Graduate training programs from other departments, how helpful are they? I notice that there are quite a number of graduate training programs across departments in my university that encourage multidisciplinary researches. For my case, I am an EECS/ Computational Biology grad student, and I am considering a training program in biophysics/nanotech. 

I don't mind taking one more course per semester, and finding co-supervisors from other departments as the program requires. My main concern: will there be any real advantages of getting that certification in term of (academic) career prospects? 

In one of his famous blog post, Sean Carroll advised: 


  Don’t dabble. Another slightly counter-intuitive one. You might think that, while most of your research work is in area A, the fact that you wrote a couple of papers in area B will be taken as positive evidence of your breadth and intellectual strength. Very wrong. What will actually happen is that your work in area B will be compared to the best people in the world who spend all their time thinking about area B, and you will probably come up wanting. Even worse, it will be taken as evidence that your interests may wander over time — so that, whereas you were hired to be an expert in area A, maybe in a few years you won’t be doing that at all. Kiss of death. Deep down, there is a strongly anti-intellectual strain within academia; you were hired to work in a specialty and that’s what they expect you to do. Once you get tenure, of course, you can do whatever you want; so it’s important that the department be reassured that you don’t want to do anything else.


I wonder if people will look down on me if they deem biophysics/nanotech a discipline too far away from computational biology (even when my thesis are dealing with all of them)?
Yes, as @JeffE attests, there is at least a balance to be struck in the diversification of your skills and perspectives versus having a clear focus that will mark out your niche. You can overdo either one. My perspective, as someone who has been involved in inter-disciplinary research for 15 years, and who has had a lot of advice from much more senior folk about this, does err somewhat on the side of Carroll. In particular, your goal is to mark out a well defined territory that is not too diffuse. "Trajectory" in your career (mainly your pub record) is a primary consideration for hiring and promotion, and it's difficult to build up a body of work if you dabble in many areas.

My own perspective resonates with Carroll's here: continual, long-term dabbling is Bad for getting tenure. It will dilute what others will be able to confidently perceive/predict about your current and future impact in a specific field. But being a "drone" who just followed faithfully in the footsteps of his/her PhD mentor, using the same perspective that might already be "old-fashioned" and not future-proof to the growing inter-disciplinary pressures (you should be able to insert your own field-specific examples here!), is also Bad. Either because you find eventually yourself bored or devalued as a "mere follower" rather than innovator, or because your micro-focused view dries up in terms of peer interest or funding.

Remember that institutions at least pay lip service to inter-disciplinary work. Some actually really support it in a meaningful way, and look for fresh, innovative thinkers to join them. As a junior academic, now is a good time to explore what's not too far from your area and learn more about how to position yourself with a unique and/or highly desirable set of skills and body of knowledge. So, this can be exactly how you end up being successful in contributing in a clear direction in exactly the way I interpret from Carroll's blog post. 

For you, ask your mentors and colleagues how they see the current and future combination of the two disciplines you are talking about, and what the interesting questions are. Then try to see how you could fit into that and do something innovative while remaining feasible and concrete. It's tricky, but finding that sweet spot should get you a long way, and it could be much more rewarding. Just be careful who you work for. Some places or people talk the talk but don't walk the walk. When it comes to decisions involving money, if your institution's administration or your peers don't know how to properly evaluate your highly innovative inter-disciplinary work then you might "fall between the cracks" and be passed over for a more traditional candidate whose work they can, at least, easily understand! Good luck