James Peter Taylor | 1979 - 2020
JTech: Junior Training and Educational Connections HotspotThe James Taylor Foundation: Big shoes to fill
These are the words that James Taylor (JT) said and lived by. This, he believed, was imperative to advance science, and in a way that facilitated diversity and inclusion. The mission of this foundation is to continue his legacy, through a multifaceted approach which will be unrolled across several stages.
In its early stages, JTech will provide support for graduate students to attend conferences in computational biology and data science, where they can present their work and form connections with other researchers in the field. Towards the goal of advancing mentorship, JTech will organize and host mentoring sessions between senior and junior faculty members at select high-profile meetings.
JTech will later expand its reach as a platform for academic mentorship. First, it will operate to spark mentoring relationships among the larger computational biology and data science community. As part of membership in JTech, faculty and students will have an opportunity to participate in periodic mentorship meetings (virtually). We expect an enthusiastic response to this opportunity, and will recruit additional team members to provide organizational structure if necessary.
In its later stages, JTech will sponsor in-person visits from students (high school or college age) to its hotspots, which currently include Johns Hopkins and Penn State. These visits are meant to attract new scholars to computational biology and data science, and in particular to form connections and opportunities for members of underrepresented minorities.
Please consider contributing to continue James Taylor's legacy.
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 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 bridge14,15.
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.
Vince Hilser, chair of the Johns Hopkins Biology department, describes James as a bedrock of the department:
He came in 2014, and it was transformational. He was this catalyst for change, with a huge positive impact. His presence in the department opened up many areas for research, as he was able to help other faculty members uncover new insights by revealing similarities between the proteins they were studying and those in other organisms.
People who worked for James thought the world of him, and many people in his group followed him from Emory to Johns Hopkins, and are still in his group today. When a new employee asked him and Anton whether it was "better to ask for permission or forgiveness" James's response was "Don't let us be a bottleneck." That was typical—always thinking of a third option where everyone else only saw two. Enis Afgan, in his memoriam, describes James:
He ran his lab not as a boss but as a friend and a colleague that inspired each individual to do their best work. He was an enabler. He was someone you tried your best not to disappoint.
While we celebrate James’ transformative vision of computational biology and bioinformatics, he was also just a lot of fun to be with. He had a finely tuned palate for good beer, he was an energetic and inquisitive conversationalist, and he had an uncanny ability to stay up late talking about science, politics, and all things related, but still be at his best the next morning. James met his future wife, Meredith Greif, when they were graduate students at Penn State. They were married in 2009. They have pursued their careers in a mutually supportive manner, him holding a faculty appointment at Emory University, and Meredith at Georgia State University. Both then moved to Johns Hopkins University. We extend our deepest sympathy to her on this shattering loss.
This memoriam can only hint at how remarkable James was as a human being. We could not capture who he was even if we were given volumes to fill. Comments have come in (and continue to come in from all over the world, and they touch on both his humanity and his intellect. Melissa Wilson, an associate professor at Arizona State and a fellow PhD student, captures this perfectly:
He is leaving a hole that cannot be filled. I met James when I started grad school at Penn State. I had no idea what to expect. We were both students, but he was clearly in a league of his own. James was one of the smartest people I've ever known, in a way that wasn't (as) intimidating. Talking with James was easy and enlightening. He advocated and put in the work for better science, in all aspects. James supported my science and my career in ways I don't think I can ever fully communicate. As a colleague, he believed in me. As a friend, he expected me to do good. He supported my growth, selflessly. Most of all, James was an advocate. He advocated for his students, for trainees, for open science, for open data, for making this world a better place.
James hated self-promotion. For him, the biggest human flaw was baseless arrogance. He believed that everything should be based on merit, which for him meant top-notch science, technical perfection, and a healthy dose of idealism. After all, he was the brightest, most unapologetic, and kindest idealist that the Galaxy project, his students, and his many colleagues and friends will ever know. This post from Karen Reddy, a colleague at Johns Hopkins, sums it all up:
James was, simply put, an amazing person. He was certainly an amazing scientist, but so much more than that. He was what we all hope to be as scientists, mentors, colleagues, and friends. We will miss you James.
Enis Afgan, Dannon Baker, Francesca Chiaromonte, Dave Clements, Nate Coraor, Jeremy Goecks, Ross Hardison, Anton Nekrutenko and all of Galaxy Team and Galaxy Community.
April 5, 2020
- Gibbs, R. A. et al. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 428, 493–521 (2004).
- Kolbe, D. et al. Regulatory potential scores from genome-wide three-way alignments of human, mouse, and rat. Genome Res. 14, 700–707 (2004).
- Hillier, L. W. et al. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 423, (2014).
- Taylor, J. Clues to function in gene deserts. Trends Biotechnol. 23, 269–271 (2005).
- King, D. C. et al. Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences. Genome Res. 15, 1051–1060 (2005).
