X windows connections

Making X-windows connections to bioinf.

Note: there are numerous reference below to accessing GCG seqlab. However, we are no longer providing GCG seqlab at UTHSCSA. This document is therefore only relevant for help in accessing other graphics programs implemented on bioinf

X-windows is a standard convention under Unix or Linux operating systems for export of graphics from one computer to another. This allows running of graphics programs on one computer while using another as the terminal. The naming of X-windows software is the opposite of most network applications. In this case the program you run to see the graphics is called a "server", and the remote computer running the graphics program and supplying the graphics is said to be the "client". X-windows servers are available for PC and Mac platforms, hence it is possible to run graphics software under Linux on the bioinformatics core facility machine (bioinf), and use your own PC or Mac as the terminal.

Bootable Linux CD option for Windows PC platforms.

Most typically, X-windows connections from a Windows PC are made by implementation of an X-windows server running under Windows (see examples below). An alternative, which is hoped to simplify the process is under development by the Bioinformatics Core Facility. A bootable CD is under development that will cause the PC to act as a Linux terminal and completely ignore the Microsoft Windows operating system. This is an alternative to the sometimes heard alternative of creating a dual boot Windows/Linux system. With the bootable CD there is no installation, configuration, or any steps affecting the resident hard drive that might alter subsequent function as a Windows computer. One simply boots the computer from the CD, clicks an icon, and enters username and password information. As part of this course, we will be asking students to test a prototype of the BCF bootable CDROM in laboratory computers around the department. One known limitation is that the prototype CD requires 128 Mb of RAM to operate. See Bootable CD assignment.

Establishing an X-windows connection (not using the bootable CD).

Assuming your computer has an X-windows server installed (see below), the simplest circumstance is that by virtue of making your ssh connection to bioinf, the X-windows connection was automatically set up. When making the ssh connection, you may have to specify ssh -X <host name> to get that behavior. In putty, the equivalent of the -X option is to click <connections><ssh><tunnels> and check "Enable X11 forwarding". [The tunneling option appeared in a recent upgrade of Putty. So if you can not find it by expanding the left Putty menu, you may need to upgrade]. See more help on ssh. After making an ssh connection and logging in to bioinf, type the name of a graphics program (like netscape, or seqlab; seqlab may have special requirements, see below). If the window pops up on your screen, then there is nothing special you have to do.

If a message like "..cannot open your display." appears then you will need to establish the connection by the following steps:

Find the X-windows server program on you machine and start it.

It will have some configuration options from which you will have to learn the IP of your computer. You can also find the IP of a Windows computer by using the winipcfg utility. (The IP is a number like 129.111.63.65. It may change from one login to the next. There is also a named associated like bioc-125.uthscsa.edu. Because of trouble we've been experiencing with the university name server, we recommend that you use the IP number directly).

You will also have to authorize bioinf to connect to your computer. Authorization may consist of adding the computer name and or IP to a list in a configuration utility. For linux or unix computers, authorization is granted by typieng xhost +bioinf.uthscsa.edu or xhost +129.111.175.204

You should authorize both the name and the IP number given above.

More specific setting for Xwin32 are given below.

From bioinf, type export DISPLAY=<your IP>:0.0
Now try running netscape and seqlab again.
Note that there seems to be a special problem between seqlab and Xwin32 signaled by the "X connection to <your IP> broken (explicit kill or server shutdown)" message. Methods to deal with that are given below.

A third option is that your X-windows server may be able to set up an Xdmcp connection. In this case, you give the name bioinf.uthscsa.edu to your X-windows server and it establishes the connection for you. The ability to get an Xdmcp query from one computer to another tends to fluctuate over time because system administrators often create security devices called firewalls that get into the way. Hence this method is convenient, but not particularly reliable within this university.

Sources of X-windows servers for PCs.

There is a relatively standard X windows interface for the PC called X-Win32 available for a fee from Starnet (http://www.starnet.com/) for about $125. There is an X server named MI/X for Macintosh Os9 or less that is free from Microimages (http://www.microimages.com/). Microimages also sells a windows version for $25. MacIntosh OsX may or may not have come with an X-windows server installed. Look for an application called X-darwin or X11, or an icon on the icon bar with a big red X on it. Otherwise X11 for OsX can be obtained from http://www.apple.com/macosx/x11/, or X-darwin can be obtained for a fee from http://www.xdarwin.org/.

Connection notes for selected X-windows servers.

To set up Xwin32 for GCG:

Run X-config.

