Matt Suntay’s jump into the PINC computing program

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 of faith because when I first heard about the PINC program, and specifically CSC 306, I thought, “Ain’t no way this could be for me. I may be stupid because I can barely understand the English in o-chem and now I gotta understand the English in Python? Maaaan, English isn’t even my first language… But they said I don’t need any prior computer science knowledge, so why not? It’s Spring ‘21, new year, new me, right?”

And let me tell you, it definitely made me a new me. I went from printing “Hello World!” to finding genes in Salmonella to constructing machine-learning models to study Alzheimer’s Disease and antibiotic resistance in E. coli. These are some pretty big jumps–my favorite, right?–and they weren’t easy to make. However, I was never scared to make any one of those jumps because of the PINC program.

When I think PINC, I don’t only see lines of code across my screen or cameras turned off on Zoom. I see friends, colleagues, mentors, and teachers. I see a community.

I see a community willing to support me in my efforts to develop myself as a scientist. I see a community providing me the platform and opportunities to grow as a researcher. And most importantly, I see a community that shared hardships, tears, laughter, and success with me.

I can confidently say that the PINC program was, and still is, monumental to my journey through science. Thanks to the PINC program, many doors have been opened to me and one of those doors I’m always happy to walk through each time is the one in Hensill Hall, Room 406 – or the CoDE lab. It was here in this lab that I met some of the most amazing people who want to do nothing but help me reach new heights. I’m so grateful and lucky to have them. So thank you, Dr. Pennings, for believing in me and continuing to believe in me. Thank you to everyone in the CoDE lab for supporting me and laughing at my terrible jokes – and real talk, please keep doing so, I don’t know how to handle the embarrassment that comes after a bad joke.

If I haven’t said it enough already, thank you so much to the PINC program. If you were to ask the me from a year ago what his plans were for the future, he would tell you, “Slow down, dude, I don’t even know I’m trying to eat for breakfast tomorrow.” But now if you were to ask me what my plans for the future are, I’d still tell you I don’t know what I’m trying to eat for breakfast tomorrow because I’m too busy writing code to solve my most current research question, whatever it may be.

For many students, including myself, one of the biggest causes of an existential crisis is, “What am I gonna do after I graduate?” To be honest, I’m still thinking that same thought, but without the dread of an existential crisis. One of the coolest parts of the PINC program is the exposure to research and the biotechnology industry, and learning that research == me and not just != the stereotype of a scientist.

Dr. Yoon, thank you for taking the time and effort to push me and my teammates forward, because even though our projects were difficult, we learned a lot about machine-learning and ourselves, like who knew we had it in us this whole time? You definitely did and you helped us see that. Professor Kulkarni, you also helped us realize that we should give ourselves more credit. 601 and 602 showed us we can be competitive and that we’re worth so much more than we make ourselves out to be. Also, I would like to give a quick shoutout to Chris Davies and Chun-Wan Yan for the wonderful seminars because those talks gave me hope and inspiration for the future. Knowing that there’s something out there for me makes going into the future a lot less scary and a lot more exciting because who knows what awesome opportunity is waiting for me?

And one last honorable mention I would like to make is to Professor Milo Johnson. He was my CSC 306 professor, and I don’t know if he is here today, but he was an amazing teacher in more ways than one. He helped me turn my ideas into possibilities and I have him to thank for helping kick start my journey through PINC. When I thought “I couldn’t do it, this isn’t for me,” he said “Don’t worry, you got this.”

So, once again, to wrap things up, thank you to everyone who’s helped me out this far and continues to help me out. Thank you to all my friends, mentors, and teachers that I’ve met along the way. And thank you to the PINC program, the best jump I’ve ever made.

Matthew Suntay – PINC graduate 2022

Scientist Spotlight: Alennie Roldan

Alennie (they/them) graduated from SFSU in 2021 and will be working as a Bioinformatics Programmer in the lab of Dr. Marina Sirota.

Pleuni: Hi Alennie, congratulations on graduating this semester! 

Alennie: Thank you! I really enjoyed my time at SFSU and I’m excited to move onto the next chapter. 

Pleuni: You told me that you are starting a job at UCSF soon. Would you mind telling me what you’ll be doing there and how you found that job? 

