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

[Yannick Wurm]

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
>> 
>> 
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