• Where is the BCBLab?
• When is the BCBLab open?
• What is the BCBLab's purpose?
• What software can I run in the BCBLab?
• I'm a student, staff member, or faculty member who would like to use the machines. How do I get an account?
• I'm a faculty member who'd like to use the BCBLab for a course I am teaching. What do I need to do to be able to use the BCBLab machines?
• How do I log in?
• What are the BCBLab computers called?
• How do I log out?
• Where can I read more about computers, programming, and Linux?
• How do I keep up-to-date on new developments in the BCBLab? How can I communicate with other BCBLab users? How do I subscribe to the mailing list?
• Who runs the BCBLab? Who do I report problems and concerns to?
• How is the BCBLab funded?

Where is the BCBLab?

The BCBLab is on the Iowa State University campus in Ames, Iowa in the basement of the Molecular Biology Building (Pammel Drive), in room MBB0101.

When is the BCBLab open?

An automatic timer-controlled lock keeps the lab open from 9am to 5pm or thereabouts (it doesn't observe the change to and from Daylight Savings Time so sometimes this is off by an hour).

What is the BCBLab's purpose?

The BCBLab is intended primarily to provide computing resources for those studying questions in Bioinformatics and Computational Biology at Iowa State.

What software can I run in the BCBLab?

To read about most of the pre-packaged software that has been installed on the machines, you can click on the icon in the lower, left-hand corner to browse the options there. Or, from a command prompt in a terminal window type "rpm -qai | more" to get a list of software packages with their descriptions.

To explore amongst some of the specialized software that is installed, you can begin looking in the /opt/structure, /opt/sequence, /opt/office, /opt/j2sdk1.3.1, or /opt/jdk118 directories. For example, at a shell prompt "ls -lR /opt/structure | more" is one way to do that.

There is a wealth of software already installed, including compilers or interpreters for several computing languages, such as C, C++, Java, Perl and Python.

Office programs such as the office suite StarOffice, the vector-based drawing and illustration program Sketch, the diagram editor Dia, the spreadsheet program Gnumeric and the graphics program GIMP (Gnu Image Manipulation Program). These programs are not identical to their proprietary counterparts, but have their own strengths and weaknesses. In many cases they can work with the same files as with proprietary products. As of 20030402 OpenOffice.org is installed on microviz11, and is planned for roll-out to the rest of the machines eventually.

Mission-specific software installed on the BCBLab machines falls roughly into two categories: Sequence Analysis and Structure Analysis. Sequence Analysis software already installed includes Bioperl, Clustal, Phyllip an others. Structure Analysis software includes CCP4, CNS, MOLMOL and NMRView. Some of these programs are stored in /opt/sequence or /opt/structure, respectively, and some are stored alongside the rest of the programs in /usr/bin. For a list of the latter, please see this list, and thei respective man page. (For example, to read more about the version of clustalw installed, issue the command "man clustalw" in terminal window.)

In general, there is one overriding question considered in picking software to run in the BCBLab:

Beyond that, installation priority is given to those programs which are available from their author(s) in source form--the more free from redistribution restrictions, the better.

After those considerations are made, we'll consider installing almost anything that can conceivably run on our hardware providing it doesn't interfere with other operations--we're not that proud ;-)

So if you have something in mind, just ask. While we can't promise we'll have all the time and resources to meet your request, you've got to start somewhere!

I'm a student, staff member, or faculty member who would like to use the machines. How do I get an account?

There are several levels of access available.

Starting Aug 28, 2000, machines with a blue background for the login screen can be logged in to using your Acropolis username and password (the same ones used to get email @iastate.edu). This allows you to access files in your Acropolis locker and to run any of the software on the BCBLab machines. Anyone with an active ISU mailing address can use the machines this way.

There are two additional resources open to those who are: Affiliated with one of the classes or professors involved in the BCB or IGERT programs or with the Lawrence H. Baker Center for Bioinformatics. The first resource is additional filespace on local disks. The second resource is the ability to log into the machines remotely for interactive use (ie, running programs remotely) and the ability to initiate, from remote systems, file transfers into or out of the local disks.

If you need access to either type of resource, please describe your specific needs in an email to bcbsupport@iastate.edu.

I'm a faculty member who'd like to use the BCBLab for a course I am teaching. What do I need to do to be able to use the BCBLab machines?

You will need to provide me with a list of the Project Vincent email addresses of the students in your course so we can be sure they can save files to the local hard drives. You will also need to work with us to ensure that the software you want to run is installed. Free software may already be installed. If not, it may be relatively easy (technically and administratively) to install. For machines with license restrictions, you will need to arrange for however many licenses as will legally allow us to run the software in the manner you wish. Contact the lab administrators to discuss your software needs.

How do I log in?

