James's office

jxtx: More than a Galaxy

By Kate Weaver

James Taylor (1979-2020) was an iconic professor in the CMDB department known for his eclectic taste in music, noteworthy shoes, wheeled-transportation, chill demeanor, dedicated skit performances, solid food recommendations, and especially his ardent support of his students and colleagues.

James was a pioneer in integrating biology and computer science throughout his training and career. He attended the University of Vermont, earning his B.S. in Computer Science in 2000. After working in industry for several years, he began his Ph.D. studies in the Center for Comparative Genomics and Bioinformatics at the Pennsylvania State University under the mentorship of Webb Miller and Francesca Chiaromonte. By encoding multi-species alignments and incorporating computational clustering, search, and learning algorithms, he identified novel regulatory regions in the genome that were frequently validated by subsequent studies. At Penn State, James worked with Anton Nekrutenko and others to start the Galaxy project, an online platform for open and reproducible data analysis. After finishing his Ph.D. in three years, he continued on to New York University where, as a visiting member of the Courant Institute for Mathematical Sciences, he continued developing Galaxy further.

James established his lab at Emory University in the Departments of Biology and Mathematics & Computer Science in 2008. He continued as a lead of the Galaxy project and worked to understand the 3D organization of the genome and gene regulation. In 2013, he was promoted to Associate Professor with tenure. Moving to Johns Hopkins University in 2014, James was named the Ralph S. O’Connor Professor of Biology and Computer Science and was promoted to Professor in 2018. While at JHU, James was a PI for AnVIL, a large NIH initiative to provide genomic researchers with cloud-based resources for genomic data access, sharing and computing. In addition to Galaxy, AnVIL, and JHU collaborations, James provided his expertise to numerous committees, advisory boards, and consortiums throughout the field to advance scientific knowledge and reproducibility.

A cornerstone of the CMDB community, James was an integral member of the department’s recruitment, hiring, and thesis committees, involved in numerous collaborations, and a fantastic instructor who shared his love of computational biology and dedication to reproducible science with all new trainees. Upon joining the faculty in 2014, he created and led a summer bootcamp and weekly lab course within the graduate curriculum to teach students computational biology and open, reproducible data analysis. The course served as many of these students’ first introduction to coding, and James received an Excellence in Graduate Teaching award in 2019 to honor his work on it.

Aside from his formal responsibilities, James excitedly discussed science, experimental design (including the need for many replicates), and ways to improve teaching with many in the department. He welcomed high school and undergrad summer students into his lab with the purpose of teaching them coding and exciting them about science, and made an effort to advocate for under-represented minorities and women in STEM whenever possible. Finally, as a mentor, James supported a vibrant and unconventional community of Galaxy and research personnel in his lab, enabling each member to thrive by providing space to try things and confidence in his students’ abilities. He treated each member as a colleague and offered encouragement in the face of difficulties and celebration of even minor successes. James did not self-promote, but he continuously promoted and supported future scientists, his colleagues, and his students.

As a close, here is some quintessential advice and words of wisdom from James:

  • Simplicity in all things.
  • Go back to the data.
  • Inbreeding is great! . . . Wait. Please quote me in context.*
  • Good ideas don’t have owners—they belong to everyone.
  • Try it first and see.
  • You’re not ‘guessing’. That’s a nasty word. You’re inferring in a completely rigorous way.
  • Hope!

*With regards to this quote, at the time, James did ask to be quoted in context, so here it is. In the Spring 2019 Quantitative Biology and Biophysics course (which James organized and taught several lectures for), he asked for examples which would cause a population to have less than complete gene flow. A student answered with inbreeding, and in classic James excitement, his response created a lasting memory for the 2018 cohort.

In Memory of James Taylor: The birth of Galaxy

By Anton Nekrutenko and Michael C. Schatz

James Peter Taylor, the Ralph S. O’Connor Professor of Biology and Computer Science at Johns Hopkins University (JHU), passed away on April 2, 2020. He was 40 years old. James was an exceptional scientist, colleague, mentor, and community builder, who worked at the intersection of biology and computer science. His life's pursuit was to understand how genomic and epigenomic information is processed during normal development and dysregulated in disease. As co-leader of the Galaxy (http://galaxyproject.org) and AnVIL (http://anvilproject.org) projects, a major thrust of James' career aimed to support the work of others, especially to empower those with limited resources. His impact was broad, as innumerable scientists worldwide benefited from his leadership, mentoring, and scientific contributions.

James completed a B.S. in Computer Science (Magna Cum Laude) at the University of Vermont in 2000. After spending three years as a senior software engineer in Vermont, he joined the Ph.D. program in Computer Science at the Pennsylvania State University in the Center for Comparative Genomics and Bioinformatics under the supervision of Professors Webb Miller and Francesca Chiaromonte. His Ph.D. work focused on developing novel machine learning approaches for identifying functional elements in the genome, leveraging the wealth of new data from ENCODE (https://www.encodeproject.org/) and the alignments of newly assembled vertebrate genomes.

