I use Mendeley as references manager because it is free, and you can create groups and share bibliography, automatically import references from the web, create a social profile, etc. 

https://www.mendeley.com/?interaction_required=true 

I have tried to start to use R for my statistical analysis because as an open statistical package there are lots of developers working to improve the codes and packages.

https://www.r-project.org/

I also recently discovered the H-CUP Project, which offers you the possibility of using databases for secondary analysis and useful open code tools for classification of diseases for research purposes.