| I was in very similar circumstances when I joined my band. The guitarist wrote all the songs, and I had no experience in writing basslines, so I had to learn along the way. I am by no means an experienced player, But I thought I'd share some of the things I learned:
I think the first and most important step to writing a bassline is to establish a rhythm. Establishing a rhythm can be as simple as following the rhythm guitar, or drums. At this stage, just use the root notes for convenience. However, you can achieve interesting results if come up with a rhythm that is different from the guitar/drums. For example, if the guitarist is playing chords as straight eighths, try playing only the upbeats(it'll probably give the song a bouncy feel), instead of both up and down beats. Or if the drummer is laying down sixteenth beats, try playing eighth or even quater notes(it will feel as if the song has slowed down). Try messing around a bit, you can use dead notes and other things, to give your lines a bit of a groove. When you come up with a rhythm, it's important to take the specific genre of music you're playing into consideration, because within most styles of music, there are common rhythm patterns. But ultimately, it comes down to what you feel sounds best.
Next you start thinking about harmony and melody(the notes, lol). It's essential that you have a basic understanding of scales & chords, so that you have a basis for analysis, and more plainly speaking, you'll have a better grasp of what's going on within the context of the song. Once you know the key of the song, and the chords that are used, you can start working scale tones and chord tones into you bassline, to either come up with a melody, or place emphasis on the harmony. For example, I play in a punk rock band, our guitarist plays nothing but power chords, so initially I've no clue of what key the song is in, I usually have to sit down and figure it out carefully. Once I do figure it out, I'll realize whether the chords he's using are originally minor or major chords, and I'll find out what scale tones are available for me to use(to stay within or either venture out of the key signature). With most punk rock, it's fine for the bassist to just play root notes, but I find you can give the song a forward moving feel, if you use chord tones and scale tones to walk from one chord into another. Hence making the song more interesting. Again, you should mess around a bit. I cannot stress enough, how theory can be a convenient tool or guideline to your writing. But as I mentioned above, it all comes down to what sounds good to you.
I'd like to add that it's important that you listen and analyze the basslines of your favourite players, and great bassists in general. You'll understand why their lines sound good, and more to the point, you'll be able to learn and ultimately incoporate their methods into your music. A good and convenient way to do this, I think, is to look through the transcribtions in bass magazines, and figure out why certain notes/rhythm patterns are used in a given situation/song, and to what effect. You can exercise the mind a bit, and brush up what you've learned, and more importantly find out what you need to learn.
Well, I hope all of this is intelligible. | 
