|New Mexico Supercomputing Challenge|
Challenge Team Interim Report
Thus stated, our goal is to accomplish two tasks: first, to identify the data from individual test samples in the stream of data output of a flow cytometer, and second, to analyze this refined data. These processes are currently done by hand, which takes much time and effort on the part of researchers. With the help of a computer program, these tasks could be completed quickly and with minimal effort; this will increase efficiency. Efficiency is especially important when working in the field of drug discovery.
The Flow Cytometer:
Before being sent through the flow cytometer, the cell samples must be prepared. A potential drug is added to the cells, and the samples are tagged with a fluorescent dye. Different types light emitting 'fluorescent tags' can be used to monitor cell responses. Different cells will receive different 'tags', thus making them different colors or intensities. Next, they are carried through the flow cytometer in a saline solution and passed at regular intervals past the laser beam. The cells deflect the laser light. If the fluorescence is altered in the presence of the test compound, this means that a reaction between the cells and the potential drug has occurred. When a reaction occurs, this is called a "hit". Hits are potential drug targets.
The colors of light deflected or emitted by the cell are optically separated and go into a detector. These detectors are called photomultiplier tubes, or PMTs. A PMT has a sensor in it, which sends a signal to a computer whenever a cell goes into it. The computer is then able to tell what fluorescence a cell has, and at which time interval the light went into the PMT. This shows up in the researcher's computer screen as a two-dimensional graph of dots showing the time when the cell came through the machine on the x-axis, and the fluorescence on the y-axis.
By looking at the fluorescence of the different particles on this graph, researchers are able to tell what kinds of reactions have taken place because every type of cell receives a characteristic fluorescence. If the potential drug causes this fluorescence to change in a sample, then the sample is a hit. Because hits may occur at rates of one sample per thousand, large numbers of samples are needed and large amounts of data are produced.
Project to date:
We plan to begin the last programming by using small amounts of data. This should make it easier to handle than using an entire data file. When we are comfortable with this, we will expand our program to accommodate larger amounts of data. Project Advisors: Mr. Allen Arsenault Dr. Larry Sklar
For questions about the Supercomputing Challenge, a 501(c)3 organization, contact us at: consult1516 @ supercomputingchallenge.org
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80 Cascabel Street
Los Alamos, New Mexico 87544