Question: What Do Bioinformaticians Use To Make High Quality Web Sites?
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gravatar for User 6659
8.4 years ago by
User 6659960
User 6659960 wrote:

Hello

In my previous computer programming experience I have only ever used windows technologies for making websites such as asp.net which includes many high quality ajax controls for professional interactive websites.

Whilst asp.net can run on linux I think I've only seen one bioinformatics website written in asp.net.

Are there tools/components/controls etc preferred by bioinformatics for making websites. I need basic features like ajax postbacks and ability to break the browser window down into sections (and not with frames!) like in galaxy and slider bar controls. In fact coverflow style web interface would be great.

This question might not appear to be specific to bioinformatics but it is because I'm interested in the trends and technologies used within this field. I notice bioinformatics has certain trends and I'm a fan of consistency - plus its easier to swim with the current than against it.

thanks

edit:

it is my understanding that biologists are not comfortable downloading and installing software and prefer analysing their data using the web. If you wanted to make a workbench type of tool available to biologists on the net then it would be advantageous to have some sorts of web components for making the browser look more like a traditional application. I know this isn't 'necessary' but it makes for a more enjoyable user experience. This was what i had in mind when i asked the question.

web • 3.8k views
ADD COMMENTlink modified 8.4 years ago by Yannick Wurm2.3k • written 8.4 years ago by User 6659960
1

Related question: http://biostar.stackexchange.com/questions/1995/what-programming-language-is-best-to-learn-for-getting-into-web-based-bioinformat

ADD REPLYlink written 8.4 years ago by Neilfws48k
11
gravatar for Pierre Lindenbaum
8.4 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum121k wrote:

Do you mean a website for the 'users' or for the other bioinformaticians ? As a bioinformatician I really don't want a beautiful interactive web site.

I want some web services based on SOAP/REST/SPARQL, bookmarkable URIs, etc...

That's why the best part of the NCBI, IMHO, is NCBI-EUtils.

ADD COMMENTlink written 8.4 years ago by Pierre Lindenbaum121k

Whereas I agree with you, I think the question has to do with making bioinformatics web sites that are to be used by biologists.

ADD REPLYlink written 8.4 years ago by Lars Juhl Jensen11k

Yes Lars. I agree with you and I never imagined that my answer would reach 10 points...

ADD REPLYlink written 8.4 years ago by Pierre Lindenbaum121k

Pierre - i notice you answer many questions relating to sql queries against ucsc. Would you mind looking at this question please? http://biostar.stackexchange.com/questions/6148/retrieve-coding-exons-in-ucsc-table-browser

ADD REPLYlink written 8.4 years ago by User 6659960
9
gravatar for Lars Juhl Jensen
8.4 years ago by
Copenhagen, Denmark
Lars Juhl Jensen11k wrote:

The JavaScript libraries Prototype and jQuery are both heavily used for coding bioinformatics web interfaces.

ADD COMMENTlink written 8.4 years ago by Lars Juhl Jensen11k

at the EBI Proteomics Services there's a guy I was talking to using jQuery for sg (in production) but forgot what it actually was

ADD REPLYlink written 8.4 years ago by Attila Csordas520
9
gravatar for Mark Fortner
8.4 years ago by
Mark Fortner90
Mark Fortner90 wrote:

You might take a look at Grails. It has UI plugins for GWT, Google Maps, Google Analytics, Google Visualization, YUI, jQuery and other frameworks. The RichUI plugin has a coverflow component. There are over 500 plugins currently available. It does all of the CRUD work for you. It supports all major relational databases, in addition to most of the NoSQL databases. It also has support for both Amazon web services, and Google App Engine. It is supported in all of the major IDEs.

Since it runs on the Java VM you can use any Java library with it (like BioJava and CDT) and it runs on most operating systems. It has built-in support for RESTful services, and a couple of plugins for SOAP services. Take a look at Grails.org for more details.

ADD COMMENTlink written 8.4 years ago by Mark Fortner90

that seems the type of thing i was looking for.

ADD REPLYlink written 8.4 years ago by User 6659960
6
gravatar for Daniel Standage
8.4 years ago by
Daniel Standage3.9k
Davis, California, USA
Daniel Standage3.9k wrote:

I've found that for building websites of any significant complexity, it is well worth the time learning how to use an MVC-based web framework. The MVC (model-view-controller) paradigm enforces some good practices that are really necessary when building large web apps, such as the separation of data and business logic (the model) from the presentation (view). There is a learning curve associated with learning how to use a framework, but like I said, the time is well worth it.

The framework I have experience with is Symfony (PHP), which has a great dev community. Some other popular (or once-popular) MVC frameworks are CakePHP, Ruby on Rails, and DotNetNuke ASP.NET).