Creating a Galaxy

During this time at Penn State, James worked closely with me (Anton Nekrutenko) and others to start the Galaxy project, a comprehensive web platform for open and reproducible computational data analysis. The first software commit to the project repository was on June 1st, 2005 by James. Today, Galaxy needs no introduction to anyone working in genomics, but at the time was a major advance above the ad-hoc command line bioinformatics analysis that dominated the field. The initial version introduced support for accessing remote data resources and visualizing the results. The project grew to incorporate thousands of analysis tools into one unified graphical user interface, accessible to anyone via a web browser. The Galaxy project remains a landmark achievement and has forever changed the way scientists analyze and share data.

After completing his Ph.D. in 2006, James worked for two years as a visiting member of the Courant Institute for Mathematical Sciences at New York University. During these two years, Galaxy became one of his principal projects as James coded several of its iconic features, including the three-pane interface, the “noodly” workflow editor, and the dynamic genome browser Trackster. In 2008, James started his laboratory at Emory University in the Department of Biology and the Department of Mathematics & Computer Science. He was promoted to Associate Professor with tenure in 2013, shortly before his move to JHU where he was promoted to Professor in 2018.

It was at Emory University, and later JHU, where the Galaxy platform exploded in popularity, driven by the growth of high throughput sequencing data and large-scale cloud computing. This combination of technologies has proven to be transformative to the field, and the Galaxy project has reached a wide audience of scientists evidenced by thousands of citations. Today thousands of scientists around the world use Galaxy daily.

The Galaxy Project is not only a software platform but also a scientific community. James’ dedication to accessible, reproducible, and transparent research promoted a community of researchers that extended far beyond the original development team. Scientists, often working completely independently from the founders, have taken Galaxy into entire new research domains. The strength of the Galaxy community is also seen every year at the community-run conference that brings hundreds of participants together to share their latest contributions and applications.

James was an ardent and principled advocate for open science, especially open access to scientific data and open-source software. James said that software may come and go, including even Galaxy, but the metadata that Galaxy collects will ultimately be his most valuable contribution to science. This metadata enables anyone to observe all analysis steps and reproduce entire analyses, providing the bedrock for future discoveries. Without such transparency and rigor, he explained, the entire field will suffer.

Beyond the Galaxy

While James is widely known for his development of the Galaxy Project, he made numerous other contributions to science and education. James collaborated with many experimentalists to analyze Hi-C data and interrogate the 3D organization of the genome. At Emory, James worked to understand how DNA binding proteins shape nuclear architecture as cell fates are specified. At JHU, James collaborated to decipher the mechanisms of the mysterious “A” and “B” compartmentalization of the genome in relation to the nuclear lamina. He applied his knowledge of the genome to identify “buttons” that promote gene regulation between chromosomes. James’ curiosity and collegiality led to new scientific directions as he evaluated ribosome profiling data to identify A and P sites, analyzed long-read transcriptome data to characterize development in worms, and interpreted transcriptome data from human retinal organoids to understand how our eyes develop, among many other projects. No matter the question, approach, or organism posed to him, James was always up for a new scientific challenge.

James’ love of science was matched by his passion for teaching. At JHU, he completely transformed and revitalized the curriculum within the graduate biology program to require training in computational and quantitative research for all Ph.D. students. This was rooted in his recognition that all subfields of biology are increasingly data-rich and quantitative. For many of the students, James’ ‘boot camp’ was their first introduction to such techniques; as with a military boot camp, the students were left mentally and physically exhausted at the end of the day. Ultimately, however, they all appreciated how it made them stronger and more empowered scientists. James’ passion for teaching extended to the annual Computational Genomics course at Cold Spring Harbor Laboratory that he co-taught with David Hawkins and William Pearson.

Galaxy, and every aspect of James’ life, benefited tremendously from James’ leadership style. Rather than an authoritarian top-down approach, he led by example, contributing code and technical oversight with exceptional mastery and precision. While he generally had a laid back personality, he was always willing to fight for his students, friends, and colleagues. Whenever I (Schatz) felt stuck about a particular administrative or logistical issue, James fired back about how the university administration should support us even more. I also knew that whenever I was not in the room, he would be there to advocate for me on my behalf. He offered these gifts to everyone, which promoted deep friendships and community for all of us around him.

Thank you James

James was always kind, friendly, and generous, and we will miss him dearly. He is survived by his wife Meredith Greif, a sociology professor also at Johns Hopkins. We all will strive to carry on his vision in his absence.

If we could talk with him one last time, we would say: Thank you, James, on behalf of your community, for being a friend, a leader, a colleague, a mentor, a student, a scientist, a programmer, and an advocate. Thank you for embracing your bioinformatics community and sharing resources in the spirit of accessibility and scientific progress. Thank you for sharing your strengths in selfless ways, for dedicating your life’s work to further scientific research in genomics and beyond. Thank you for caring, participating, and leading the way. You leave behind many teams and communities, many people who worked on the things that you started, many who thought that they would have more time to work with you on projects and reach new scientific heights. Please know that we will go forward and continue what you started, keeping you close, building on your work, and expanding on the many foundations that you provided. We will try to be better friends, leaders, colleagues, mentors, students, scientists, and advocates for each other, because we know, through your work and your many examples, that this is what you wanted us to do.

Acknowledgements

We would like to thank Alexis Battle, Jeremy Goecks, Robert Johnston, Ben Langmead, Jeff Leek, Rajiv McCoy, Kelly Moffat, and the Galaxy team for their careful edits and suggestions. We would also like to thank the entire bioinformatics community for their outpouring of support.