Archive by Author

Meet Faye Orcales – Genentech intern, PINC alum and CSC 508 Mentor.

21 Sep

Pleuni: Faye Orcales is a recent SFSU alum and I am lucky enough to be working with her this year thanks to an NSF supplement for post-bacc students. She is also a PINC alum and PINC mentor (for my class CSC 508: Machine Learning and Data Science for Personalized Medicine). This past summer, Faye was an intern at Genentech. We asked her to write about her experience!

My name is Faye and I’m a recent graduate from San Francisco State University. I obtained a bachelor’s degree in Cell and Molecular Biology with a minor in Computing Applications from the PINC Program.

I’m currently working under Daniel Le as a bioinformatics intern for Genentech’s Next Generation Sequencing Department.

Faye worked with Daniel Le at Genentech in the summer of 2021 (https://www.linkedin.com/in/daniel-le-compbio/)

In my junior year I got introduced to coding when I had to take a mandatory elective course. At first, I didn’t think I would like the subject. In contrast I found out that I had a genuine interest in coding, and mentioned it to a counselor. They told me about the PINC Program at SFSU, which is a coding program offered primarily to students majoring in biology, chemistry, or biochemistry. My interests aligned with the program, so I spent my last two years of university taking coding classes along with my regular biology courses.

I first obtained research and informatics experience under PINC’s Summer Program in 2020, where I worked with Dr. Rori Rohlfs and a group of other students. I went on to do more research with Dr. Pleuni Pennings in the CoDE Lab where I utilized machine learning to study impacts on fitness cost in Hepatitis C.

“I’ve known about Genentech ever since I was in middle school”

In senior year my PINC Program Director Dr. Nina Hosmane informed me about Genentech’s Summer Internship Program. I’ve known about Genentech ever since I was in middle school, so I’ve seen the scientific innovations that Genentech has built throughout the years. I decided to challenge myself and apply to the internship because I wanted to strengthen my coding skills and see what industry standard research looks like.

I was able to obtain the internship with much support from my connections in the PINC Program. They took the time to help me strengthen my resume and provide me interview resources. I highly recommend to anyone interested in applying to Genentech, or somewhere similar, to have their trusted peers or professors give them lots of feedback on their application materials.

My work ethic and inspiration to pursue higher learning came from my parents. My family came to the United States as immigrants when I was very young. I’ve seen my mom stay up long nights studying and my dad juggle three jobs all while raising two kids. My parents’ hard work allowed our family to survive in a new country, and taught me the importance of education and perseverance.  

“My scientific inspirations came from my middle school science teachers.”

My scientific inspirations came from my middle school science teachers. They were all women of color, so their representation had a big impact on me. Every lab I did in their classes were memorable. Their passion for science influenced my current curiosity for life and the universe.

In the future I would like to become a physician-scientist. At first, I only wanted to become a doctor. After my experience in the PINC Program and Genentech, I realized that I still wanted to continue doing research as a career. To have the best of both worlds, I hope to one day get accepted into an MD-PhD program to fulfill my biggest career goal.

Outside of research and science, I’m a big fan of food. Whenever I can, I love trying out new restaurants with friends. Luckily, I live in the bay area which is rich in cultural diversity.

The PINC Summer Program 2021 got 30 Bio/Chem Students into Coding and Research at the Same Time!

13 Sep

by Dr. Pleuni Pennings

One of our students said it best: 

“PSP led me through my first research project and allowed me to present on the summer project. PSP has given me confidence in my ability to do scientific research and analyze the results of the research. Most importantly, I had the opportunity to improve my public speaking through our research symposium at the end of the program.”

What is the PINC Summer Program? 

The PINC Summer Program is a part-time program where students work in teams with a peer-mentor. They learn coding skills as well as work on a research project with their mentor and a faculty advisor. At the end of the 9-week program, the teams give a talk about their work at a research symposium. 

We have run a similar program since 2017 and written about it here. Most importantly: (1) The program is part-time on purpose to allow students to join who have other obligations, like jobs and families; (2) the students work in teams and all work takes place during team meetings – this way there is always a friendly person nearby (on zoom these days) when you are stuck; and (3) the coding skills they learn are applied to biology or chemistry research immediately.   

Who participated in the 2021 PINC summer program? 

Many people are involved in the PINC Summer Program. 

First of all, there are about 30 student participants, more about them in the next paragraph. The 30 students were organized in 6 teams. Each team had a peer mentor and a faculty advisor. The peer mentors were Angela Lane (grad student and CC lecturer), Carmen Gonzalez, Elissa Vazquez, Liz Mathiasen, Jason Hernandez and Patra Holmes (all PINC students and GenPINC scholars). The faculty advisors this year were Drs Gretchen Lebuhn, Jaime Chavez, Rori Rohlfs, Jessica Weng, Nicole Adelstein and Derrick Groom. 

In addition to those groups, the staff consisted of Torey Jacques (mentor trainer), Dr Sophie Archambeault (weekly workshop organizer), Rochelle-Jan Reyes (all-around organizer). Pleuni Pennings, Nicole Adelstein and Rori Rohlfs were responsible for the entire program. 

More about the students

The PINC Summer Program reaches a diverse group of students, in terms of ethnicity, gender and majors (see image). 

