A warm hello from the USF campus.  Having finished grading exams, I’m hoping to update the project blog more frequently for you over the summer.  Commencement exercises concluded Saturday evening, and today, the CSI construction perimeter is taking shape around Harney plaza.

But May has seen a lot of prep work already, even during the last weeks of classes and the final exam period.  From the Golden Gate Avenue side of campus, you can see a pleasant green wooden wall behind the trees between Harney Science Center and the Memorial Gymnasium.

Capturing What Nature Provides

Here’s a May 16 construction photo of what’s happening behind that fence.

Near the University Center, the crew has been digging a pit for an enormous rainwater cistern.  The new Center captures rainwater for efficient re-use.  That’s one of many aspects that is pushing the project steadily toward, we hope, a LEED Gold rating for sustainable design and energy efficiency.

Demolition Preview: Guard Shack Pile

Generations of new students, visitors and employees remember the guard shack next to Memorial Gymnasium.  As of early May, this was removed as part of site preparation (primarily to facilitate truck traffic and pedestrian visibility/safety.)  The early May photo below captures the moment right before the shack remnants were removed completely.  (Visitors note:  a temporary guard shack now sits between Memorial Gym and the Hayes Healy Building, just a bit to the east.)

The “one way” sign is accurate, as the summer will see a steady stream of material taken away from main campus, as the excavation of Harney plaza gets going.

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Some of you might recall our ongoing “bridge program” that brings postdoctoral candidates from UCSF to teach our introductory lab sections in the sciences at USF. We continue our conversations with the large, multi-faceted leader of worldwide human health research, and most recently, this has led to a pilot program with UCSF’s Helen Diller Family Comprehensive Cancer Center, and specifically its Translational Informatics program. Last Fall, Frank McCormick presented to a packed house at USF, and he mentioned specifically the need for recruiting programmers into the front lines of the cancer struggle.

The pilot program takes a few Masters students in Computer Science at USF over to the Cancer Center where they can apply their chops to biomedical problems. Much credit here must go to our Adjunct Professor Patricia Francis-Lyon, who specializes in bioinformatics (in short, the application of computer techniques to various problems and bio data piled higher than the Crysler Building.)

Meet the Students

This semester, three bold USF students have signed on to this experiment: Adrian Bivol, Paul Howe, and Rodrigo Thauby, all Masters students in USF’s Computer Science program. They’ve each agreed to sit down with us for Q&A.

Did you have an interest in cancer research and cancer treatment before this opportunity came along?

 

I was certainly aware that cancer was an extremely complex biological and informational problem. I also have a biology background, and cancer has been a fascinating topic for me. I am extremely pleased that I had the opportunity to work with a top team at a prestigious research institution.

 

What’s been the most surprising thing about the collaboration so far?

 

The challenge is far greater than I expected, even knowing full well that I was venturing into unknown territory. The task requires integration of knowledge from many disciplines, including: genetics, biotechnology, cancer biology, statistics, computer and information science.

 

Okay, I understand there are two separate projects that you three are pursuing, with Adrian on a project related to pancreatic cancer data, and with Paul and Rodrigo working together on a tool that will help the cancer center generate pathology reports. Could you take a hack at describing this in a way that a digital fumblethumbs like myself might get an idea of what you’re doing?

We are working with the cancer center on developing a tool to assist with the process of pathology report annotations. Pathology reports contain valuable information such as biopsy procedure results and the like. Unfortunately, there is no standard procedure for working with these reports in a digital environment. This means that technicians must work with printed copies, highlighting desirable sections which are then manually entered into a database.

Our tool provides a digital workflow for choosing reports, automatically extracting report data and allowing users to add new annotations directly from a web browser.

 

Pancreatic cancer is a severe form of cancer, with very poor prognosis, despite treatment. In recent years there has been a revolution in how cancer research is performed, based on developments in genetics and information technology. Cancer is now considered a genetic disease, and technology now allows a genomic investigation into the mechanisms of the disease. My goal is to process and analyze data from lab experiments performed on pancreatic cancer cell lines. We use statistical, machine learning, and other computational techniques to try to “break the molecular code of cancer”.

Interesting!  The two projects both seem to be as important as they are different.  They also underline the extent to which the Center takes on “the whole enchilada,” from research to treatment.

What has been your favorite part of working in a team at UCSF?

