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I wish someone would build an integrated BART+MUNI+CalTrain app. When I evaluated transit apps over a year ago, I liked the UI of iBART the best but ultimately went with iCommute because it had MUNI+BART in 1. Still had to get a separate app for CalTrain and then another separate app for San Jose Transit for when I was down there.
In case you (or others) aren't aware of it, the built-in maps app does give directions using all of these forms if you ask it to show mass transit instead of driving or walking directions.

Also in the Bay Area, 511.org is another way to get these directions (but I don't think the mobile experience is as good as the maps app.)

True. Though the built-in maps app definitely leaves something to be desired. One big benefit it does have is its coverage.

What Maps is missing is a decent list of stuff though... offline routing, real-time arrivals, alerts and system maps.

Maps on iOS is really more of a driving app than a transit app. As a result, transit is a buried and minimized feature in Maps.

Thanks for your insights on your app choice for MUNI + BART. For what it's worth, we do have a separate Caltrain app called Ride Caltrain.
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Routesy is awesome and does exactly what you want!
I feel a little sorry for other entrants in the MTA competition- it came across as being a competition for independent developers making apps in their spare time. Certainly, it seems like 90% of the entries were exactly that.

Impossible to compete with a Y-Combinator backed startup, really.

untog, we hear you there. Though there are three things we should note to put this in better context.

1. The MTA's goal ultimately was to get apps to help their riders as much as possible, regardless of where the apps came from.

2. We're recently YC funded and this began as a side project for us during college.

3. Had this competition occurred earlier in our life as a company, we still would have jumped at it, even knowing a more mature company could come in and take first. Having looked at the rankings and downloads of all the apps involved before and after the contest, we can say that this was more of a net win for this category of Apps than it was for Embark in particular.

For Windows Phone users in Chicago, I can't recommend CTAWatch highly enough. I haven't tried Embark yet, but CTAWatch has become my favorite public transit app across iOS, Android & WP7:

http://www.triton-tek.com/solutions/mobile/apps/cta-watch

Disclaimer: I have no ties to the developer or company selling the app - I'm just a very happy user.

Congrats on the award!

Is there money to be made in this space? Ads? Exit to Google? I find it to be a small market for ycombinator to invest in, but maybe I am missing something.

Some features I've wanted to see in mass transit apps:

* Notify the user when they are about to reach their destination (so that you know to get off). I think there are ways to do this now but it isn't integrated into the maps app.

* Give me mass transit directions to a destination knowing that I am already on a train/bus.

Unfortunately that isn't possible in a lot of cities because the mass transit is underground- if you can't get a GPS lock, you don't know where the user is.
You could prompt the user to explicitly say when they board the train and then use the approximate time to destination stop to alert the user. It might not be optimal, but it would be a great...right?
Google Maps for Android has transit navigation that notifies you went to get off the bus or train. I've only used it on surface transit, but it worked pretty well for me.
What's the business model?
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