If you are sitting at a machine in MBB0101, simply enter your Project Vincent username and password at the login screen (currently this screen has a blue gradient background, with "K Desktop Environment" across the top of a window in the middle of the screen). side).

If you are on a machine elsewhere on campus and have arranged for remote access (ie, are on the "bcball" list or have otherwise requested and been granted remote access, you need to have an SSH client on your machine and use it to connect. The full use of SSH is beyond the scope of this document, but it is almost exactly as simple to use as Telnet. Start the SSH client, type in the address of one of the BCBLab machines (see next question), select the SSH protocol for communication and start the connection. Follow links from this page to read more about ssh.

If you are connecting from off-campus, please send email to us and tell us a) what your ISU email address is and b) what the IP number of your machine is. If you do not have a static IP number, we at least need to know the name of your Internet Service Provider.

What are the BCBLab computers called?

Right now, there are eleven computers described by this document microviz02.bb.iastate.edu, microviz03.bb.iastate.edu, microviz04.bb.iastate.edu, microviz08.bb.iastate.edu, microviz09.bb.iastate.edu, microviz10.bb.iastate.edu, microviz11.bb.iastate.edu, microviz12.bb.iastate.edu, microviz13.bb.iastate.edu, microviz14.bb.iastate.edu and microviz15.bb.iastate.edu.

How do I log out?

If in MBB0101, move the cursor to the lower left hand corner of your screen and click to open the menu. The logout option should be there. Make sure you wait to confirm that you really want to log out.

If connected remotely, type "exit" followed by the Enter or Return key of your computer.

Where can I read more about computers, programming, and Linux?

	Those who want some introductory reading might do well to start by reading
	some of the documentation which is freely-available online.  Local copies
	of the Linux HOWTO's can be found on the upgraded machines at
	        file:/usr/doc/HOWTO/HTML/en/index.html

		Some online beginner's tutorials


	Some documents that might be of particular interest are:

		file:/usr/doc/HOWTO/HTML/en/META-FAQ.html
		file:/usr/doc/HOWTO/HTML/en/INFO-SHEET.html
		file:/usr/doc/HOWTO/HTML/en/Unix-and-Internet-Fundamentals-HOWTO.html
		file:/usr/doc/HOWTO/HTML/en/Reading-List-HOWTO.html

		file:/usr/doc/HOWTO/HTML/en/mini/Programming-Languages.html
		file:/usr/doc/HOWTO/HTML/en/GCC-HOWTO.html
		file:/usr/doc/HOWTO/HTML/en/Parallel-Processing-HOWTO.html
		file:/usr/doc/HOWTO/HTML/en/C++Programming-HOWTO.html
		file:/usr/doc/LDP/lpg/lpg.html
	
		file:/usr/doc/HOWTO/HTML/en/Vim-HOWTO.html
		file:/usr/doc/HOWTO/HTML/en/Emacs-Beginner-HOWTO.html
		file:/usr/doc/HOWTO/HTML/en/Printing-Usage-HOWTO.html

         (on the bcbmachines, just type the above URLs into your browser)

These documents, and more, are also available online available online.

How do I keep up-to-date on new developments in the BCBLab? How can I communicate with other BCBLab users? How do I subscribe to the mailing list?

For peer-to-peer help and collaboration, all BCBLab users are encouraged to subscribe to the bcblab@iastate.edu mailing list and to participate by asking and answering each others' questions about the use of the facillity. Subjects for discussion on the list may include:

• the mundane details of day-to-day use
• the larger questions of usage policy
• what generally-available software should be installed
• upgrade suggestions
• other topics about the lab's use

The lab management will also use this mailing list to send updates about the lab's configuration and usage.

To subscribe to bcblab@iastate.edu, please fill out this online subscription form.

Who runs the BCBLab? Who do I report problems and concerns to?

Two P&S staff members, Mike Brekke (from Volker Brendel's lab) and Joe Anderson (computing support for BBMB, ZG & Botany) oversee most of the day-to-day running of the BCBLab, assisted by a number of student workers (Brad Powers, Chris Campbell, Balaji Sukhumaran, Danielle Frey, Nate Pierce), while Kathy Wiederin provides valuable logistical support from the BCB Office. The bcbsupport@iastate.edu mail alias forwards messages to several of these people--if you have a problem that is not appropriate for addressing to the main bcblab mailing list, you can send email to bcbsupport@iastate.edu.

How is the BCBLab funded?

Purchase of client hardware and system software was largely funded by money from CAC under a request written by Rich Honzatko (anyone else?).

Purchase of server hardware was funded by an NSF-IGERT Training grant administered by Dan Voytas.

Most of the software packages running in the BCBLab have been made available as source code by their authors, too numerous to mention here, but often available in the documentation for the packages themselves (look under /usr/doc on any BCBLab client machine running Linux, or visit FreshMeat to find out more about most of this software and how you can get it).

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