- Chimpanzee Sequencing and Analysis Consortium. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437, 69–87 (2005).
- Hillier, L. W. et al. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. Nature 434, 724–731 (2005).
- Giardine, B. et al. Galaxy: A platform for interactive large-scale genome analysis. Genome Res. 15, (2005).
- Wang, H. et al. Experimental validation of predicted mammalian erythroid cis-regulatory modules. Genome Res. 16, 1480–1492 (2006).
- Taylor, J., Tyekucheva, S., Zody, M., Chiaromonte, F. & Makova, K. D. Strong and weak male mutation bias at different sites in the primate genomes: insights from the human-chimpanzee comparison. Mol. Biol. Evol. 23, 565–573 (2006).
- Taylor, J. et al. ESPERR: learning strong and weak signals in genomic sequence alignments to identify functional elements. Genome Res. 16, 1596–1604 (2006).
- Harris, B. lastz. (Github).
- Giardine, B. et al. GALA, a database for genomic sequence alignments and annotations. Genome Res. 13, 732–741 (2003).
- Afgan, E. et al. Galaxy CloudMan: delivering cloud compute clusters. BMC Bioinformatics 11 Suppl 1, S4 (2010).
- Afgan, E. et al. Harnessing cloud computing with Galaxy Cloud. Nat. Biotechnol. 29, 972–974 (2011).
- Grüning, B. et al. Practical Computational Reproducibility in the Life Sciences. Cell Syst 6, 631–635 (2018).
- Batut, B. et al. Community-Driven Data Analysis Training for Biology. Cell Syst 6, 752–758.e1 (2018).
We just lost James Taylor (1979-2020). His legacy — open, reproducible science — will continue.
James Taylor, a leader of the Galaxy Project, and one of its original members, passed away on April 2, 2020.
The community response (see below) has been tremendous, which reflects the breadth and depth of his impact. If you have something you would like to add then please share your thoughts here, and we will add them below.
The cause of James' death is not yet known, and given how overwhelmed the medical profession is in Baltimore, we may never know. Given how quickly this overtook him it is very unlikely to have been COVID-19. We will add any new information here as we learn it.
Thank you for your support during this awful time,
The Galaxy Project
April 3, 2020
By Enis Afgan, Johns Hopkins
I met James on Friday, Feb 13, 2009. Perhaps that was a sign for what’s to come. It was a job interview for my postdoc. Preparing for the interview, I had searched for a picture of James to know who to look for but I had no success. He was quite concerned about privacy and the social web of the time had not undermined his efforts. When I finally walked into his office, I saw James for the first time: a person about my age wearing jeans, a button-up shirt with top two buttons undone, and a sport coat with elbow patches. It had a somewhat raggedy appearance but elegant at the same time. I guess you’d call it edgy today. Having had a very traditional educational upbringing where faculty was referred to as Dr. This or Professor That and generally wearing professional attire, I was a bit surprised with his appearance (as you may be able to tell given I remember it a decade later). We proceeded to chat about my work and some of the Galaxy efforts he was spearheading that continue to be worked on to this day. The point of this is that James left a long-term impression on me, and it didn’t take long. He had the special ability to be concise and impactful.
Continuing in the vein of a non-traditional mentor (at least by my past experiences), we would have most of our lab meetings over dinners at pubs or at the SweetWater brewery. One particular dinner stands out. We were discussing the impact of cancer research on actual patient care. One thing led to another and the conversation evolved into a discussion about death. James, always pushing the norms, proceeded to elaborate about a not completely unrealistic path of capturing one’s consciousness in a digital format and saving it forever. With time, he argued, it would be possible to reconstruct the consciousness back into physical form and ultimately live forever. Books have been written about such topics but the point remains that James was happy alive and inspired to live forever.
Instead, here we are. Roughly a decade later, I’m writing a eulogy to the man I admired and who has inspired me and hundreds of others to work hard and think on our own. James made a great scientific impact on the world. I am sure others will write about his scientific and technological accomplishments so instead I wanted to focus on the generous and likable human being that he was. He ran his lab not as a boss but as a friend and a colleague that inspired each individual to do their best work. He was an enabler. He was someone you tried your best not to disappoint. In addition, he taught me what is good beer so how can you not love a man like that. I’m going to miss working with you James.
By Jeremy Goecks, OHSU
I enjoyed our conversations the most. All across the world for more than a decade, James and I would find each other at the same conferences and meetings, and we’d head out in the afternoon or evening and have wide-ranging conversations about science, politics, software engineering, medicine, lifelong goals, academia, food, alcohol, and more. He was easy to talk with, no matter how long it had been since we last spoke. He made you feel heard, and he had an intelligence and earnestness, mixed with a slightly smartass sense of humor, that was unique. When I sat down with James, I always knew I’d learn something new or come to appreciate a topic in a different way. And I’d leave the conversation with the feeling that comes when you connect with such an amazing human being. As I remember James, the feelings I had after our conversations will be the ones that I hold onto.
