Professor James Peter Taylor's Death - Open Source Technology - Good Ideas Don't Have Owners—They Belong To Everyone

Ed.'s note: Another unexpected death related to open source technology in this case, Professor James Peter Taylor at Johns Hopkins University. Johns Hopkins University is at the center of everything that is happening around the coronavirus in the US running their "death map" of alleged coronavirus fatalities. James Taylor through his Galaxy Project was building an open source network for bioinformatics for labs to use around the world. Taylor's specialization was studying molecular biology, genetics and genomes. In the fields of molecular biology and genetics, a genome is the genetic material of an organism. It consists of DNA (or RNA in RNA viruses). Coronavirus is coming under intense investigation based on studies of its genome. With Taylor's work on open source bioinformatics, it would have made it easier to track the coronavirus genome because of its RNA map.

Continuous and Discontinuous RNA Synthesis in Coronaviruses

We've posted on the significance of "knowledge is power" and no where can this idea be more significant related to open source systems and transparency. There are private corporations that covet knowledge and will go to great extremes to either steal it or prevent others from accessing it. We are not going to speculate on the death of James Taylor without knowing a lot of detail, but this is very similar to the unexpected and shocking death of Philip Donald Estridge. Estridge was killed when the Lockheed Martin L1011 Delta Air Lines Flight 191 at Dallas/Fort Worth International Airport he was a passenger on crashed on August 2, 1985. Philip Estridge was considered the "father of the IBM PC" and he too wanted open source architecture but for hardware and software for the PC that he was instrumental in selling leading IBM's blue team.

PHILIP ESTRIDGE DIES IN JET CRASH; GUIDED IBM PERSONAL COMPUTER
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Source: The Scientist

Computational Biologist James Taylor Dies

The Johns Hopkins University professor was a co-developer of the Galaxy platform, an open-source bioinformatics tool used in labs around the world.

By Lisa Winter | Apr 7, 2020

James Taylor, a computational biologist at Johns Hopkins University who developed a popular open-source bioinformatics platform, died April 2 at the age of 40.

Taylor is known for his work with the Galaxy Project, an open-source tool originally designed to help process data for genomicists.

Taylor earned a computer science degree in 2000 from the University of Vermont, and afterward received his PhD in the field from Penn State University in 2006, during which he helped develop the Galaxy Project. He worked as an associate professor at Emory University for five years, according to a memoriam from Johns Hopkins University. During this time, he continued his work with Galaxy, broadening it to a global scale and writing many papers about the platform that have been cited thousands of times. He left Emory and joined the staff at Johns Hopkins, where he became known for his collaborative spirit.

"He came in 2014, and it was transformational," Vince Hilser, the chair of the biology department, says in the statement. "He was this catalyst for change, with a huge positive impact."

Taylor was one of the founders and developers of the Galaxy Project in 2005. The platform allowed scientists to better understand genomic and epigenomic activity across individuals and species without every researcher needing to learn computer programming. Galaxy is now used to analyze bioinformatics data with increased accuracy and reproducibility in many fields, ranging from drug discovery to ecology, and has been used in nearly 9,000 scientific publications, according to its website.

Since the onset of the SARS-CoV-2 pandemic, Taylor used his Twitter account to speak out on the need for shared genomic data and criticize the lack of proper supplies for those working on the front lines.

Throughout his career he had been involved with the National Institutes of Health's National Human Genome Research Institute and ENCODE, a member of the National Center for Genome Analysis Scientific Advisory Board, and many others. He also co-chaired the Portal Working Group of the AnVIL Project, another cloud-based bioinformatics tool.

Please go to The Scientist to read the entire article.
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Source: Galaxy Community Hub

James Peter Taylor | 1979 - 2020

Good ideas don't have owners—they belong to everyone (@jxtx)

James Taylor started his professional path at the University of Vermont, where he received a BS in Computer Science in 2000. In 2003, after working as a software engineer in the private sector, he found that his real purpose in life was elsewhere. That year he began his graduate studies in Computer Science at Penn State and joined the nascent Center for Comparative Genomics and Bioinformatics. He used to refer to the Center as 'BX'—a contraction of BioinformatiX. The name stuck; 'BX' is still a part of many URLs (e.g. the original Galaxy URL at http://g2.bx.psu.edu) and is the origin for the name of the bx-python software package. The interdisciplinary faculty of the Center included Francesca Chiaromonte, Ross Hardison, Kateryna Makova, Webb Miller, and Anton Nekrutenko. This group became the core of James’ academic family, a family that has now lost its most brilliant and prolific child.

