posts:socks: Fix 'SSH tunneled' -> 'SSH-tunneled'

[blog.git] / posts / Open_source_force_spectroscopy.mdwn

diff --git a/posts/Open_source_force_spectroscopy.mdwn b/posts/Open_source_force_spectroscopy.mdwn
index e95140011584d3860b1e0b49f6e3bdb9e32bb639..5f9fa960bde02beed4dbd4468063bc5a3de11101 100644 (file)
--- a/posts/Open_source_force_spectroscopy.mdwn
+++ b/posts/Open_source_force_spectroscopy.mdwn
@@ -1,6 +1,7 @@
 There are a number of open source packages dealing with aspects of
 [[single-molecule force spectroscopy|force_spectroscopy]].  Here's a
-list of everything I've heard about to date.
+list of everything I've heard about to date (for more details on
+calibcant, Hooke, and sawsim, see my [[thesis|Thesis]]).
 
 <table>
        <thead>
@@ -109,7 +110,42 @@ analysis code in [[Python]].  The driver is curious; it uses the
 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
@@ -120,6 +156,21 @@ code for details.
 [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]]