Dr Chris Davies’ PINC/GOLD/gSTAR Program 2022 Graduation Speech

Being A Better Scientist

Image of Dr Chris Davies giving his speech. On the right you see the slide with his name and title: Christopher Davies, PhD. Antibody Engineering Department. Genentech Early Research and Development (gRED). Genentech, Inc.

Chris Davies: “Today, we are here to recognize and celebrate these students who began, endured, and successfully completed the PINC, GOLD, or gSTAR certificate programs. I want to begin by saying congratulations and well done. Bringing together the fields of computing and data science with biology and chemistry is a pathway towards the future, that is now. The growth of technology to analyze large data sets, create applications, and the ability to code has never been more important in a generation than it is now. To the dreamers and organizers of these programs, I am happy to say your dream has come true amongst these students today.

For those of you that do not…

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Matt Suntay’s jump into the PINC computing program

Being A Better Scientist

Matt Suntay is one of the students in the PINC program and also a research student in my lab in the E. coli / drug resistance / machine learning team. A few days ago he gave a speech at our PINC/GOLD/gSTAR graduation event. I thought it was a great speech and Matt was kind enough to let me share it here both as a video and the text for those of you who prefer reading.

“To those of you who may know me, you all know I’m pretty adventurous. For those of you who may not know me, first off, my name is Matthew Suntay, and I have jumped off planes, cliffs, and bridges – and each time was just as exhilarating as the last. But, let me tell you about my most favorite jump: the leap of faith I took for the PINC program.

I call it a leap…

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Meet Hailey Garma, SFSU and PINC Alum and Scientific Researcher in Genentech’s Development Sciences Rotation Program (DSRP)

Being A Better Scientist

My biggest advice when pursuing an internship, career, degree, etc. is to be your authentic self, know you are good enough, and do what is best for your growth.

How did you decide to get a degree in biology? What interested you in making this choice?

My interest in science stems from wantingto understand how thehuman body works in order to have a better knowledge whenunderstandingmedical conditions mylovedones suffer from. WhenI was a child, my father had a stroke — my family’s frustrations from not fully understanding how my father was affected by this incident and the doctors not having all of the answers is what initially piqued my interest in studying science,I wanted to be able to understand and answer those questions.

Why are you interested in a career in Biotech? What inspires you…

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Congratulations to the 2020 SFSU PINC graduates!

Yesterday on May 27th, 2020, we celebrated the 10 PINC students who finished their 5th CS class and who will all graduate with a minor in Computing Applications!

We are extremely proud of these students and what they accomplished! All students worked on a capstone project in the last two semesters.

The graduates

Johana Aleman, Andrea Guevara-Castro and Maria Flores worked on a project named “Hidden Figures” with Dr Rori Rohlfs and Dr Anagha Kulkarni and mentor Karuna Nayak.

Their short video is here: https://www.powtoon.com/c/dptVSQWWrog/2/m

Adrian Choppa, Kaila Marie Gemenes, Natassja Punak and Imani Warren worked on a project to create a virtual reality game for the Tourniquet Master Training (TMT) by Stanford Technology Enabled Clinical Improvement Center. They worked with Dr Anagha Kulkarni and Dr Ilmi Yoon and mentors Jose Castanon, Ben Tingle.

Their short video is here: https://www.linkedin.com/feed/update/urn:li:activity:6669710335370522624/

Hailey Garma, Austin Sanchez and Caroline Solis worked on a flow cytometry project with Dr Anagha Kulkarni, Dr Nicole Adelstein and Dr Shadi Toghi Eshghi (Genentech) and mentors: Erick Velez, Sally Mostafa.

Their short video is here: https://www.linkedin.com/posts/hailey-garma-483ab512b_computerscience-flowcytometry-science-activity-6669023311613317120-HVJs/

Graduation speakers

We were excited to listen to the following speakers:

Joy Branford from Genentech

Our dean Dr Carmen Domingo, CS chair Dr Arno Puder and Biology chair Dr Laura Burrus.

PINC alum and current PhD student at UTSW Alia Edington.

Coding with Stuart Castaneda, a PINC Mentor

Meet Stuart Castaneda! He is a PINC Mentor and graduate student at San Francisco State University. His current research delves into the HIV-1 subtype B’s different mutation classes and their fitness costs. Stuart utilizes coding to analyze this data! To read more about Stuart, his research and career outlook, as well as what he does as a PINC mentor, please check out his interview below.

  1. How did you get into coding?  

I was curious on how coding could be applied to various biological questions. More specifically I wanted to know how scientist design systems and models to analyze biological data. I learned about the PINC program through a colleague and thought the program would be a perfect fit to solving my questions about coding. I believe my first programming language I was introduced to was Python. After the first class I established a great foundation with the basics and was able to transfer the experience to learn new computer program languages.

