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:

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:

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:

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:

Dr Moorjani has done very exciting work using ancient DNA to understand the history of human populations in Asia and Europe (

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:

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.

Students learn data science skills in the 2018 Big Data Summer Program

AllBDSPStudentsEight teams of mostly undergrad students from Biology, Biochemistry, Economics and other disciplines spent 9 weeks during the summer of 2018 learning “Big Data” skills.  Each team was led by a senior undergrad or graduate student, with support from a professor. The program was run by Drs Rori Rohlfs (biology), Nicole Adelstein (chemistry), Sepideh Modrek (economics) and Pleuni Pennings (biology).

During the 9 weeks of the program, students worked in small groups for 10 hours a week on campus. In the first weeks of the program, each team worked through an online class, and then they applied their new skills to a research project. For example, one team learned data science skills in R and then analyzed data on the experience of students in our local REU program. Another team learned machine learning skills and then worked on a project to determine the subtype of an HIV sequence using machine learning algorithms.

Many of the students in the program were recruited to the different labs on campus to continue doing computational research. Several students joined the PINC program to take their first CS class.

Two peer-reviewed articles about the PINC program

The professors involved in the PINC program have collaborated to write two papers on the PINC program. Here are the abstracts and links to the pdfs.

Promoting Inclusivity in Computing (PINC) via Computing Application Minor

Ilmi Yoon, Pleuni Pennings, Anagha Kulkarni, Kaz Okada, Carmen Domingo

Abstract— We aimed to build a new educational pathway that would provide basic training in computer science for women and students from underrepresented (UR) groups who otherwise may not take computer science classes in college. Specifically, this on-going project focused on creating a 2-year Computer Science (CS) program consisting of exciting new courses aimed at biology majors. Biology traditionally attracts large numbers of women, a significant number of students from UR groups, and has compelling needs for CS technology. The interdisciplinary program is training the next generation of innovators in the biological sciences who will be prepared to cross disciplinary boundaries. The program consists of the following: (1) computer science courses with content related to biology, (2) cohorts of students that progress through the program together, and (3) a small group peer mentoring environment, and (4) facilitated interdisciplinary research projects. Graduates from this program, referred to as “PINC” – Promoting INclusivity in Computing – will receive a “Minor in Computing Applications” in addition to their primary science degree in Biology. The program is now in its second year and thus far 60 students have participated. Among them, 73% are women and 51% are underrepresented minorities (URM). The majority of students in the PINC program stated that they would not have taken CS courses without the structured support of the PINC program. Here we present the data collected during this two year period as well as details about the Computing Application minor and programmatic components that are having a positive impact on student outcomes.

Promoting Diversity in Computing

Anagha Kulkarni, Ilmi Yoon, Pleuni Pennings, Kaz Okada, Carmen Domingo

Abstract: In this paper we present a pilot program at San Francisco State University, Promoting INclusivity in Computing (PINC), that is designed to achieve two goals simultaneously: (i) improving diversity in computing, and (ii) increasing computing literacy in data-intensive fields. To achieve these goals, the PINC program enrolls undergraduate students from non Computer Science (non-CS) fields, such as, Biology, that have become increasingly data-driven, and that traditionally attract diverse student population. PINC incorporates several well-established pedagogical practices, such as, cohort-based program structure, near-peer mentoring, and project- driven learning, to attract, retain, and successfully graduate a highly diverse and interdisciplinary student body. On successful completion of the program, students are awarded a minor in Computing Applications. Since its inception 18 months ago, 60 students have participated in this program. Of these 73% are women, and 51% are underrepresented minorities (URM). 74% of the participating students had nominal or no exposure to computer programming before PINC. Findings from student surveys show that majority of the PINC students now feel less intimidated about computer programming, and vividly see its utility and necessity. For several students, participation in the PINC program has already opened up career pathways (industry and academic summer internships) that were not available to them before.

Screenshot 2018-06-10 10.24.41
Figure 2 from Kulkarni et al, 2018 shows that the PINC program (the two bars on the right) attracts and retains a higher fraction of women than the CS major (on the left) . Original caption: Gender distribution of students at the start and end of the CS bachelors program, and PINC program. For CS bachelors, start: CSc 210, and end: CSc 699. For PINC pro- gram, start: CSc 306, and CSc 698.

PINC Professors Picture 2
Dr Anagha Kulkarni, Dr Ilmi Yoon, Dr Pleuni Pennings, Dr Kaz Okada.

Dr Carmen Domingo, PINC Co-PI and Interim Dean of the College of Science and Engineering at SFSU.