There are a number of open source packages dealing with aspects of
-single-molecule force spectroscopy. Here's a list of everything I've
-heard about to date.
-
-============= =========== ======================================================
-Package License Purpose
-============= =========== ======================================================
-[[calibcant]] GPL v3+ Cantilever thermal calibration
-[fs_kit][] GPL v2+ Force spectra analysis pattern recognition
-[Hooke][] LGPL v3+ Force spectra analysis and unfolding force extraction
-[[sawsim]] GPL v3+ Monte Carlo unfolding/refolding simulation and fitting
-[refolding][] Apache v2.0 Double-pulse experiment control and analysis
-============= =========== ======================================================
+[[single-molecule force spectroscopy|force_spectroscopy]]. Here's a
+list of everything I've heard about to date (for more details on
+calibcant, Hooke, and sawsim, see my [[thesis|Thesis]]).
+
+<table>
+ <thead>
+ <tr><th>Package</th><th>License</th><th>Purpose</th></tr>
+ </thead>
+ <tbody>
+ <tr><td>calibcant</td><td>GPL v3+</td>
+ <td>Cantilever thermal calibration</td></tr>
+ <tr><td>fs_kit</td><td>GPL v2+</td>
+ <td>Force spectra analysis pattern recognition</td></tr>
+ <tr><td>Hooke</td><td>LGPL v3+</td>
+ <td>Force spectra analysis and unfolding force extraction</td></tr>
+ <tr><td>sawsim</td><td>GPL v3+</td>
+ <td>Monte Carlo unfolding/refolding simulation and fitting</td></tr>
+ <tr><td>refolding</td><td>Apache v2.0</td>
+ <td>Double-pulse experiment control and analysis</td></tr>
+ </tbody>
+</table>
calibcant
=========
[fs_kit][] is a package for force spectra analysis pattern
recognition. It was developed by Michael Kuhn and Maurice Hubain at
-Daniel Müller's lab when they were at TU~Dresden
+Daniel Müller's lab when they were at TU Dresden
([paper][fs_kit_paper]). It has an [[Igor]] interface, but the bulk
of the project is in [[C++]] with a [wxWidgets][] interface. fs_kit
is versioned in CVS at `bioinformatics.org`, and you can check out
The last commit was on 2005/05/16, so it's a bit crusty. I patched
things up back in 2008 so it would compile again,
-[[!inline pages="./Open_source_force_spectroscopy/*.patch" archive=yes quick=yes]]
+[[!inline pages="./Open_source_force_spectroscopy/*.patch"
+ sort="title" archive=yes quick=yes]]
but when I emailed Michael with the patches I got this:
So, it's a bit of a fixer-upper, but it was the first open source
package in this field that I know of. I've put up a [[PDF
-version|fs_kit_tutorial]] of the tutorial Michael sent me in case
+version|fs_kit_tutorial.pdf]] of the tutorial Michael sent me in case
you're interested.
Hooke
=====
-[Hooke][] is a [[force spectroscopy]] data analysis package written in
+[Hooke][] is a force spectroscopy data analysis package written in
[[Python]]. It was initially developed by Massimo Sandal, Fabrizio
Benedetti, Marco Brucale, Alberto Gomez-Casado while at Bruno Samorì's
-lab at U~Bologna ([paper][hooke_paper]. Suprisingly, there are
+lab at U Bologna ([paper][hooke_paper]; surprisingly, there are
commits by all of the authors except Samorì himself). Hooke provides
the interface between your raw data and theory. It has a drivers for
reading most force spectroscopy file formats, and a large number of
generally compared to simulated data to estimate the underlying
kinetic parameters. [[Sawsim]] is my package for performing such
simulations and fitting them to the experimental histograms
-([paper][sawsim_paper). The single-pull simulator is written in
+([paper][sawsim_paper]). The single-pull simulator is written in
[[C]], and there is a nice [[Python]] wrapper that manages the
thousands of simulated pulls needed to explore the possible model
parameter space. The whole package ends up being pretty fast,
NanoScope scripting interface to drive the experiment *through* the
NanoScope software by impersonating a mouse-wielding user (like
[Selenium][] does for web browsers). See the `RobotNanoDriver.java`
-code for details.
+code for details. There is also [support for automatic velocity clamp
+analysis][refolding-vclamp].
+
+The official paper for the project is by [Aioanei][]. The earlier
+paper by [Materassi][] may be related, but Aioanei doesn't cite it in
+his paper, and Materassi doesn't give a URL for his code.
+
+Hardware
+========
+
+Nice software doesn't do you much good if you don't have the hardware
+to control. There are a number of quasi-open hardware solutions for
+building your own AFM (and other types of scanning probe microscopes).
+There's [a good list on opencircuits][opencircuits]. Interesting
+projects include:
+
+* Glenn Durden's [STM][GD] (1992–1998)
+* Jim Rice's [Homebrew STM][JR] (1995)
+* The Peddie School's [STM Project][PS] (1997–2002)
+* Jürgen Müller's [home-built STMs][JM] (1999–2006)
+* John D. Alexander's [STM Project][JDA] (2000–2003)
+* The Münster Interface Physics Group's [SXM Project][MIPG] (free
+ except for commercial use, 2000–2005).
+* Joseph Gatt's [Amateur STM][JG] (2003)
+* Maxim Shusteff's [AFM for the instructional laboratory][MS] (2006)
+* Dominik, Ivan, and Sandro's [STM-DIY project][DIS] (2009)
+
+Other software
+==============
+
+The [Gnome X Scanning Miscroscopy (GXSM)][GXSM] project provides GPL
+software to perform standard SPM imaging. The list of supported
+hardware is currently limited to the SignalRanger series by SoftdB,
+via GXSM-specific kernel modules like `sranger-mk23-dkms`. There is
+an obsolete [[Comedi]] driver for GXSM that Percy Zahl wrote back in
+1999, but [it has been deprecated][issue1649579] since at least 2007.
[fs_kit]: http://fskit.blogspot.com/
[fs_kit_paper]: http://dx.doi.org/10.1111/j.1365-2818.2005.01478.x
[refolding]: http://code.google.com/p/refolding/
[refolding_paper]: http://dx.doi.org/10.1093/bioinformatics/btq663
[Selenium]: http://seleniumhq.org/
+[refolding-vclamp]: http://code.google.com/p/refolding/wiki/BatchApproachRetractionAnalysis
+[Aioanei]: http://dx.doi.org/10.1093/bioinformatics/btq663
+[Materassi]: http://dx.doi.org/10.1063/1.3194046
+[opencircuits]: http://www.opencircuits.com/Atomic_microscope
+[GD]: http://web.archive.org/web/20010810000325/http://nemesis.com.au/alfa/mystm.htm
+[JR]: http://web.archive.org/web/20010210003357/http://atom.snu.ac.kr/stmwebpage.html
+[PS]: http://web.archive.org/web/20021219052018/http://www.peddie.k12.nj.us/Research/STMProject/e.html
+[JM]: http://www.e-basteln.de/
+[JDA]: http://www.geocities.com/spm_stm/Project.html
+[MIPG]: http://sxm4.uni-muenster.de/
+[JG]: http://www.angelfire.com/electronic2/spm/
+[MS]: http://www.media.mit.edu/nanoscale/courses/AFMsite/
+[DIS]: http://www.stm-diy.ch/
+[GXSM]: http://gxsm.sourceforge.net/
+[issue1649579]: http://sourceforge.net/tracker/?func=detail&aid=1649579&group_id=12992&atid=479639
[[!tag tags/programming]]
[[!tag tags/theory]]
projects / blog.git / blobdiff