Koch Lab:Data/MT Gliding Assay Readme File: Difference between revisions

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This is the readme file for kochlab gliding assay and microtubule tracking data.
This is the readme file for kochlab gliding assay and microtubule tracking data.<br>
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== 2013/2014 Update ==
"Kochlab" has shutdown and we were unable to preserve the kochlab.org domain. All the data are preserved, but we can not yet provide convenient access. I will update links below to provide alternatives, based on the preserved data set on the University of New Mexico's Institutional Repository (LoboVault): http://hdl.handle.net/1928/12559 --[[User:Steven J. Koch|Steve Koch]] 12:11, 15 July 2014 (EDT)
==Credits==
Raw data acquired by Andy Maloney.  Tracking software by Larry Herskowitz and Steve Koch.  Tracking automation by Larry Herskowitz.  Data analysis and interpretation by Andy Maloney, Larry Herskowitz, Steve Koch.  Kinesin-1 provided by Haiqing Liu (LANL).
Data are licensed CC0, as noted above.  You are not required, but if possible it would be cool if you give credit to us in any derived work.  Also, we might enjoy working with you if it is productive.  Contact info can be found here: [[Koch_Lab:Contact]].
==Data==
Raw data can be found at the following link.
* <s> http://www.kochlab.org/files/Passivation/</s> (kochlab.org has shutdown)
* http://hdl.handle.net/1928/12559 (This links to the data set on LoboVault)
=== Guide to accessing data ===
The data can be browsed with the above [http://hdl.handle.net/1928/12559 link], using a web browser. More convenient downloading of the data can be achieved by anonymous FTP:
* Host:          libstore.unm.edu
** Anonymous username, blank password
* Remote site:  /12559/koch/surface_passivation/data
Please contact Steve Koch with questions: sjkoch@unm.edu
==Software==
(2013/2014 Update: Unfortunately, all of the kochlab.org links are broken. However, the software is preserved just not easily publicly accessible (at least not yet). Please email Steve Koch with requests. --[[User:Steven J. Koch|Steve Koch]] 12:25, 15 July 2014 (EDT))
Our software will all be open-source.  However, currently we have not yet gone through the steps to make sourceforge projects.  Below is all of the software we used to analyze images, but it will probably be difficult to use without some instructions (which we haven't yet written).  Unfortunately, some of even the compiled versions will require a NI-Vision license.  Whereas all the source code will require LabVIEW development platform.
===Microtubule image tracking, automated===
* LabVIEW 7.1 executable, installer, and source code (.llb library file) available here: http://kochlab.org/files/Software/Microtubule%20Gliding%20Assay%20Software/Automatic%20microtubule%20tracking
** The .zip file will give you everything
** The .exe file will run if you have LabVIEW 7.1 and NI Vision 7 installed on your machine.
** The installer will give you the necessary run-time engines.  However, you will need to purchase a pricey NI Vision license to run the installed software.
** If you have LV 7.1 and NI Vision, the .llb file will provide you the source code.
** This is the May 14 version of software.
* Raw image data can be obtained for our shared folder here: http://kochlab.org/files/GMA_RawImageData/Maloney.Andy
===Track smoothing and speed calculation, automated===
* LabVIEW 7.1 executable, installer, and source code (.llb library file) available here: http://kochlab.org/files/Software/Microtubule%20Gliding%20Assay%20Software/Manual%20tracking%20and%20automatic%20track%20speed%20analysis
** The .zip file will give you everything
** The .exe file will run if you have LabVIEW 7.1 and NI Vision 7 installed on your machine.
** The installer will give you the necessary run-time engines.  However, you will need to purchase a pricey NI Vision license to run the installed software.
** If you have LV 7.1 and NI Vision, the .llb file will provide you the source code.
** This is the May 14 version of software.
* Test files available [http://kochlab.org/files/GMA_RawImageData/Maloney.Andy/10Mar30/16%2042%2046Beta%20Casein%2010/Testing%20Automation here] and also in many of the sibling directories.
===Group speed analysis, automated===
* LabVIEW 7.1 executable, installer, and source code (.llb library file) available here: http://kochlab.org/files/Software/Microtubule%20Gliding%20Assay%20Software/Group%20speed%20v%20time%20auto%20analysis
** The .zip file will give you everything
** The .exe file will run if you have LabVIEW 7.1 installed on your machine.
** The installer will give you the necessary LV runtime engines.  I believe you do not need any other licenses (in contrast to above which require NI Vision runtime license), but I have not checked this.
** If you have LV 7.1, the .llb file will provide you the source code.
** This is the May 14 version of the software.
** Test files available here: http://kochlab.org/files/data/MTD
==Related Publications==
* Steve's presentation: [http://precedings.nature.com/documents/4479/version/1 Osmotic stress and water isotope effects in kinesin-1 gliding motility assays]
* Andy's poster: [http://precedings.nature.com/documents/4469/version/1 Speed effects in gliding motility assays due to surface passivation, water isotope, and osmotic stress.]
* Larry's poster: [http://precedings.nature.com/documents/4468/version/1 Open Source Kinesin-1 Stochastic Simulation and Gliding Assay Tracking Software]
==Related Notebook and Other Postings==
* [[User:Andy_Maloney/Notebook/Lab_Notebook_of_Andy_Maloney/Table_of_Contents/Table_of_Contents_Category_View|Andy Maloney's notebook]]
* [[User:TheLarry/Notebook/Larrys_Notebook|Larry Herskowitz's notebook]]
* [[User:Steven_J._Koch/Notebook/Kochlab|Steve Koch's notebook]]
* Example videos for now can be found on youtube: http://www.youtube.com/user/KochLab  Example:
<html><object width="480" height="385"><param name="movie" value="http://www.youtube.com/v/bPiFvOQsD-I&hl=en_US&fs=1&"></param><param name="allowFullScreen" value="true"></param><param name="allowscriptaccess" value="always"></param><embed src="http://www.youtube.com/v/bPiFvOQsD-I&hl=en_US&fs=1&" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" width="480" height="385"></embed></object></html><br>
Example with tracks overlayed:
<html><object width="425" height="344"><param name="movie" value="http://www.youtube.com/v/heaK44PW5ko&hl=en&fs=1"></param><param name="allowFullScreen" value="true"></param><param name="allowscriptaccess" value="always"></param><embed src="http://www.youtube.com/v/heaK44PW5ko&hl=en&fs=1" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" width="425" height="344"></embed></object></html>

