From 73682b6d1cf6c92115ffb41c5d1a82adf02fce32 Mon Sep 17 00:00:00 2001 From: "W. Trevor King" Date: Sat, 23 Apr 2011 15:10:46 -0400 Subject: [PATCH] Cleanup open source force spectroscopy markup. --- posts/Open_source_force_spectroscopy.mdwn | 43 ++++++++++++++--------- 1 file changed, 26 insertions(+), 17 deletions(-) diff --git a/posts/Open_source_force_spectroscopy.mdwn b/posts/Open_source_force_spectroscopy.mdwn index 7987ea3..99c10f5 100644 --- a/posts/Open_source_force_spectroscopy.mdwn +++ b/posts/Open_source_force_spectroscopy.mdwn @@ -1,16 +1,24 @@ 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. + + + + + + + + + + + + + + + + + +
PackageLicensePurpose
calibcantGPL v3+Cantilever thermal calibration
fs_kitGPL v2+Force spectra analysis pattern recognition
HookeLGPL v3+Force spectra analysis and unfolding force extraction
sawsimGPL v3+Monte Carlo unfolding/refolding simulation and fitting
refoldingApache v2.0Double-pulse experiment control and analysis
calibcant ========= @@ -27,7 +35,7 @@ fs_kit [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 @@ -38,7 +46,8 @@ their code with: 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: @@ -53,16 +62,16 @@ 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 -- 2.26.2