In terms of prior experience, 6 students had prior research experience, while 24 didn’t. 5 students had previously taken a coding class at SFSU while 25 didn’t. The 5 students who had coding experience were all part of the PINC program. We placed them all in the same team. Out of the 25 students with no coding experience, 9 signed up for CSC 306 (intro to python) in the fall of 2021. 

  • Major Demographics of PSP 2021. 60% of students are majoring in Biology, 30% in Biochemistry, and 10% in Chemistry.
  • Race & Ethnicity Demographics of PSP 2021. The largest communities within this cohort were of Hispanic or Latinx descent (33.3%), Asian descent (30%), or identified with 2 or more ethnicities (16.7%).
  • Sex Demographics of PSP 2021. 70% of the cohort identified as female, 26.7% as male, and 3.3% as gender non-conforming.

How did it go?

Overall, the program worked well this summer, with a few hiccups. In one team, several students had to leave the program midway for personal reasons. We recruited one new student from another program (SCIP) to join the team that had gotten a little small. 

At the end of the summer all teams did a presentation in our end-of-summer research symposium. It was really fun to hear the students talk about their research! Almost all students spoke for at least a few minutes. 

Most students who did the post-program survey are expecting to use coding in their career. 

We got answers such as “I want to pursue a career in medicinal research, and I envision using my coding skills to analyze and communicate my research with other scientists who share my interest in study.” However, a few students didn’t see it this way: “No I don’t because programming is a little too hard for me. I don’t see myself doing it seriously but for fun and for educational purposes, yes.”

Here are a few other interesting quotes from the post-program survey: 

“PSP has really showed me how fun research and science can be if you’re in a group with people you get along with.”

“I think it was helpful because we were a small group with our mentor and advisor which made it more “relaxing”. We could easily ask questions, and reach to each other. It was a nice dynamic overall.”

“Relentlessly positive, but slightly chaotic”

What’s next?

During the program, we held a lab matchmaking event in order to help students meet faculty and see if their interests align with faculty labs from SFSU and UC Berkeley. At the end of the summer, several students joined a lab. Secondly, several signed up for a coding class. Some felt like they were too busy during the fall to do either coding or research. For a few students, we don’t know what their plans are. 

Funding

The PINC Summer Program 2021 was paid for by a grant from the Genentech Foundation (PI Dr Frank Bayliss). The budget was $60,000 (roughly $9,000 for support staff, $6000 for the directors, $17000 for the mentors and $22,000 for the faculty advisors). 

How learning to code is like learning to drive a car

31 Aug

Written by Pleuni Pennings

I was in my late thirties when I learned to drive a car. I grew up in The Netherlands, in an area with excellent bike and train infrastructure and I never felt the need to learn how to drive a car. Also, I didn’t want to spend money or time on learning to drive a car. But when I finally learned to drive a car, it turned out to be very useful! It gave me independence, and it gave me options I didn’t have before.

Recently, I added to my skillset. Two weeks ago, for the first time in my life, I drove a car over significant distances in The Netherlands. I thought driving in The Netherlands was scary – but when I finally did it, it wasn’t as scary as I thought!

Now, am I the best driver in The Netherlands? Surely not!
But it’s real nice to be able to borrow my dad’s car to visit my cousin who runs a lego workshop to rent some legos. It gives me independence. And it makes my son happy too (see picture below).

If you are learning to code, you should consider your coding journey as a journey towards independence. After one semester or one summer of coding, you are not a star coder (sorry to break it to you 😉 ). But you have started! You have learned new things. You have learned new jargon and new tools. And maybe you can now analyze a small dataset by yourself. Or you know enough about coding to be able to ask for help in a smarter way. And next semester or next summer, or when you have time, you will learn more. And one day you’ll be able to drive a car in The Netherlands!

4 ways learning to drive a car is like learning to code

  1. It gives you independence. Before I always had to ask my mom or my husband to drive if I needed to use a car, now I can do it myself. For coding tasks, you may depend on a lab mate or software like SPSS or SAS, but it’s just nicer if you can do it yourself.
  2. It is not about being the best driver or the best coder. I can drive, but I will never be the best driver in any group of people. But who cares? I get from A to B safely and that’s what matters. For coding, it’s the same thing. If you want to use coding in your studies or work, you don’t need to be the best coder. You just need to get from A to B (or from raw data to a nice plot).
  3. Practice is key. When I first got my license, I didn’t have access to a car and I didn’t drive for a few years. Clearly, that was not very good for my driving skills or confidence. Later, when I did have a car available, I would regularly take it to drive to a friend who lived just 5 miles away to have a coffee. These short trips helped me feel comfortable in the car. If you’ve learned some coding skills, try to find a way to keep using it, even if it is just for short 5-mile drives.
  4. It opens up jobs and opportunities. For many jobs, you need to be able to drive a car. Not just jobs such as taxi driver, but also jobs that are utterly unrelated to driving. For me, I got the job at SFSU when I lived in Menlo Park. Public transport from Menlo Park to SFSU is so bad, that I really couldn’t do the job if I wasn’t able to drive to the SFSU campus. With coding it can be the same thing. I am a biologist and I am interested in evolution of viruses and bacteria – yet I couldn’t do that research without coding skills.

Happy coding!