Activity (RSS)

It seems that using the cache to store the results of the database search for the genotypes was causing some issues. Since the DB wasn't the bottleneck of the p...

I was exploring the polymorphic marker problem a bit and ran some analyses on the current production snplotyper and on the production.snptloyper.mcw.edu product...

It seems that using the cache to store the results of the database search for the genotypes was causing some issues. Since the DB wasn't the bottleneck of the p...

Im still finding some problems with the polymorphic markers (on the Dev branch). Attached are some screenshots from an analysis on Chr 1 between some ACI strain...

This was one of the things that I was going to need to deal with when we release the source code, since it's going to be different for everyone.

I think I had t...

Yes - that is the problem. R is located at '/Library/Frameworks/R.framework/Resources' on my machine (I didnt use macports for the install). I had just found th...

The R_HOME variable is set in config/initializers/startup.rb

for me it's set to ENV['R_HOME']='/opt/local/lib/R/' and below that, it properly sets the variable ...

I tried to run an analysis with the hierarchical clustering option turned on and it threw an exception:

Here's the developement log entry:

[Thu Jan 15 16:45:22 ...

I'll start putting stuff into here, compiling literature references, links to other tools and databases, etc. plus the existing screencast (which I should updat...

There is a new homepage for SNPlotyper and some links to support pages (help, contact, tutorials, related) that are just placeholders.

Real useful content needs...

The snp limit has been removed, but as you add more, it will get significantly slower.

You can now create an analysis via a get request by going to /analyses/api_visualize?parameters

While this exists, it's not going to be useful until we get stan...

The marker was being set in the genotype loop, but it was only using the last value that it found. I've changed it to logical AND the values so if any of them i...

The majority of the analysis code has been moved into models and now has specs.

I've added some spacing between the columns, updated the row colors.

There isn't valid CSS yet to rotate the text to a vertical layout. This is coming in CSS3, ...

Currently all the table cells run together making it very hard to distinguish sections of the table from each other. Needs to be improved so its legible! I've a...

Using the current master branch of SNPlotyper, it is not correctly indicating which SNPs are polymorphic anymore. At the moment, every SNP is polymorphic, even ...

admin controller has been split into snps and strains controllers and code moved into the models.

Add admin section to create groupings of strains so that we pass one value instead of multiple.

GBrowse and other applications need to send GET requests to SNPlotyper to open the visualize page without manually entering data.

The 400 SNP limit exists when a user is manually creating an analysis. This won't exist in the API/remote version, and may eventually be removed in the user ver...

The strains are being referenced by the MySQL table id, which will cause issues for external applications if the data is ever updated. Suggest that we update th...

Refactor the analyses controller so the code is moved into the models. This should make the controller easier to test and follow.

Refactor the admin controller so the code is moved into the models. This should make the controller easier to test and follow.
The models should also be easier ...

If possible, it might be worth updating all the data in the system. It would also be a good time to standardize the strain id used in the application, see tick...

When the data was originally loaded into SNPlotyper there was a glitch which meant the FHH SNP genotypes were not loaded. These need to be added to the database...

updated the css and logo image

Change the logo to remove the prototype text in the image.