Ways of developing non-core skills during PhD studies?
My goodness, but this is a tough one.  We all learn and maintain our skills in our own unique way.  Especially in industry or when operating independently, so it's difficult to say what would work for you.  I'm in a similar situation except that I'm a developer first and I've been tasked with 'just making security happen'.   Much like with you and bio-med, there is an awful lot that is changing in the landscape of info-sec and staying sharp in both domains is a real challenge.  

That said; your mileage will vary but here are some techniques that work for me. 

Find overlapping areas:
When I started to move toward developing a new aspect of my skill set I looked for areas where the old and the new overlap.  Luckily for me; this was a pretty easy thing to do with infosec and software development.  The benefit here is that it allows you to leverage your existing skills in a new area.  If can can find areas where you can turn two jobs into one you can ease your way into it, rather than just sitting down one weekend and deciding "I'm going to learn X.".

Sit down one weekend and decide "I'm going to learn X.":
Sometimes there is no easy overlap to ease your way into a new tech or topic. In those cases I've found that a couple of days in power study mode can be a real benefit.  Strap on the headphones, coffee up it that's your thing, and just read the literature &amp; work problems.  If it's tech then do tutorials.  If it's topic then vacuum up as much as you can.  

Find mentors: Maybe you can't find the all encompassing guru of everything you want to do, but that's OK.  Someday that guru will be you.  In the meantime find people with expertise in your subject areas to help you fill in the gaps. 

Keep it fun:
If at all possible and whenever possible. If you hate what you're doing then you're not going to do it well. At least that has been my experience. 

Don't give in to the temptation to 'dumb it down':  You're a smart person.  You've taken the time to learn a new skill. You've actually read the materials.  You work hard to develop and maintain a system that crosses a number of subject matter domains.  Don't let people off easy when they ask hard questions; give them hard answers.  My approach is to ask them 'do you want an answer or a response?'  If all they want is a response that's OK. I give them a short and succinct response.  If they want an answer then I do my best to provide the most exhaustive and thorough explanation of what I do, that I can.  When I work hard to learn a new skill I don't need to show it off but I won't let it be taken for granted either. 

Well, that's what I've got. All the best to you in your endeavors. If you ever need Java help feel free to grab me on chat and I'll get you an email address.