By: Cindy Yeh, Graduate Student, (Dunham Lab, Genome Sciences), University of Washington
Only 26% of the computing professional workforce is made of women, less than 10% of whom are women of color (ncwit.org). This is in contrast to the gender distribution in the life sciences, which is much closer to 50%. As technology continues to play an increasingly important role in our lives, addressing this gender disparity by giving young women access and exposure to computational thinking early is imperative.
I was introduced to programming as a high schooler, but never really learned how to code until I started my PhD program at the University of Washington in the Genome Sciences Department. Programming felt more intuitive when I was trying to implement a biological concept, such as finding the longest matching pattern in a DNA sequence using a suffix array or extracting information from FASTA files. Learning computer science can be intimidating, but I figured if this method allowed me to better understand its logic, it could be a great way to introduce young women to coding and make technical fields more accessible. Indeed, many research studies have found that integrated approaches are much more effective than traditional, non-interdisciplinary curricula. Furthermore, developing integrated lessons require many hours of professional development for which many teachers may not have time (Lin et al., 2018; Struyf et al. 2019; Salami et al., 2015; Stohlmann et al., 2012; Thibaut et al., 2018).
In 2017, as first year graduate students, my colleague, Andria Ellis, and I received a small grant from the National Center for Women in Information Technologies (NCWIT) to run a one-week, half-day summer camp for high school girls called Genome Hackers. We wanted our program not to have our participants walk away as experts in computer science or genomics, but to introduce them to concepts that they otherwise would never have the opportunity to learn prior to college. The idea was that if they were challenged by these topics in the future, they would seem less abstract or intimidating. We also wanted to teach real-world applications of computer science and how it specifically is used in genomics. With a team of graduate student instructors, our participants learned how to perform PCR to isolate and amplify a particular gene and subsequently Sanger sequence the PCR product to retrieve raw sequences. Simultaneously, we taught them the basics in programming through Python. By the end of the camp, the participants had written transcription and translation scripts, where they can directly take their Sanger sequencing results and determine the amino acid sequences of their gene. Furthermore, they shared their sequencing results with other students and generated a phylogenetic tree to investigate the relatedness of the same gene from various species. They also used their final amino acid sequence to generate a predicted protein structure compared across species as well.
Figure 1: 2017 participants learning how to pipette
Genome Hackers culminates in a poster session where the students share with scientists in the department (and with their family and friends!) their many accomplishments over the course of the week. This really helps tie the week together, and participants walk away with something concrete that they can show off. Furthermore, our camp is affordable ($50/week with scholarship available); this is in contrast to many other biotechnology camps where fees can be a deciding factor for many applicants, usually costing, at the minimum, $300, per week (these can sometimes cost upwards of $500 per participant!).
Figure 2: Participants working hard on their transcription and translation scripts
After receiving overwhelmingly positive feedback from graduate students, faculty, teachers, and parents, we will be running Genome Hackers in 2019 for its third year in a row. We are also running iterations of this camp through two other campuses (SoundBio Labs and University of Chicago). Here we will determine what aspects of our current curriculum are easy to implement and what areas need improvement. Our final goal is to package our program into something any high school biology teacher or graduate student can pick up and implement on their own without my or Andria’s presence.
Figure 3: 2017 participants presenting their findings to those teachers, parents, and scientists at University of Washington
Figure 4: 2018 participants presenting their findings to those teachers, parents, and scientists at University of Washington
Several of our former participants have now also participated in Girls Who Code at Fred Hutch or gone on to pursue technical degrees. One former participant has even returned to Genome Hackers as a near-peer mentor and may lead her own session this year. I never would have guessed that this was something I would accomplish (or even want to accomplish) as a graduate student. While I did put a lot of energy towards outreach and service as an undergraduate, being able to take what I have learned in the lab as a graduate student and materialize it into teaching high school students has been one of the most rewarding activities I’ve ever pursued in and outside of my scientific career. Andria and I are also both very lucky that our PIs (Cole Trapnell and Maitreya Dunham, respectively) appreciate outreach activities and continue to encourage us to pursue them.
Figure 5: Group photo from 2018. Cindy and Andria and are the ends of the front row.
We are always searching for new ideas or collaborators who may be interested in running their own version of Genome Hackers. We have a website (genomehackers.org) and an e-mail (genomehackersuw@gmail.com) and are very interested in hearing your comments.
Figure 6: Students’ confidence and interest levels before and after Genome Hackers
Participant Testimonials:
“I have been taught coding before, but I feel like […this program] introduced a new coding language very well.”
“I liked how I got to see how programming aided genome scientists.”
“My favorite part was getting to learn a new coding language, and combining two of my passions.”
“I wasn’t very interested in coding, but after actually doing some coding I now really like it and I might look into doing coding for a career with biology.”
“I will remember creating my first science poster. It felt amazing learning how to reach a conclusion and finally getting to have something to show for it.”
“I was really proud of myself for figuring out how to code a DNA strand into RNA.”
References
Lin, Y.-T., Wang, M.-T., Wu, C.-C., 2018. Design and Implementation of Interdisciplinary STEM Instruction: Teaching Programming by Computational Physics. The Asia-Pacific Education Researcher 28, 77–91. doi:10.1007/s40299-018-0415-0
Salami, M.K.A., Makela, C.J., Miranda, M.A.D., 2015. Assessing changes in teachers’ attitudes toward interdisciplinary STEM teaching. International Journal of Technology and Design Education 27, 63–88. doi:10.1007/s10798-015-9341-0
Stohlmann, M., Moore, T., Roehrig, G., 2012. Considerations for Teaching Integrated STEM Education. Journal of Pre-College Engineering Education Research 2, 28–34. doi:10.5703/1288284314653
Struyf, A., Loof, H.D., Pauw, J.B.-D., Petegem, P.V., 2019. Students’ engagement in different STEM learning environments: integrated STEM education as promising practice? International Journal of Science Education 41, 1387–1407. doi:10.1080/09500693.2019.1607983
Thibaut, L., Knipprath, H., Dehaene, W., Depaepe, F., 2018. The influence of teachers’ attitudes and school context on instructional practices in integrated STEM education. Teaching and Teacher Education 71, 190–205. doi:10.1016/j.tate.2017.12.014
