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I think the OP is thinking along the lines of a tuning/respec of a sci officer to FIT the Bort.
My own suggestion would be "Get a better ship"-the Bort's basically a space-station with some mobility, if space-whales are your bag, then tuning your Sci as if you were a Federation sci in a SLOW cruiser would be the direction to go-i.e. lots and lots of resists and area-affect skills, high scores in flow cap, Gravitons, and particle, for combat skills don't bother with weapons specialization, just max out your weps training and maybe projectiles, then focus most of your weps on torpedoes and mines, with appropriate projectile Doffs, A technician to shorten your cooldown timer, and that nifty Duty officer who helps you get an aftershock gravity well.
for BOFFs, focus on powers that boost your shields, resists, or can be used to support your mates for the ens. and Lt abilities(TSS and Hazards are ALWAYS nice), and big drainy-crushy AOE powers in the LTC and C spots. (Grav well 3, Tyken's, Photonic shockwave, etc.)
The Bort's got no handling, so don't arm it as if it HAD handling-beam arrays, turrets, and torpedoes (for the spread in conjunction with other CC, and because torps use less energy than beams or cannons), set your powers to high sheild/high Aux/low engines and low weps (you're not going to use them as much as you will sci abilities or your photonics...which are boosted off Aux, not Weps). Your role as a sci in a Botasque' is to try and 'anchor' your teammates while passing out the heal and resist buffs, lay down suppression fire (AOE) and the like-you're not the main hitter and you're not going to be scoring lots of individual kills-your job is to make it easy for the REST of your team to get kills (and maybe not die in the process.)
"when you're out of Birds of Prey, you're out of ships."
Consider that just a proof of concept. As far as Science goes, there isn't to much skill wise that buffs your inherent captain abilities. So for sure skill your captain along the lines of abilities that you will actually be using in a Bortas. Top rank sci abilities may not be on the menu. Your call really. Other than those top rank items it would be hard to mess up.
Also, sub nuc comes out of the pointy end of your ship. So if you're going to fly a sci in a Bortas, you're going to want to learn how to aim the pointy end at the bad guys whenever you want to. Just takes a bit of practice.