Breaking Language and Computational Barriers

Dr. Josué Rodríguez-Ramos is a Postdoctoral fellow at the Pacific Northwest National Laboratory. He is a Puerto Rican microbiome scientist and bioinformatician with expertise in microbiology, computational biology, viral ecology, microbial metabolism, and biochemistry. He is a specialist in multi-omic analyses and the integration of metagenomics, metatranscriptomics, and metaproteomics data. 

Josué was an NMDC Ambassador in 2023 and has remained engaged through the NMDC Champions Program since then. He continues to be an active, collaborative member of the NMDC community who advocates for FAIR data and inclusive practices in microbiome research. His work focuses on creating “a future of microbiology where nobody gets left behind” –Josué Rodríguez-Ramos. 

Josué presented some highlights from his time as an Ambassador at the NMDC Town Hall during the 2024 Department of Energy Genomic Science Program, Enabling Capabilities and Resources annual PI meeting. He described how he translated the Ambassador training slides into Spanish to make them more accessible for his audience. He then presented on how his workshop at the University of Puerto Rico and the NMDC EDGE product directly led to a publication about the sea cucumber gut microbiome. We followed up with Josué to get more details about his experiences as an Ambassador and with the NMDC EDGE product.

Dr. Josué Rodríguez-Ramos presenting at the NMDC Town Hall at the Department of Energy Genomic Science Program, Enabling Capabilities and Resources annual PI meeting.

Read more about Josué’s experiences as an Ambassador and bioinformatician below (answers have been lightly edited for clarity): 

Why did you decide to host a workshop at the University of Puerto Rico?

I did my undergraduate studies over at the University of Puerto Rico, Mayagüez and I knew that they were always eager to push their sciences to the next level. I was still in contact with my undergraduate mentor from over there and so I thought it would be a great space to collaborate in to connect some undergrads to some of the people in the field.

How did you approach altering the instructional content for this audience (e.g., language, undergraduate researcher experience level) and why was that important to you?

A lot of the science classes that were taught in Puerto Rico were taught in Spanish, but all of the books were always in English. I always thought this was strange because sometimes the words in Spanish just don’t add up. Especially in things like chemistry: chemical names and what not. So when I went in to give the workshop, I wanted to translate all of the materials into Spanish so I could ensure readability. It was also an interesting thing for me because most of my informatics knowledge I got from my PhD at Colorado State University in English. So trying to go back and learn the terms in Spanish was pretty cool.

How has NMDC EDGE helped to make bioinformatics accessible to your workshop participants?

I think that the NMDC EDGE online interface is a really useful tool for folks from the workshop. My undergraduate lab is a teaching lab, and so students are taught the knowledge they need to generate these metagenomes and how they are usually processed, but some of the software omics tools they use are compute-heavy. NMDC EDGE allows them to not have to run these analyses locally and instead do it online at no cost to them.

How has NMDC EDGE impacted your own research?

I used NMDC EDGE alongside my workshop participants to process some metagenomes that they had from a sea cucumber. That workshop results were actually published into a full-fledged scientific article [1], which was awesome to see. For some of the students this is their first publication in a scientific journal, so it was really cool to see.

Sea cucumber evisceration (right), the ejection of the organism’s internal organs, is thought to be a stress or defense response [1,2]. Photo credit: Rivera-Lopez et al., 2024 Data in Brief

I think that if we can broaden our reach of which institutions we do workshops at with the NMDC Ambassador’s Program we can start getting more folks that could leverage the NMDC EDGE web app to process their own data and publish their results. Compute can be expensive, so providing this service will be very useful for folks.

What did you enjoy most about being an NMDC Ambassador and what are you most excited about regarding your new role as an NMDC Champion?

I really enjoyed interfacing with some of the folks in the scientific community. I think that people have a lot of good ideas of how they want things done and what they can do themselves and so listening to that and working with them to execute their vision was awesome. I’m excited for more of that.

References

1. E. O. Rivera-Lopez, R. Nieves-Morales, G. Melendez-Martinez, J. A. Paez-Diaz, S. M. Rodriguez-Carrio, J. Rodriguez-Ramos, L. Morales-Valle, C. Rios-Velazquez, Sea cucumber (Holothuria glaberrima) intestinal microbiome dataset from Puerto Rico, generated by shotgun sequencing. Data in Brief 54, 110421 (2024).
2. A. Okada, M. Kondo, Regeneration of the digestive tract of an anterior-eviscerating sea cucumber, Eupentacta quinquesemita, and the involvement of mesenchymal–epithelial transition in digestive tube formation. Zoological Letters 5, 21 (2019).

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