A computer upgrade shut down BART

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BART is unique and doesn't share much in the way of infrastructure with any other public transit system. You can't build a scalable startup targeting BART because you'd have a maximum of one customer.

The Boring Company has attempted to develop tunnel boring technology which theoretically could someday allow for cheaper expansion of all subway and light rail systems. Although in practice they haven't accomplished much and their existing projects aren't even used for rail transit.

https://www.boringcompany.com/

There are also several eVTOL startups aiming to improve quality of life through rapid point-to-point transportation. But I doubt they'll succeed on any widespread basis due to battery and noise limitations.

There isn't much different about bart. Slightly wider wheel spacing and such are things anyone making trains can handle.

the real problem is thinking they are different or that they need to innovate. Trains are common and they need not innovation but minor improvements over time.

I've heard that makes procurement way more difficult, you can't just order a train car in the standard gauge from many manufacturers. It's like big and tall sizing, yes, any place can make it, but there just isn't that large volume to create a liquid market.

But is this a problem that can account of the day-to-day difficulties of managing and using BART? Yes, procuring new train cars is more difficult (and likely more expensive), but BART has lots of other problems to tackle.

The problem isn't just the rolling stock. Everything in BART is at least somewhat custom including control systems and software. Very little can be shared with public transit systems in other metro areas so there are no economies of scale. Thus BART has to do a lot in house or depend on a limited set of specialized vendors at great expense.

If you had to buy a special car to be allowed to drive on Bay Area roads because they weren't the same as the roads in Chicago or Boston then a Honda Civic would cost $1M.

  then a Honda Civic would cost $1M.

For $1M you could build a single San Francisco Cable Car. Plus it's built locally.