Programming pages.
Mailcap files, defined in RFC 1524, allow you to tell you mail clients, web browsers, and other programs how you want to view and edit various MIME types. Since interaction with your mailcap files often occurs deep within the bowels of your program, I've written up a very simple Python script to test your mailcap entries: mailcap-test.py. Enjoy!
Available in a git repository.
Repository: cookbook
Author: W. Trevor King
I've been running a home-rolled recipe webapp for a year now, and it
worked fairly well in a bare-bones sort of way. However, I recently
had to make some changes to my personal website (since EveryDNS and
aparently most other free DNS providers were bought by Dyn), which
prompted me to translate cookbook
into a Django app. Thanks to
the wonders of Django, Grappelli, and django-taggit, the code
is now leaner, meaner, and prettier!
See the README for details.
Available in a git repository.
Repository: h5config
Author: W. Trevor King
Since the number of packages mooching off pypiezo's configuration scheme was growing, I've split it out into it's own package. Now there's a general package for all your HDF5-based configuration needs.
The README
is posted on the PyPI page.
Available in a git repository.
Repository: pypid
Author: W. Trevor King
I've just finished rewriting my PID temperature control package in pure-Python, and it's now clean enough to go up on PyPI. Features:
- Backend-agnostic architecture. I've written a first-order process with dead time (FOPDT) test backend and a pymodbus-based backend for our Melcor MTCA controller, but it should be easy to plug in your own custom backend.
- The general PID controller will automatically tune your backend using any of a variety of tuning rules.
The README
is posted on the PyPI page.
Available in a git repository.
Repository: insider
Author: W. Trevor King
Insider is a little Django app I wrote to help my brother, Garrett, track insider trading with a simple, familiar web interface. It's a pretty simple app, partly thanks to Bradley Ayers' django-tables2, which does the table formatting. Just goes to show that a good scripting language and framework make developing simple apps a breeze!
The README
is posted on the PyPI page.
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 |
calibcant
Calibcant is my Python module for AFM cantilever calibration via the thermal tune method. It's based on Comedi, so it needs work if you want to use it on a non-Linux system. If you're running a Linux kernel, it should be pretty easy to get it running on your system. Email me if there's any way I can help set it up for your lab.
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
(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
their code with:
$ cvs -d:pserver:anonymous@bioinformatics.org:/cvsroot checkout fskit
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,
0001-Added-math.h-include-to-fs align histogram2d.h.patch
Posted Sat Apr 23 15:00:17 2011
0002-changed-abs-double-to-fabs-double-in-fs fit spectr.patch
Posted Sat Apr 23 15:00:17 2011
0003-Updated-wxWindows-code-to-compile-on-wx-2.8.patch
Posted Sat Apr 23 15:00:17 2011
0004-Added-wxglade-entry-to-Makefile-for-regenerating-aut.patch
Posted Sat Apr 23 15:00:17 2011
but when I emailed Michael with the patches I got this:
On Thu, Oct 23, 2008 at 11:21:42PM +0200, Michael Kuhn wrote:
> Hi Trevor,
>
> I'm glad you could fix fs-kit, the project is otherwise pretty dead,
> as was the link. I found an old file which should be the tutorial,
> hopefully in the latest version. The PDF is probably lost.
>
> bw, Michael
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 of the tutorial Michael sent me in case you're interested.
Hooke
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; 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 commands for manipulating and analyzing the data.
I liked Hooke so much I threw out my already-written package that had been performing a similar role and proceeded to work over Hooke to merge together the diverging command-line and GUI forks. Unfortunately, my fork has not yet been merged back in as the main branch, but I'm optimistic that it will eventually. The homepage for my branch is here.
sawsim
While programs like Hooke can extract unfolding forces from velocity-clamp experiments, the unfolding force histograms are 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). 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, flexible, and convenient.
refolding
Refolding is a suite for performing and analyzing
double-pulse refolding experiments. It was initially developed by
Daniel Aioanei, also at the Samorí lab in Bologna (these guys are
great!). The experiment-driver is mostly written in Java with the
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.
Available in a git repository.
Repository: pypiezo
Author: W. Trevor King
This is a piezo-actuator control library based on pycomedi. It also contains some atomic-force-microscope-specific logic. The higher-level library pyafm extends the AFM-control framework with coarse positioning.
The README
is posted on the PyPI page.