Some quick notes on mini trip to DOE-JGI & UCSF

Well, just got back from a very brief trip to give a talk at UCSF.  I was invited by graduate students via the following email message

The students in the DeRisi Lab at UCSF are thrilled to invite you as our selection for the California Institute for Quantitative Biosciences (QB3) and Integrative Program in Quantitative Biology (iPQB) Invitational Speaker Series!  This is a new type of speaker series at UCSF where students from a laboratory directly nominate and invite speakers from outside UCSF to deliver lectures about cutting-edge topics in quantitative biology.  All nominations are discussed by a QB3/iPQB student committee, and a speaker list is compiled from many outstanding nominations.  The invited speakers are scientists who gathered especially strong support from their nominating lab and the QB3/iPQB student committee, and who have an outstanding record in delivering exciting research talks grounded in quantitative methods. As our selected nominee, your travel, lodging and food expenses will be covered by funds from QB3/iPQB.

It was impossible to say no – I am always thrilled to be invited by student groups.  It took a bit to coordinate when I would come (I am notoriously bad at planning and answering such invitations).  But eventually, with a little prodding, I answered and we picked a date. I of course then asked to change the date and we settled on February 17.

I actually headed out Wednesday AM because I had some appointments at the DOE Joint Genome Institute in Walnut Creek where I have an Adjunct Appointment.  While there I got to see their Pacific Biosciences machine – we are getting one at UC Davis soon (well, they tell us it will be soon – we are supposedly going to be the first commercial machine delivered).

PacBio machine at JGI

I heard a talk there by Jason Holder from MIT who works on biofuel related topics and then I met with him for an hour or so after his talk.  He pointed me to a book I was somehow unaware of: The Cathedral and the Bazzar which discusses two different models of free software development.  I will be reading it.  Thanks, Jason.

After meeting with Jason, my plan was to go hang out with my brother in Berkeley before heading into San Francisco to a hotel to stay overnight so that I would not have to get up at a crazy early hour in Davis.  UCSF had reserved me a hotel room at the Griffon Hotel on the Embarcadero.  Alas, my brother was sick and I did not want his cooties.  As it was already about 4 PM, I bailed on visiting people at Genentech which had been another possibility (since Genentech is a bit South of SF it seemed like there would be traffic heading there).  So I just went to the hotel.  I got free valet parking b/c I have a hybrid car and then checked in and dumped my stuff and went immediately out to the Embarcadero to see the water.  Living in Davis, CA is nice, most of the time.  But whenever I get near a large body of water I mostly just want to stare out at it.  So I walked around, took some pictures and walked around some more.

I then had dinner at Perry’s on the Embarcadero.  Had a very strange interaction with the service crew.  I got seated, was happily sitting reading email on my phone when the barkeeper came over and asked if the waitress had taken my drink order yet.  I said, no but it was not a big deal.  He said something to the effect of “Well, she should have been here.” and he took my order.  Then the waitress came over a few minutes later and apologized for being a bad server – as though the barkeeper had told her I complained, which of course I had not done.  Then every few minutes she kept coming back to fill up my water glass and I tried to tell her not to worry about it but she kept seemingly apologizing for a slight I never noticed in the first place.  Not exactly relaxing.  But the food was OK (had a veggie burger and salad) and I lingered there a while before “retiring” to work on my talk.

Got up early the next AM and decided to drive over to UCSF so I had my car there rather than having to return to the hotel later.  So I packed up and heading over to Mission Bay.  I parked and grabbed my giant umbrella I thankfully had in the car, and walked through the driving rain to Cafe Terzetto where I had breakfast and coffee and tried to finish working on my talk.  Coffee was OK – nothing special but tolerable.

Then I headed off to Genentech hall and called up my host, Peter Skewes-Cox from Joe Derisi’s lab and he took my on up to Joe’s office. I met with Joe for a while which was great.  I have known him for years since my brother worked in the same lab as Joe many many years ago when they and Pat Brown and others were developing microarrays.  Joe is always up to something interesting and he told me about many things including using his 3D printer to make virus models.  I guess he used these as part of his HHMI Holiday Lecture this year, which you can view here.

After meeting with Joe for a while Peter took me to another room where I spent about an hour just talking about life, science, open access, and other things with students.  I was very impressed with the collection of students at UCSF.   Then Peter said we should go to get ready for my talk.  Hmm … that was surprising since I thought my talk was at 4 PM.  Apparently, it was at noon.  And though I had hoped to edit a few slides and take out a few since I had too many, we went down to the seminar room and I had five minutes to organize my slides and thoughts.  But I think it worked out OK.  I gave my talk, got a lot of questions and then headed out to lunch with students.

 I also got to chat very briefly with Jamie Fraser, who I had last seen at a Giant’s playoff game in October.

Jamie Fraser and Michael Eisen, rooting for the Giants

We had lunch at the cafe on campus, which was a bit slow but good (had another veggie burger). And eventually we headed on up to Michael Fischbach‘s office. Had a great time talking to him and a collection of students in his group.  All doing very interesting and impressive stuff on comparative genomics of microbes, especially in relation to production of secondary metabolites.

And then, too soon, it was off to meet Patsy Babbitt and one of her lab members and then Carol Gross and some people in her lab.  And then off to dinner – Peter escorted me and some students to a really good mexican place (no clue really where or what it was called).  And we had a good dinner there and eventually Peter dropped me off at the garage where my car was and I headed home.

However, I did one mischievous thing before heading home.  I posted to twitter about how I thought Matt Damon might have been in the back of the room at my talk, and feigned ignorance about this being remotely possible.  I did this because the students and others were talking the whole day about how over the last few days, a film crew was on campus filming a movie starring Matt Damon and Jude Law.  And I figured, someone would see my tweet and make the connection and suggest that it was in fact possible that he was at my talk.   Then I drove home.  Meanwhile, some people fell for the trick and started to send me messages about how Damon might in fact have been in my talk.   Oh well, I guess you can’t believe what you read on the internet.

Author: Jonathan Eisen

I am an evolutionary biologist and a Professor at U. C. Davis. (see my lab site here). My research focuses on the origin of novelty (how new processes and functions originate). To study this I focus on sequencing and analyzing genomes of organisms, especially microbes and using phylogenomic analysis

One thought on “Some quick notes on mini trip to DOE-JGI & UCSF”

  1. Yes, the “Cathedral and the Bazaar” is a classic, although it sort of fails to address the fact that to have the supposedly superior bazaar-style development, you have to have a large base of users who are actually interested in contributing code. At least in the cases where I'm familiar with, this tends not to be the case — you can't just throw code out to the public and expect people to improve it for you, unless (as in the classic case of the Linux kernel) it represents something millions of people really want (in Linux's case, a free PC UNIX clone in the era where a commercial license was out of the reach of the students and academics who most wanted it)


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