A new cross-town partnership

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?

Adrian Bivol

 

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?

Adrian Bivol

 

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?

Paul Howe

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.

 

Adrian Bivol

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?

Rodrigo Thauby

 

 

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?

Rodrigo Thauby

 

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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