Gaggle Bridge


The Gaggle

The Gaggle is a framework for exchanging data between independently developed software tools and databases to enable interactive exploration of systems biology data.

We offer two tools extending the Gaggle:

  • Gaggle Bridge, allowing to connect several Gaggle Boss instances, and
  • Gaggle SuperBoss, a more secure Gaggle Boss implementation which additionally includes all features of GaggleBridge.

Citation

Gaggle Bridge as well as Gaggle SuperBoss are briefly described in our publication:
Battke F, Symons S, Herbig A, Nieselt K: GaggleBridge – Collaborative data analysis. Bioinformatics (2011) 27(18): 2612-2613.


Gaggle Bridge

Gaggle Bridge (extends the Gaggle) allows to connect several Gaggle Boss instances on different computers. Connections can be established either directly, or via SSH, which is helpful to work together in different firewall-protected locations.

Using Gaggle Bridge

  1. Run a local instance of a Gaggle Boss, and start your Geese
  2. Run Gaggle Bridge (Java WebStart)
  3. Click on “Connect local boss” to establish a connection to your local Gaggle Boss instance.
  4. Connect to a remote boss by clicking on “Connect Boss”. In the dialog, enter that name of the target boss (you can choose this freely), the name or the IP address of the computer it is running. Don’t change the Boss RMI port unless you know what you are doing.
    You can also connect to a remote boss using a SSH tunnel (either connecting to a boss on the SSH login server, or connecting to a host via a SSH gateway). Do do so, enable SSH tunneling in GaggleBridge and supply the SSH login information. If this does not work for you, please check that your SSH server is configured correctly (see below).

SSH server configuration

    Some SSH servers are configured to not allow so-called “Gateway Ports”. If this is the case, GaggleBridge SSH tunneling will not work on that server. GaggleBridge users will most likely see the error message

    Connection refused to [SSH gateway ip/hostname]

    If you are using OpenSSH, just add the line

    GatewayPorts Yes

    to your sshd_config file. It is usually found at

    /etc/ssh/sshd_config

    After saving the file, the SSH server must be restarted. On Linux systems, this can be done by calling

    /etc/init.d/ssh restart

Gaggle SuperBoss

Gaggle SuperBoss extends the original Gaggle Boss by some features for added security and convenience. It is compatible with every Goose available.

Features:

  • Reject Connections: Gaggle SuperBoss asks every time a Goose tries to connect. If an unwanted Goose connects, it can be rejected, and can not send or recieve data.
  • Only local communication: Gaggle SuperBoss can filter out incoming data from GaggleBridges.
  • Force Disconnect Geese: Gaggle SuperBoss can forcefully disconnect any Goose, even those that refuse to terminate when asked by the Gaggle Boss.
  • History: Gaggle SuperBoss keeps track of the data it distributes. Any past data transmission from the current session can be resent, for example.

You can run the Gaggle SuperBoss (Java WebStart) from here.