# Talk:Koch Lab:Publications/Drafts/Versatile Feedback

## To Do

• Provide more context Rcyeh 00:39, 2 March 2008 (EST):
• Re-reading the paper two-and-a-half years after I wrote it, I feel that it is still not general enough, and doesn't provide sufficient context. If the reader were unable to jump into my head (and read my Master's thesis), I would have lost her or him by the second paragraph of the "Program Design" section.
• Reformat the list of modules into bullets, and provide an explanation of what each one does, prior to the example combinations.
• The improved traceability is a false argument until we say that the modules are so fundamental that they changed rarely. We were more likely to replace modules (Force Clamp AOD vs Force Clamp Piezo) than improve/enhance/tweak them. If we were to replace the contents of the modules without changing their names, the traceability of old data would be lost.
• There are clearly sections Steve can improve, and probably lots of data he has to contribute figures.
• The find tether center algorithm we used is actually more complicated than just odd-ordered polynomial. I wrote an algorithm to model the data as a rolling bead combined with WLC, which was much more stable. This little bit of code could be useful to others.
• This reminds me that in addition to the overall architecture, some of the subroutines (including data analysis: e.g., geometry iteration) could be valuable and easily usable by other users. Another example is the loading rate clamp which relies on computing the instantaneous ssDNA stiffness. Perhaps with some of these nuggets included we'd feel better about submitting for peer-review? Not sure, something to keep in mind.--Steve Koch 23:32, 2 March 2008 (EST)
• Richard C. Yeh 22:09, 4 March 2008 (EST): I think these are the major content of the article: a fully fleshed-out example of how to do things right.

--Richard C. Yeh 21:40, 4 March 2008 (EST): Steve -- do you have a copy of Single Molecule Techniques: A Laboratory Manual (Cold Spring Harbor Laboratory, 2008)? Searching through on Amazon reveals some mention of software. Chapter 13 describes force and position clamps (p. 288) alluding to an embedded processor. The most detailed it gets is in Chapter 17, on AFM (p. 380). There is a telling quote to the developmental state of affairs, though: "because of the complexity of coordinating high-precision-imaging equipment, peripheral devices, and the appropriate software, the lab or facility should have adequate expertise to engineer such a system from scratch." (p. 218, probably on fluorescence microscopy).

OPTICAL TRAPS
13. Optical Traps to Study Properties of Molecular Motors
J.A. Spudich, S.E. Rice, R.S. Rock, T.J. Purcell, and H.M. Warrick
14. High-Resolution Dual-Trap Optical Tweezers with Differential Detection
C. Bustamante, Y.R. Chemla, and J.R. Moffitt
15. Imaging and Nanomanipulation of an Actomyosin Motor
S. Nishikawa, T. Komori, T. Ariga, T. Okada, M. Morimatsu, Y. Ishii, and T. Yanagida
MAGNETIC TRAPS
16. Single-Molecule Studies Using Magnetic Traps
T. Lionnet, J.-F. Allemand, A. Revyakin, T.R. Strick, O.A. Saleh, D. Bensimon, and V. Croquette
FORCE PROBES/ATOMIC FORCE MICROSCOPY
17. Probing Polysaccharide and Protein Mechanics by Atomic Force Microscopy
M. Rabbi and P.E. Marszalek