PUMAdb : Data Repository Help

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The Repository allows database users to save and exchange retrieved and analyzed data from database, such as .cdt and .pcl files. The Repository is accessed through the web and it allows you to save data on our server at every step of the data retrieval and analysis pipeline. You can also analyze and re-analyze the same data sets in various ways making the comparison of different analyses easier. In addition, you can share your data files with others in your group or give access privileges to outside collaborators, as you would with an experiment. This help page describes how to use the Repository.

Size of the Repository

Each user will have a space quota for the Repository of 400 MB. The amount of memory used by files currently in your repository is shown on the bottom of the page. Once you have reached your quota, you will not be able to save new files to your repository until you delete some old ones. Therefore we ask that all users curate their own files, i.e. delete the unnecessary ones to save space. Warning: Once a file is deleted from the Repository it is not recoverable.

Accessing the repository

There are several ways you can access the contents of your Repository. If you already have files saved into the Repository select the Repository List link from the "Index of Programs" page under the "List Data" section. This link will show all the files you have in your repository and it will allow you to navigate to see other users' repository files for which you have access to view.

In addition, if you have already deposited a file to your repository, then there will be an selection entitled "Display My Repository" under the "My BioAssay Data" menu,

You can also see the same Repository list when you save a file in the repository during data retrieval or analysis.

Sharing Files in the Repository

You can make files in your Repository accessible to other database users and you can see files in other users' repositories to which you have been given access. In general, access to files the Repository is controlled the same way as access to experiments is controlled: members of a default group (lab group) can see each other's repository without restriction and you can give view access to your files to any other database user or group.

To give additional access to groups or individual users click on the respective edit ( ) icon on the right side of the window. On the next page you can either add or remove access to the file. At this time we don't allow public access to files stored in the repository.

To access files in the Repository of other database users, select a name from the pull down list after "View the repository of" on the bottom of the page. Hit the "submit" button and you will see the list of files available to you in that repository.

Repository Options

The top of the page lists whose repository you are in. If it is not yours, you can always go back to it using the MY REPOSITORY links. To navigate to another user's Repository, use the pull-down menu at the bottom og the page: "View the repository of", hit submit and you will get a list of the files you have access to.

The saved files in the Repository can be sorted by any of the column names that are highlighted. For Example, clicking the 'Size' column orders the files according to increasing size.

Upload files

You can upload files from your desktop computer to your repository. You can upload either a .pcl file or a .cdt file together with .gtr and .atr files if you have them. You can upload by clicking the 'UPLOAD' link on the right side of the page.

Bulk Delete

In order to manage your repository, and remain within the alloted quota, it may be necessary to delete numerous deposits based on date/age or size. Use the BULK DELETE link (posted at the top and bottom of the repository page) to remove multiple deposits that are no longer needed.

Icons and Options

There are 2 primary types of deposits within the repository.

  1. PCL
  2. CDT
These are deposited either from the primary database analysis pipeline or by direct upload. These 2 deposit types have both shared and specific options, as detailed below.

Shared Deposit Options
Allows you to look at the selections you made during data retrieval, filtering, etc.
You can download the entire file to your computer. The downloaded file will be compressed (in the .tgz format) and can be unpacked with Stuffit Expander or similar software. The resulting file is a text file of the type shown in the table (see the File Formats help for various formats found in the database).
After confirmation the file will be deleted. Once a file is deleted it is lost and cannot be recovered.
You can edit the name and the description of the file, and give access to other users or groups to see the file.
PCL-specific Deposit Options
You can filter the data that was retrieved from the database. See the Data Selection for Analysis help for more information on data selection.
You can perform "synthetic gene averaging" on the dataset. See the Synthetic Gene Collapse help for more information.
Perform K-nearest neighbors data imputation (KNNimpute), as described in Troyanskaya et al. Bioinformatics 17 (6): 520. (2001).
Click to perform SVD analysis on the data. See SVD Analysis Help for information on SVD.
Selecting this icon allows you to perform clustering analysis on the data. Take a look at the Analysis Methods help page for more information about clustering methods.
Click to visualize PCL data in a scatter plot. See Plot PCL Help for more information.
CDT-specific Deposit Options
Shows a static 'Cluster Image View' of the cluster, if avaialble.
Shows a static 'Spot Image View' of the cluster. This icon is available if the spot coordinates were retrieved from the database.
Shows a static 'Joint Cluster and Spot Image View' of the cluster. This icon is available if the spot coordinates were retrieved from the database.
Clicking this icon allows you to look at the file in an interactive fashion using GeneXplorer.
Clicking this icon allows you to look at the deposit in an interactive fashion using the Java TreeView applet.