  1. How did learning coding skills impact your career/career goals?

After learning how to code, I knew that I would always want a component of coding during my research career. My current research requires coding to analyze and estimate fitness costs of different mutation classes in HIV-1 subtype B. Coding makes this process of analyzing large datasets fast, and reproducible. A great skill I learned during PINC is to annotate my code. This allows others to understand what my code does step by step.

  1. What do you do as a PINC mentor?

As a PINC mentor I try to get to know my mentees and help them with any problems they find during the course. These problems can range from homework to understanding concepts covered in class. So far, I’ve only helped in the first class that all PINC scholars take, CSC 306. In this class scholars are introduced to Python, a computer language that I was first introduced to, and learn the basics of coding. I believe having a mentor in this first class is a great necessity, since this is their first step into the coding world.

  1. What do you like about being a mentor? 

My favorite part about being a mentor is helping my mentees understand computer science concepts. It allows me to think of analogies and visual aids that could explain these concepts that they are having trouble with.

For example, my favorite concept to explain to students is how for loops work. Imagine you’re driving on the road and you are directed into a racetrack. This racetrack will be our “for” loop. As you drive around the racetrack you notice a sign on the jumbotron saying “If you want to exit do 100 laps”. This is your conditional statement that must be met in order to exit the racetrack. The screen keeps track of the number of laps you’ve done and always compares it to 100. As you do your 100th lap the screen says “Exit” and one of the gates lead you back on to the road.

  1. Do you have any advice for students wanting to join the PINC program? 

Don’t be intimidated by learning a new computer language. Learning to code can be daunting at first, but if you have the time and determination, anyone can learn. 

  1. What do you think are the benefits of being a part of the PINC program, both as a mentor and a mentee?

There are several benefits that I received as a mentee in the PINC program. As a mentee I was guided by my mentor on how to approach concepts and problems. Our program coordinators hosted networking events, and professional panels. My favorite experience as a mentee was working as a team with my fellow colleagues. Just like programming professionals, we were tasked to work on a year-long project and had actual deadlines to finish our product. As a mentor I have the opportunity to pass down what I learned to my mentees. This experience as a mentor has given me translational skills to teach future colleagues.

  1. What are your next steps?

My next step is to finish my research project, and graduate with my master’s in science from SFSU. My current project deals with analyzing sequence data of HIV-1 subtype B. I plan to prove that CpG creating mutations are costly to HIV-1 subtype B. This class of mutation has been shown in previous studies to be costly in one region of HIV. My project hypothesizes that these mutations are costly throughout the genome. I plan to begin my PhD in Bioinformatics, at the University of Michigan later this year!

Dr Priya Moorjani visits the PINC program

PINC students talking to Dr Priya Moorjani (lower left, with grey jacket on her chair).

Dr Priya Moorjani is a population geneticist and assistant professor at UC Berkeley. You can read about her and her group on their website: https://moorjanilab.org/

Dr Moorjani has done very exciting work using ancient DNA to understand the history of human populations in Asia and Europe (https://science.sciencemag.org/content/365/6457/eaat7487.editor-summary).

Yesterday, she came to SFSU to give a talk in our seminar series and to meet with student from the PINC program. The PINC students had many questions about PhD programs, computer languages, how to deal with failure and how it is to be a woman of color in the academic world.

Thank you, Priya, for visiting us!

Dr Moorjani (upper left) with a group of PINC students. Selfie by Pleuni Pennings.

Register now for Intro to Programming CSC 306!

In the fall of 2019, the SFSU PINC program is welcoming a new cohort of PINC minor students.

The first class of the minor (CSC 306) is an intro to programming in Python and will be taught by Dr Pleuni Pennings on MW 3:30 – 4:45 in Thornton 329.
CSC 306 is a gentle introduction to the world of programming and students need absolutely no prior knowledge. The class is open to students from Biology / Biochem/ Chemistry. Students can simply sign up for the class, we no longer ask students to apply to become a PINC student. Pre-Biology students very welcome! 

If you want to do the entire minor, it consists of 5 classes usually taken over 4 semesters. Master students can sign up for the classes, but cannot get the minor.

If you have any questions, please email pennings @ sfsu . edu.

The promotion video above was made by Niquo Ceberio with the help of Jhony Zavaleta who both took CSC 306 in the fall of 2018. The two students who are interviewed in the video are Emily Samperio (who is now taking CSC 698) and Maria Flores (who is now in CSC 220).

PINC students are going places!

We try to keep track of where PINC students go and recently, many PINC students have been successful in getting into PhD programs or interesting jobs.

Last year, Cecelia Brown did an internship at IBM Research and started a PhD program at Stanford. Ezequiel Lopez started a job doing data analysis for the SF BUILD program on our campus. But graduation from PINC doesn’t necessarily happen at the same time as graduation from SFSU, so many of the PINC 2018 students are now graduating and going different places. 

