In addition to software development issues I would like to use Jira
for managing literature links and document files within a group of
about 50 people to be able to share documents, comments, ...
Are there any templates or definitions available somewhere which
could be used as a starting point? I'm rather new to Jira (just a
few days working with it)
Using Jira (instead of confluence) would allow as to use a single tool
for our application chemists and I guess that search, sorting of
papers into components and alike would be more easy - but I'm using
confluence only from time to time in an active way.
There is an article from Atlassian on this topic. See http://confluence.atlassian.com/display/CONFEVAL/Using+JIRA+for+a+Knowledge+Base
To be honest, I think that Confluence would be a better solution for this, it supports templates, revisions and sharing documents and comments out of the box. I've heard of several cases where Confluence was used for literature management and creating complete books :)
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