There used to be a time, when scientists were rewarded for challenging every assumption in their theories. I have been re-reading Darwin's book and was surprised to find out how much space and energy he spent to argue against potential flaws and pitfalls in his theory. He seem to have covered every imaginable species and trait, and did not leave anything untouched. Darwin had difficulty getting his book completed, and he could have easily taken another five or ten years to finish it, if he did not get rushed after hearing Wallace proposing a similar theory. The famous book is actually an 'abstract' of his theory.
Today's 'scientists' push papers to get grants to push papers to get grants. By today's standard, Darwin did not get anything done beyond 'submitting an abstract'. You cannot be like that. So, I suggest you stop asking too many questions about your tools, and follow these simple rules -
(i) You get more grants, if you can show more papers and many 'high-visibility' papers. Try to keep those two numbers high.
(ii) Give your paper a catchy and inflated title. That criterion has become almost essential to get into high visibility journal.
(iii) Write a strong abstract, and try to focus your bioinformatics work to make sure you have enough strong points for the abstract.
(iv) Figures are the next important part of the paper. Make sure you spend enough time to polish them up.
(v) Submit letter-type paper so that you do not have to spend too much time writing the remainder of the paper.
(vi) Materials and methods section - try to copy as much as possible from other published work. That way you can blame others, if someone objects about one or other step in the procedure.
(vii) If you are writing too many papers following (i) - (vi), the editors and reviewers will keep you busy, and you will not find too much time to read biostars, blogs, twitter, etc. Your primary problem is that you have too much time in hand. That is unacceptable, if you want to run a lab as a successful PI today.