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Michael Chute on OS X, Bioterrorism Research

By Blane Warrene MacNewsWorld ECT News Network
Jul 16, 2004 11:07 AM PT

At the onset of the Persian Gulf War in 1991, United States military leaders realized they did not have an effective method for detecting biowarfare agents in the atmosphere. Thus the Biological Defense Research Directorate (BDRD) was born within the Naval Medical Research Center in Silver Springs, Maryland.

Michael Chute on OS X, Bioterrorism Research

During the past 10 years, the BDRD has been pioneering methods -- called assays -- for detecting biological threats against military personnel. This has included research and development for detection in air, water and soil, resulting in one case in an assay for identifying anthrax.

Michael Chute, lab manager with the BDRD, recently spoke with MacNewsWorld and shed some light on his group's efforts and their use of Apple technology for research and development.

MacNewsWorld: Can you provide an overview of your current research efforts?

Michael Chute: To date much of our research has been molecular, biological and immunological, focusing on creating assays for detecting biowarefare agents in the environment. We recently spun up new sections that involve genomics, or DNA profiles of the biowarfare agents, and in vaccines, identifying DNA-based vaccines to the threat agent. We are in monkey trials on some, so progress is being made, and the next step would be human trials.

One of the side benefits of research such as ours is it ultimately can also benefit the non-military science spectrum over the long run.

MNW: We understand you use an Apple Workgroup Cluster. Can you explain your adoption of this platform for your research?

Chute: The shift to DNA and protein level analysis generates huge amounts of data we need to mine. We developed requirements internally that assumed we would not have dedicated information technology resources for support and did not want the licensing issues that come with Microsoft.

While we have traditional IT resources here, they are tasked with supporting the entire facility and not just our labs, so we would not have someone who could hold our hands while running a system.

More importantly, from a scientist's perspective, running on Unix was a must, so we looked at Linux and OS X solutions. While price was important, unfortunately the last few years have been a boon for our kind of research as instability has arisen internationally. Our budget permits us to buy just about whatever we want.

In the end, ease of use and data security was the rule. I spoke with people using Linux clusters, and while they were effective, they entailed more significant IT resources. No need for a bunch of scientists mucking around when they do not have the time to learn system administration.

Beyond that, due to the nature of our work, we needed to keep our data processing and storage secured internally. The G4 Xserve cluster, combined with BioTeam's iNquiry software package, matched for our needs.

MNW: Did you setup the cluster yourself? Any lessons learned?

Chute: Yes, in about six hours without any real difficulty. The joke around here is the hardest part was finding the screwdriver to assemble everything. Joking aside, it was straightforward to install. We use a four-node cluster of G4 Xserves, and most of the errors I ran into were based on my own misconfiguration that would break the system. I was able to use either Apple or BioTeam support to resolve any issues.

Since the setup and management is pretty straightforward, we can troubleshoot and support the little problems that come along. We know we can go back to the vendors for any serious problems.

What we came away with from setting up the system was that we were hungry for more power. We plan to add eight more G5 Xserve nodes to expand our capability. We can then configure the cluster to choose the best servers to run a particular procedure on, which should create more efficiency than we have even now.

MNW: Why did you select BioTeam's iNquiry?

Chute: iNquiry has a large number of open source programs wrapped up inside of it for various scientific pursuits. We utilize it for our genomics and vaccinology work. Additionally, by way of an XML interface in iNquiry, we can also integrate it with a proprietary software program we wrote here that analyzes micro array data.

That was the one area where we needed extra training. I went up to the BioTeam facility and was a gopher for them while getting training. They hopefully will then launch a formal training program for users.

MNW: In a general sense, how do scientists perceive Apple?

Chute: A majority of tools used in scientific research are either Unix-based and, in some cases, command line based, like BLAST, so a Unix-based platform has obvious attraction.

Second, keeping an interface simple is key, so Apple often wins users there as well. Finally, the myth that PCs are cheaper than Macs is untrue when you look deeper, anyway -- you have to "trick out" a PC to get to the performance level a Mac provides out of the box.

MNW: What is missing from your current setup?

Chute: Aside from adding the eight G5 nodes to our cluster, we also are now using Xserve RAID for data backups. However, we are looking to add a solution using tape storage or perhaps an optical drive so we can also backup and send data offsite.

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