James was a tremendous academic scientist, which is much more impressive than it sounds. Research, teaching, and service obligations are all required of professors. Most of us do some of these things well; James did them all well and enjoyed them to boot. As you’ll hear time and again when others talk about James, he inspired people in all his roles as an academic scientist. The Galaxy Project will likely be James’ greatest professional legacy, and it is a testament to his ability to inspire. The Galaxy community of users, developers, and trainers, which is now worldwide and numbers in the tens of thousands, reflect his vision for open science and education. Through the efforts of this community, James' vision will continue to be developed and have impact far into the future.
Years ago, I asked James how long we should keep working on the Galaxy Project. At the time, Galaxy was a big deal, but there were other interesting projects we had started as well. His response was brief: “we should keep going until we get bored or the money runs out.” I didn’t really get it at the time, but now I think he may have been sharing one of his key principles for how to live. James just didn’t do stuff he wasn’t interested in, but he worked tirelessly to develop the resources he needed to live the life and do the work that he wanted. He seemed genuinely happy with his life and work, a man who was happy with what he’d accomplished but nonetheless had big plans for the future. My dear friend James, we did not get bored and the money did not run out. It’s difficult to accept that we won’t be able to keep going together, but I’m so grateful for our friendship and the time we had.
By Michael Sauria, Johns Hopkins
James Taylor was such a vital and energetic force, I am still at a complete loss for words for this unthinkable tragedy. James and I have known each other for more than a decade, as mentor, boss, colleague, and friend. In the beginning, we decided to take a chance on each other, me as his first student, he as my advisor. I have never looked back. James was an inspiring person, showing you the breadcrumbs leading down an interesting path, and then watching you follow them with encouragement and confidence to a place neither of you had been before. I think one of his most amazing traits was to maintain his sense of wonder and excitement well past when most of us begin to lose it. The outpouring of love and support in the wake of this show just how many people he has inspired and helped with his boundless enthusiasm and vision.
But more than losing an amazing boss and scientific juggernaut, I am going to miss the James that many fewer people got to see or know. There were special moments, on a long ride to a conference, chatting over a beer, or sometimes in the most unexpected situations when "Science James" would slip away and playful geek would come out on full display, whether discussing comic books, the singularity, Doctor Who, music, books, and anything else in his extensive catalog of personal interests. He always felt like the coolest and nicest person that you wanted nothing more than to please and be liked by.
The graduate students at his first professorship nicknamed him 'the rock star'. I don't know if they ever realized how accurate and far from the truth at the same time this was. If anyone had an amazing sense of style and presence, from the shoes up, it was James. But he was also a humble and soft-spoke person, never looking to steal the spotlight or dominate. Instead, he was an advocate, both for those he personally worked with, and for all of the scientific community, pushing for honesty, fairness, transparency, responsibility, accessibility, and reproducibility.
While his loss is a wound that may never heal, I am immeasurably enriched for having known, learned from, worked with, and shared so much of my life with James. Thank you for everything.
In Memoriam, Professor James Taylor, Johns Hopkins Department of BiologyProfessor Taylor was a trailblazer in computational biology and genomics research. He had an enormous impact as a scientist, teacher, and colleague, and his loss is devastating to many – both here in our Hopkins community and around the globe.
Vince Hilser, chair of the biology department, describes Professor Taylor as a bedrock of the department. “He came in 2014, and it was transformational. He was this catalyst for change, with a huge positive impact.” His presence in the department opened up many areas for research, as he was able to help other faculty members uncover new insights by revealing similarities between the proteins they were studying and those in other organisms.
James' work and personality touched many of us, and we share a deep sense of loss from his passing. On behalf of the Bioconductor community, we offer our deepest condolences to James’ family, friends, trainees, and colleagues.
OBF joins many others in mourning the loss of a pillar of the bioinformatics community.
When I’m writing this I’m cautious of not exaggerating. I gave up on that. James made an enormous impact in the bioinformatics community. With Galaxy, he co-founded a platform that enabled many thousands of researchers to do reproducible analysis. Much of what I’m doing now, builds on his legacy. But even more importantly, his vision on Open Science touched many more people, most of them will never be aware of it. It fits his generosity.
James, you wanted Galaxy to belong to its Community, not just to the founders. This reflects your style of leadership, and the Community is in a good shape to face the future because of it. But having to write this now wasn’t part of the deal. I expected and looked forward to keep on working with you throughout my career.
We’ll find a way forward with the Galaxy Community. I’m not sure how yet, but I do know we’ll often refer back to you. And with time, the sorrow will dampen and we’ll think fondly back, glad to have known you.
