Workshop: Using clouds for parallel computations in systems biology


Located at the Oregon Convention Center, Portland, Oregon

Monday, November 16, 9:00am - 5:30 pm.

In afflication with SC09

The aim of this workshop is to bring together researchers in the computing, systems biology and computational biology fields. The workshop will focus particularly on applications of cloud computing.

Modern genomics studies use many high-throughput instruments that generate prodigious amounts of data. For example, a single run on a current sequencing instrument generates 30-40 GB of sequence data, or one-third of a genomics sequence space (current archives of complete genomic data comprise 51 GB). The situation is further complicated by the democratization of sequencing; many small centers can now independently create large sequence data sets. Moreover, the immense amount and variety of 'omics data that must be integrated together with genomics data in order to model and study organisms at a systems level creates unique opportunities in computational biology. Consequently, the rate of sequence and related data productions is growing faster than our ability to analyze these data.

Cloud Computing provides an appealing possibility for on-demand access to computing resources. Many computations fall under the "embarrassingly parallel" header and should be ideally suited for cloud computing. However, challenging issues remain, including data transfer and local data availability on the cloud nodes.

This workshop aims to bring together computer scientists, bioinformaticists, and computational biologists to discuss the feasibility of using cloud computing.


  • Existing applications of cloud computing in Systems and Computational Biology (SCB).
  • Performance studies of SCB applications.
  • Tools for cloud computing in SCB.
  • Bridging computational needs and clouds/HPC.


    1. What are the characteristics of applications that would be appropriate for effective utilization of cloud architecture?
    2. What are the hardware bottlenecks that prohibit cloud architectures from being easily adopted by high throughput biological data analytics?
    3. What are specific tools that need to be developed or enhanced in order to make cloud architectures easily adopted for biological data and bioinformatics algorithms?


    We are soliciting both research and position abstracts (up to 500 words) related to the topics mentioned above along with responses to the charge questions listed (no more than 2 pages).

    The workshop will combine invited talks, talks selected from abstract submissions to this call (20 minutes Abstracts should be emailed to (please use PDF, ASCII or DOC format).


  • Abstract and charge response deadline: September 14, 2009
  • Acceptance notification: October 2, 2009
  • Workshop: Monday, November 16, 9:00 am - 5:30 pm.


    Clouds for Systems Biology Workshop: