accessing AIMS with MacX

Randall L Scholl rscholl at magnus.acs.ohio-state.edu
Fri Mar 12 15:09:53 EST 1993


		ACCESSING AIMS VIA MacX USING A MACINTOSH II



	The following instructions are designed to assist you in
setting up "MacX", the X-Window host system for Macintosh, to
communicate with AIMS.  When this is successfully completed, you will have
the following functions from your Macintosh computer:

	1. 	Connection to AIMS with a single mouse "double-click."

	2. 	Full mouse function within AIMS. i.e., all selections can be 	
		accomplished utilizing the mouse so that the interface becomes
		fully graphical, in the fashion of personal computer windowing
		systems.

	3.	Ability to view color photographs of plant phenotypes
		(currently 50 available and many others to be added
		soon), pictures of gel and autoradiographs for all RFLP
		DNA stocks and graphical genetic maps of all of the
		chromosomes.  

		We plan to utilize, in the future, the graphical capability
		of this system to represent restriction maps, physical
		maps and pedigrees of stocks.
	
	Note that all of these can be achieved from a Macintosh
computer which is attached to the Internet, and there are no
requirements other than installation of the MacX program.


I. Hardware Requirements


	Macintoshes with at least 5 megabytes of RAM and an ethernet
connection should be able to access AIMS via MacX.  MacX can
function with either System 6.x or 7.x.


II. Installing MacX on your computer

A. SOFTWARE INSTALLATION

	It is recommended that you have the MacX documentation in
front of you when you install the software.  The requirements and
procedures are different for different systems.  In general, MacX
will run on System 6.x or 7.x. MacX version 1.2 (newest) is 
preferred for system 7 computers with high memory.  This is
because some older MacX versions require 24 bit processing rather
than 32 bit processing, which is itself a requirement for memory of more
than 5 Megabytes.  Following the MacX installation instructions
should result in successful installation of MacX.  MacX is
obtainable from Claris software.  Your university might have a
site license for MacX - in which case you can obtain it free or at
a greatly reduced cost (retail cost of MacX 1.2 is approximately
$185).

 B. COLOR vs  BLACK AND WHITE OPERATION

	Color operation allows viewing of plant images in color, and
also allows gray-scale display of gel and autorad images, as
opposed to the dithered mixture of black and white dots that is
utilized by the black and white version of the program.  However,
the program runs slower in color.  If you have a IICi or IISi computers (or
higher), the speed will not be a problem.  You may find MacX too
slow if you use color operation with an LC.  In any case
your Mac will probably need at least 5 Meg of RAM to utilize MacX
in color. The steps required to prepare MacX for color and black
and white operation are described below.  Running MacX in color requires approximately 2,500 to 3,000 K of RAM devoted to the program, and black 
and white MacX requires 1500K of RAM.  

	1. Setting up for Color Operation

	The default setting for RAM allocation to
MacX is 1500K.  Hence if you want to run MacX in color you need to
increase the memory allocated to MacX.  This is done from the
Finder. The steps to be performed to increase the memory allocation
are:  1) Highlight the MacX program icon by clicking once on it.
2) Go to the "File" heading on the top Menu Bar and depress the
mouse button so that the pull-down menu appears.  3) Keeping the
mouse button depressed, move to the "Get Info" line and then
release the mouse button.  A box with information about MacX will
appear. 4) One of the items in this display tells the memory
allocation to MacX - Change this from 1500 to 3000.  You may then
close this box and proceed. You should not have to change any
setting within MacX, as it is initially set up for color
operation.  

	2. Setting up for black and white operation.

	The default memory allocated to MacX is adequate for black
and white operation, so this does not need to be changed. 
However, MacX may still open in color mode, unless you set it to
black and white, specifically (especially if you have a color
monitor).  Converting  MacX 1.2 to black and white  may be achieved as
follows:  1) Open MacX by double clicking on the MacX icon.  2)
Move the pointer to the "Edit" menu and depress the mouse button.
3) With the mouse button depressed, move the pointer to
"Display preferences" and release: A window will appear.  3)
In the monitor section of the window, choose black and white, 4)
Close this window by clicking on the close box, 5)
Quit MacX by choosing "Quit" from the "File" pull-down.  6) NOTE:
You should be presented with an option to "Save Changes"
at this time; choose "Yes."  7) You will be asked to give a file name 
for saved changes - you can name it anything, e.g., "aims".  In the
 future, when you want to open MacX using the settings you just
 specified, open this new file rather than MacX itself. Setting 
MacX 1.1.7 to black and white can be performed as part of the command 
creation process described in section III.

