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