JAMF Archive

BioCompanion as published in 1995

THIS IS THE REFERENCE CODE AS PUBLISHED.

		Doelz, R.   
		Optimal production of biological documentation: the JAM format.
		Comput. Applic. Biosci. 11, 224-226 (1995).

The version you are currently viewing is the one printed and distributed via the Internet from the server of BioComputing Basel. Version 3.1 of the BioCompanion was published with version 2 of the JAMF software. The server that was indicated in the documentation has ceased to exist.

Version 3.2 of the BioCompanion was not publicly available for free but was shareware that was distributed with GCG's software release 9. For the purpose of enhanced editing, JAMF was partially rewritten and the proprietary version 3.x of JAMF was used from 1996 onwards. The Biocompanion is available in a current version from the publisher . It has significantly changed both in software and content.

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Chapter 2: Elementaryrequirementsandusage

Elementary requirements and usage

Needed Equipment

The BioCompanion assumes that you work in an open environment, including access to the Internet as well as to a local network to a more centralised facility provided in-house or in a reasonable (network) distance.

If you do not have access to the internet, only a few items will not apply. Most of the work is achieved locally, and executed on loal equipment. Special hints on security are inserted whereever appropriate to make you aware of the problems in internationally accessible environments.

Desktop

To work in a sophisticated manner, you should have

EITHER a PC or Macintosh computer with mouse, keyboard, screen (17 inch recommended), and a reasonably large hard disk (at least 300 MB)

OR an X-Windows terminal with a monitor of at least 17 inch

ALWAYS a network connection to the in-house network

NOTE: In the past, connections to centreal facilities using terminals were widely used. This method of access is no longer recommended as it usually excludes the use of graphics. Many programs still utilise text modus and are supported as well, but the access via personal computers or even workstations should be favoured. Personal computers are, depending on age and equipment, hybrids of terminals and workstations.

On-Site or Remote Central Computing Facilities

If you work on a computer that is maintained as a central facility, you share this computer with others. The data of your colleagues are also stored on the same machine. At large sites, a computer can have hundreds of users. Therefore, these computers run a multi-user operating system . To access such a system, you must have the following prerequisites:

account name

password (your secret authentication)

name of computer and knowledge how to access it

Ask your nearest computer knowledgeable person for details about where to get this information.

Prices

Many computing services in academia are offered for free or negotiable cost. In commercial environments, and some institutions in academia, subscription fees will need to be paid in order to access resources. You should not be afraid of these costs, as the expected benefit is much larger than the cost.

Hardware (like PCs, terminals, and local printers) and software (like word processors and terminal emulators ) residing on your desk usually have to be purchased by you or your department. If the network connection is unsatisfactory (e.g., too slow, wrong plugs, etc.), 'better' links are unlikely to be installed readily. Try the existing ones first before complaining. If you cannot get an account on a system where molecular biology and other software is installed, you are in a less favourable position, because you will have to organise everything yourself.

At Basel University, you may use either the university- maintained VMS cluster, or the UNIX cluster run at the BioComputing facility. The functionality of both sites is identical but usually Biozentrum members use the university-owned VMS cluster. the following institutions are to be contacted:

Local Site Information for Accounts (VMS Operating System):

 
    Hosts: YOGI, BALU, etc.  
    Universitaetsrechenzentrum   
    Klingelbergstrasse 70  
    4056 Basel   
    (Bitte beachten Sie die Oeffnungszeiten.)

Please, note that you have to contact the BioComputing facility as well in order to get access to the GCG program package (completion of separate account form required).

Local Site Information for Accounts (UNIX Operating System):

 
    Hosts: biox, bioy, yeti, bioa, bioz, etc.  
    EMBnet Switzerland   
    c/o BioComputing   
    Biozentrum der Universitaet   
    4056 Basel

Contact EMBnet Switzerland for details of EMBnet services.

In order to Connect...

You should have the appropriate hardware/software prerequisites before you start.

Cabling : Any desktop device must be somehow connected to the main computer or network, which usually requires a plug in the wall. Make sure that the responsible person at your site is informed if you want to connect your equipment, for advice and support.

Desktop Equipment - Workstation Type: If you have a workstation, PC or Macintosh, you need software (commercial or public domain) for connection to the IP network . Note that, depending on the application you want to run, your desktop device must run specific software which makes it possible to display "windows" on the screen. The usage of this so-called X-Windows system is described below .
NOTE: Even if you have all cables ready, you MUST call the responsible person BEFORE you connect. World-wide connectivity REQUIRES that your host is properly named and configured.

