A quick word about isolation exercises:
These are generally contraindicated. A lot of drills people have come up with over the years are not something you'd see a cyclist doing on the road, so why would we do them indoors? However, riding indoors means we also don't face all the same conditions as riding outside - no wind, no turns, no downhills - so certain exercises can help challenge the body in ways that only sitting or standing can not.
Here are my own rules when it comes to isolation:
*Hands on the handlebars! You wouldn't take them off your bike if you were on the road, so don't do it in class! I've heard instructors tell their class to stand up to climb, but then alternate putting either arm behind their backs or worse, letting go entirely. Not safe. You shouldn't be leaning on the handlebars, but if you put every last ounce of your weight over your knees in an awkward position, you're asking for trouble.
*Isolation exercises should still mimic a normal riding position and serve some sort of function. Hovering over the saddle and staying really low is something a rider might do in strong headwinds. Focusing on pulling up on the hamstrings is a way to train the legs to have a more efficient pedal stroke. When eliminating the bounce of riding to isolate the quads, this also trains the legs to pedal more effectively rather than using the whole body to bounce up and down. The more you move your whole body, the more energy you take away from your legs.
*Don't do it if it hurts. I always tell my riders - especially noobs - that if you feel any kind of strain or pain in your hips and knees, just sit and ride. If you were riding your bike out on the road, you would naturally settle into the most comfortable riding position, anyway. These are just exercises to mix up the routine but ultimately, if you're not ready to try them, it's okay to "sit it out" so to speak... just keep working, of course!
This is one of my favorite playlists and it includes a mix of hills, runs, hamstring and quad drills. I've got a little something from every decade starting in the 1960's and working up to today. Have fun!
"Rock of the Ages"
1. warm up - flat road, optional individual leg-warm/up 30s each - "Light My Fire" The Doors
2. seated run - add a gear, quick cadence, work up to 70% effort - "I Wanna Be Sedated" Ramones
3. 3 position climb - add a gear start in pos. 1, stand in pos. 2 on the bridge, add a gear in pos. 3 on the chorus. Back to pos. 1, leave the resistance on and repeat the cycle (should be heavy by the end!) - "Livin on a Prayer" Bon Jovi
4. flat recovery/run - recovery pace for the verse, pick it up and run on the chorus - "Basket Case" Green Day
5. isolation - light to medium resistance - sit and run at 70% for the verses, stand in pos. 3 for the chorus chorus; try to eliminate all bouncing so that ONLY the legs are moving - "Dance, Dance" Fallout Boy
6. climb to the max - started seated at med. resistance, adding a gear every 30-45s. until you have to stand (don't drop below 60rpm - once you can't maintain that cadence, you can stand) - "Ain't No Rest for the Wicked" Cage the Elephant
7. recovery/endurance run - 1st minute is recovery on a flat road, then add a gear back in and pick up the pace to 80%/top of your aerobic zone. Hold this pace as you add a hair of resistance at 1-min. intervals - "Whole Lotta Love" Led Zepplin
8. rolling hills/seated climb - alternated seated run at light resistance on the verse, add a couple gears and run in pos. 3 at med. resistance on the chorus ("Laaaay-laaaa") - when the music slows for the super-long outro, take it to heavy resistance and climb it out 'til the end - "Layla" Derek and the Dominos
9. recovery/run - flat road, recover for 1st minute, then pick up the pace and run on the chorus, take it up to 90% this time - "Rebel Yell" Billy Idol
10. hovers - medium resistance: start in pos. 1, transition to pos. 3 on the bridge, then take it back and hover over the saddle (work those Hammies!) on the chorus - "Mysterious Ways" U2
11. last hill - keep it at med. resistance, sit and climb, add a few gears to make it steep and stand up to charge up the hill on each music break (when the music picks up) - "Seven Nation Army" White Stripes
12. run it out - flat road, recover for a minute then pick the pace back up to 80%. Take it to an all-out sprint on the chorus - "Walk" Foo Fighters
13. Recover and stretch! - "Everlong (Live)" Foo Fighters