And a small sample of what's been shared about James elsewhere online from his community:
James was a cornerstone of the department and of the scientific community. But most of all he was the exemplar of a colleague and just a wonderful human being
James Taylor was an amazing colleague, scientist, and friend. I love him very much and I will miss him very much.
James was a truly wonderful mentor, scientist, and human being. He was so brilliant, but so approachable. He was a giant in the field and I was so lucky to have the chance to work with him. He will be deeply missed.
I am in shock and saddened over the horrible news that James Taylor has passed away.
He was a cornerstone of the bioinformatics community, and with his leadership Galaxy grew to tremendous heights.
So heartbreaking, a true loss. My sincerest condolences to his family and all his friends. He will be sorely missed.
Massive contributions to bioinformatics and an amazing person.
This is a such a tragic loss. Thank you, James, for being such a supportive mentor and friend. We will miss you.
What a tragedy. He was a terrific researcher and an awesome human being. A huge loss for the world.
You were a hero James — we'll do our best to carry on your work. RIP, we will all miss you terribly!
This is devastating news. James Taylor will be missed by our entire community and well beyond. All my condolences to his family
This is just such devastating news. I have known James for the best part of seven years, as we set up Galaxy in Australia and James, of course, immediately agreed to visit in 2013 to help make that happen. He was visionary, looking to create free, open platforms for global science.
He was also enormously good company, going out for beers and in depth discussions on any and all topics. I thoroughly enjoyed James' company in social and academic forums...but far more importantly than that, he both led and built software and data science communities that will define community-focussed global bioscience from here on.
Personally, it's crushing - I am so sorry for his family and friends, of which of course I count myself - but the loss to the world of science eclipses that. We are all the poorer for losing James. If it is any consolation, he accomplished so much - the world of science is changed because of James.
I am in shock. James was a great scientist, great person, and a cornerstone of the Jetstream effort.
I'm so very sorry to hear this news. A wonderful person and scientist who made awesome contributions to science. He will be greatly missed. Heartfelt wishes to his family, friends and all the Galaxy crew.
My condolences. The galaxy project has grown such a supportive and positive community around it, and Dr. Taylor was right at the center of it.
I am utterly shocked and terribly saddened to hear this. James has been a wonderful colleague, collaborator, and a great mentor to many students.
Our hearts are heavy. James Taylor has passed away. A kind and generous person. His contributions to science are innumerable and he was just getting started. Deep condolences to his family and many friends and colleagues all over the world.
James was a scientific giant, dedicated to sharing what he knew with everyone no matter their background and one of the kindest people I knew. We will miss James so much.
I am so shocked and saddened by the news of James's death. This is such a huge loss to the bioinformatics community. Galaxy has been an inspiration to our Cistrome project. James will be sorely missed!
James was, simply put, an amazing person. He was certainly an amazing scientist, but so much more than that. He was what we all hope to be as scientists, mentors, colleagues, and friends. We will miss you James.
Heartbroken to hear this. Kind person, great scientist and open science advocate. He will be dearly missed, especially by the Galaxy community
This is devastating news. I had the privilege of working with James since he was a grad student and we are still collaborating with him on the VISION Project. He was brilliant, creative, insightful, and passionate about bioinformatics, biology, and full transparency in data & analyses.
I am so sorry — these are dark days and James was always such a hopeful ray of light — I cannot properly express my shock hearing of his passing. May we all conduct our lives with the urgency he did, have the positive impact on society that he did, and thereby honor his legacy.
Deeply saddened at the loss of James Taylor. I remember first reaching out to James at the start of my PhD. I had the great pleasure of rotating in his lab, which not only helped me develop my bioinformatic skills, but also ultimately set me on my career trajectory. I owe a lot to James. In addition to happily agreeing to be on my thesis committee he was an immense source of knowledge and an overall great colleague. I’m grateful for having had the opportunity to work with him. James - you will be missed dearly.
I am shocked. A supremely talented scientist and a wonderful collaborator gone way too soon. We will miss you. Rest In Peace, my friend.
Devastating news. James had such a large impact on how we work in and teach bioinformatics. He was a great person to work with and had great enthusiasm.
I've had tremendous respect for James and his dedication to open science and, to sum it up briefly, making the world a better place for everyone. He was an amazing human and a scientist and will be missed dearly.
This is shocking. James was an inspiration and admired vision and community building, above all. Was lucky to get to know him, and will be terribly missed, RIP
Some lead from above, but the best leaders lead from within by lifting up everyone around them into a strong community. I will miss you dearly my friend and leader James.
James was a trailblazer and wonderful person. What a terrible loss.
My heart goes out to his wife, his family, his lab, and to our scientific community. He was an exceptional person in every way that matters. 2020 is now officially cancelled.
I learned galaxy from you, sir. Your legacy will be continued. Rest in peace.