Alennie: I’ll be working as a Bioinformatics Programmer in the lab of Dr. Marina Sirota. The work is very in line with the interdisciplinary concepts I learned through the PINC program–– coding meets life science and health data. Prior to getting the position, I heard about an event, “NIH Diversity Supplement Virtual Matchmaking,” from the PINC and SEO mailing list. At the event, I met with many different UCSF PIs and learned about their research. I kept in contact with some of the PIs I met whose research I thought was very interesting. From there I scheduled different meetings and interviews with each PI to see if we’d be a good match. I ended up moving forward with the Sirota lab because I wanted to be involved in their research and felt that I could learn a lot from the experience. 

Pleuni: When did you start to learn coding? 

Alennie: Honestly, I feel like my first stint with coding began with Tumblr. In middle and high school I picked up some HTML to personalize my Tumblr page. It was exciting to input strange strings of numbers and letters and churn out wacky graphics. When I stopped using Tumblr I didn’t seriously pick up coding until summer 2019 for the BDSP, where I learned that there were so many different ways programming could be used. 

Pleuni: Did you always want to learn coding? 

Alennie: When I was younger, I’d watch the crime show “Criminal Minds’” with my mother. One of my favorite characters was Penelope Garcia, the show’s FBI Technical Analyst. She fills the tech-savvy role of the group and I always enjoyed seeing how she’d help solve the case by unlocking “digital secrets” or finding classified information. Based on portrayals like that, I always considered coding as an exclusive skill limited to cyber security and creating complex software. So I was always interested in coding, but the idea of learning how seemed too daunting. 

Pleuni: You did the entire PINC program – which part did you like most? Which part was frustrating? 

Alennie: I enjoyed the creative freedom of the PINC program. Many of the classes I took had final projects that encouraged us to come up with our own ideas. It was satisfying and challenging to take all that I’ve learned so far and use that knowledge to come up with my own projects. One of my favorite projects was for CSC 307: Machine Learning for Life Science Data Scientists. The goal of my group’s project was to address the lack of diversity in dermatology datasets by applying a machine-learning model that could identify various skin disorders; our dataset consisted of skin image samples from People of Color. The assignment was especially rewarding because it allowed me to combine my passion for health equity, social justice, and programming into a single project. 

The most frustrating part of the program was primarily due to the pandemic. It was difficult to communicate with my professors and classmates through a remote format. The experience sometimes felt isolating because I had been so used to seeing my mentors in-person or meeting up with classmates to work on an assignment/project. Thankfully, I had met many of the same classmates in person before switching to virtual learning so I felt like I had some familiar faces to interact with. 

Pleuni: Sometimes it looks like coding is something for only some kinds of people. There are a lot of stereotypes associated with coding. How do you feel about that? 

Alennie: This is a very good question, as there are many layers to the coder/programmer stereotype. If you were to ask people to draw a picture of a coder, the most common image you’d likely see is a lonely man furiously typing in a darkened room, hunched over in his chair and focused on screens covered with indecipherable numbers and symbols. Simply put, we often imagine a typical coder as a cisgender white man who typically exhibits loner or awkward behaviors. It’s a very narrow and negative stereotype which ultimately promotes negative connotations regarding neurodivergent individuals and excludes Women and People of Color from the narrative. 

The stereotype does little to encourage or welcome most people. But in reality, the coding community at large desperately needs a diverse range of people who can contribute their unique perspectives. Stereotypes can be discouraging and unwelcoming, so it’s important for institutions to emphasize inclusivity to show how students can be fantastic coders and still be true to their unique identities. 

…it’s important for institutions to emphasize inclusivity to show how students can be fantastic coders and still be true to their unique identities.

Pleuni: I know you are applying to medical school. Do you think it is useful for a doctor to know about computer science? 

For example, by having some knowledge in computer science a doctor could aid in the design of an app that patients can use to let them know if they’re experiencing side effects to their medication, create a website that shows local doctors who are LGBTQ+ friendly, or even better navigate electronic health records. The possibilities are endless! 

Alennie: I believe that computer science can be very useful to a physician because it can improve how they can take care of people. Since they are face-to-face with patients everyday, healthcare professionals are in a position where they can recognize and understand what unique problems need to be addressed in their communities. 

Pleuni: Do you have any tips for students who are just starting out? 

Alennie: Embrace your creativity! We often think of coding as a sterile and strict subject, but as you create new programs, websites, apps, etc you realize how much creative freedom you actually have. Learning how to code can be very daunting so when you personalize programs to fit your style or reflect things that you like, it makes the journey seem less scary and more fun. When I started coding, I had the most bare-bones of tools at my disposal, but I could still find ways to inject things to make my code feel like it belonged to me. The very first game I programmed, a basic recreation of Pong, I signed with my favorite color, pastel pink.

