What Do Bioinformaticians Use To Make High Quality Web Sites?
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11.4 years ago
User 6659 ▴ 970

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.

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11
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11.4 years ago

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.

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

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

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Pierre - I notice you answer many questions relating to sql queries against ucsc. Would you mind looking at this question please? Retrieve Coding Exons In Ucsc Table Browser

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9
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11.4 years ago

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

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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

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11.4 years ago
Mark Fortner ▴ 90

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.

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that seems the type of thing i was looking for.

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11.4 years ago

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.

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11.3 years ago

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.

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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.

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+1 for Django, a great python webframework

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one more vote for django

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+1 for django, especially for database driven applications

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11.4 years ago
Bio_X2Y ★ 4.2k

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

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

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wow! impressive

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11.3 years ago
Joachim ★ 2.9k

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).

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11.4 years ago

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.

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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.

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11.3 years ago
Boboppie ▴ 550

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

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11.3 years ago
Yannick Wurm ★ 2.4k

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

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