[Bioperl-l] New Article on Approaches to Web Development for Bioinformatics

Alex Amies alexamies at gmail.com
Sat Mar 3 22:09:51 EST 2007


Thanks for your comments.

You are right that I could have said a lot more about web services.  I
plan on doing that but I haven't got there yet.  Actually, with all
the hype about web services I have been surprised to find the
programming model so complicated.

As you mention, I certainly could have thought out my own URL's better.

I have been surprised not to find more PHP activity in bioinformatics.
 To me, besides being a lightweight and pleasant language to program
in it is incredibly economical for hosting Internet applications and
there is a huge open source community around PHP in general.  The same
can be said of Perl.  It is because of my own ignorance and lack of
time that I have not investigated Python and Ruby.  I may do in the
future and write about them.


On 3/3/07, Mauricio Herrera Cuadra <arareko at campus.iztacala.unam.mx> wrote:
> Hi Alex,
> I think you've put a very nice & concise introductory article. I'd like
> to comment a little on some sections I've read:
> * Introduction
>  > "Given that you have an idea for analyzing or presenting data in a
>  > particular was, a complete bioinformatics web application depends of
>  > these basic pieces, which is what this article is all about:
>  >
>  >    1. A source of data...
>  >    2. An application programming language...
>  >    3. A web application platform...
>  >    4. Optionally, a data store...
>  >    5. Optionally, you would reuse software tools..."
> Even though you do a small mention about Web Services at the very end of
> the article (under Application Integration -> Programmatic Integration),
> I believe that Web Services can be another optional (or even basic)
> piece of a web application. In fact, many web applications consist only
> of Web Services without HTML user interfaces.
> * Application Development Languages
>  > "There are many different programming platforms and tools available to
>  > solve bioinformatics problems.  It can be bewildering at first, but it
>  > makes more sense to build on top of some of these tools rather than
>  > build from scratch.  Some the problems with using these tools for a
>  > bioinformatics portal are
>  >
>  >    1. Many tools are written...
>  >    2. Some tools have particular prerequisites...
>  >    3. Many may not be in a form...
>  >    4. The context that gives meaning...
>  >
>  > Standardization on a particular platform can help manageability but
>  > for most organizations a compromise between standardization and
>  > adoption of several different platforms will allow many people to
>  > develop software in platforms that they are already comfortable with
>  > and allow the reuse of a large amount of freely available software..."
> I would add to the problems list the fact that building web (or other
> kind of) applications on top of a platform whose codebase is evolving
> constantly, can make them very difficult to maintain. The case of
> EnsEMBL comes to my mind here: they opted to stick with BioPerl 1.2.3 as
> a core library and haven't moved onto a higher version of it because the
> EnsEMBL code is so vast, that a simple upgrade of BioPerl would break a
> lot of their code. AFAIK, it's because of this and the slowness at some
> parts of BioPerl that EnsEMBL is gradually saying goodbye to BioPerl.
> Also, I think that depending on the amount of available code you plan to
> import into your application, sometimes having a whole platform at the
> very bottom can add unnecessary extra weight to your application. More
> weight could be equal to less speed, this is critical in web development.
> * Application Integration -> Navigation
>  > "The basic way that users will navigate into and around your
>  > application should be using HTTP GET and POST requests with specific
>  > URL's. Users bookmark these URL's and other applications will link to
>  > them. Most applications developers did not realize it at first, but
>  > these URL's are, in fact, an interface into your application that you
>  > must maintain in a consistent way as you change and evolve your
>  > software. Otherwise, they will find dead links..."
> Just as I clicked the bookmark button for your article :) The same
> principle could apply to its filenames. A URL of the form:
> http://medicalcomputing.net/tools_dna17.php is less indicative of the
> real content of the article and can mislead potential readers.
> Optimising the URL's will make them better to be indexed by search
> engines, something like:
> http://medicalcomputing.net/web-development-bioinformatics17.php would
> do the trick.
> To conclude my comments, I was surprised to see a section about BioPHP
> and not about other more-known toolkits like BioPython or BioRuby. What
> about their role in web development? Python is also a common language
> for web programming and with all the recent *hot* stuff like Ruby On
> Rails, it's very likely that both Bio* toolkits are more than ready for
> deploying web applications. I'm Cc'ing this to their respective mailing
> lists to see if someone wants to give you some feedback about them in
> order to complement your article. Other than that, I really liked your
> work :)
> Cheers,
> Mauricio.
> Alex Amies wrote:
> > I have written an article on Approaches to Web Development for
> > Bioinformatics at
> >
> > http://medicalcomputing.net/tools_dna1.php
> >
> > There is a fairly large section on BioPerl at
> >
> > http://medicalcomputing.net/tools_dna13.php
> >
> > I hope that someone gets something useful out of it.  I also looking for
> > feedback on it and, in particular, please let me know about any mistakes in
> > it.
> >
> > The intent of the article is to give an overview of various approaches to
> > developing web based tools for bioinformatics. It describes the alternatives
> > at each layer of the system, including the data layer and sources of data,
> > the application programming layer, the web layer, and bioinformatics tools
> > and software libraries.
> >
> > Alex
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> --
> arareko at campus.iztacala.unam.mx
> Laboratorio de Genética
> Unidad de Morfofisiología y Función
> Facultad de Estudios Superiores Iztacala, UNAM

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