I recently had the pleasure of working with Jeffrey Perkel, the technology editor at the scientific journal Nature, on a career column explaining “Why it’s worth making computational methods easy to use”. Jeff had reached out after watching one of my live-coding Youtube videos and asked if I would be willing to share my thoughts and experiences in creating these videos, the lessons I learned along the way, and generally why I spend time creating such content. I wrote down and shared some rather rambling think-piece as an initial attempt at writing the column and then iterated with Jeff through the many rounds of revisions to emphasize a set of more actionable, service-oriented take-aways. I learned a lot working with Jeff and about the process of publishing service-oriented columns in general.
Since the published column changed quite a bit through the editorial process, I thought it’d be fun to share the original piece as I had written it. Unedited. Perhaps someone will appreciate my unfiltered, meandering thoughts, however unorganized and verbose.
On The Digital Frontier: Exploring Avenues For Enhancing Access To Scientific Resources
What does a scientist look like? Well, that depends on who gets to become a scientist.
I got to become a scientist in part thanks to the people who contribute scientific resources on the Internet. As a young explorer of this digital frontier, I would sit for hours in front of the computer at the public library, using the Netscape web browser to access scientific resources people created for everything from bird speciation to weather formation. In this era before digital platforms like Facebook, Twitter, and so forth, I became motivated to learn to code so that I too could make my own contributions to this World Wide Web. I sought to formalize my computational training via programming coursework in school. However, as a hands-on learner, I struggled to stay engaged with the introductory course material, which often focused on reading textbooks and memorizing factoids. Again, the Internet became an avenue for me to access scientific resources people had created for learning programming. And within the community supported spaces of the public library and public school system, such access to scientific resources enabled me to embark on my own journey towards becoming a scientist.
I eventually pursued a PhD in bioinformatics and integrative genomics at Harvard University so that I could not only consume scientific resources but also contribute new scientific resources via research. Outside of research, I taught young girls after school about science through hands-on learning, engineering ears to amplify sounds and writing string search algorithms to identify genetic mutations. In one lesson, I asked my students, “What does a scientist look like?” One young girl casually noted how she couldn’t become a scientist because she’s “not a math person.” To encourage her and my other students to envision themselves as scientists, I created personalized picture storybooks depicting each of my students engaging in various scientific disciplines. I further built a website at CuSTEMized.org and wrote software to enable the generation of our personalized picture storybooks on-demand so that others can also have access to this resource, creating impact that has gained recognition from teachers and parents as well as organizations like TEDx and the Nature Research Awards. From my small classroom of 10 to now over 50,000 personalized picture storybooks created, the digital frontier is providing effective avenues for scaling and enhancing the speed and ease of access to these scientific resources to help shape who sees themselves as a scientist.
Now, as an assistant professor of biomedical engineering at Johns Hopkins University, I mentor a team of students to contribute new scientific resources in computational biology, specifically in the analysis of spatially resolved transcriptomics data to better understand how cells are organized within tissues. And as I have matured, so has the digital frontier. Numerous digital platforms are now available to enhance access to the scientific resources we’ve created. For example, we recently created a computational tool called STdeconvolve for reference-free deconvolution of such spatially resolved transcriptomics data, which we describe in the form of a scientific paper, made accessible through digital platforms such as bioRxiv. We further made the tool’s source code available as open-source software, made accessible through digital platforms such as GitHub and Bioconductor as well as our own lab website. In addition, we enhance access by sharing code tutorials for using the software on our lab blog as well as video tutorials on YouTube. We still enable access to our work through traditional platforms such as by publishing through peer-reviewed open-access journals such as Nature Communications. Likewise, we still give talks explaining the approach at scientific conferences and seminars. But now, we are also able to expand access by making recordings of these talks available on the Internet. Such expanded access on the digital frontier has further enabled interactivity, providing students with the space to ask questions and seek feedback on their own journeys towards becoming scientists.
As creators of scientific resources, we must work to ensure that what we create is accessible. Enhancing access plays a critical role in ensuring equity towards diversity and inclusion, as making scientific resources accessible means engaging with broader audiences with diverse learning needs, with visual learners watching videos and hands-on learners following tutorials, ultimately to the benefit of all who wish to learn and engage with science. The digital frontier now provides numerous, continuously evolving avenues for enhancing access. And as the digital frontier continues to evolve, so too will traditional platforms have to evolve away from being the gatekeepers of access to scientific resources towards being the curators of scientific resources that ensure discoverability of quality information. To encourage such work in making scientific resources accessible, we must consider how systemic incentive structures, policies, and metrics of productivity can be reevaluated and revised to take such work into consideration. We must further ensure that such work can be sustainably supported by the community for the benefit of the community. Overall, the digital frontier has broadened the available avenues we can take towards enhancing access to scientific resources in shaping the current and next generation of scientists.
So, what does a scientist look like? The answer will be up to all of us.