Lab Web Framework, Any Suggestions?

Question

[daniel.soronellas]

Hi everybody,

I am planning to use an existing web framework to build a collaborative site for people in lab and possible external collaborators.

I saw that in bioinformatics current approaches to this field involve Shiny from Rstudio developers and iPython notebook.

I was wondering which could the best framework to build a site that could share paper results (figures and tables, materials, methods, protocols, paper-related bibliography) as well as the possibility to eventually incorporate automated R functions like clustering and heatmap plotting, point plot for correlation analysis, etc..., and finally could also integrate a local installation of UCSC genome browser or any related...

I think it could be a powerful app, but I'm not sure where to start

So I ask to the community if anybody has experience with this kind of projects, and could recommend me a suitable way to handle all this

Thanks for your help, This is an amazing Q&A community!

Answer 1

[Pierre Lindenbaum]

I would use a 'simple' mediawiki installation like openwetware.org did. You can add some plugins to mediawiki (I remember I wrote one to display the content of the UCSC brower at a given location: http://plindenbaum.blogspot.fr/2010/08/mediawiki-extension-displaying-ucsc.html)

My laboratory has recently started to use http://www.redmine.org/ to manage its projects.

[Daniel Standage]

An alternative to mediawiki is dokuwiki, which uses flat text files for the back end instead of a MySQL database, which simplifies the setup somewhat. I've used dokuwiki for several years now for several different projects: it has been my personal lab notebook for 2-3 years, I used it at a previous job for a knowledge base, and our lab uses it for collaboration and as a CMS for class websites and the lab website.

[Konrad]

I set up the same constellation in our lab: MediaWiki for general content. Redmine for task management. We are also doing our journal club paper collection in the Wiki using the PubmedParser extension.

[Daniel Standage]

I second this! A wiki is a great starting point for collaboration and collaborative documentation. My experience with collaboration is that > 90% of the issues are issues with people, not issues with technology. Getting people to actually share consistently, organize themselves, etc is the real battle--if they are motivated and organized, I don't think it matters much what tool you use, it'll get done. If they are not motivated and organized, it doesn't matter how nice of a system you build for them, they won't use it and it will be a waste of time and resources.

If by some chance you do have a spectacular group of collaborators, and after using a wiki for a while they complain about missing features, then you might look into writing extensions or perhaps moving to something richer.

[daniel.soronellas]

Thanks for your suggestions! I will start by looking all resources and decide which is the good way!

Answer 2

[Sean Davis]

I use a static site generator, nanoc, for my own site. Sphinx can be quite powerful for building static sites, also; it isn't just for python documentation. As for app development, I like using flask (python) for web app development, but that is mainly because I find myself in the python world often enough. Shiny and ipython notebooks also have a place as does simply knitr and markdown. You may want to think of several distinct apps, though, rather than trying to find one framework that will fit all needs.

[daniel.soronellas]

Many thanks! very useful!

Answer 3

[jeff.mcwhirter]

You might want to check out RAMADDA - http://geodesystems.com (disclosure: I am the developer of RAMADDA)

RAMADDA is a comprehensive and extensible content, information and data management platform. It is easy to install, configure and maintain and provides data management, wikis, weblogs, document management, lists, and lots (and lots) of other cool features. It is released as fully functional shareware and is freely available for non-profit use.

I don't know much about bioinformatics but I have built out some support for genomics data and services (kind of like Galaxy) as well as for bio-imagery (Dicom, ome-tiff) - http://geodesystems.com/repository/alias/bio

The Service Integration Framework allows you to plugin your own tools