He came to UIUC back on the job hunt, gave an awesome presentation. Sadly I didn't know him well but met him many times through GCC and BOSC (I hazily recall late night laughs w/ beers involved). He was nice, amazing, awesome. I am so sorry for your loss Galaxy community. This hurts
My friend James Taylor is dead. I'm heartbroken and thinking of all of his family and friends. He is leaving a hole that cannot be filled.
I met James when I started grad school at Penn State. I had no idea what to expect (I'd only learned of PhD programs within the previous year). We were both students, but he was clearly in a league of his own.
James was one of the smartest people I've ever known, in a way that wasn't (as) intimidating. Talking with James was easy and enlightening. He advocated and put in the work for better science, in all aspects.
James supported my science and my career in ways I don't think I can ever fully communicate. As a colleague, he believed in me. As a friend, he expected me to do good. He supported my growth, selflessly.
Most of all, James was an advocate.
He advocated for his students, for trainees, for open science, for open data, for making this world a better place.
I will miss him so terribly.
What a beautiful tribute, Melissa. James was my colleague in the Hopkins Biology department. His loss has left us reeling.
The first time I saw James was at ISMB 2007 in Vienna when he gave a Demonstration on Galaxy's tool integration framework - the room was packed and everyone was deadly silent whilst he live xml'ed.
We are all poorer for this today.
A great visionary and a lovely person too. We are all shocked and saddened. Such a loss to us all. Thoughts are with his family and friends.
James was so approachable. Though we never got the chance to collaborate directly, when I first met the James Taylor I remember feeling that approachability in that someone so famous in our field would always take the time out to talk to me about science or about whatever the topic of the moment was. We had many conversations - some just a glance across a busy crowd at a conference where that would be our only acknowledgement, some, hours long chats. The first memory that came to mind thinking back now was the many weeks he spent at CSHL instructing at courses in the fall. There were months when he was on campus more than I was. The particular memory that flashed when I heard this news was finishing a beer with him around 2 am in the cold outside the bar at Blackford. The bar had long closed, but we were having a crazy conversation along with one other course instructor about awful American TV shows. The conversation was of course punctuated with thoughts on comparative genomics. James was brilliant, but it wasn’t this that made him a star, helped him build a global community, or an enduring vision. He was a lovable and decent human being who will be fondly remembered. His work and the community he helped to create will live on. For every researcher who continues his legacy and works to live up to his achievements, don’t forget to bring along also his charm, curiosity, compassion, and love.
Terribly sad news. He was kind enough to let my high school daughter tour his lab and was so supportive of her interest in science. My sympathies to his family and colleagues.
Very sad news and a great loss for the scientific community. James Taylor was a visionary leader in open science and reproducible research. My condolences to his family.
Rest in peace. I will always remember you.
I feel very lucky to have been taught computational biology by James Taylor throughout this first year at Hopkins. Wish this could have continued and will miss him greatly.
Deeply saddened by this. Such a tremendous loss for science!
Completely in shock and saddened by this. He will be so missed.
I was fortunate to be introduced to James via the IU/TACC Jetstream project, where he promised to consume large quantities of CPU time on behalf of the Galaxy project. His vision and his plans for achieving it were both straightforward and clear. In short: Give us a key to your system (an API key, in this case), and we will make sure it's used for good. And he delivered, spectacularly! While this straightforward approach might at first appear naive, he articulated his plans clearly and proved soundly that he could do it. He was always ready to share examples of discoveries that had been enabled by Galaxy. In later visits on other topics, I was impressed by his astute understanding of how the research community works and how to make (important, substantive) things happen. People like him are rare and special, and a joy to encounter and work with. This is a heavy loss for the research community.
I still remember the nice after meeting time we had with Nate in Collioure. I had nothing but the greatest respect for him and his work. Hope you rest in peace James.
We will miss you James. Thank you for all you contributed. My sincere condolences to his family and friends. This loss is a burden that will be shared by many.
James was a great force for openness, community, and science. He was a truly lovely man. I first met him in Oslo in 2013 and he was immediately welcoming even though he had no idea who I was. Over the years that followed we shared beers, meals, conversations, games and laughs. The thing I'll most remember about him is the glint of pride he got in his eye whenever he saw the wonderful Galaxy community get together. He and Anton created something amazing.
My sincere condolences to James' family, his colleagues and the rest of the Galaxy world.
The bioinformatics community has produced many stars; James was a galaxy.
Extraordinarily sad news in these already troubling times. This is an enormous loss for the field and for the community. Virtual hugs to those who need one from me. Vale James.
As an undergrad, tinkering with pipelines and tutorials on Galaxy was how I started to learn about bioinformatics. James Taylor’s work to make these resources accessible and free changed my life.
I just do not know what to say. My thoughts go to his family, friends, and to the great Galaxy Project community to which he was a father. Sincere condolences.
This is so heartbreaking. I didn't interact with James that many times IRL, but those few moments witnessed strongly about his generosity and humbleness. This puts tears to my eyes and a makes my heart heavy. Rest in peace dear fellow human!