Edit: I forgot to mention that these frameworks have all types of schnazzy UI elements that are typically pretty easy to integrate.

ADD COMMENTlink written 8.4 years ago by Daniel Standage3.9k
6
gravatar for Simon Cockell
8.4 years ago by
Simon Cockell7.3k
Newcastle
Simon Cockell7.3k wrote:

I'm surprised Django hasn't received a mention so far - a Python web framework based on the MVC paradigm mentioned by Daniel. I use it because it makes it easy for me to plug my existing Python code into a web-based system, and the separation of look and feel from operating logic makes a lot of sense. Also the database abstraction is very cool. Throw in some JQuery and JQuery-UI elements, and large, flexible websites can be built pretty simply.

Creating useful resources, like a RESTful API using Django is also very simple, especially with third-party resources like Tastypie. I agree with Pierre, a pretty website is nothing without the tooling to back it, and allow programmatic access to the tools/data.

ADD COMMENTlink written 8.4 years ago by Simon Cockell7.3k
1

Python makes a good choice for scientific apps due to libraries like NumPy, SciPy, and matplotlib. These put a lot of the numeric goodness that you'd find in R or MatLab at your disposal in a general purpose language.

ADD REPLYlink written 8.4 years ago by Cbare60

+1 for Django, a great python webframework

ADD REPLYlink written 8.4 years ago by Thaman3.2k

one more vote for django

ADD REPLYlink written 8.3 years ago by Biomed4.5k

+1 for django, especially for database driven applications

ADD REPLYlink written 8.3 years ago by Biomed4.5k
3
gravatar for Bio_X2Y
8.4 years ago by
Bio_X2Y3.7k
Ireland
Bio_X2Y3.7k wrote:

I came across the X:Map Genome Browser recently, and it looks impressive. They use the Google Maps API.

ADD COMMENTlink written 8.4 years ago by Bio_X2Y3.7k
2

We use google maps and jquery for the front-end and grails for the back-end :-)

ADD REPLYlink written 8.4 years ago by Tim_Yates110

wow! impressive

ADD REPLYlink written 8.4 years ago by Thaman3.2k
3
gravatar for Joachim
8.4 years ago by
Joachim2.8k
San Francisco, California
Joachim2.8k wrote:

I read your edit and for developing desktop-like applications that can run in a browser, you might be interested in either of the following frameworks:

These frameworks allow you to use windows within a browser (but you do not have to use them) and they come with pre-made widgets such as fairly smart tables, tab-views and the like.

Personally, I use qooxdoo and I am fairly excited about their release schedules and their support on the qooxdoo mailing-list. They have demos on their web-page, but you can also watch the screencast I once made about the system I am currently writing in qooxdoo: http://bergmanlab.smith.man.ac.uk/?p=704 (this database is now further developed in my spare time and updates about it can be found at http://joachimbaran.wordpress.com/tag/flystockdb/ ; the screencast is a bit out-of-date since in the newest version you can drag & drop features too and do some other nifty things).

ADD COMMENTlink written 8.4 years ago by Joachim2.8k
2
gravatar for Chris Evelo
8.4 years ago by
Chris Evelo10.0k
Maastricht, The Netherlands
Chris Evelo10.0k wrote:

There already are a lot of useful technical answers on this page. But for me the core answer would be: "they use those websites themselves, and thus use themselves to test the sites".

Problem with many sites is that they do not or no longer do what they were intended to do and since the developer never uses them he doesn't realize that, which results in many sites being obsolete even without the developer knowing that. Of course if you do use it yourself you will also improve it.

ADD COMMENTlink modified 8.4 years ago • written 8.4 years ago by Chris Evelo10.0k

Very good point Chris. Too many web tools are technically well made, but they are a pain to use. Others are just plain buggy. If the developers actually used the tool themselves, they would notice.

ADD REPLYlink written 8.3 years ago by Lars Juhl Jensen11k
1
gravatar for Boboppie
8.4 years ago by
Boboppie530
Cambridge, UK
Boboppie530 wrote:

GMOD has a collection of interoperable open source software components for visualizing, annotation and managing data. Most of them are web based.

ADD COMMENTlink written 8.4 years ago by Boboppie530
1
gravatar for Yannick Wurm
8.4 years ago by
Yannick Wurm2.3k
Queen Mary University London
Yannick Wurm2.3k wrote:

http://www.sinatrarb.com/ is a very elegant, very fast way of making a website. (eg a wrapper around a tool)

ADD COMMENTlink written 8.4 years ago by Yannick Wurm2.3k
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