[Biophp-dev] Web vs CLI (was: Bioinformatics.org's PHP)

Greg Tyrelle biophp-dev@bioinformatics.org
Thu, 10 Apr 2003 14:32:42 +1000

*** S Clark wrote: 
  |If Greg doesn't mind, I can also upload the sample code he sent me
  |somewhere for perusal (or he can do it himself presuming I get
  |"adding developers to the project" worked out...)

I have no objections.

  |> Personally, I think (Bio)PHP is better suited for web apps.  It
  |> suffers from two limitations when it comes to developing (non-web)
  |> applications: 1) it falls short in its OO features, 2) it's a lot slower
  |> than compiled languages like Java (although there is the
  |> Zend PHP compiler, but its steep price is a definite turn off!).

On this point I agree, "(Bio)PHP is better suited for web application
development". This is one of the reasons I'm taking an initial interest
in the project: using BioPHP modules to facilitate developing web
applications for bioinformatics.

  |Well, I would tend to counter with "better than WHAT for web apps?", though
  |that's just my natural streak of "devil's advocate" showing through. 

In that case you could argue that if it isn't better than a
Bioperl/CGI solution for developing web apps why bother with Bio(PHP) ?  

Being (more) tightly integrated with the web is one of PHP's
strengths.  And one of the areas where the other Bio* projects tend to
be lacking is intrinsic web integration.

  |> Well, yeah, I suppose it should be able to do BOTH. [web and non-web]
  |Yup - again for me, this is mainly another "choice is good" issue, though
  |keeping in mind the ability to work outside of web pages makes it possible
  |to implement longer processes than would be feasible on a web page.

I agree that "choice is good" but how will that relate to development
focus ? 

For example should the sequence class include HTML rendering methods
or should it be a generic sequence class that can be rendered as HTML
using an HTMLRender class or Page class ?

A BioPHP specification, development guidelines, road-map style document
might be a useful starting point ?


Greg Tyrelle  (http://www.kinglab.unsw.edu.au/~greg)

"Logic only gives man what he needs, 
 magic gives man what he wants" - Tom Robbins