All the Birds in the Sky

Science vs. Magic! Two nerds befriend each other in school, one a latent witch, and the other a developing technological genius. But life separates them and they grow up apart, each fully developing their power and training it as much as possible. Then, naturally, science and magic go to war and they find themselves on opposing sides, which could end everything.

All the Birds in the Sky is the first of Charlie Jane Anders' stories I've read (I used to be a devoted reader of io9.com, so I've like her writing for a long time). It's cleverly done, and is a really well realized world of magic and science (though the science feels rather magical throughout). Well worth a read.