Alennie recreated the classic game of Pong with a little extra flair for one of their coding projects.

Pleuni: Thank you, Alennie! Please stay in touch!

Scientist Spotlight: Berenice Chavez Rojas

Berenice Chavez Rojas graduated from SFSU in 2021 with a major in biology and a minor in computing applications. She is moving to Boston to work in a lab at Harvard’s Medical School.

Pleuni: Hi Berenice, congratulations on graduating this semester! 
I know that you are starting a job at Harvard soon. Would you mind telling me what you’ll be doing there and how you found that job? Did your coding skills help you land this job?

Berenice: I’ll be working as a research assistant in a wet lab. The model organism is C. elegans and the project will focus on apical-basal polarity in neurons and glia. I found this job on Twitter! Having a science Twitter is a great way to find research and job opportunities as well as learn new science from other scientists. While I won’t be using my computational skills as part of this job, the research experience I have been able to obtain with my coding skills did help me. 

“coding always seemed intimidating and unattainable”

Pleuni: When did you start to learn coding? 

Berenice: I started coding after I was accepted to the Big Data Summer Program two years ago [Note from Pleuni: this is now the PINC Summer Program]. This was also my first exposure to research and I’m grateful I was given this opportunity. This opportunity really changed my experience here at SFSU and it gave me many new opportunities that I don’t think I would have gotten had I not started coding. Following the Big Data Summer Program I started working in Dr. Rori Rohlfs’ computational biology lab. I also received a fellowship [https://seo.sfsu.edu/] which allowed me to stop working my retail job, this gave me more time to focus on school and research. 

Pleuni: Did you always want to learn coding?

Berenice: Not at all, coding always seemed intimidating and unattainable. After my first exposure to coding, I still thought it was intimidating and I was slightly hesitant in taking CS classes. Once I started taking classes and the more I practiced everything began to make more sense. I also realized that Google and StackOverflow were great resources that I could access at any time. To this day, I still struggle and sometimes feel like I can’t make any progress on my code, but I remind myself that I’ve struggled many times before and I was able to persevere all those times. It just takes time!

The forensic genetics team at the Big Data Science Program in the summer of 2019. Berenice Chavez Rojas is in the middle.

“At the end of this project, I was able to see how much I had learned and accomplished”

Pleuni: You did the entire PINC program – which part did you like most? Which part was frustrating?

Berenice: My favorite part of the PINC program was working on a capstone project of our choice. At the end of this project, I was able to see how much I had learned and accomplished as part of the PINC program and it was a great, rewarding feeling. As with any project, our team goals changed as we made progress and as we faced new obstacles in our code. Despite taking many redirections, we made great progress and learned so much about coding, working in teams, time management, and writing scientific proposals/reports.

Link to a short video Berenice made about her capstone project: https://www.powtoon.com/c/eKaZB3kkxE5/0/m

Pleuni: Sometimes it looks like coding is something for only some kinds of people. There are a lot of stereotypes associated with coding. How do you feel about that? 

Berenice: I think computer science is seen as a male-dominated field and this makes it a lot more intimidating and may even push people away. The PINC program does a great job of creating a welcoming and accepting environment for everyone. As a minority myself, this type of environment made me feel safe and I felt like I actually belonged to a community. Programs like PINC that strive to get more students into coding are a great way to encourage students that might be nervous about taking CS classes due to stereotypes associated with such classes. 

“talking to classmates […] was really helpful”

Pleuni: Do you have any tips for students who are just starting out?

Berenice: You can do it! It is challenging to learn how to code and at times you will want to give up but you can absolutely do it. The PINC instructors and your classmates are always willing to help you. I found that talking to classmates and making a Slack channel where we could all communicate was really helpful. We would post any questions we had and anyone could help out and often times more than a few people had the same question. Since this past year was online, we would meet over Zoom if we were having trouble with homework and go over code together. Online resources such as W3Schools, YouTube tutorials and GeeksforGeeks helped me so much. Lastly, don’t bring yourself down when you’re struggling. You’ve come so far; you can and will accomplish many great things!

Pleuni: What’s your dog’s name and will it come with you to Boston?

Berenice: His name is Bowie and he’ll be staying with my family here in California. 

Pleuni: Final question. Python or R?

Berenice: I like Python, mostly because it’s the one I use the most. 

Pleuni: Thank you, Berenice! Please stay in touch!