James was my PhD advisor. For 6 years he patiently helped me become a better scientist and supported me for years after.
James you are one of the smartest and kindest person I have ever met and I will miss you very much!
What tragic news. My heart goes out to all those who loved him, his family, friends, colleagues, the Galaxy team and community.
Many aspects of what we are going through right now will pass with time. James' impact on many of us personally and on how science is done will live on and I suspect grow with time.
Almost every project I've worked on since entering the field of bioinformatics has referenced Galaxy Project directly or indirectly. Sad for the loss of a great scientist, but inspired by the camaraderie of the community around good science, especially given current events. RIP.
James has been a part of our community since 2003 and this devastating news is hitting us hard, and doesn't feel possible. His brilliance and positive energy were undeniable and affected everyone lucky to have met and work with him. We we will miss you James.
We are deeply saddened by the loss of a wonderful person that was part of our CSHL courses family for many years. Im just heartbroken with the news. We will miss you Dr. Taylor, thank you for all your kindness. It was an honor working with you.
As I write this from Colombo, Sri Lanka, one can only think of the impact that James has had across the entire world at such a young age, and how his untimely loss has taken away so much from it. The software and community that James was a chief architect of, has positively affected hundreds of thousands of scientists around the world. The loss felt by all of us in this vibrant, welcoming world-wide community that he helped to create, cannot be captured in words. Rest in peace James, the community and impact you have created will live on in your name.
This makes no sense. So incredibly sad to hear this. My heart goes out to all who knew and loved him
James Taylor always wore the coolest shoes. He inspired me to buy my own sparkly shoes, as he inspired me & my cohort of grad students to push our own boundaries of knowledge. He was a generous & kind collaborator. I will miss him.
Damn right he did!
His course on Galaxy is part of what inspired me to enter this field. Years later I felt honored to work with him. A great mind, gone too soon. This is devastating news... sincerest condolences to his family and colleagues.
This is devastating and shocking. What a terrible loss for the community and humanity. Deepest condolences to his loved ones.
what a shock. he was a great collaborator, always generous and a pleasure to work with, and he made a huge impact on the field. what a loss, I can't believe it.
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James was visionary. And he had this rare quality of making you want to follow him. It is called charisma. It really changed my priorities and I don't regret any of these changes. His disappearance is a heartbreak.
I remember James from when we met at GCC in Portland 2018. He was thoughtful with an edge. He had a mystique to him. We shared a conversation about the craziness of skate bombing mountains in Vermont. His Coursera Galaxy courses made a big impact on my early training as the whole Galaxy project is for us; impacting. It's just so crazy to lose him so soon.
What a terrible loss for the Galaxy Project and the open source/access community - it is so sad. The Best we can do is to continue working with even more dedication on all the great projects he has been part of.
I am shocked and heartbroken at losing a friend and mentor. James was a visionary scientist, and he exemplified the values of collaboration and community. He inspired everyone around him to be the best scientist and human being they could be. My heart breaks for his wife and family, his lab, colleagues, collaborators, trainees, and all the scientific communities touched by his passion. James - we will all miss you terribly.
I am a researcher in Genetics, and took a series of Coursera Genomic Analysis courses, in which Prof. Taylor was the instructor. As a teacher I am passing on what I learned there, and by coincidence this week I am teaching an on-line version of his course for students and researchers at the Federal University of Rio de Janeiro, helping us to have some intellectual activity during this quarentine. Two or three days ago I was reviewing some of his lectures !!! That is a real global influencer. We are here in Rio de Janeiro in the middle of a crisis, and still we are learning from his. I thank him a lot.
Such a huge loss. James made huge contributions to open-source, accessibility, and reproducibility. Anyone who runs a bioinformatics tool on the cloud does so thanks to James's work.
RIP to a Real One.
My deepest condolences to his family and the Galaxy family. This is an incredibly loss for the bioinformatics community, we have lost an advocate for open and reproducible science.
The bioinformatics open source community has lost a visionary. Condolences for the family. This is terrible news.
James Taylor's passing leaves a galaxy-sized void in the world of computational biology. An inspirational colleague and a brilliant, unselfishly kind mind.
Terrible news in a world where I was starting to get immune to bad news.
So sad to hear this — the impact of his work and thought leadership on bringing genomics into the cloud computing age cannot be overstated. It just feels really wrong to lose such an amazing talent.
Deeply saddened to hear about the loss of James Taylor. My clearest memory is from him offering a very friendly & encouraging comment on a simple lighting talk I gave as a young engineer at a Galaxy conference years ago. Meant lots to me and a testament to his generosity. I didn't interact with James that many times in real life, but those few moments witnessed strongly about his generosity and humbleness. This puts tears to my eyes and a makes my heart heavy. Rest in peace dear fellow human!
