE"
• Karen Lipkow, CSBC, Cambridge - "How do transcription factors find their targets?"
• Nick Luscombe, EBI, Hinxton - " A classification model to predict enhancer functions in the early Drosophila embryo"
• Aswin Seshasayee, NCBS, Bangalore - "Functional and comparative genomics of DNA transactions in bacteria"
• Robert Cannon, Textensor, Edinburgh - "Algorithms and architecture for cloud based stochastic simulation"
• Shahid Khan, MBC, Chicago & LUMS-SSE, Lahore - "Sequestration of CaMKII in dendritic spines in silico"
• Lorenzo Dematté, Centre for Computational and Systems Biology (COSBI) & VENUS-C -"   Scaling up Systems Biology: Model construction, simulation and visualization"
• Robert Grossman, Bionimbus Cloud, Chicago
• Nicolas Le Novere, EBI, Hinxton (tbc)

The workshop will start at 9am and end at 17:30, followed by a drinks reception.

REGISTER NOW - Registration closes 29 March

With places limited to 100 and applications register now to ensure your place at the workshop. We encourage registrants to only register if they will participate so as to ensure that places are filled.

For more  details  and to register: http://www.escience.cam.ac.uk/euindiagrid/bioworkshop/

EU-IndiaGrid2 Smodlyn Tutorial - 30 March

The Smodlyn tutorial is an opportunity for Grid application users to learn about  the Smoldyn algorithm which has demonstrated the power of Grid computing. Smoldyn is a stochastic simulator of cell-scale biochemical reactions at high spatial and temporal resolution and 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 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 at kl280 at cam.ac.uk.

Places at the tutorial are limited to 20 and applications are subject to final confirmation from the organisers. This EUIndiaGrid/CSBC tutorial is free and includes refreshments and buffet lunch but not accommodation or travel.

Register now for the Smoldyn tutorial 30 March.

Find out more here

More about Smodlyn - from http://www.smoldyn.org/

Smoldyn is a computer program for cell-scale biochemical simulations. It simulates each molecule of interest individually to capture natural stochasticity and for nanometer-scale spatial resolution. It treats other molecules implicity, so it can simulate tens of thousands of molecules over several minutes of real time. Simulated molecules diffuse, react, are confined by surfaces, and bind to membranes much as they would in a real biological system.

Smoldyn is easy to use and easy to install. It is both more accurate and faster than other particle-based simulators. Smoldyn's unique features include: a "virtual experimenter" who can manipulate or measure the simulated system, support for spatial compartments, molecules with excluded volume, and simulations in 1, 2, or 3 dimensions.