Mauricio, 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. Alex On 3/3/07, Mauricio Herrera Cuadra <[EMAIL PROTECTED]> 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 > > [EMAIL PROTECTED] > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > -- > MAURICIO HERRERA CUADRA > [EMAIL PROTECTED] > Laboratorio de Genética > Unidad de Morfofisiología y Función > Facultad de Estudios Superiores Iztacala, UNAM > > > > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
