Similar to Youtube, would allow for a person to share a unique URL with a third party that will ignore standard authentication and allow access to a single specific view. This is specifically designed to make sharing easier without forcing a person to have an account with a password setup.

Check both the file name and the file hash when uploading files. It is possible for two files to contain identical data, but have significance of being run at different times and therefore needs to be added to the system. Can't exclude on hash only...

To help prevent the uploading of duplicate files, we need to add a SHA1 checksum calculation to ensure each file is uploaded only a single time to the site. This will help reduce load on the database and also prevent ambiguity if one or more users are repeatedly attempting to upload the same files.

In the event of User A attempting to upload the same file User B has uploaded previously (but kept private) we should prompt User A to request access to the file uploaded by User B rather than upload and process the file in duplicate.

When you're on a matrix view and you scroll down and click on a cell to view the raw read scores, it will auto scroll back to the top when you close the dialog box.

Add a popup showing score values in the color only view when mousing over a color block

Fix a problem with the matrix view where entries with no reads are still getting score values when they should not be. Need an alternative for when a group doesn't even exist within a file included in the view.

Fix a problem with the matrix view not correctly showing in Firefox. It has to do with the CSS used to draw the colored boxes. In chrome width: 100%; height: 100% files the but in firefox it's not doing the same.

Make sure any file or experiment that has not yet been processed by the system cannot be used as the basis for a new view. Only processed files/experiments can be used for this purpose.

Create a large form popup when clicking on a matrix view block that shows a table consisting of raw read values and sgRNA strings.

Build a view for looking up individual files. This view needs to include information about the file, links to download the file, and also views for viewing the raw data of the file or the collapsed grouped view of the file. All versions should be downloadable for use in other applications.

Build an automated process for creating advanced Datatables searching functionality based on column definitions. Apply this to all DataTables within the site, including custom Matrix views.

Allow for advanced functionality such as range searching and boolean searching/exact match/Wildcard searching.

Anywhere we use the term "background" change it to "control"

Need to build a more complex permission system. We need the ability to isolate uploaded screens and created views to allow for restrictions specifically to individual users and groups of users based on configurable preference. This will likely involve setting permissions individually on both files/experiments and views.

Add a Matrix View Legend Showing a Mapping of Files to Column Headers to make it easy to see which column header points to which file, and also allow for easy clicking through to the file view for further interrogation.

Some sgRNA are mapped to multiple groups. These are not being included in the calculations for log2 fold change for all groups in which they are a member.

Allow a user to remove views they no longer are interested in having available.

Change the way gene annotation is selected to utilize a more recent dump of Entrez-Gene rather than BioGRID annotation. This allows for a more easily maintained annotation set for genes.

Change the DataProcessingCRON to remove the pre-processing of score values on raw data into gene summaries. This is no longer required due to switching to our more advanced View Generator platform. This will require uncoupling several classes from the main code for Dataset Processing.

Add the ability to dictate what order your files are placed when creating a view like the Matrix view. Currently, files are ordered randomly which can result in related files being placed quite distantly from one another, especially in cases where many files are selected as a part of the view.

Add a popup containing gene annotation to groups listed in the first column of the matrix view, with links to the BioGRID.

Add a download link for downloading view data in tab delimited text file format. Specifically it should work for all views, including those created just for viewing annotated raw data.

Incorporate tools to allow for each file involved in a view to have a different annotation mapping file. This allows for the mixing and matching of different datasets, but allows the final view to still attempt to align results successfully.

Requires changes to build View Tool.
Requires changes to ViewGenerator
Requires changes to View Display to show selected options.

Create a simplistic dashboard view that is presented to users when logging into the site. First version should just be a simplistic view with links to functional areas of the site.

When using the Create View tool, the files shown at the bottom are not limited to those selected when picking experiments to start with.

There are two operations that need to be run regularly, DataProcessing and ViewGenerator. Place both of these in a shell script, so that they can be run with flock as a single call in CRON.

Don't show the linkout to view a file for new or in progress files from any table where you can view files. This needs to be done to prevent the view from showing off data that has not yet been processed into the database.

Do something to highlight the cell you clicked on when engaging the raw reads popup for the matrix view. Also, incorporate the score into the popup itself.