[BioRuby] gsoc suggestion: microframework for simple scientific web wrappers

Thu Feb 6 18:47:51 UTC 2014

You can always mentor and discuss implementations on this list to get others thoughts.  That’s the fun of it, both for the student and the community.

chris

On Feb 6, 2014, at 6:24 AM, Yannick Wurm <y.wurm at qmul.ac.uk> wrote:

> Thanks, glad you like the idea. 
> 
> The thing is I'm not technical enough to supervise the implementation... so I could only co-supervise with the help of a strong technical thinker. 
> 
> This could fit under sci-ruby's remit as well. 
> 
> Cheers,
> Yannick
> 
> 
> 
> On 6 Feb 2014, at 06:34, Pjotr Prins <pjotr.public14 at thebird.nl> wrote:
> 
>> This is a very good idea, and ties in with earlier bio-ngs work and
>> our future plans in pipeline software management. 
>> 
>> GSoC also likes 'infrastructure' type projects - it was found out the
>> last summit.
>> 
>> Do add it to the OBF project proposal list. Also mention bio-ngs and
>> your project.
>> 
>> Pj.
>> 
>> On Thu, Feb 06, 2014 at 12:09:58AM +0000, Yannick Wurm wrote:
>>> Dear all,
>>> 
>>> a small thought about a potential GSoC project. 
>>> 
>>> Many bioinformatics software consist in a binary that you run on the command line with one or few input files, some parameters and generates some output files. Let's consider only software that generates potentially human-readable output. 
>>> 
>>> Most of us on this mailing list have no problem running that kind of software on the command-line. But for the majority of biologists that's still impossible: they need a point and click interface instead. 
>>> 
>>> So if you're the person who needs to implement that point and click interface, how do you do it? 
>>> 1. create a wrapper for galaxy [1]. This has become easy.. but puts the burden on your enduser to have or set up a galaxy installation (not trivial), and the galaxy user experience is debatable.
>>> 2. use sinatra.rb (we did this for our sequenceserver wrapper for blast) - it worked but involved way too much manual labor.
>>> 3. be old-skool (build your own from php/etc).
>>> 
>>> 
>>> Clearly 1 isn't always appropriate & locks you into a weird framework, and 2. is still to much work. Padrino & rails are overkill for the simplest apps. With Ruby providing such great web development frameworks, why isn't there an easier/faster way to generate a web wrapper around a piece of scientific software? 
>>> 
>>> Perhaps I'm missing something. 
>>> 
>>> Alternatively, creating a "wrapping scientific software" framework could be a viable GSoC project. 
>>> 
>>> Build it upon Sinatra, create a rigid framework where the basic locations of files that the developer needs to edit are predetermined (similarly to rails). Single page/webform for the user to enter data; single output/download page after the run was successful. No need to store any user-data on the server. The framework should include the following features: 
>>> * easy way to verify presence, executability and version of binary (or script) that is being wrapped
>>> * easy way to specify number of input files, and potential constraints on them  [this stuff should be specified once; appropriate HTML should be auto-generated (bootstrap)]. 
>>>   * most basic constraints: size and/or extension
>>>   * more advanced constraints: user-extensible function that verifies the format
>>> * easy way to specify possible parameters and constraints on their types 
>>> * easy way to show/include local data (HMM models, sequence databases etc...)
>>> * easy way to make text-output look good
>>>   * eg. inserting specific headers or indexing at specific regexps (for table of contents)
>>>   * eg. csv output should be shown as a table
>>> 
>>> I'm not the best qualified person to consider exact implementation details, but if someone wants to go ahead with it I'm happy to provide more general thoughts. 
>>> 
>>> Cheers,
>>> 
>>> Yannick
>>> 
>>> [1]: http://galaxyproject.org
>>> 
>>> 
>>> -------------------------------------------------------
>>> Yannick Wurm - http://yannick.poulet.org
>>> Ants, Genomes & Evolution ??? y.wurm at qmul.ac.uk ??? skype:yannickwurm ??? +44 207 882 3049
>>> 5.03A Fogg ??? School of Biological & Chemical Sciences ??? Queen Mary, University of London ??? Mile End Road ??? E1 4NS London ??? UK
>>> 
>>> 
>>> _______________________________________________
>>> BioRuby Project - http://www.bioruby.org/
>>> BioRuby mailing list
>>> BioRuby at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioruby
> 
> 
> _______________________________________________
> BioRuby Project - http://www.bioruby.org/
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby