[BiO BB] [Portal Web Design for Bioinformatics] How to start and cross platform issues

[Stefan Goetz]

Hi Robert.
for such an approach and in case you are planing to create something big 
and long-lasting, I would go for Java Technology (Servlets,Struts, JSPs, 
JSF (or even Wicket or GWT)) in combination with an application server 
(Tomcat or similar). On the client side plain html+css and 
javascript/ajax. With Java you are platform independent, you have a big 
user community (and biojava) and find wrappers to connect to other 
programing languages important to bioinformatics like R, Python, Perl etc.
As a development platform I would recommend you Eclipse with SVN/Git and 
Ant or Maven.
Good luck,
Stefan


Robert lzw wrote:
> Thanks a lot, guys, for the detailed messages, which is very helpful. Now I
> know where to start at least.
>
> My understanding is that platform decides which tools / frameworks would be
> available to you. So that is a big decision for a starter...
>
> Robert
>
> On Fri, Sep 25, 2009 at 3:00 PM, Chris Upton <cupton at uvic.ca> wrote:
>
>   
>> And remember, large numbers in the life sciences and in bioinformatics use
>> Mac OS X.
>>
>> Chris
>>
>>
>> On 9/25/09 11:34 AM, "J.W. Bizzaro" <jeff at bioinformatics.org> wrote:
>>
>> Hi Robert,
>>
>> The separation of server-side software (e.g., PHP, ASP, etc.) from
>> client-side software (browser and plugin) is an aspect of the Web that has
>> made it so flexible and successful.  As long as the software that you choose
>> to run on the client-side (e.g., JavaScript and plugins such as Flash, etc.)
>> is widely supported on multiple platforms, it doesn't matter what you choose
>> to run on the server-side.
>>
>> So, you can set up a server that runs on Windows, Mac OS, Linux, Commodore
>> 64, or whatever, and people can access your site on any platform that
>> supports the client software that you use, if you even use anything beyond
>> HTML.
>>
>> Technically speaking, many bioinformatics portals work on the
>> "model-view-controller" (MVC) paradigm, intentionally or not.  Here's some
>> more information on the topic:
>>
>>  http://en.wikipedia.org/wiki/Model-view-controller
>>
>> Applied to the Web, the model resides on the server (e.g., in MySQL), while
>> the view and controller reside on the client (e.g., browser and plugin).
>>
>> If you choose to use a plugin and not just JavaScript, be sure that it is
>> supported on multiple platforms.  Microsoft solutions are always best
>> supported on Windows computers, including plugins.  Mac OS is a second-class
>> citizen to Microsoft, and Linux barely exists.  For Linux, it is often left
>> up to a third-party developer (e.g., Novell) to develop clones of Microsoft
>> applications (e.g., Novell Mono attempts to bring .NET to Linux).  ActiveX
>> and Silverlight are two examples of where Microsoft doesn't make their own
>> plugins for Linux (AFAIK).
>>
>> Cheers,
>> Jeff
>>
>> Robert lzw wrote:
>>     
>>> Hi there,
>>>
>>> I am a newbie to web design for bioinformatics and going to design a
>>>       
>> portal
>>     
>>> web page similar to the following link:
>>> http://www.eh3.uc.edu:8080/GenomicsPortals/
>>>
>>> It looks that the above portal was designed on Unix/Linux using
>>>       
>> JavaScript
>>     
>>> and Microsoft FrontPage 5.0 processing datasets in MySQL database. As I
>>>       
>> only
>>     
>>> have MS Visual Studio 2008 Prof software, I plan to go with ASP.NET and
>>> ADO.NET to do it for processing datasets in SQL databases.
>>>
>>> Does anybody know if this will work? Can the portal web pages designed
>>>       
>> based
>>     
>>> on Windows .NET framework be browsed without any problem on Linux/Unix.
>>> i.e., other platforms than the Windows? Regardless, any suggestions on
>>>       
>> how
>>     
>>> to start designing such a portal web page (books, online resources,
>>> framework and tools) would be highly appreciated. I need a general,
>>>       
>> correct
>>     
>>> direction to follow. Thank you very much in advance.
>>>
>>>       
>> --
>> J.W. Bizzaro
>> Bioinformatics Organization, Inc. (Bioinformatics.Org)
>> E-mail: jeff at bioinformatics.org
>> Phone:  +1 978 621 8258
>> --
>>
>>
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>>     
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>   


-- 

--------------------------------------------
Stefan Götz
Bioinformatics Department
Centro de Investigación Príncipe Felipe (CIPF)
C/E.P. Avda. Autopista del Saler, 16-3 
(junto Oceanográfico)
46013 Valencia, Spain
Tel: +34 963289680 Ext. 1011
Fax: +34 963289574
E-Mail: sgoetz at cipf.es
http://bioinfo.cipf.es
--------------------------------------------

FIRST INTERNATIONAL COURSE IN AUTOMATED 
FUNCTIONAL ANNOTATION AND DATA MINING
VALENCIA/ORLANDO September-October 2009
http://bioinfo.cipf.es/blast2gocourse
============================================