Best Practices/Methods For Developing Bioinformatics Related Web Applications

Question

[ete]

Hello everybody!

I'm planning to transform a few windows programs which I wrote into web applications. Can anybody give me some tips, suggestion or experience with this (Framework, Hosting)? I will use Python. I was thinking about GAE but unfortunately you can not run processes on it. I will need BLAST, Primer3 and Bowtie.

Any help is appreciated!

Stefanie

[ete]

I have to write it myself because I will also run it locally (confident data) as well as public on a webhoster. Since it is a private project it should be as cheap as possibler Does anybody tried luban?

[Istvan Albert]

Galaxy has a very liberal license - there is no limitation against keeping it private.

Also I have not heard of the tool that you link to. But I have tried many others with similar goals. I found them to be litte more than fun diversions, once things get realistic these frameworks run out of options/customizations very quickly. Making them do something that the original author did not foresee leads to far more complicated code than doing it directly in HTML/javascript.

[Pierre Lindenbaum]

cross posted on SO: http://stackoverflow.com/questions/13915504

Answer 1

[Sean Davis]

I'd suggest using a galaxy instance.

If you really really need to write it yourself, take a look at Celery for the backend and flask for the front-end.

Answer 2

[Istvan Albert]

I have had good experiences with a Python + Django + Linode - stack.

Of course the details of your problem may require a different hosting or application server.

[Jeremy Leipzig]

which distro did you choose for Linode?

Answer 3

[Damian Kao]

bottle.py - http://bottlepy.org/docs/dev/

I like it because it's fully self contained.

edit*

I forgot to mention, this is only really good for a small amount of traffic. Like hosting a small app for analyzing data for use in your lab or something. Not for enterprise level stability.

[Aaronquinlan]

How does Bottle compare to Flask?

[Istvan Albert]

flask seems to be at a lower level - closer to exposing the WSGI standard and IMHO that makes a bit more complicated

[Damian Kao]

Honestly they both do the same things. Flask is a bit more complicated since it leverages a couple of other frameworks. Bottle requires one file and that's it. I prefer simple stacks for stuff like this.

Answer 4

[Pierre Lindenbaum]

from SO: http://stackoverflow.com/questions/10493188 "Simplest framework for converting python app into webapp?"

Answer 5

[Yannick Wurm]

Hello Stefanie, have a look at what we did for our BLAST frontend, Sequenceserver. Perhaps it can help provide some ideas. This was done in ruby - using Sinatra.rb, and a few additional technologies (ERB, Twitter Bootstrap, jQuery...).