SSH connections to molbiol for the PC

In order to use your molbiol account we recommend a program that creates a secure (SSH) connection to the molbiol server, "orac". This connection will encrypt traffic between the server and your computer - including your password. It will help to protect all molbiol account holders by preventing username and password "sniffing" on the internet.

It is no longer possible to transfer files between a local machine and the server using FTP. Instead, you can make use of the secure SSH connection to transfer files using SFTP.

Once connected, SSH programs by themselves are only capable of handing text. However, when used in combination with X window software (e.g. with eXceed on a PC), it is possible to use graphics-based, X applications such as Staden, Artemis, and AceDB.

Step 1. Install SSH

The SSH client for PC's (SSHSecureShellClient-3.2.9.exe) is available for download. Once downloaded, this application will install the SSH client on your PC. Note: you need to have administrator rights on the machine to be able to do this (or contact your local IT support to do it for you). After installation, the following guides should help you set up SSH to connect to your molbiol account.

Step 2. Configuring SSH on a PC for a single user

Once you have installed the SSH client, you will be able to start SSH (via "SSH Secure Shell" in start > all programs) before setting it up to connect to molbiol.

Configuration

• click "Profiles" (see Fig 1)
• click "Add Profile..."

Fig 1. Configuring SSH client

• type a name for the new profile (e.g. orac) (see Fig 2)
• click "Add to Profiles"

Fig 2. Adding a new SSH profile

• again, click "Profiles"
• click "Edit Profiles..."
• next to "Host name", type: orac.molbiol.ox.ac.uk (see Fig 3)
• next to "User name", type your molbiol username

Fig 3. Add molbiol address and username

• click "OK" to close the "Profiles" window
• click on "File" and then "Save Settings"

• once again, click "Profiles"
• click "Edit Profiles..."
• click on "Tunneling" (see Fig 4)

Fig 4. Tunneling

• ensure that the box next to: "TunnelX11 Connections" is ticked (see Fig 5)

Fig 5. Tunnel X11 Connections

• Click "OK" to close the "Profiles" window
• finally, click on "File" and then "Save Settings"

The SSH client is now configured to allow a secure connection to molbiol.

Configuring SSH on a PC for multiple users

Where a single PC is used by more than one person in a communal area, it is often more convenient to install and configure SSH only once so that it can be used by any user on the machine.

Once you have downloaded and installed the SSH client on your PC (see above), we have prepared a single SSH settings file for use by multiple users:

• Download the compressed settings file ( - using: save to disc )
• This file is a self-extracting zip file. Double-click the downloaded file to extract the settings file. By default, this will be created in a new folder: "C:\CBRG"
• Create a shortcut to the settings file (right-click > Create Shortcut). Note: you need to have administrator rights on the machine to be able to do this (or contact your local IT support to do it for you).
• Move the shortcut to the following location (when using Windows XP)
  C:\Documents and Settings\All Users\Desktop

All users on the machine will now be able to access their molbiol accounts via a secure SSH connection using these settings by double-clicking the shortcut from their desktop

Step 3. Guide to using SSH and SFTP

A connection to molbiol can be made by clicking on Profiles and selecting "molbiol". You will be prompted for your molbiol password.

Terminal Window
When a successful connection has been made, the terminal window will display a welcome message (see below) to let you know. If required, further terminal windows can be brought up by clicking the icon.

  
       *** Welcome to the Computational Biology Research Group *** 

     -------------------------------------------------------------------
     *  If you find ANY problems with the service please E-mail genmail * 
     -------------------------------------------------------------------

Secure File Transfer
You can use the SSH client to securely transfer files between your PC and your home directory on molbiol. Clicking on the icon will bring up the secure file transfer window (see Fig 6). This window will display the directory structure of your PC in the left pane and the directory structure of your home directory on molbiol in the right pane. Files can be dragged and dropped between the two systems. You can alter the read-write-execute permissions of any files on molbiol by right-clicking the file in the right pane and selecting "Properties".

Fig 6. SSH Secure File Transfer Window

Disconnect
The disconnect icon should be used to break the connection with molbiol prior to closing the SSH client (or if you leave your PC unattended).

Step 4. Install and configure eXceed

On our old machine "enterprise", eXceed was used to establish the connection to the server. In contrast, eXceed now uses the secure connection to molbiol that is created by the SSH client and no longer connects directly by itself.

These instructions are intended for Windows XP. We assume that you are using eXceed version 9 or version 10. The latest version is available under site license from the OUCS shop. You will need to pay for the media pack if you get a disk set. At the end of this guide, eXceed may be used in combination with the secure connection created using SSH (see above) to connect to molbiol.

Configuration:

1. After installing eXceed, open Xconfig
   • (start > all programs > Hummingbird Connectivity > Exceed > Xconfig)


2. Click the Security, Access Control and System Administration icon.
   • Select the File option and then click the edit button. This will bring up a notepad window and will allow you to edit the contents of the xhost.txt file. If you have used molbiol before, this file will probably contain an entry for "molbiol.ox.ac.uk". You should replace this entry with the following two lines:
     localhost
orac.molbiol.ox.ac.uk
     (note: any lines starting with "#" can safely be left in the file)
   • Save the changes made to the xhost file (File > Save) and close notepad.
   • Click the green tick at the top of the xconfig screen to save the changes and return to the starting menu.


3. Click the Network and Communication icon
   • In the options for "Mode", select "Passive"
   • Click the green tick at the top of the xconfig screen to save the changes and return to the starting menu.


4. Click the Display and Video icon
   • Under "Window Mode", select "Multiple"
   • Click the green tick at the top of the xconfig screen to save the changes and return to the starting menu.


5. Exit the Xconfig window.

Running Xwindow applications:

1. In order to run an Xwindow application, eXceed needs to be running in the background.
   Open eXceed (start > all programs > Hummingbird Connectivity > Exceed > Exceed). An eXceed button will be added to the taskbar at the foot of the screen (- although no window will be opened).


2. Start SSH (start > all programs > SSH Secure Shell > Secure Shell Client) and connect to molbiol (click on the molbiol profile that you made previously (see above)


3. After logging in, you will be able to open any of the Xwindow applications on molbiol. (You can test this by typing xeyes or xclock).

Troubleshooting:

• (Windows only) If you see the following error message after attempting to run any Xwindow application: Error: Can't open display:
  ...check that you have enabled "Tunnel X11 connections" when setting up the SSH profile for orac (see above)



• (Windows only) On some PCs, you may experience problems with eXceed that are caused by the integrated firewall. Oxford University Computing Services (OUCS) has a help page to guide you through the changes required to the firewall settings on your PC to allow traffic via eXceed.