III.  Establishing communication with AIMS using your MacX

	Once you have installed and configured your MacX as described
above, you are ready to run AIMS from this program!  Here are the
steps for doing this:

1.	Open MacX by double-clicking on the icon of your saved file
	or the MacX icon.

2.	Under the "Remote" menu, make certain that there is no check
	marks beside the item "Access control."  If there is, remove
	it by selecting this item.

3.	Again depress on the Remote heading and select the item, "New
	Command."  A box will appear which needs to be filled in to
	create the new communications command for MacX.

4.	The first issue to address is the "host."  For accessing AIMS,
	genesys is the host computer.  First, select the "Host"
	button (to the right of the box); a new box will appear.
	Enter the IP number of Genesys, 35.8.12.72, in the line at
	the bottom of this box. Then click on "OK."  This should take
	you back to the original command-editing screen.

5.	The first line on the left side of the window is titled
	"Remote Command."  Enter the following in this area:

	source .macrc; setenv DISPLAY "option-Rdisplay"; aims	
		      
 	 All characters of the command must be typed as shown in
	the case shown.  HOWEVER, note that the option-R here stands for 
	typing r while the option button is depressed.  This will result in a
	"registered trademark" character - make certain that
	there is no space between the trademark character and the
	word display.  ALSO, the quotation marks are to be typed as
	part of the command, as shown!

6.	Next, fill in the "command name" line. This can be anything; it
	is your local name for this command.

7.	In the Display line, choose "color rootless" or "black and
	white rootless" depending on which mode you wish to utilize.
	NOTE: For MacX 1.1.7 this is all you need to do to specify
	monitor mode:  The specific construction of the remote
	command allows the monitor to be specified in this fashion.  

8.	Enter "guest1" in the "User" line.  Be sure to use lower
	case.

9.	The password to be entered is "spartan1", the usual genesys
	password. Note, that the password will not show, so be
	careful to type it correctly.

10.	Note, that you can edit your command so that it will execute
	automatically when you open MacX. To do this, click on the 
	box labelled, "Execute at Startup", so that the box has an
	"X". 

 11.	Once all of this information has been entered correctly, you
	are ready to execute the MacX communications command.  This
	is simply done by clicking on "Execute".  


12.	Once you have executed the command, the AIMS login window
	will appear. You are now in AIMS.  It operates exactly as
	described in the original AIMS tutorial, except that
	you can now simply click on appropriate choices to manipulate the
 	program. The next steps are to type your AIMS login and password.  

13. 	If you wish to execute this command again before quitting
	MacX or RETRY it if you typed the password wrong, you may
	drag-select under the "Remote" item at the top of the screen
	and release on the name you have given your command, which
	should now appear as an item at the bottom of this list. This
	will also work in the future when MacX is open.

14.	EXITING  AIMS is accomplished in the usual way - just select
	X and then Exit AIMS from any window.  This should result in
	an exit from AIMS and Genesys.  The next step is to quit the
	MacX application.  NOTE: When you exit MacX after your FIRST
	session, you will want to save the command so that it can be
	executed without typing in all of the above information each
	time.  To do this, simply reply YES to the prompt that asks
	you if you wish to save changes to MacX, when you are
	exiting.  The sequence is:  a)Select "Quit" from the "File"
	pulldown menu. b) Respond by clicking on "Yes" when asked if
	you want to save changes;  c) You will then be asked to give
	a name for the file to record the information.  Give this
	file any name you want.  MacX will then be closed.  

15.	IMPORTANT:  The next time you wish to communicate with
	Genesys through MacX, you can simply OPEN THIS NEW FILE by
	double-clicking on it, rather than opening MacX directly! 
	This will open MacX, AND execute your communications command
	automatically, so that you only need to enter the "spartan1"
	password, when prompted, to open the AIMS login screen. 

Good Luck! Feel free to contact us with questions.  NOTE: If you
cannot bring up AIMS with your MacX using the above commands,
other command options are available which sometimes work when
these do not.  If you have such problems, send us an e-mail
message, and we will send alternate instructions.

You may direct questions to: aims-manager at genesys.cps.msu.edu

A NOTE ABOUT X-WINDOWS AND IBM COMPATIBLE COMPUTERS:

	In principle, X-windows for pc's should operate just as
successfully with AIMS as MacX does. Installation of these
programs is somewhat more complicated than for MacX, and you
should be careful to purchase a program that is compatible with
the communications hardware/software of you computer.  The basic
commands of X-Windows are similar for all systems, and the above
command syntax should provide a good


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