ALTERNATE PROTOCOL 1: INSTALLING AND RUNNING WormBase LOCALLY
All of the protocols above assume that a user will work with one of the main WormBase servers, with his or her own computer operating merely as a client. However, for people who want to use WormBase intensively, it can be highly useful to set up a local installation of WormBase on one's own desktop or laptop computer. Doing this frees one from needing a network connection and allows a single machine to be dedicated to one's own research needs. Local installations of WormBase are not for the faint of heart, because WormBase is UNIX-based and requires installing several different, complex software packages for it to run. However, work is underway to make installation more reliable.
WormBase software should be portable to any standard Unix-like operating system. At present it has been ported to Linux (Welsh et al., 2002) and Mac OS X (Pogue, 2005). The minimum suggested specifications for the computer's hardware are: a CPU running at 1 GHz; 1 Gb RAM; 1 Gb of swap space; 25 Gb of free disk space; and a high-speed connection with the Internet. In practice this minimum of CPU speed and RAM will yield a usable but annoyingly sluggish database. Better specifications are one 2 GHz CPU, 2 Gb of RAM. Better still is to have two processors running at 1 GHz or more, 2+ Gb of RAM, and two hard drives, preferably SCSI rather than IDE. The advantage of two hard drives is that WormBase uses two separate databases (ACeDB and MySQL) which work better if put on separate disks.
The computer's operating system must have a usable version of the GNU Compiler Collection (gcc: http://www.gnu.org/software/gcc/gcc.html). It must also have basic utilities for compiling and running open-source software. A standard distribution of Linux will satisfy these criteria, as will Mac OS X if auxillary XCode (http://www.apple.com/developer) and Fink (http://fink.sourceforge.net) utilities are installed. Several other software packages are also required, foremost among them MySQL (http://www.mysql.com; Reese et al., 2002), GMOD (http://www.gmod.org) and BioPerl (http://bioperl.org; Stajich et al., 2002; Tisdall, 2003). Full installation instructions, with a complete listed of required software packages, are available at http://wormbase.org/docs. Almost all of the software required for running WormBase is freely available in open-source form (Stone et al., 1999). One exception is the Washington University distribution of BLAST maintained by the laboratory of Warren R. Gish. While this program is available free of charge to academic users in precompiled (executable binary) form, a license from Washington University is required before it can be downloaded and used. See http://blast.wustl.edu for details.
The data files for each release of WormBase are assembled and archived by curators at the Wellcome Trust Sanger Institute, at ftp://ftp.sanger.ac.uk/pub2/wormbase/live_release.
Installing WormBase on a local computer
Installing WormBase locally requires skill with Unix system administration, Perl, Apache, and MySQL. Even if one has these skills, the installation is fairly complicated. Painstakingly follow the instructions at http://wormbase.org/docs. For a standard, prepackaged Linux distribution, one will need to compile and reinstall several basic packages from source code, such as Apache (http://httpd.apache.org) and mod_perl (http://perl.apache.org). If defects in the installation instructions or incompatibilities in the required software are found, please describe the bugs to WormBase via the Feedback page (http://wormbase.org/db/misc/feedback), or send E-mail to firstname.lastname@example.org.
If installing WormBase on a computer with two hard drives, place the ACeDB component of WormBase on one drive and the MySQL component on the other; this should significantly improve performance.