Rank: 599 based on 150 downloads (last 30 days) and 11 files submitted
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Jonathan Karr

E-mail
Company/University
Stanford University
Lat/Long
37.43141, -122.17427

Personal Profile:

I'm a graduate student in Biophysics and Translational Medicine at Stanford University. My career goal is to understand and reverse engineer the complexity of biology to enable (1) personalized and predictive medicine and (2) rational bioengineering. My approach is to develop comprehensive computational models, and to compare model predictions to experimental data. I believe these models are essential to reverse engineering biology.

Professional Interests:
systems biology, translational medicine

 

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Files Posted by Jonathan View all
Updated   File Tags Downloads
(last 30 days)
Comments Rating
25 Mar 2013 Coverage Report Generator Generates Cobertura-style XML coverage report Author: Jonathan Karr coverage report, cobertura, hudson, jenkins, xunit, junit 13 3
21 Dec 2012 Mat file header utilities Utility functions for reading and writing .mat file headers Author: Jonathan Karr file 6 0
21 Dec 2012 Computer info Returns username, hostname, and IP address of the current machine. Author: Jonathan Karr user, host, username, hostname, ip address 2 0
21 Dec 2012 Mat file utilities Utility functions for differencing mat files and structs. Author: Jonathan Karr mat file, struct, diff, difference 7 0
21 Dec 2012 Empirical formula Class for representing empirical formulae including support for basic math (+, -, *, etc.) Author: Jonathan Karr empirical formula, element, chemistry 2 1
Comments and Ratings by Jonathan View all
Updated File Comments Rating
01 May 2013 queryMySQL Platform independent MySQL database solution with blob support. Author: Jonathan Karr

Hi Akhmad,

For security reasons we had to lockup our MySQL server, so unfortunately you can't use that test database anymore. The schema is described in test.sql. You can set this up on your own machine. See the examples on line 37-53 for how to work with blobs.

Best.
Jonathan

25 Mar 2013 Coverage Report Generator Generates Cobertura-style XML coverage report Author: Jonathan Karr

Sorry for the confusion. I don't believe the Control System Toolbox is required.

06 Nov 2012 queryMySQL Platform independent MySQL database solution with blob support. Author: Jonathan Karr

Hi George,

Unfortunately our server was attacked recently and I had to lock it down. This means the examples won't work anymore. You'll need to run them on your own MySQL server. The necessary schema is in test.sql.

Best.
Jonathan

06 Nov 2012 queryMySQL Platform independent MySQL database solution with blob support. Author: Jonathan Karr

Hi George,

I should also add that you are correct that MATLAB requires that classes be imported after addpath statements are executed. MATLAB will complain if you run the commands together until you've set the path. I usually work around this by setting the MATLAB path at the beginning of the session and then never setting the path inside any other function.

Best.
Jonathan

18 Jul 2012 queryMySQL Platform independent MySQL database solution with blob support. Author: Jonathan Karr

Hi Agustin,

I just tried this example where I repeatedly open and close connections without any issues.

for i = 1:1000
db = MySQLDatabase('covertlab.stanford.edu', 'test', 'test', 'test');
db.prepareStatement('select * from tinytest where id=1');
result = db.query();
assert(~isequal(-1, result));
db.close()
end

Are you working with the most recent version of the code (downloaded after June 22)? I recently changed the way database connections are created based on a suggestion from Matteo. Perhaps you won't have the issue with the newer version.

I'm not sure what the issue is. What happens if you keep the connection open rather than reopening it for each query? I can try to help if you can provide a more complete example of the problem.

Best.
- Jonathan

Comments and Ratings on Jonathan's Files View all
Updated File Comment by Comments Rating
01 May 2013 queryMySQL Platform independent MySQL database solution with blob support. Author: Jonathan Karr Karr, Jonathan

Hi Akhmad,

For security reasons we had to lockup our MySQL server, so unfortunately you can't use that test database anymore. The schema is described in test.sql. You can set this up on your own machine. See the examples on line 37-53 for how to work with blobs.

Best.
Jonathan

27 Apr 2013 queryMySQL Platform independent MySQL database solution with blob support. Author: Jonathan Karr FAUZI, AKHMAD

[HELP ME]

How i can save my image from Matlab to MySQL database in Type Data BLOB??

Please give me some tutorial with this Code in here,

my email: akhfauz.sisfo@gmail.com

Thanks Verry Much for your help

25 Mar 2013 Coverage Report Generator Generates Cobertura-style XML coverage report Author: Jonathan Karr Karr, Jonathan

Sorry for the confusion. I don't believe the Control System Toolbox is required.

18 Mar 2013 Coverage Report Generator Generates Cobertura-style XML coverage report Author: Jonathan Karr James

Why is Control System Toolbox required?

22 Dec 2012 Empirical formula Class for representing empirical formulae including support for basic math (+, -, *, etc.) Author: Jonathan Karr Crozier, Richard

Jonathan, I think this could be a useful piece of code, but you have not documented it. If you have gone to the effort of writing and shareing the code, I suggest going the extra effort to document it so others might be interested in using it.

Top Tags Applied by Jonathan
junit, mtest, testing, unit test, xunit
Files Tagged by Jonathan View all
Updated   File Tags Downloads
(last 30 days)
Comments Rating
25 Mar 2013 Coverage Report Generator Generates Cobertura-style XML coverage report Author: Jonathan Karr coverage report, cobertura, hudson, jenkins, xunit, junit 13 3
21 Dec 2012 Mat file header utilities Utility functions for reading and writing .mat file headers Author: Jonathan Karr file 6 0
21 Dec 2012 Computer info Returns username, hostname, and IP address of the current machine. Author: Jonathan Karr user, host, username, hostname, ip address 2 0
21 Dec 2012 Mat file utilities Utility functions for differencing mat files and structs. Author: Jonathan Karr mat file, struct, diff, difference 7 0
21 Dec 2012 Empirical formula Class for representing empirical formulae including support for basic math (+, -, *, etc.) Author: Jonathan Karr empirical formula, element, chemistry 2 1

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