James was a wonderful mentor to me. We will all deeply miss you. Such a huge loss to the community. RIP
Had the pleasure of working with James on the AnVIL project. A great scientist and a greater human being. Condolences to his family, friends, and colleagues.
My world feels vastly diminished. James we will miss you.
The truth is, the world is diminished without him in it.
We are proud to have collaborated with James for many years. Our hearts go out to the Galaxy team and his family. He will be missed. He already is.
He made an impact on scientists (and scientists-in-training!) all over the world, and will be deeply missed.
He also had the coolest stickers on his laptop.
Deepest condolences to friends/family. Cant even describe the scale of impact of contributions to the bioinformatics community. He will be missed greatly.
I was using Galaxy when I found out... 2020 sucks. I want a redo.
We will miss you James. Thank you for all you contributed. My sincere condolences to his family and friends. This loss is a burden that will be shared by many.
I am so shocked and sad to learn that James Taylor, a pioneer in cloud and open-source genomics is dead. I feel privileged to have been one of many whose professional lives he transformed teaching the CSHL genomics course. I will miss his kindness and generosity the most.
The bioinformatics community has produced many stars; James Taylor was a galaxy.
I had the chance to hang out with Jamesx for the first time at a dinner after a seminar talk I gave at JHU's IDIES. I had the pleasure of hanging out with him multiple times since. He was kind, funny, brilliant & cool as f&%k; and despite it all, so down-to-earth. I will miss him.
We are so sorry to hear of James Taylor's death. As co-lead Galaxy, a professor of biology and computer science at Johns Hopkins and a treasured member of the international Galaxy community, his legacy will continue have profound impacts around the world
Shocked to hear this. Always looked forward to a good talk with a drink whenever our paths crossed. His impact on the field is immense. My condolences to his family...
Sending a big hug to James's family and loved ones. He had such a positive impact on so many of us.
Condolences to all touched by James. As a user of Galaxy, I hope his star shines on brightly in our community.
Whatever bioinformatics I know today, it all started with the help of Galaxy during my PhD years. Even though I didn't know James personally, I've been following his fascinating research. A huge loss for everybody...
Thank you James Taylor for teaching me and so many others Galaxy. Meaningful and life-saving work will come from your genomics efforts. RIP
I am still shocked by this. James was such a great person and scientist. I got to know him through the course at CSHL. In addition to being passionate about science, he was just as passionate about teaching and bringing computational biology to the masses.
Hard to overstate the outsized impact he had on the biological sciences. And he was a lovely person.
he was indeed ageless, & im so sad that he is gone, I am a big fan of James & Anton & the Galaxy Project. A visionary project, democratizing open bioinformatics. The Gaalaxy community is large, and will continue and do well, but we will all miss James!
Okay google. Play James Taylor. Missing you James. (He didn’t actually like JT the singer, although I think it captures his introspective reflective personality.)
This is so tragic, I'm so sorry to James and his family and colleagues. Working on Galaxy in the early days was one of the best things in bioinformatics. I will always cherish that.
09/06/2014 - Dr. James Taylor and I realized we had a mutual love for the Canadian show Trailer Park Boys at a happy hour post-bootcamp during my first week of grad school. His first email to me was to let me know the new season of TPB was on netflix. Will miss him greatly.
I worked with James Taylor from 2000-2002 when he was in Vermont. I got him into mountain biking and he turned me on to Modest Mouse. He was a wonderful human and the smartest person I've ever known. I am not surprised at the lives he's touched.
James Taylor was an NHGRI-funded investigator who made significant contributions to the field of genomics — having developed the Galaxy data-analysis platform, having worked as an AnVIL PI, and having participated in ENCODE. He will be missed by us at NHGRI.
So sad to learn of the passing of James Taylor. Met James long ago via the OBF/Galaxy/WormBase. A truly positive an inspiring force. Quick snap of James (with Greg von Kuster) at the 2009 Biohackathon on Okinawa.
As someone who began their bioinformatics genomics journey by using Galaxy's ultra-friendly user interface, I am very sad to find out that one of its founders, Dr. James Taylor, died this week at just 40. Thanks for making my first assemblies so much less intimidating!
I did not know you, but your influences on me has been great. Galaxy laid the bioinformatics foundation for myself and the rest of my lab. Your contribution to science has been immense and I am sad that it has been cut short. RIP James Taylor
I'm so sorry to hear this. James' influence and work has enabled so many people and discoveries, and will continue to do so for many years to come. We share your loss and our thoughts are with you all.
I met James over five years ago though the Galaxy Community, and I believe that his personality and role as co-founder helped shape that positive and welcoming atmosphere. Looking back it is clear that he and Anton convinced funders of the importance of community building, evident in how the Galaxy Project funded and has continued to fund dedicated staff for community, outreach and training. James cared both about people and principles - he was also vocal on open science and open data, embodied in the Galaxy platform's ethos of reproducible research. Just days ago, he was tweeting complaints about how in a pandemic so much new covid19 viral sequence data was not being shared openly (as in the NCBI/INSDC), but instead under restricted terms in the GISAID database. It is clear from the posts of his students, mentees, collaborators and friends, that while he would have achieved much more, he has already built a legacy we can all be proud of.
