no, i doubt there is a way to print txt before ending. I know this can be done with asp (but it will still continue to load the page).
what you can do is increase your script execution time. on php.ini, the option is:
max_execution_time
the default is 30 i think...
an alternate approach would be to compile PHP as a CGI and also a module. Then create a dummy program called "startbio.php". This will invoke the system command "/usr/local/bin/php myprogram.php &". This is assuming you are on a UNIX machine. The & will run it as an independant process.
Then startbio.php can print out "program has been started".
BTW: what is a bioinformatic program? If you doing serious processing with PHP for research, i'd really like to see this script! I myself have never used PHP to do anything besides web stuff (ecommerce, content mgmt systems, etc). I always use C or C++ to do complicated stuff :-)
-sridhar