 

 

The best thing was the complete freedom we had to tackle this problem. Mark and his team at UCSF were very welcoming of our thoughts on which technologies we could use and make this project our own. We are also very excited about the possibility that this project will make people’s tasks easier at UCSF, hopefully a solution to a very real problem.

 

Finally, I know it’s really just started, but has this experience changed your vision of possible career paths?

 

I think Paul and I were both surprised by the practical applications that software has in the scientific world. Personally, I was very enthusiastic to learn about problems that we are not exposed to on a normal day-to-day basis, and as such gives me an opportunity to do something innovative. I’m not sure where the future will take us, but this experience made the possibility of working in this field an attractive possibility.

 

 

Thanks much, you guys! And all best wishes for the work ahead. Many thanks to Sorena Nadaf Director of Translational Informatics and Chief Information Officer at the Helen Diller Family Comprehensive Cancer Center, and his many colleagues involved in this pilot program. And thanks again to USF’s Patricia Francis-Lyon for all her work on the USF side of this equation.

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For nearly 10 straight hours, main campus was beset by a buzz of enthusiastic students describing their work to one another, to professors from other programs, and even to a lost tour group of recovering hippies searching for the house where Jefferson Airplane lived. This was the (… clears throat …) “First Day of Celebration of Students’ Research and Artistic and Scholarly Creative Activity,” or FDCSRASCA (bless you!) for short.

Budding psychologists, artists, economists, mathematicians, chemists, and you-name-it, put up their creative work and their faculty-led research projects in poster format. Think less “science fair,” and more “academic conference.”

Ready for more after the day-long general session, about 100 science students joined an evening event to bring all science disciplines together (for the first time, as far as I’m aware), in the Harney Science Center.

Poster-fulls of boldface credit go to professors Megan Bolitho (Chemistry), EJ Jung (Computer Science), and Chris Thompson (Exercise and Sport Science).

Check back here, as I’ll try to get the digital booklet of student work and put the file here. For now, enjoy Shawn Calhoun’s flickr site for the event and browse his great photo-documentation of daily USF in general. (And note the open-access creative commons licensing to boot.)

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We’re trying something a little new in Harney next week, and all are welcome to attend.

When: Next Tuesday, April 12, starting at 5:30 p.m.
Where: 2nd floor (main floor) of the Harney Science Center

While we’ve had subject-specific events highlighting student work, this will be the first one in recent memory where you can view student research projects from across the USF science programs. It will not be comprehensive, with every single research project represented, but a dozen or so fantastic projects spanning an impressive range of topics will be on display, presented by the student researchers themselves.

Here’s a downloadable flyer. Hope to see you there!
Science-poster-night

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We recently had the chance to talk with USF Chancellor John Lo Schiavo, S.J., right after his 86th birthday. As you all know by now, the Center for Science and Innovation will be named in his honor.  

At the groundbreaking in December, Fr. Lo Schiavo said that “we stand ready to begin the second golden age of the University of San Francisco.” Many of us felt chills that were not solely due to the foggy, winter gusts around us.  It was an inspiring statement of the project’s vision and potential.

With cake only recently consumed, he kindly agreed to some Q&A.

What birthday memory brings the biggest smile to your face?

When I was a little kid, four or five years old, I believed we all grew on the night of our birthday, with our entire growth for the year in one night.  I remember running downstairs and asking my mother how much taller I was than the night before.  She explained to me that it didn’t work that way.

Favorite type of cake, birthday or otherwise?

For me, any chocolate cake is good.

In your comments at the groundbreaking, you mentioned the history of USF sciences, with some surprising facts about USF before 1906.

The teachers were exiled Italian Jesuits who had been students in European Universities.  We had the best laboratories west of the Mississippi.  The church was as large, maybe larger, than our present church.  There was even a swimming pool on campus.  In the big earthquake and fire of 1906, St. Ignatius College was completely destroyed.  Because of two World Wars and the Great Depression, we really didn’t start rebuilding until after World War II.

Do you recall any surprising stories from the construction of Harney Science Center (circa 1965)?  Any things we should be on the lookout for as we begin the CSI?

Not really, because that was a period of intense construction, with one building after another.  In no particular order, Cowell, University Center, the Jesuit Faculty building, a wing of Phelan Hall, the Law School building, and Harney.  There was always some part of campus fenced off, and we were used to all the trucks and noise.

We’re about to replace Harney plaza, which is hard to imagine.  Do you have any recollections that stand out about events in that plaza, good or bad?

