LabCAS ("Laboratory Catalog and Archive Services") is a web-enabled environment that allows users to publish, share, search and download a wide variety of biomedical datasets. This page contains information for end-users of the LabCAS portal and services.

Data Publishing

At present, data can be published into LabCAS in two possible ways: by using the LabCAS User Interface to upload and trigger ingestion of data; or by uploading data directly to the LabCAS server. Before publishing, data should be "curated" i.e. organized in a meaningful directory structure, and provided with enough metadata to make them useful to other users.

Data Structure

Data in LabCAS is organized according to the following logical hierarchy:

Examples:

Before publishing data into LabCAS, you should organize them in a meaningful directory structure conforming to the model above.

Metadata

In LabCAS, metadata can be associated to data at all 3 levels: collections, datasets, and files. When publishing, it is recommended that the following metadata fields be supplied to make the data searchable and more useful (mandatory fields are underlined). When using the LabCAS UI to publish data, some of these fields are automatically populated based on the user login, or the value of other supplied fields.

Collection

Dataset

File

Any other custom metadata can be supplied and stored as well, at all levels of the data hierarchy.

Publishing via LabCAS UI

The LabCAS web portal provides a web-enabled workflow for uploading data to the server, and trigger publication to the LabCAS archive. The user is guided through the process of selecting the files from their own desktop, and populating the required and recommended metadata fields. Because uploading data through the browser is not very efficient, this process is recommended for datasets that are not very large (up to a few GB in size).

Uploading Data to the LabCAS Server

Very large datasets should be transferred to the LabCAS server via some means other than a web browser. At this time, LabCAS offers two ways to upload data directly: SFTP and WebDAV. Both protocols are supported on a variety of platforms including Linux, Mac OSX, and Windows. Before uploading data, please make sure to:

Then proceed through one of the two methods below.

SFTP

In this section we describe how to upload data using a Unix-like system (macOS, Linux, FreeBSD, Solaris, etc.) and on Windows.

Unix

On Unix-like systems, do the following:

Windows

On Windows systems, you first generate a public/private key pair:

  1. Download and install both PuTTY and WinSCP. Both are free, open-source software packages.
  2. Installing PuTTY makes a new program available, PuTTYgen. Start this.
  3. At the bottom, select SSH-2 RSA and enter 2048 bits. (This should be the default.)
  4. Press "Generate".
  5. Move the mouse around in the blank area to generate random numbers until the progress bar is filled.
  6. Click "Save public key" and save the key to a file. Mail that file to JPL and we'll install it in the right place. Alternatively, you can click in the Public key box, select ALL the text, and paste that in an email. This key should be a single long line of text that starts with "ssh-rsa AAAA…"
  7. Enter a passphrase (and confirm it) then press "Save private key". Choose a filename (say "LabCAS") and save it to your Documents folder.
  8. Close PuTTYgen.

At this point, you'll need to await confirmation from JPL that your public key has been installed. Once you hear back, you can start uploading data with the following:

  1. Open WinSCP.
  2. Press the "Advanced" button.
  3. On the left side, under "SSH", click "Authentication".
  4. Under "Authentication parameters", click the ellipsis … button under "Private key file".
  5. Select the private key you saved in the Documents folder in step 7 (above). Click "OK".
  6. Under "Session", select SFTP. For Host name, enter zipper-vm.jpl.nasa.gov; for user name, enter "sftpxfer".
  7. You will be warned the first time you're connecting to an unknown server. Press the "Copy Key" button. Then press "Yes".
  8. Enter the passphrase for the private key you created in step 7 (above). Check the box by "Remember password for this session". Then press "OK".
  9. You now have a window on the left with your local files and on the right. To send a file, select it on the left and click "Upload". Or simply drag and drop. You'll be prompted the first time to set up transfer settings. The defaults are fine, so check "Do not show this dialog box again" and press "OK".

WebDav data upload

Note that at this time uploading data through SFTP or WebDAV will NOT automatically trigger data publishing (although it will in the near future). Please contact the LabCAS team to let them know new data is available, and to coordinate the publishing phase.