Determine the relation between storage size and genomes, Computer Networking

Genome4U is a scientific research project at a large university in the United States. Genome4U has recently started a large-scale project to sequence the genomes of 250,000 volunteers with a goal of creating a set of publicly accessible databases with human genomic, trait, and medical data.

The project's founder, a brilliant man with many talents and interests, tells you that the public databases will provide information to the world's scientific community in general, not just those interested in medical research. Genome4U is trying not to prejudge how the data will be used because there may be opportunities for interconnections and correlations that computers can find that people might have missed.

The founder envisions clusters of servers that will be accessible by researchers all over the world. The databases will be used by end users to study their own genetic heritage, with the help of their doctors and genetic counselors. In addition, the data will be used by computer scientists, mathematicians, physicists, social scientists, and other researchers.

Genome4U has developed new techniques to sequence a person's genome quickly, accurately and most importantly at low cost.  The research group is a contestant for the $10,000,000 X-Prize offered by Archon-Genomics (see for details).  With their current funding they expect to complete the pilot project with capability to store the research data for 1,000 individuals by December 2012. And can sequence 5,000 individuals every month thereafter.

In addition to genetic information, the project will ask volunteers to provide detailed information about their traits so that researchers can find correlations between traits and genes. Volunteers will also provide their medical records. Storage will be required for these data sets and the raw nucleotide data. This detailed medical information is expected to require not more than 100 Mega-Bytes of storage for each individual.

Since the data is to be publically shared, an initial community of 25,000 active users are expected, and this community expected to double every 18 months.  Active users are expected to access 10% of the entire database daily which is expected to create huge demand on the networking infrastructure. For user navigation, search and management HTTP will be used as well as FTP for genome data transfer.

Also, the data center with the NAS and the research center with equipment to enumerate genome sequence are in different university campus buildings. To store one genome information in the NAS, 25% of traffic overhead is generated.

You have been brought in as a network design consultant to help the Genome4U project and the management team has asked you to help them organize their requirements.

They would appreciate your analysis to answer the following questions:

1. List the major user communities.

2. List project technical goals. Specify expected tradeoffs.

3. Calculate data storage requirements in the table below (10 marks). (Hint: do not forget RAID 6 waste of disk space)


By December 2012

Next each month

Storage size



Number of NAS servers



4. Estimate additional bandwidth requirements between data and research center buildings in kbps. Assume that a Month is 20 work days and equipment works 10 hours per day.  (Show all your calculations)

5. Can you determine the relationship between the storage size, number of genomes, number of users and network capacity requirements? If possible express this as an equation.

6. Characterize the network traffic in terms of flow, load, behavior, and QoS requirements. You will not be able to precisely characterize the traffic but provide some theories about it and document the types of tests you would conduct to prove your theories right or wrong.

Posted Date: 3/18/2013 7:03:57 AM | Location : United States

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