[Pipet Users] New directions for Piper?

J.W. Bizzaro jeff at bioinformatics.org
Thu Feb 20 07:50:02 EST 2003

Hi Nicolas.

It's good to hear from you again.

Nicolas Chauvat wrote:
> * don't develop a web application using Apache+PHP, use Apache+mod_python and 
> you'll benefit from all the qualities of a real programming language.

I've become somewhat familiar with PHP over the last couple years.  I 
don't want to get into language wars, but there are some impressive 
features of PHP.  I particularly like how a script can effortlessly 
switch back-and-forth betwen HTML and PHP code, without even writing a 
single print or echo statement.

I really do prefer Python for general-purpose programming, esp. when OO 
is needed.  But, I've found that it is indeed best to use "the right 
tool for the job".  For example, I had recently looked into matrix 
programming and had narrowed my options down to 2: Python/NumPy or 
Octave.  If you read the Python/NumPy manual, you'll see that there are 
tons of caveats about Python mistaking common mathematical programming 
notation (a la Octave/Matlab) for Python notation (Example: ' in matrix 
math means inverse; in Python it means single quotation mark).  You 
don't have that problem with Octave, because the language was written 
for math programming.  Now, I'm  sure Python/NumPy can do whatever 
Octave can (and more), but the catches will make it more useful for 
programs that *have to* use Python.  Otherwise, you are better off doing 
what I prefer these days: pipeline heterogeneus scripts on the command-line.

I even use sed quite a bit :-)  which is another example.

> * HTML is good for displaying information, not for manipulating information.
> The interface you're describing will be difficult to make and to use if
> done with HTML.

I agree and have even made that argument myself when describing the 
Piper desktop project I was working on.  I have found, however, that (1) 
being able to shift nodes around quickly and interactively may be fun 
but is really not that important, (2) with imagemaps and pop-up windows, 
I can get pretty much the same features, and (3) the big killer: 
everyone has such different hardware and software configurations (and 
sits at so many different computers), that *anything* that can run 
without a download is a GreatThing[tm], for them and for me.

If I had a huge team of developers with me, I might still prefer the 
downloadable client, but I've had such a hard time finding help, that 
I'm going to put manageability at the top of my list.  Even finding 
developers to help with Bioinformatics.Org is difficult: money makes the 
world go around.

> If you really want to stick with a browser-based approach and
> can't stand distributing a client (Python+GTK?), then look into Javascript,
> DOM2 and CSS that can provide you with many missing parts (drag and drop,
> refreshing parts of the screen only, etc.)

I haven't looked into using DOM2 with HTML.  I'll check it out.  Thanks.

J.W. Bizzaro                                jeff at bioinformatics.org
President, Bioinformatics.Org       http://bioinformatics.org/~jeff
"As we enjoy great advantages from the inventions of others, we
should be glad of an opportunity to serve others by any invention
of ours; and this we should do freely and generously."
                    -- Benjamin Franklin

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