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| *[[/Paper|Text of the paper]] | | *[[/Paper|Text of the paper]] |
| *[[/Why|Why you should use our software]] | | *[[/Why|Why you should use our software]] |
| *[[/Software|Software Documentation]] | | *[[/Software]] |
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| ===About this project===
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| By: Richard C. Yeh (rcy3cornelleduProject Admin) - 2008-03-04 03:03
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| Optical tweezers have transitioned from a laboratory toy some two-and-a-half decades ago to become a tool used in probing fundamental biochemical steps. With the release of Neumann & Block's 2004 "Optical Trapping" article in Review of Scientific Instruments, it seems that the hardware used to build optical tweezers has become more standardized. In the meanwhile, most labs with optical tweezers just wrote their own ad-hoc software to perform data acquisition and instrument control.
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| We think it is now appropriate to forward our software as an open-source project for use by tweezers developers. This project is an umbrella for the following:
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| 1. A user interface that allows manual or automated control of the instrument.
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| 2. Individual modules that perform various modes of data acquisition and feedback control of the instrument: force clamp, position/velocity clamp, force-loading clamp.
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| 3. Hardware device drivers.
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| The primary contribution of the initial version of the software, which we wrote in November-December 2000, is the ability to create and run scripts of feedback steps, which could be put in any combination or order. Each step had its own logic to determine when it was finished. For example, a typical DNA stretching experiment might have the following steps:
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| 1. Locate the tether center
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| 2. Apply a force clamp of 3 pN to make the tether taught
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| 3. Apply a velocity clamp to lengthen the tether with a given constant speed, monitoring the force, until the tether reaches 75 pN.
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| 4. Apply a force clamp of 75 pN until the DNA tether dissociates.
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| Each step would terminate once its stopping condition was reached. For steps 2 and 3, it might be that a particular maximum tether tension was reached. For step 4, it might be that the tether tension fell below some minimum threshold. These and other kinds of stopping conditions made repeated experiments more consistent.
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Revision as of 22:17, 22 March 2008
This is a draft of a paper that describes a useful software controller design for automated experimental setups. The particular application is dynamic single-molecule experiments performed with optical traps, but we believe the abstraction of hardware control into modular, functional feedback steps with user-programmable stop conditions offers a good example that can have application in other fields.
The draft was mostly written by Richard Yeh, with some help from Steve Koch. We are posting on OpenWetWare in draft form, because we probably will not try to publish in a peer reviewed journal soon, and the draft as is may have some positive impact.
