Rank: 515 based on 243 downloads (last 30 days) and 11 files submitted
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Jonathan Karr

E-mail
Company/University
Mount Sinai School of Medicine
Lat/Long
40.78866, -73.95287

Personal Profile:

I'm a fellow at the Mount Sinai School of Medicine. 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
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(last 30 days)
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25 Mar 2013 Coverage Report Generator Generates Cobertura-style XML coverage report Author: Jonathan Karr coverage report, cobertura, hudson, jenkins, xunit, junit 28 4
21 Dec 2012 Mat file header utilities Utility functions for reading and writing .mat file headers Author: Jonathan Karr file 20 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 18 0
21 Dec 2012 Mat file utilities Utility functions for differencing mat files and structs. Author: Jonathan Karr mat file, struct, diff, difference 20 0
21 Dec 2012 Empirical formula Class for representing empirical formulae including support for basic math (+, -, *, etc.) Author: Jonathan Karr empirical formula, element, chemistry 17 1
Comments and Ratings by Jonathan View all
Updated File Comments Rating
26 Jul 2013 queryMySQL Platform independent MySQL database solution with blob support. Author: Jonathan Karr

Hi Carlos,

This is an error with the MySQL Java driver.

Can you share the error? Without seeing the error its hard to say what the problem is.

Best.
Jonathan

09 May 2013 queryMySQL Platform independent MySQL database solution with blob support. Author: Jonathan Karr

Hi Carlos,

I've never seen this error before.

First, comment out the try/catch block on lines 402, 410-412. Which line throws the error?

Best
Jonathan

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

Comments and Ratings on Jonathan's Files View all
Updated File Comment by Comments Rating
26 Jun 2014 Coverage Report Generator Generates Cobertura-style XML coverage report Author: Jonathan Karr Löfberg, Johan

Code does work in recent version of MATLAB (r2012,2014 tested) on Windows. The problem is capitalization of drives in which.m vs absolutepath.m.

The first returns C:\... while the second returns c:\...

This causes a failure on line 190 in Coverage.m

Cannot import as done in the example either, so I have to call the method as

report = edu.stanford.covert.test.Coverage('src', '..');

10 Jun 2014 queryMySQL Platform independent MySQL database solution with blob support. Author: Jonathan Karr Romain

Hi again,

I find my problem with '\n', it's just that Excel generate some CSV file with FIELDS TERMINATED BY '\r\n' and not just '\n'!

Sorry about that !

10 Jun 2014 queryMySQL Platform independent MySQL database solution with blob support. Author: Jonathan Karr Romain

Nice work here !
Only issue I have with these files is to load a CSV file into a database with lines terminated by '\n' (example : LOAD DATA INFILE 'ExampleFile.csv' INTO TABLE example FIELDS TERMINATED BY ';' LINES TERMINATED BY '\n'.
It looks like there are some problems to find this line return. Indeed the same request works on mysql, and the same request with lines terminated by '!' (for example) works with your package.
I've try to fix this problem but without succes for now.

Anyway thanks for this package !

23 Oct 2013 queryMySQL Platform independent MySQL database solution with blob support. Author: Jonathan Karr John

Hi Jonathan- thanks for the useful utility. I've noticed that with these tools, retrieving data from a database takes significantly longer than writing data, even if you try to grab large amounts at once (such as selecting everything in an entire table, which I would think is the most efficent). Running a Matlab profile on the code, it seems that in the function MySQLDatabase.m, line 190 is taking most of the time:
fieldName = this.getValidFieldName(char(metaData.getColumnLabel(i)));

Have you experienced this? Any thoughts on how to speed it up?
Thanks

12 Oct 2013 queryMySQL Platform independent MySQL database solution with blob support. Author: Jonathan Karr Shteingart, Hanan

files which are not part of clean matlab installation are missing:

mkconstarray.m
padarray.m
checkstrs.m

You can find them over the web.

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