Mostly good.  Lots of things happened there over the years.  I remember big rallies in the plaza before basketball games and other games.  Those were a lot of fun.  The students would all come to the games in white shirts, and after the game, they’d have a dance in what is now the McLaren complex.  At the time, it was a dining hall.

Any science-related story you want to share?

Well, I have to admit Physics wasn’t my favorite subject in the seminary, in Spokane.  Once, in a section of optics, with concave and convex lenses and all that, the professor, a Jesuit priest, asked a test question.  ”How do you treat nearsightedness?”  We were supposed to give the right type of lens, but I just wrote: “Eat plenty of raw carrots and other vegetables.”

Thanks, Fr. Lo!  This Physics Professor says whatever you’ve been eating has been working.  From the emerging new heart of campus to its namesake, here’s wishing Fr. Lo Schiavo a very happy 86th birthday, with many happy returns.

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We learned recently that Juliet Spencer, Associate Professor of Biology, has again lassoed a prestigious research grant from the National Institutes of Health, (NIH).   Her grant pace is comparable to that of some scientists at larger universities, the folks who have swarms of PhD students and miniscule teaching commitments.

Juliet joined us in 2003, after spending about four years in local biotech.  Her great “real world” experience has been a huge boon for USF, the Biology Department, and our students.

On the occasion of her new grant (totaling roughly $400,000 of new funds for USF, her lab, and her student research assistants), we pestered Juliet with some questions about the new honor and the scientific task at hand.  Many thanks for taking the time, Juliet!

How would you explain this particular project to a non-scientist?

We are studying a common human virus called cytomegalovirus, or CMV. Believe it or not, most people are infected with CMV but show no symptoms and don’t even know they are infected. For healthy people it’s not usually a problem, but for immune compromised people, like transplant recipients, or AIDS patients, CMV can cause very serious disease. The project that was just funded will allow us to investigate whether being infected with CMV has any impact on the development of cancer. We don’t think the virus causes cancer, but we are going to examine whether being infected might increase the chances of a tumor becoming more invasive and forming secondary tumors. If this is true, treating some cancer patients with antiviral drugs might help improve their prognosis.

I’m not sure that most people understand how difficult it can be to secure such a grant, since there are so many applications now.  Just to give readers some context, do you know what % of grant applications were awarded funds in this specific program?

In 2010, 19% of these grants were funded.

Have your colleagues in biology been a good resource for such successful grant writing?

Yes, this is my third proposal funded by the NIH, and I’m very fortunate to have colleagues in the Biology department who are willing to take time to critique my grant proposals. I believe my success has been due in part to the fact that I can incorporate their feedback and address those comments before submitting the final proposal. This helps me present a really solid research plan, and I’m very grateful to the NIH for their continued support.

What will this grant mean to the students in your laboratory — will there be more students, or just better supported students?

Both – the grant will provide stipends for student researchers, both undergraduates and Master’s students. It will also help us buy the supplies for students to conduct these molecular experiments, as well as travel to conferences to share our results and get input from other scientists in the field.

What are you most excited about with the coming of the new science center? Our readers know it is focused on teaching, but do you see a positive research by-product in it?

I look forward to the opportunity to teach our students in new, modern laboratories. In terms of research, I think that having state-of-the art teaching labs will help generate even more interest and enthusiasm for careers in research among our students.

Godspeed to Juliet and her students. The issue of how cancer spreads is fairly wide open, and obviously it’s a critical question for medical science.

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This week, we had an open university forum on the coming construction.  Representatives from Cahill Contractors and our own project manager Kristy Vivas, gave a presentation on what’s to come and then took a bunch of questions from the audience (of staff, faculty, and students.)

The goal is to complete the new Center within 2013, if all goes well.  When it opens for business is a different story, since we’ll have a lot of equipment to move and systems to check, etc.  But that’s only two years away — unbelievable.

Dig numbers

• 20,000 cubic yards of material will be excavated from Harney plaza.
• That will be hauled away in about 1800 dump truck sorties.

Most of that, ideally, will be complete about six months from now, before Fall 2011 classes begin on campus.

Near-term dates to remember

• Spring break will see the construction camp take shape in the parking lot adjacent to University Center.  That will be the staging area for equipment, materials, and work crews.
• In April, the crew plans to install the large underground cistern that will store rainwater for the new Center (winning some LEED points and complying with new city regulations, as I understand it.)  This big tank will live under the eventually-restored UC parking lot, nestled between Harney, University Center, and Memorial Gym.
• May 24 will be the first day of our “big dig.”
• During July of this year, we’ll witness the installation of an enormous construction crane.  It will dominate our skyline for the next couple of years, and the installation will be site to behold.  Maybe we can have some sort of picnic:  Gin and tonics, croquet, and gawking at a crane the size of St. Ignatius church.