James Taylor at the Galaxy Community Conference. July 8, 2019. Freiburg, Germany. Photo by Bérénice Batut.

James concluded his PhD work under the supervision of Webb Miller and Francesca Chiaromointe in just three years—during which he blossomed as a methods developer and as a scientist. He published extensively on comparative genome analysis, gene regulation and molecular evolution—a total of eleven papers1–11 which were hugely instrumental in advancing the research of the Center. Ross Hardison, former head of the Center, remembers:

I may have been on James' thesis committee, but I learned far more from him than he did from me. In those days, the major data sources for functional genomics were alignments of genome sequences from different species—a specialty of Webb Miller. James was an early developer of machine learning methods to find signals in those multi-species alignments that were predictive of gene regulatory regions. He realized that those methods required substantial dimensional reduction—a specialty of Francesca Chiaromonte—to be effective. He had an amazing command of the statistical, computational, and biological frameworks in which he was working. With his high energy and creativity, he generated effective, publicly released predictions of regulatory elements by 2006. An enduring highlight of my career was my experimental lab testing many of those predictions, and finding that an impressive portion of them did affect levels of gene expression in transfected cells. James and I continued to work together on many projects, always with the goal of finding out what is important in our genomes. It is hard to think of continuing on without him.

Midway through his graduate studies James became entangled in a messy project that was given the name "GalaXY". This name was coined by Robert Harris, a fellow graduate student and LASTZ12 developer, by adding 'X' and 'Y' to the name of Galaxy's predecessor, GALA13. GALA was the brainchild of Ross Hardison and Webb Miller, who wanted to link genome alignments and annotations and provide tools for operating on those data. They convinced James and Anton Nekrutenko to take it on as a potentially interesting side project. It is hard to pinpoint the exact time when James and Anton started working on Galaxy together, but most likely it was in the middle of a long night of random pub traversals in Glasgow, Scotland, during the 2004 annual meeting of the International Society for Computational Biology (ISCB).

After graduating from Penn State, James gained post-doctoral experience as a visiting member of the Courant Institute of Mathematical Sciences at the New York University (2006 - 2008). During these two years, and ever since, Galaxy became one of his principal projects. Its now iconic features such as the three-pane interface, the "noodly" workflow editor, and the dynamic genome browser Trackster, were built by James while at NYU.

James' move to Emory University as an assistant professor in 2008 coincided with the rapid emergence of cloud computing, and it became obvious that the future of Galaxy was cloud-dependent. Together with his new team—Enis Afgan, Dannon Baker, Kanwei Li, and Jeremy Goecks—James quickly adapted Galaxy to cloud infrastructure, making it the first comprehensive data analysis resource in Life Sciences to cross this bridge 14,15.

From the very beginning, James' vision for the future of Galaxy was about creating and supporting a community of developers and users. This took shape with the Galaxy Developer Conference held at Cold Spring Harbor Laboratory in the summer of 2010, which has since become a yearly event that draws more than 200 attendees. He believed that to be successful and, most importantly, useful, a project must be open and cannot be owned by a single lab or a PI16. He was firmly dedicated to this idea. Today Galaxy is not associated with a particular group or an institution. It is a community effort supported by hundreds of developers worldwide. This, perhaps more than anything else, ensures that James' legacy will endure.

James once said that he would change his middle name to Reproducibility if it would help move the cause forward. He was an advocate for reproducible science long before it became fashionable, and he made it a central tenet of Galaxy. He could be downright evangelical about it. Martin Morgan of Bioconductor, a collaborator on the AnVIL Project, shared:

We in the Bioconductor community knew James as a Galaxy project leader, a strong advocate for open and reproducible science, and an enthusiastic and inspirational colleague. James recognized Bioconductor as a kindred spirit, and bridged the relationship between Galaxy and Bioconductor through his leadership of the NHGRI AnVIL project. James' leadership has had deep consequences for the way Bioconductor now navigates toward large-scale cloud-based computing.

James was particularly concerned with the inadequate state of quantitative education in life sciences. He developed many of the early training materials that became the foundation of the Galaxy Training Network17. He continued to make important contributions to biomedical education after he joined the Biology Department at Johns Hopkins University (JHU) in 2014. At JHU he participated in the development of massive open online courses (MOOCs), and he taught data analysis and scientific computing to biologists.

Please go to Galaxy Community Hub to read the entire article.
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