tag:blogger.com,1999:blog-108572922011-04-21T14:48:15.707-07:00This blog is sort of a homepage for fs_kit, an open source software to analyze force spectra.fskit Teamhttp://www.blogger.com/profile/04034411275301443155noreply@blogger.comBlogger21100tag:blogger.com,1999:blog-10857292.post-1108495520199454952006-02-15T11:22:00.000-08:002005-05-16T15:29:39.786-07:00fs_kit is a program that helps you automate tasks in the analysis of force spectra. It can find peaks, align spectra and classify peaks based on the alignment. An article about fs_kit has been published in the <a href="http://dx.doi.org/10.1111/j.1365-2818.2005.01478.x">Journal of Microscopy</a>.<br /><br />fs_kit is released under the GNU General Public License. This means that you are free to make it better and contribute.<br /><br />Binaries are available in the form of a GUI version and a command line version. The GUI version makes your life easier for simple tasks. However, to access the full functionality you will need to edit the settings file with an editor. The command line version has the big advantage that you see the output of the program even when it crashes. Yes, crashes are possible, because spectra can do all kinds of things that the program may not be prepared for. Hopefully, it will run fine in most cases.<br /><br />A <a href="http://fskit.mckuhn.de/tutorial.pdf">tutorial</a> is available.<br /><br /><span style="font-weight: bold;">Prerequisites</span><br /><ul> <li>There are binaries for Apple Mac OS X 10.3. A Microsoft Windows binary is planned, but it currently won't compile with the external libraries. Compiling fs_kit on Linux is possible.<br /></li> <li><a href="http://www.wavemetrics.com/products/igorpro/igorpro.htm">WaveMetrics IGOR Pro</a> for visualisation of spectra</li> <li>The GNU Scientific Library (<a href="http://sources.redhat.com/gsl/">GSL</a>) and <a href="http://www.wxwidgets.org/">wxWidgets</a>. (See installation instructions.)<a href="http://www.wxwidgets.org/"><span style="font-weight: bold;"></span><br /></a></li> </ul><span style="font-weight: bold;"><span style="font-weight: bold;"></span> Installation on Mac OS X<br /></span> <ol> <li>Download and install <a href="http://fink.sourceforge.net/">Fink</a>. You need administrator access to do so. (You also may need to install <a href="http://developer.apple.com/tools/xcode/">XCode</a>.)<br /></li> <li>Use Fink to install the packages <a href="http://fink.sourceforge.net/pdb/package.php/gsl">gsl</a> and <a href="http://fink.sourceforge.net/pdb/package.php/wxmac">wxmac</a>. (wxmac is not required for the command line version of fs_kit. wxMac 2.5 is currently classified as unstable, as it is still under development. However, use of version 2.5 is <a href="http://www.wxwidgets.org/dl_mac2.htm">recommended</a>. You might need to <a href="http://fink.sourceforge.net/faq/usage-fink.php?phpLang=en#unstable">follow these instructions</a> to enable unstable packages.)</li> <li>Download <a href="http://bioinformatics.org/groups/?group_id=298">fs_kit for Mac OS X</a> (under File Releases).<br /></li> <li>Follow the <a href="http://fskit.mckuhn.de/tutorial.pdf">tutorial</a> to get acquainted with fs_kit.<br /></li> </ol> <span style="font-weight: bold;">Installation on Windows<br /><span style="font-weight: bold;"><br /></span></span>A compiled version for Windows is currently not available. <a href="http://fskit.blogspot.com/2005/02/why-is-there-no-windows-binary.html">More info here</a>. You can, however, check out the source from CVS and compile it, for example under Cygwin.<br /><br /><span style="font-weight: bold;">Who's to blame for all this?<br /></span><br />fs_kit has been mainly developed by Michael Kuhn, with contributions by Maurice Hubain. Michael will start his PhD work at the EMBL in Heidelberg (on a totally different topic than force spectra!) Thus, we are always open for new developers to work on this!<br /><br />Contact info: michael.pencil.kuhn@gmail.com (Remove the writing utensil and one of the dots.)<br /><br /><br /><span style="font-size:78%;">This post is from the future so that it stays on top of the list. :-)</span><div class="blogger-post-footer"><img width='1' height='1' src='https://blogger.googleusercontent.com/tracker/10857292-110849552019945495?l=fskit.blogspot.com' alt='' /></div>fskit Teamhttp://www.blogger.com/profile/04034411275301443155noreply@blogger.comtag:blogger.com,1999:blog-10857292.post-1108700770865133682005-02-17T20:19:00.000-08:002005-02-17T20:26:10.866-08:00I have tried to compile fs_kit with Dev-C++, but it won't work. wxWidgets is available as package for it, so that should be not the problem. It is more of a problem that the GSL isn't available anymore as a package specifically for MinGW, the compiler in Dev-C++. I compiled the GSL with a separate installation of MinGW, and I'm getting some errors. I don't have the time to fix them now, but I hope it can be done eventually. If someone could try it, that would be great.<div class="blogger-post-footer"><img width='1' height='1' src='https://blogger.googleusercontent.com/tracker/10857292-110870077086513368?l=fskit.blogspot.com' alt='' /></div>fskit Teamhttp://www.blogger.com/profile/04034411275301443155noreply@blogger.com