First access <start> <display><settings> and make sure your display is at maximum color depth.
Find your IP in the DISPLAY window.
In the Windows tab, you will generally want to select "single" and pick height and width consistent with your screen display. However, these setting may be modified to taste after you see how the targetted graphics program displays In some cases, you may need to increase the resolution of your screen display to get enough pixels to reasonably display a particular graphic.
In the INPUT tab select "3 button simulation" to be ON (unless you have a 3 button mouse). This makes clicking with both mouse buttons send a middle click. You should probably check "panning".
On the security tab, add bioinf.uthscsa.edu and 129.111.175.204; also check "Access Control" and "Use XAuth".
On the "other" tab check "Pseuodocolor Mode". Under some circumstances some programs display better without Pseudocolor mode while other won't display at all. You can adjust this setting to taste after you get basic connectivity.
Accept settings by OK.

Run Xwin32 itself and minimize it.
Use ssh to connect to bioinf.
Type export DISPLAY=<your IP>:0.0
Most graphics programs can be run at this point, and their display will appear in the X-windows window which you can activate by clicking on its icon on the task bar. SeqLab however has a special problem which is indicated by the message "X connection to <your IP> broken (explicit kill or server shutdown)." If you get this message for seqlab or other graphics programs, then do the following to run with an exported Desktop.

Running X-windows with an exported graphics desktop.

In some cases, we have found this a necessary step to access GCG seqlab, in particular. Note: GCG seqlab has been discontinued at UTHSCSA

Complete the connection as indicated above.
Then run either the kde or xfce desktop's by typing startkde or xfce. Kde has more functions to it, but has also failed to export to some X-windows servers. Xfce is simpler and loads faster. It only displays a toolbar at the bottom of your X-window display, so be sure to scroll down to the bottom to see it.
Note: The startkde and xfce startup scripts have a habit of getting lost during bioinf system upgrades. If the command is not found, then notify Bo Demeler or Jeremy Mann and they will restore it.
Find the Xterm icon on the desktop and click on it.
In the resulting terminal window, type seqlab (or other graphics program name).

Some special notes using StarNet's Xwin32.

Xwin32 in it's config menu (accessed by starting it out of <start><programs>, or by right clicking on the xwin icon, systemtray symbol, or xwin window banner) allows setting the window to be single, or multiple. Some applications work better in multiple and some better in single. kde has been known to crash or display blank desktops in multiple window mode. When using single window mode, there is an option to click full screen in the config menu. Do not use that. There is no convenient path back to the Microsoft windows desktop once you blot out your screen that way. To escape that situation, you can use <alt><tab> to access another program that is running on the (now invisible) taskbar. Otherwise, all you can do is use <alt><F4> to terminate xwin32 and start over.

In the single windows mode it is best to set an explicit window size approximating your desktop. If by no other means, find this by trial and error. The single window appears with a banner and iconify, and maximize buttons. Also right clicking the banner gives you access to config. For accessing displays larger than your physical screen size, you can set the single window screen size larger than your physical screen size, and then through the banner buttons make it display in scroll bars. This can be a little inconvenient if the program displayed already has scroll bars. Then you get two sets of scroll bars, which is a little clumsy but workable.

Some special tricks through X-windows to bioinf.

You can activate a Netscape browser either by typing netscape at the command line, or by clicking the Netscape icon on an exported desktop. This Netscape browser will save files directly to your bioinf directory system. Hence, you can use it to save sequences directly from NCBI Entrez into your bioinf directory system.
If you export the kde desktop, you can install StarOffice on it, which will let you edit Microsoft .doc files and other Microsoft file types within the bioinf environment. To install, open a terminal shell and type /usr/local/staroffice6.0/program/setup, and follow the prompts.Choose a "local" installation. To create an icon, right click on screen, <create new>, <link to application>, and in the "execute" tab browse to staroffice6.0/soffice and enter. Your kde desktop should also be set up with Acrobat reader (for .pdf files), Ghostview (for viewing postscript files), and xview and GIMP (see below) for capturing, viewing, and editing screen shots and other bitmap images.
You can use the screen capture utility xview exported to your PC to capture screen shots from other graphics programs being exported to your PC. See X-window screen captures with xview. Note: if your PC has a native screen capture utility, you can use that also. Finally, a fully powered bitmap image editor with a screen capture facility, GIMP, should be present on your desktop, or in any case may be run by typing gimp in a terminal window. For instructions on using GIMP see Screen capture from various platforms.

Last updated 6/2/2004. - Steve Hardies