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Last year, we were happy to earn a B+ from The College Sustainability Report Card. But now we’ve raised our grade to a plucky A-. As I mentioned last year, this is not an exercise in grade inflation — these folks give out some nasty grades.

For now, we’re tied for the top score in the Bay Area with Stanford, with higher marks than Santa Clara University, Berkeley, Saint Mary’s College, Mills, et alia, to say nothing of the D+ hammer lowered on University of Akron. Ouch.

Read here for more detail on our improvements, and keep up with the campus Green Team right here.

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We’ve introduced you to all sorts of people here, but now I’d like to introduce you to the Center’s true MVP, Kristy Vivas, lead project manager.

Kristy has to interface with nearly every single facet of the project: architects, city officials, construction contractors, university neighbors, academic deans, faculty, you name it. Each group has their own concerns, their own requests, and even their own language. Kristy navigates all of these, on time and somehow combining a no-nonsense, bottom-line approach with an ever-present smile. I’ve researched projects at many other campuses, and I can’t being to tell you how important this is to a successful project.

An undergrad and masters alumna of USF, Kristy joined USF as a staffmember in 1999 and has been with the CSI since the early planning stages.  Now she’s going to be rolling up her sleeves for construction.

Questions with the Project Manager

Kristy, welcome! What has been the most surprising aspect of this project so far?

The sheer excitement by many faculty, staff and students and the many neighbors who are supportive of this project.

What, if anything, makes this project different from other construction projects, from the project management point of view?

The very tight site constraints with occupied buildings at each edge of the site coupled with the desire to mitigate the impact to the University community and neighbors.

Yeah, I’ve heard it compared to building a ship in a bottle. What did you learn about working with science professors?

The professors that I have worked with throughout this project, many times on a daily basis, have been very willing to help. As you can imagine there is a lot of questions as to what we will need in the new building vs. what we have in existing Harney and sorting through whether what we have had in the past was due to a necessity or because of past circumstances. Change is not always easy and the professors I have been closely working with have taken it with stride and have been very active participants in the process. I have enjoyed working with them and appreciate their humor and energy towards this project.

What is the most technically difficult part of this construction project?

Due to the LEED Gold goal and the desire to match the floor to floor heights of existing Harney we are constrained for space with MEP (that’s “mechanical, electrical, and plumbing”) and are forced to get very creative in ways to provide utilities to the labs and classrooms in a way that will make the building aesthetically pleasing and comfortable to use.

As a side note, I learned (from Kristy and others) that 1966 floor-to-floor heights in science building were generally much lower than in new science buildings, where extra space is left for all sorts of air ducts, specialized gas supply lines, velvet ceiling drapes for physics and astronomy, et cetera. We wanted a seamless connection between the new project and existing Harney, so the designers engineered it such that we get the best of both worlds: old school clearances with new school facilities.

Many thanks, Kristy. Now you can return to doing 11 things at once, instead of 12.

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The words may bring to mind current gold prices, the bubblegum craze of years gone by or huge soap bubbles for kids, but no. The Biggest Bubble: Avoiding Ecological Collapse is the appropriately provocative title of the fourth annual Jose de Acosta lecture on the Environment.

Denis Hayes is president of the Bullitt Foundation and chairman of the board of trustees of the American Solar Energy Society. He was national coordinator of the first Earth Day in 1970, and he served as the director of the federal Solar Energy Research Institute (during the Carter administration.)

Here’s an abstract he’s provided for his talk.

Bubbles have regularly afflicted economic systems since the 16th century Dutch Tulip mania. They occur when prices (of tulips, swamp land, web site hits, or CDOs) don’t accurately reflect reality. Hayes argues that the biggest bubble of all — encompassing the entire global economy — is an ecological bubble. We are liquidating the earth’s natural capital and not reflecting this on our books. We are destroying the vibrancy of ecosystem services but not internalizing this as a cost. Hayes will propose several sensible policies that, if adopted, could deflate this international bubble before it leads to a catastrophic collapse.

So mark your calendars, and please join us!

Tuesday, February 22
Reception @ 6:30 p.m.
Lecture @ 7:00 p.m. in the Maraschi Room on main campus.
Followed by Q&A.

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