The Bio-Mirror Project
Bio-mirror Public Service: a worldwide bioinformatics public service for high-speed access to up-to-date DNA/protein biological sequence databanks. In genome research, these databanks have been being growing at a tremendous rate, so much so that existing Internet speeds hampers distribution.
What is the Challenge? (The Need)
Bioinformatics is a melding of biology, computer science, informatics and information engineering into a single discipline that enables new discoveries in biology and related fields. Today, scientific advances require an understanding and integration of this library with computational expertise. Many questions in biology, medicine, and agriculture today can best or only be answered using extensive bioinformatics tools and resources.
The Bio-mirror project is devoted to facilitate timely access to important large data sets for this research. It is an international collaboration for rapid public access to molecular biology and genomic data. Currently, collaborators include bioinformatics centres in Japan, Australia, Singapore, China and Korea. At present, the Bio-mirror enables high-speed network access to DNA and protein sequence and structure data. This warehouse of core bioinformatics data is updated on a daily basis, the nightly update exceeds 10 megabytes. Bio-mirror is perhaps the world's largest public database at 200 Gigabytes and doubling every year or sooner.
John Fraser at the Bioinformatics group at Auckland University says: "We are supposed to be at the leading edge of Biotech; however, we are in the stone age as far as access to this public resource is concerned." Auckland University knows about a major Biotech company in the dairy sector spending tens of thousands of dollars a month on data, while Auckland University exchanges a removable hard disk by physical mail with an Australian Bio-mirror node (Australian National University)! - "We are stuck in a time warp!"
New Zealand does not have a node - because it does not have a Internet2 class (1 gigabits per second [Gbps] or above) connection. New Zealand scientists access this absolutely critical raw material for Biotech innovation in drips and drabs within the limits set by GENBANK. Incidentally, GENBANK also specifies the windows time during which NZ scientists may access the database (http://www.ncbi.nlm.nih.gov/) and limits the download volumes - because we do not contribute by way of having a node.
Professor Mike Hendy from Massey University, who specialises in developing tools that may be of huge scientific and commercial value in interpreting the data contained in the Bio-mirror, is frustrated at trying to work within a five university co-operative venture: The Allan Wilson Centre for Molecular Ecology and Evolution (http://awcmee.massey.ac.nz/index.htm).
John continues, "It is a fundamental requirement to operate in a first world fashion - particularly given the rhetoric of the government to grow the economy around Biotech driven growth."
It is not just a question of accessing the Bio-mirror, it is also about adding to the database to project New Zealand's capabilities abroad and actually taking a role as a peer in the global biotech community.
Bio-mirror is on Internet2 (former name for NGI), which operates at speeds of 1 Gbps+, allowing it to refresh changes to the database in a mere 30 minutes each day. Without an NGI-style connection (such as in New Zealand), we either have to exchange disks by mail every other week or remain stuck in the dark ages as far as access to essential raw information for Biotech is concerned.
How Can NGI Help? (The Use)
It is really quite simple. In order for our scientists to attain and maintain full participation in the global biotech community, we need a Bio-mirror node locally in New Zealand. That is not going to happen unless we have NGI - that is the pre-requisite condition to participate in the Bio-mirror project. This is so because the nodes are resident on networks such as Abilene, which is an Internet2 (NGI) backbone network. Abilene spans over 10,000 miles and operates at 2.4 Gbps, a speed 45,000 times faster than a 56K modem. So without NGI in New Zealand we remain stuck in the Biotech "have not" of the digital divide! â¦And all the talk about leadership in Biotech remains a rhetoric.
Mike Hendy puts it quite well: "I am not sure how long the top researchers will survive the carrier pigeon between hard drives mechanism."
The Bottom Line (The Value)
The Allan Wilson Centre is a fantastic example of cross-institutional collaboration in biotech in New Zealand. The centre is designed to draw resources that are distributed over five universities. Such a centre needs top scientists, who of course need top tools. Bio-mirror is an example of such a tool, and increasingly scientists who are not getting access and moving overseas. NGI can contribute to stemming this exodus of fine New Zealand brain overseas. The challenge is: how does one put a value on this? Traditional methods are impossible to apply to predict the future, however it is fair to concede that the huge growth projection in world class biotech intellectual property and scientists will simply not be realised without access to fundamental tools of the trade such as the Bio-mirror.
Based on official projections, one may say that the negative impact of an NGI-less New Zealand is in excess of $500 million over the next decade - worse still - the time warp can get so bad we can get stuck in it permanently.
The economic opportunity that we are missing in commercialising work, such as that done by Prof. Hendy, can easily be see by looking at outcomes of the bioinformatics tools and services used by other first world economies such as the United Kingdom (http://www.ebi.ac.uk/services/index.html). This is a multi- million-dollar opportunity cost for our economy that we are missing out on.
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