FamFetch set-up and start

FamFetch is the general interface used to query the families databases developed using the HOBACGEN model. This is a standalone Java application that requires some settings before it can be ran on your computer.

Java installation

The first thing you need to do is to install a Java Virtual Machine (JVM) on your computer if this kind of software is not available on your computer. This is likely to happen mainly under Windows as most of the other operating systems now include Java in their distribution. The preferred version of Java required to run FamFetch is 1.3 (avoid using 1.4 as it contains a lot of bugs).
Java is available for most of the existing plateforms and it should not be very difficult to find the binaries corresponding to your architecture. Here are pointers where you can download the versions corresponding to common operating systems: Windows, Linux, Solaris and MacOS X.

In the case of Windows or Unix machines, you will need to add to the list of the directories where programs are searched the path leading to the java binary. Ask your system administrator if you don't know how to configure the PATH environment variable for Windows or Unix.

FamFetch installation

The client program is named FamFetch and the latest version is 2.0. The directory containing the whole distribution can be reached at URL:


<ftp://pbil.univ-lyon1.fr/pub/famfetch/>

All the Java classes required to run FamFetch are stored into a java archive file named famfetch.jar. This archive does not need to be expanded to install FamFetch. For all types of computers and systems, you must retrieve this file using the binary mode of your FTP client and save it in the directory where you want to have the program located. You have also to get the Help file to be able to access the on-line help when running FamFetch. Note that this file need to be retrieved using the ascii mode of your client. The set-up procedure then differs following your operating system:

Windows 95 and higher:
Retrieve the command file FamFetch.bat and edit it by replacing all occurrences of string C:\Appli\FamFetch by the path leading to the directory containing the files famfetch.jar and Help.
MacOS 8.0 to 9.1:
On Macintosh computers, depending on the JVM installed, the FamFetch installation process varies greatly. If you use the MacOS Runtime for Java (MRJ) virtual machine (which is a part of the MacOS distribution since system 8.5), simply download the FamFetch.bin file. For this purpose, use the MacBinary II mode of your FTP client and save the file in the directory where the famfetch.jar and Help files are already stored. Note that you can download the latest version of the MRJ using the address listed in the Java installation section.
FamFetch runs well with MacOS 8.0 to 9.2.2 associated with MRJ 2.1 but it has not been tested on Macintoshes running a version of MacOS prior to 8.0. Also, do not use versions of MRJ prior to 2.1.
MacOS X
For Mac OS X, you only have to retrieve the compressed archive file FamFetch-2.0-OSX.tgz and double click on it to decompress. The directory contain the FamFetch executable.
All Unix (including Linux):
Retrieve the C-shell file FamFetch.csh and edit it by replacing the string /Appli/FamFetch by the path leading to the directory containing the two files famfetch.jar and Help.

In any case it is recommended to have at least 128 (preferably 256) Mbytes available on your computer to run FamFetch. On micro-computers, turn on the virtual memory system in a way to reach that limit if you don't have enough RAM.

FamFetch start

The procedure to run the program also differs following your platform. On Windows and MacOS 8.0 to 9.1 operating systems, simply double-click on the FamFetch.bat or FamFetch file. On Unix computers, go to the directory where the FamFetch.csh file is stored and type FamFetch.csh. Another possibility is to copy or move this shell file to one of the directories that are listed in the PATH environment variable.

When the program is started for the first time, it is initialized with default parameters, particularly a default server is used. A common thing to do is to change the preferences in a way to use the closest server available. To do that, select the option Prefs in the File menu and use one of the possibilities listed in this table. It shows the main places where the server has been installed:

Server	Port	Script	Databases
pbil.univ-lyon1.fr	80	/cgi-bin/query_http	HOGENHOM HOVERGEN HOPPSIGEN NUREBASE RTKdb
www.infobiogen.fr	80	/cgi-bin/query_http	HOBACGEN
bioweb.pasteur.fr	80	/cgi-bin/hobacgen/query_http	HOBACGEN
genome.ornl.gov	80	/cgi-bin/HOBACGEN/query_http	HOBACGEN

Server: names of the server, Port: port number on which the HTTP service is running, Script: path to and name of the CGI-script that is started when the server receives a query, Databases: list of the available homologous genes databases available.

FamFetch help

General documentation is available here. More documentation on the search of phylogenetic trees in databases is available here

Acknowledgements

This project is supported

by the European Commission ( TEMBLOR, contract-no. QLRI-CT-2001-00015, RTD programme "Quality of Life and Management of Living Resources") as a part of the Integr8 project.

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