Desktop Equipment - Terminal Type: You can use a terminal, PC or Macintosh as an input/output device. If your PC or Macintosh is not connected to ethernet (a cable which may look like a TV cable or an oversized telephone connection), but to a serial line (i.e., COM1 (PC) or communication port (Macintosh)), you need software (commercial or public domain) for terminal emulation (e.g., the public domain program 'kermit' ).
NOTE: If you run a terminal or terminal emulator you will most probably not be able to use the X-Windows system , which is required for running various applications including GCG's graphical user interface WPI .
NOTE: If you run a terminal or terminal emulator you will most probably not be able to use the comfortable, graphic versions of 'gopher' or 'mosaic' . You will be restricted to use the versions of 'lynx' (a text-only browser for the WWW system) and 'gopher' of the host to which you are connected.

Hardcopy Devices: If you wish to use a local printer attached to your PC or terminal, you need to make sure that this printer supports 'pass-through' printing. Note that, depending on your local configuration, printing can also use the network , which implies that various devices at different physical locations are accessible. Biology software, like the GCG package, might require specific settings and is described later .

The following assumes that the hardware and communication software are properly installed and that you use a device with keyboard input. PC (Windows) or Macintosh applications might offer a click-and-enter interface where you just need to give the name of the computer to connect to (e.g., a graphical user interface to 'telnet').

SECURITY NOTICE: You will most probably be able to connect to any computer in the world once you are connected to a central computer and use this as a 'base' for 'internet surfing'. If you do this, you will access environments, programs, databases and computers which are not under local control. Rules which are available for local use, therefore, might not apply in the usual way. This consideration is particularly important for environments beyond firewalls (commercial companies).

Local Site Information for Access:

At Basel University, you can use a PC, Macintosh, or workstation-based desktop system and access the molecular biology software residing on the central computing facility via 'telnet' (TCP/IP). External institutes and some smaller departments are not yet networked and have to use the the serial line method (LAT).

Serial Line Access (LAT server): The service is running on BALU (VMS) as well as on bioa (UNIX).

Open a window if you are on a PC or Mac, otherwise hit <RETURN>. If you get a prompt which identifies a LAT terminal server (LAT: Local Area Transport, a DEC-proprieraty protocol for local area networks), e.g.,

Enter Username>

enter your account name and hit <RETURN> again. (You could also abbreviate your name here, at this point there is no check.) If you get

local>

you will be able to connect to your host on the local network. E.g., to connect to the host BALU, type

local> connect balu

from another host running TCP/IP: The service is running on balu.urz.unibas.ch (TCP/IP, VMS) as well as on basel.ch.embnet.org (TCP/IP, UNIX).

PC or Mac System

If you run a computer which is capable of opening 'telnet' communications directly, you need the application 'telnet' or a similar utility. A famous public domain program for various systems is available from NCSA, ask your computer expert for details. The naming and addressing works as described below.

IMPORTANT: The network setup must be done correctly. Your PC or Macintosh computer will not behave correctly on the network if it has not been configured to do so. You need a 'network configuration', which is a set of data obtained from the computer centre's specialists. These data have to be entered in the 'network configuration' panel or the 'MacTCP' tool before the connection is made. Frequently, errors occur if the NAMESERVER addresses were not entered correctly.

It can be that your computer does not understand TCP/IP names because it is not connected to a name server . Then, you need to find out the so-called 'address' of the remote computer. This address is typically a set of four numbers separated by dots. The WWW browser and other networking software will most certainly fail if the name server system does not operate properly.

VMS System

If you have an account on a VMS machine, and you wish to connect to another system which runs TCP/IP , the command to connect to the host basel.ch.embnet.org would be

$ TELNET BASEL.CH.EMBNET.ORG

The command 'telnet' may fail if it is unknown on your local computer. TCP/IP is an optional product on VMS systems and needs to be configured or purchased separately. Ask your system manager for assistance. It can be that your VMS system does not understand TCP/IP names because it is not connected to a name server . Then, you need to find out the so-called 'address' of the remote computer. This address is typically a set of four numbers separated by dots. For example, to connect to a node called 131.152.8.4, type

$ TELNET 131.152.8.4

This command might fail because the remote computer is currently unavailable for communication. Then, the error message would be

network is unreachable

or similar.

UNIX system

If you have an account on a UNIX machine, and you want to connect to another system which runs TCP/IP , the command to connect to the host basel.ch.embnet.org would be

% telnet basel.ch.embnet.org

It can be that your UNIX system does not understand TCP/IP names because it is not connected to a name server . Then, you need to find out the so-called 'address' of the remote computer. This address is typically a set of four numbers separated by dots. For example, to connect to a node called 131.152.8.4, type

% telnet 131.152.8.4

This command might fail because the remote computer is currently unavailable for communication. Then, the error message would be

network is unreachable

or similar.

from another host running DECNET: The service is running on BALU (VMS).