Meet Francisca Catalan, SFSU PINC alum and research associate at UCSF (spotlight)

Francisca Catalan, SFSU PINC alum and research associate at UCSF

1. How did you get into coding? 

I took a regular CS class my second year at SF state. I thought it would be a good skill to have as an aspiring researcher and saw that it fulfilled one of my major requirements. It was a PowerPoint-heavy 8 am class three times a week. I didn’t talk to anyone else in the class and by the end of the semester I found it very difficult to show up. I passed the class but was really devastated about my experience. I thought I could never learn to program, though I never gave up completely. A couple semesters went by and I saw a friendly flier announcing PINC, SFSU’s program that promotes inclusivity in computing for biologist and other non-computer science majors. I eagerly signed up and started the “Intro to Python” class soon after. Then, with some more programming under my belt, I joined Dr. Rohlfs’ lab and began doing research in the dry lab for the remainder of my undergraduate career.

2. What kind of work do you do now? 

I currently work at UCSF as a dry lab research associate. Our lab focuses on an aggressive form of brain cancer, glioblastoma. We try to find gene targets for new drug treatments and research the cell type of these cancerous cells in order to fight drug resistance. My main duties now include creating pipelines for our single cell, RNA-Seq, and Whole Genome Sequencing data. You can read about our lab’s latest study in our new publication on cancer discovery! DOI: 10.1158/2159-8290.

https://cancerdiscovery.aacrjournals.org/content/candisc/early/2019/09/25/2159-8290.CD-19-0329.full.pdf

3. How did learning coding skills impact your career?

Coding has opened so many pathways for me. I was able to find a great job at UCSF soon after graduating with my Bachelor’s of Science in cell and molecular biology and minor in Computing Applications. It has also given be a giant boost of confidence! As a woman of color in STEM, I often felt underrepresented and out of place, but those feelings now quickly subside when I can help my colleagues answer coding questions! It’s motivating to feel like a necessary component of your community when often time you feel pushed out. It’s also impacted my career choices! I know now I want to be a professor in the future, I want to provide access to programming to others in hopes it will open pathways like it did for me!

4. Do you have any advice for students who are just starting? 

Yes! Don’t give up! It can be really difficult to learn coding, but know that it’s not you, talking to a computer can just be hard sometimes! Continue practicing and ask questions, google your heart out. Take breaks when necessary, remember to breathe, and keep in mind all the amazing science you will be able to do once you have these skills under your belt!

Being a better programmer: learning Python with Udacity.

When I started my “Being a better scientist” project, after reading Gretchen Rubin’s Happiness project, I decided to start with a one month focus on “Being a better programmer”. I made three resolutions.

1. Learn python by finishing Udacity‘s python course.
2. Look it up, write it down.
3. Annotate, annotate, annotate.

Like many biologists, I am a self-taught programmer. I use C++ and R, but for a long time I have wanted to learn a new language. One that is easier than C++ and faster & more suited to my needs than R. I love using R, so I think the new language will not replace R, but I think it could be useful for some of my projects. Plus, I think that by doing a programming course, I will learn stuff that could be useful for working in any language.

A few months ago I already started a python class at the online university Udacity. Even though I enjoyed the course a lot, I got stuck after 3 units (out of 7). This month, I will finish this course. Today, I just finished unit 4. In the next three weeks I will do units 5, 6 and 7.

What I like about the Udacity CS101 course:
1. The course is entirely web based and is VERY interactive. There are tons of little quizzes and programming exercises.
2. In the programming exercises, you can check the answers by executing the code and running some tests, and then have it checked by Udacity. If my code is almost correct, the response may be something like: “Try again, your code didn’t pass the following test …” – which is very useful and motivates me to, indeed, try again.
3. The lecture parts are short (2-7 minutes) which is good. The lectures are also interesting and teach some computer science theory.
4. It is free. I know I should be willing to pay for a useful course, but honestly, I don’t think I would have started it if it wasn’t for free.

What I don’t like about the Udacity CS101 course:
1. Before I started, I had no idea how long it would take to do the course. It is split in 7 units, but I didn’t know if a unit corresponds to an hour of work, a week of work or a semester of work. Turns out it is about 10 hours for me (rough guess).
2. The course lets you build a web crawler and by doing that, you learn all the python you need for the task. Although I think it is good that they focus on a specific task, I am not interested in web crawlers, and I would prefer to build something related to biology. How about some alignment software?
3. The time it takes to execute code (on the Udacity servers) is somewhat long which is slightly annoying.
4. Very few of the Udacity teachers are women. Maybe that’s why the fun examples are about cars and superheroes.