Key differences from the original Bioshare

Bioshare has been completely rewritten with a strong emphasis on security and usability. Whereas Bioshare previously only provided file security through obscurity (files could be viewed by anyone with the URL), the new Bioshare offers permissions (view, download, upload, delete, administer) on a per “share” basis. Unless the user chooses to make the share open to anyone with the URL, only specifically designated users will be able to access the files.

Where there were originally the concepts of a project and a subproject, there is now only the concept of the “share”. A share is simply a collection of files and folders to which the share owner may assign user permissions. All “subprojects” from the old Bioshare have now become “shares”. Each share retains the same permissions as the subproject that it was derived from.

Share Interface

This is the main interface for managing Share files. Functionality will may vary, depending on the permissions a user has for that Share. Depending on permissions a user can browse, download/view, upload, and delete files and folders.

Bioshare interface

Click to see full screen version

Downloading

Users can download files in a few ways. The simplest is just to click on the name of the file. For some files (such as images), the file may be directly shown in the browser, for other file types, the file may just be downloaded.

If a user wants to download multiple files/folders at once, they should select the checkboxes next to those items. Once selected, the user can click on the “Download” dropdown and select “Zipfile” to, you guessed it, create a zipfile containing the selected items. There is, however, a more efficient method to download: rsync. However, in order to use this method, you will first need to upload a copy of your SSH public key (under Account->SSH Keys)

Uploading

User’s can either upload through the web browser, or by using rsync.

Deleting

To delete files or folders, select the checkboxes next to the items to be deleted, then click the “Delete” button just above the file table.

Adding a new folder

To create a folder, click on the “+Folder” button and enter a name. Be aware that only letters, numbers, and spaces are allowed.

Searching

To search the current folder (and any subfolders), click on the “Search” tab. The search accepts a single term, and may contain the wildcard “*”. Examples: *.xls , *human*.fasta , etc.

Permissions Interface

If a user has the administer privilege for a share, they can modify its permissions. From the Share interface click on “Permissions”.

Click to see full size version

Secure Share

By default all Shares are “Secure Shares”. This means that only authenticated, authorized users will be able to browse and download files. If the secure option is not selected, anyone with the URL will be able to browse and download files. Please note that write, delete, and administer privileges are only available to the share owner, or those with explicitly given permissions. Unauthorized users can never do more than browse or download, regardless of this setting.

User Permissions

Here share administrators can give permissions to other users. Users are identified by email address. If an email address is not associated with a current user, an account will be created for that email address. A warning will be issued if a new account will be created.

Permissions are assigned once they have been selected next to the email address and the administrator has clicked on update. Any newly added user in the list will be emailed.

RSYNC

One of the major problems that Bioshare aims to solve is sharing large files. While browsing, downloading, and uploading fewer, smaller files over the web works, it isn’t very efficient. As an alternative approach, Bioshare offers the use of the rsync command to transfer files to and from a Share. Rsync is a utility that runs on the command line which is generally available on Mac or Linux, and may also be installed on Windows.

Advantages of rsync over standard methods that use HTTP are:

  • Efficiency: Only new or modified files are transferred.
  • When a transfer fails, rsync can be rerun, and only untransferred files will be downloaded/uploaded.

In order to use rsync, users must upload their RSA SSH public key. This can be done in the Bioshare interface from Account->SSH Keys. More information on how to generate SSH keys and how to use rsync to come…

SSH Keys

Using SSH keys allows secure communication (via rsync in this case) with Bioshare without the need for a password. All that is needed is a private/public key pair. The public key is what must be uploaded to Bioshare.

Generating RSA Keys

Linux

Check to see if you already have an RSA SSH key:

cd ~/.ssh

ls

If you do not already have a key named id_rsa.pub, run the following command:

ssh-keygen -t rsa -C “your_email@example.com”

It is recommended that you enter a passphrase to protect your key. Once you have a id_rsa.pub file, in Bioshare, go to Account->SSH Keys and upload this key. Once you have successfully uploaded your public key, you should be able to run rsync commands such as:

rsync -vrz bioshare@bioshare.bioinformatics.ucdavis.edu:/000008rm0rl8ktw/ /local/destination/folder

Note that in order to upload via rsync, you must have both write and delete permissions for that share. Downloading via rsync only requires download permissions.

FAQs

I can’t access the files at the URL that someone sent me, what’s going on?

By default, all Shares now require that users are logged in and have adequate permissions to view and download files. If another user sent you an old Bioshare link, you should request that they either a) assign you the necessary permissions, or b) open up access to anyone with the URL.

Where are my projects and subprojects?

Where there were originally the concepts of a project and a subproject, there is now only the concept of the “share”. A share is simply a collection of files and folders to which the share owner may assign user permissions. All “subprojects” from the old Bioshare have now become “shares”. Each share retains the same permissions as the subproject that it was derived from.