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I've lived in the Peninsula…

I've lived in the Peninsula in Los Altos for the past 10 years and occasionally frequent SF. Personally, I'd avoid Napa/Sonoma. Late December will be past the fall color and the vines will have no leaves but you will skip all crowds and have a killer meal if you go. I second whoever said to skip East Bay. There isn't any reason. and I don't really find Berkeley similar to Ann Arbor. 

In general, I think you'll find SF is pretty much tech people everywhere these days (me being one), you can't really escape it. But it's a great city still and you'll have a great time! here's my thoughts given you wanted to veer a bit from the typical tourist spots. 

- Go to presidio, the entire park is amazing but I'd especially recommend visiting Lodge at the Presidio and the parade grounds. There's 3 fairly good restaurants right there too, unfortunately you'll be out of season for the sunday food trucks. Also you can go see the Yoda statue (squint and you'll find it). 

- West and South of the Golden Gate is Lincoln Park golf track, some very cold ocean beaches, Lands End, etc. Its worth going by if you are also spending time in Presidio. 

- De Young and California Academy of Sciences

- Noe Valley, Bernal Heights, and Hayes Valley are hipster neighborhoods but good restaurants everywhere. Several pretty solid breweries can be found throughout city. 

- if you can tolerate weather, rent road bikes in sausalito and ride through marin. There's 30 mile routes you could take and see some really beautiful sights

- go to muir woods but take the hike from muir woods to stinson beach (~5 miles if i remember). you can take a bus or uber back to trailhead. make sure to stop in stinson beach at the cafe and get hot donuts freshly made as you wait

- marin headlands. This is where you'll get the view of looking down at the Golden Gate

- drive down and take the tech company campus tours - Apple visitor center is always open, Google, take your pic in front of the like button at Facebook. Stop to eat in Los Altos and act like a local tech person. 

 

Touristy but still worth it:

- Ferry building farmers market

- Grace Cathedral / Washington Square / Nob Hill area (can also quickly lead you to Lombard street and Pac Heights)

- Pier 39 if you must do fisherman's wharf

- Carmel / Monterey / Pebble Beach (and 17 mile drive) are not to be missed. It'd be driveable from SF to go down. You could either hit the Monterey aquarium all day or drive through Monterey along the coast to 17 mile drive and go to Pebble Beach. The bench at Pebble beach overlooking 18th green is well worth it if you are a golfer. You can stop at A.W. Shucks downtown Carmel for casual seafood. 

- can you get to Tahoe? ~5 hour drive so likely would require a night stay? It'll be stunning. 

Sophos Anti-virus

Mac users need to download Sophos Anti-virus. Sophos just released a free version for home users. We use it at work on our macs and it's relatively painless. 

How about moving some of the

How about moving some of the service to Amazon's cloud compute services S3 + CloudFront (CDN)? Quick Google searching shows at least some interest from Drupal developers for using S3. S3 is dirt cheap. 

What do you intend to be

What do you intend to be doing? I always liked working with things I can see immediate results (web programming, etc.). Second the notion to use Eclipse though. Eclipse is an absolute beast so I would recommend having a pretty nice computer to run it. 

I haven't read a programming book in awhile as you can honestly pick up a book from the local library or just use Google to find something that is much more current. That being said, I would pick up a book that is tailored to whatever you intend to be doing. Knowing Java will only get you so far til you then want to do something with it. At which point, then you need another large book to resolve the what to do (Java Swing, Android, Servlets, etc. etc.)

App I've never written a mobile app before but I was teaching myself the Android SDK to write such a one for this site. My thoughts were to use the rss feed to get the post details, twitter to get updates from various sites, and delicious to get the post links (mgolicious, etc.). The problem is with the message boards since Brian would need to enable the json or xml hooks to get messages and/or post updates.
Multi-tasking Considering that you can *already* do any of the following at the same time on an Android the iphone multi-tasking looks weak: - listen to pandora - get driving directions via Google Nav and interrupt pandora to give turn instructions - talk to someone over bluetooth and interrupt the nav guidance not to mention you can always get chat messages, etc. in the background. iphone's attempt at multi-tasking still seems weak.
Two Factor Unfortunately, when you make the requirements so hard, people either write passwords down on a piece of paper or jitter the differences very minor between forced password changes. The company I used to work for made it so hard to pick a password but enforced almost no deltas between new and old passwords so my password always incremented by one digit every quarter. hardly secure. At least some financial type websites have stepped it up in the past few years and enabling some form of Two Factor authentication. My Chase account requires having possession of my cellphone which will be sent SMS's with one time passwords when Chase can't figure out which computer I'm using. E-trade has RSA tokens, etc. Hopefully more support is coming from websites to enable Two Factor. Then you have Facebook who purposely tries to make it hard on you from using SSL-secured pages since it requires more compute power.
Java Odd that it wouldn't be installed by default. Try this link -- http://www.mjmwired.net/resources/mjm-fedora-f12.html#java pages specific to your version of linux are typically better than the vendor page which can't cover every corner case.
Not a bad idea for a mashup Not a bad idea for a mashup mobile app. Does air run on iPhone or android? You could use yelp for theatre ratings. Not sure about rotten tomatoes but one alternative is to setup a search feed to google and have them return you movies reviews in a wellformed API.
Perl Perl would not be my first choice for languages to pick up. You could probably get many of the same goodies with something simpler like Python. Python also has libraries to google data APIs so you can keep writing to your google spreadsheet. There is no such Perl library implementation of the google data APIs. As I said though, IMDB might not be too happy that you are scraping data.
IMDB apparently has content IMDB apparently has content licensing requirements now (new since March 1, 2010). http://www.imdb.com/licensing/ I was going to suggest that you use the URLFetch javascript support and call an IMDB API. Then you would just have a row with a cell containing each url that you need. That was when I came across the bad news about content licensing. I would suggest looking at the scripting APIs that are available. They are pretty powerful.
NBC considers these premium NBC considers these premium streams subject to having a paid comcast cable (or other) account. So unless you already have cable, the online streams are not accessible. It's really frustrating since the Olympics are supposed to be about openness and the sport. Not this crap about primetime only. I would be more than willing to pay per stream for events given the choice to do so.