I'm just a citizen scientist active in human genome analysis especially regarding Y-DNA J2 and ancestral and relatives haplotype clusters. I cheer and am thankful of public science services like Galaxy Project and hereby would like to send my thanks to James Taylor et al for what they provided to every interested person.
I am heartbroken. When I think of James I remember him relaxing in the sun during one of the GCC hackathons. At the time I was attending as a lowly delegate from Africa, and engaging with a Galaxy project PI was quite a leap. We got talking and got to know each other over meetings and beers over the years. I cannot believe he is gone. His family and friends are left with a gaping hole in their lives. My strength to you (us) all. Sincere condolences to James' family and everyone in the Galaxy community from SANBI and myself.
60 percent of my laptop stickers are due to @jxtx and team. Glad to be with them during this.
Jeff, and we are really glad to have you.
I remember James as embodying an uncompromising commitment to community-driven science to the point of making it feel like a family; how do we help each other to move science forward. It was noticeable in each conversation we had and this imprint he made will always stick with me. When you stop and think about how much scientific progress was made because he had a strong hand in breaking down silos and building global bridges, that impact is both lasting and expanding.
I never knew James personally but I just wanted to say that I saw him from afar many times during my academic career and he was always surrounded by laughing and joy. We will not soon forget the joy and spirit he left with us all.
James was an incredibly kind teacher and friend. You could tell he was truly passionate about teaching and building others up around him. He cared deeply for his students and was willing to invest in anyone who wanted help. It was clear he was truly passionate about making computational tools and skills accessible to as many people as possible and I suspect that this will be one of his greatest gifts to the world.
I still remember going up to James during one of his lectures and expressing that I was skeptical of many of the available bioinformatic tools. I was a bit shocked when he replied, "You should be incredibly skeptical. You should use most of them and trust none of them." I really admired this intellectual honesty, how he was able to teach and rely on many tools while still being highly objective and critical of them. That is something I will always remember about him and carry with me as a guiding principle in the years to come.<br /
One of the privileges of being an academic is the opportunity to meet truly remarkable people, those who not only possess incredible intelligence but also incredible character. James was undoubtedly one of those individuals and his passing is a true loss.
What sad news! He will be dearly missed, especially by the Galaxy community. My condolences to his family, his friends and the team.
I am so saddened to hear this. I felt a bond with James over his commitment to reproducible science. I admired his drive and integrity. This is a great loss.
I met James in November 2002 at an open-source software conference. He was working professionally as a software developer and was speaking of his desire to go back to school to study bioinformatics. I’ve watched his career from afar as he’s done amazing work. I know he will be missed.
I am feeling a deep sadness knowing that a true scientist has passed away. I have not met Dr Taylor, but I felt him like my friend I learnt a lot from his participation in Galaxy and online courses and I am sure his legacy will never ever be forgotten. My condolences to his family and colleagues.
I was lucky to have conversation with him a couple of times during GCC 2019, His legacy will be remembered in the complete path of the Galaxy Project.
James was so helpful to various projects I've been involved in over the years. and lately he was a valuable voice of technical and educational experience in various NIH-driven projects. Beyond his obvious talent as a scientist, and a supportive colleague, he was a thoughtful and considerate person. It was always a pleasure to work with him. My thoughts go out to his family, trainees, close colleagues, and the entire community on this terrible loss.
People who interacted with James in any capacity thought the world of him.
Community building is so hard and so important. If we are talking about sustainability, this almost ever means to maintain and grow a community. Galaxy will be soon 15 years old. You and your team did it! Thanks for everything that you have given us James. I will miss you.
The world of genomics, bioinformatics, and to a great extent, current biology has lost a pioneer. Galaxy has been there for almost a decade and a half and was so ahead of its time. Your work has advanced science significantly and will be carried on. RIP & condolences to family
This is truly very sad, my deepest condolences to his family, friends and to the Galaxy community. I had the chance of meeting James briefly during the last GCC, a very nice person and true advocate of open science and open source. RIP James.
I came in today and found this in front of James’ office.
I met James at a Galaxy Community developers conference in the first year of my PhD and was taken aback by how friendly he and his team were and welcoming to all as equals. A great admirer and user of his work and saddened by this loss.
Your kind words about James bring tears. Our family thanks you all.
It's been a couple weeks now, and I still feel like it is so surreal that this could have happened. I didn't know James super well but he will always be the voice I hear announcing the state of the Galaxy during the community conference. He had a hand in so many initiatives and was so central to the communities I'm a part of, I'm left wondering how the world will possibly go on without his leadership.