Nicole Rodrigues (PINC 2018) got accepted in the Biochemistry, Molecular, Cellular and Developmental Biology program at UC Davis. She also received an honorable mention for her GRFP proposal!
Francisca Catalan (PINC 2018) got accepted into the Bioinformatics PhD program at UCSC.
Sita Chandrasekaran (PINC 2018) is going to be a PhD student in the UCSF-UCB joint Bioengineering program.
Ryan Winstead (PINC 2018) will be doing an internship at IBM Research this summer. 
Mayra Banuelos (PINC 2018) was selected for the Opportunities in Genomics Research Undergraduate Scholars Program at Washington University.
Emily Fryer (PINC 2018) started a job at the Carnegie Institute’s Department of Plant Biology on Stanford’s campus as a Bioinformatics Research Assistant.
Alia Edington (PINC 2019) is going to do a PhD at UT Southwestern. 
Hailey Garma (PINC 2020) is going to the SIREN REU program (Summer Intensive Research Experiences in Neuroscience) at the University of Michigan.
Maria Flores (PINC 2020) is going to the Jackson labs this summer for an REU program.
Caroline Solis (PINC 2020) is going to do an internship this summer at the Center for Bioinformatics and Computational Biology at the University of Maryland, College Park.

PINC students visit Pugh lab at Stanford

Dr Carla Pugh is a surgeon, researcher and educator. In her lab, she builds anatomical models with sensors that interface with computers to help medical professionals learn how to use touch better, in other words, to train their haptic skills. Touch is key for many medical examinations (e.g., finding a lump in a breast) but it is hard to train people to do such examinations correctly. To learn more about her work have a look at this Ted Talk: https://www.tedmed.com/talks/show?id=292997

On March 4th, 2019, Students from the PINC program at SFSU and the Howard West Program at Google were invited to visit her lab and learn about her work.

A special treat for the PINC students was that we got to talk to Cecilia Brown, a PINC alum who is now a PhD student at Stanford.

PINC students and Howard West students at Stanford, with Alycia Onowho and Dr Ilmi Yoon (lower left corner), Dr Carla Pugh (in the middle with the blue top) and Cecilia Brown (next to Dr Pugh, with the Stanford hoodie). Photo by Cassidi Goll (Stanford).
PINC and Howard West students listen to Dr Ilmi Yoon (SFSU), Dr Olumide Malomo (Howard West) and Dr Carla Pugh (Stanford). Photo by Cassidi Goll (Stanford).
Oned of the students tries out one of the training models. Photo by Cassidi Goll (Stanford).
Cassidi Goll shows two breast models with sensors that are used to train haptic skills (touch).
PINC students and Howard West students listen to Dr Carla Pugh in her lab. Photo by Cassidi Goll (Stanford).

NSF grant will support PINC in next 5 years!

The PINC program started in 2016 as a collaboration between the CS and Biology Departments at SFSU. Now, two years later, we are extremely happy to announce that were awarded 1.3 million dollars from the NSF to continue our efforts in the next 5 years!
The money will be used to run separate PINC sections for CS classes, to hire PINC mentors, to run the PINC summer program and to do research on how we can best support women and students from underrepresented groups in their CS journey.

The “splicing team” did computational research on alternative splicing during the 2018 summer program.

Abstract of the NSF proposal

This project aims to address two pressing needs in STEM education: 1) increasing the number of students graduating with expertise in data and computer science; and 2) improving diversity in STEM fields. The project team at San Francisco State University (SFSU) will achieve these goals by developing and implementing a Computing Application minor. This minor will use evidence-based approaches to attract, retain, and support students, with attention to students from groups that are underrepresented in computer/data science, including female students. By tailoring activities to students’ majors, the project expects to increase student engagement and help students experience how data and computer science are applied in their majors and future professions. Students in the minor will have opportunities to work with local industry and governmental agencies. In addition, this project will link to the NSF INCLUDES project at SFSU. As a result, the Computing Application minors will be able to work with high school students as computer science mentors and role models. These experiences can support development of critical skills, including leadership. The project aims to provide a sustainable and scalable model for introducing data and computer science to science majors that can be adopted by other institutions, and that can broaden participation in those fields.

The Computing Application minor will be a four-semester, five-course sequence designed for STEM students who have no prior computer/data science knowledge and who are taking a full course load in their major. The project will provide participating students with learning experiences related to their majors, train computer science faculty in evidence-based science teaching methods, and invite students to share their knowledge with the K-12 community. To reduce stereotype threat and imposter syndrome, the project will employ a cohort-based structure that uses peer, faculty, and industry mentors to create a nurturing and supportive community of learners. The project will identify pedagogies that promote students’ interest in computer/data science and their motivation to use it in their majors. These research results can inform other efforts to broaden the diversity of people who have computational expertise, and who decide to pursue graduate degrees and careers in computer/data science.