If you have an account on a VMS system, and you need to connect to another system which runs DECnet (Phase IV), the command to connect to the host biox would be

$ SET HOST BIOX

It may happen that the command fails because the computer name is not known on your local computer. Then, the error message would be

%F, remote host is unknown

In this case, you must determine the full address of the computer. Consider the following example: If the area number of the host is 47, and its host number is 36, the calculation is to multiply the area by 1024 and add the host number. In this example (47 * 1024) + 36 gives 48164. The command to be typed is then

$ set host 48164

This command might fail because the remote computer is currently unavailable for communication. Then, the error message would be

%F, remote host is unreachable

$ set host /X29 02285463552423

Once You Have Made the Connection ...

You will see a 'Welcome' message and then the following:

User Name

The machine expects your account name which should be entered followed by <RETURN>.

Username:

NOTE: Spelling is NOT case dependent on VMS systems.

Password

Next, a verification of the authorization is requested.

Password:

NOTE:

Spelling is NOT case dependent on VMS systems. VMS computers typically keep a 'password history' which avoids that the same password can be used twice. There is also a check for frequent words which should not be used as passwords.

If You Successfully Logged In

You will see the system prompt and you may type in commands. On VMS, the prompt is usually a $ character:

SECURITY ADVICE: You should never leave your terminal or PC unattended if you are logged in to the computer. To ensure data security, you should avoid using other people's accounts. Obtain your own!

If You Need to Change Your Password

You should change your password either upon the first login, or shortly afterwards (data security is very important). If the system manager has setup your password to be 'invalidated' upon your first login, you are forced to change your password.

The password should follow the following rules:

Do NOT use names of persons, cities, objects.

If you use words (rather than random characters), use at least two

Use at least 6 characters from 0 to 9 and a to Z.

ALWAYS use at least two numbers in the middle of your password

NEVER write down your password in public.

If you need to write down your password somewhere at a secret place, apply some encryption (add words, numbers, etc.) and do not add your user name, the name of the computer (or its address) to make sure that accidental discovery does not hurt.

NEVER tell your password to anyone else.

Do NOT let other people work on your account.

The password can be changed as follows:

$ set password

 
Old password:   (your old password)  
New password:   (your new password)  
Verification:   (new password again)

SECURITY ADVICE: You should never change your password to a value communicated to you by electronic mail, telephone, or other unsecure sources. You should never reply to requests from these sources to communicate your password. Passwords are 'secret' by definition and unknown to the system manager. Only the system manager is privileged and authorised to override your password protection in special cases (e.g., to make a backup of user data). Requests to set your password to a given value are a hint to a possible hostile intrusion attempt and should be made known to the system manager immediately.

Disconnect from the Computer

Note that turning off the screen power does NEITHER turn off the computer, NOR interrupt the network connection to the computer reliably. In order to stop working, you have to 'log out'. The procedure is simple:

$ logout

Emergency Break: Serial Line

If you are logged in via a serial line, you can try to send a 'BREAK' signal in order to get back to the server you started from. The BREAK command is generated by a variety of keystrokes, depending on your keyboard, terminal, or emulator . Common keystrokes are <ALT><L>, <CTRL><L>, or any combination of these with <OPTION> or <ALT GR>. <ALT><H> usually helps on DOS systems. After you have issued the BREAK command, you still have to 'log out':

Local> logout

Emergency Break: 'rlogin'

If you are logged in via an 'rlogin' session, you can try to send an 'ESCAPE' signal in order to get back to the host you started from. The ESCAPE command is usually 'tilde period' (<~><.>). This should get you back to the prompt of the original computer. Scree trace of this action:

session closed.

Emergency Break: 'telnet'

If you are logged in via a 'telnet' session, you can try to send an 'ESCAPE' signal in order to get back to the host you started from. The ESCAPE command is occasionally displayed at the start of the session and is usually <CTRL><]>. This should get you back to the TELNET> prompt. There, issue the command 'quit':

 
  
^]  
  
TELNET>  quit

Emergency Break: 'set host'

If you are logged in via a 'set host' (=DECnet) session, you can try to send <CTRL><Y> repeatedly in order to get back to the host you started from.

<CTRL><Y> <CTRL><Y> <CTRL><Y>

 
Are you repeating ^Y to abort the session ... ?

Emergency Break: PC / Macintosh

If you are logged in via a personal computer or a windowing system, where the 'login' occurred in a window, you can try to close the window in order to close the connection. Rebooting the computer is obviously only a choice for personal computers (as opposed to multi-user systems). The use of X-Windows does occasionally exceed the limits of the memory or other resources. Frozen windows or keyboards will enforce the need to reboot.

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