Latest revision as of 09:25, 15 July 2014

This is the readme file for kochlab gliding assay and microtubule tracking data.
<html><!-- Open Data Link --> <a href="http://opendefinition.org/"> 

 <img alt="This material is Open Data" border="0"
 src="http://m.okfn.org/images/ok_buttons/od_80x15_blue.png" />

</a> <!-- /Open Data Link --> <p xmlns:dct="http://purl.org/dc/terms/" xmlns:vcard="http://www.w3.org/2001/vcard-rdf/3.0#"> 

 <a rel="license" href="http://creativecommons.org/publicdomain/zero/1.0/">
   <img src="http://i.creativecommons.org/l/zero/1.0/88x31.png" style="border-style: none;" alt="CC0" />
 </a>
 <br />
 To the extent possible under law, <a href="http://openwetware.org/wiki/Koch_Lab" rel="dct:publisher"><span property="dct:title">Steven J. Koch and other KochLab members</span></a>
 has waived all copyright and related or neighboring rights to
 <span property="dct:title">KochLab Data</span>.

This work is published from <span about="http://openwetware.org/wiki/Koch_Lab" property="vcard:Country" datatype="dct:ISO3166" content="US">United States</span>. </p> </html>

2013/2014 Update

"Kochlab" has shutdown and we were unable to preserve the kochlab.org domain. All the data are preserved, but we can not yet provide convenient access. I will update links below to provide alternatives, based on the preserved data set on the University of New Mexico's Institutional Repository (LoboVault): http://hdl.handle.net/1928/12559 --Steve Koch 12:11, 15 July 2014 (EDT)

Credits

Raw data acquired by Andy Maloney. Tracking software by Larry Herskowitz and Steve Koch. Tracking automation by Larry Herskowitz. Data analysis and interpretation by Andy Maloney, Larry Herskowitz, Steve Koch. Kinesin-1 provided by Haiqing Liu (LANL).

Data are licensed CC0, as noted above. You are not required, but if possible it would be cool if you give credit to us in any derived work. Also, we might enjoy working with you if it is productive. Contact info can be found here: Koch_Lab:Contact.

Data

Raw data can be found at the following link.

Guide to accessing data

The data can be browsed with the above link, using a web browser. More convenient downloading of the data can be achieved by anonymous FTP:

  • Host: libstore.unm.edu
    • Anonymous username, blank password
  • Remote site: /12559/koch/surface_passivation/data

Please contact Steve Koch with questions: sjkoch@unm.edu

Software

(2013/2014 Update: Unfortunately, all of the kochlab.org links are broken. However, the software is preserved just not easily publicly accessible (at least not yet). Please email Steve Koch with requests. --Steve Koch 12:25, 15 July 2014 (EDT))

Our software will all be open-source. However, currently we have not yet gone through the steps to make sourceforge projects. Below is all of the software we used to analyze images, but it will probably be difficult to use without some instructions (which we haven't yet written). Unfortunately, some of even the compiled versions will require a NI-Vision license. Whereas all the source code will require LabVIEW development platform.

Microtubule image tracking, automated

Track smoothing and speed calculation, automated

Group speed analysis, automated

Related Publications

Related Notebook and Other Postings

<html><object width="480" height="385"><param name="movie" value="http://www.youtube.com/v/bPiFvOQsD-I&hl=en_US&fs=1&"></param><param name="allowFullScreen" value="true"></param><param name="allowscriptaccess" value="always"></param><embed src="http://www.youtube.com/v/bPiFvOQsD-I&hl=en_US&fs=1&" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" width="480" height="385"></embed></object></html>
Example with tracks overlayed: <html><object width="425" height="344"><param name="movie" value="http://www.youtube.com/v/heaK44PW5ko&hl=en&fs=1"></param><param name="allowFullScreen" value="true"></param><param name="allowscriptaccess" value="always"></param><embed src="http://www.youtube.com/v/heaK44PW5ko&hl=en&fs=1" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" width="425" height="344"></embed></object></html>

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