← Back to news

James 'JJ' Johnson

James "JJ" Johnson passed on March 1, 2024 in Minneapolis at the age of 71 after a long battle with cancer. JJ was a Galaxy community rock star most known for his indispensable contributions to the Galaxy Proteomics community. Being the kind and gentle person that he was he helped build up the Galaxy-P community since 2014.

JJ was a senior software developer who could take a concept and make it into a reality. He attended most of the Galaxy community conferences (including the first one and the GCC 2022 in Minneapolis). Some of his work is captured in the Galaxy Training Network Hall of Fame and two great interviews.

He will be missed by family and friends from all over the world and by his cat Freyja. JJ's works will live on in so many Galaxy tools and workflows for years to come.

Remembrances of JJ

Somewhere around the year 2011 I was introduced to JJ in his role at the Minnesota Supercomputing Institute. He had been working on using this software platform called "Galaxy", which we were interested in using for our ongoing research. JJ was tasked with helping us learn this platform. From there, JJ became a steady and critical member of our team. I could list out many, many accomplishments we achieved over the years working together: developing software tools to analyze complex data on genes and proteins that impacted everything from human health and cancer, to understanding how ground squirrels (i.e. gophers!) hibernate, to the bacterial present in environmental samples. JJ's skill and dedication to his work played a key role in all of these projects. I take solace in the fact that the software tools used for these studies will live on in their value for years to come, so, in some ways, JJ will still be with us.

More than the scientific accomplishments, however, JJ's impact on all he worked with will be remembered. Despite his deep expertise in software development and ability to handle very complex technical details, his humility was always on display. He would always defer credit on his accomplishments, and deflect our praise when he solved a complicated problem that helped move us forward. Even though the day-to-day work was very technical, he always kept an eye on the bigger picture reasons for the work we were doing together - to contribute to the scientific body of knowledge, and, hopefully, help us better understand complex problems that could improve people's lives. His dedication to the work only deepened when he himself was diagnosed with cancer - I'm sure it focused the motivations for our work even more. The other enduring memory of JJ is his easy-going, gentle nature that made him such a joy to work with. I'll always remember his sense of humor, pulling out a Swedish joke that poked fun at his own personality quirks.

As a career focused on scientific research progresses, you realize that the joys of the work are far beyond just scientific discovery. It is the people you get to know along the way that leave the lasting memory. JJ will be one of those colleagues that holds a special place, not just for me but everyone he worked with.

Tim Griffin
University of Minnesota

JJ was an inspiration in many ways and below I will mention just a few incidents that highlight why he was so special and had an impact on so many lives.

The white board: JJ was an excellent software developer and as part of teamwork we all relied on him to either develop a software tool, or come with a software tool that delivers an output based on the concept. This involved a lot of discussions, testing and optimization. JJ had an office at MSI with a window and whiteboard. I remember meeting him in his office and discussing functionalities needed in a software tool for proteogenomics. I used the whiteboard during the brainstorming session and left. The software tool was available and used as part of the bioinformatics workflow and the manuscript was published. I visited JJ’s office two years after this and his whiteboard still had the same content. I asked him - why is the content still there? His reply was - “I just thought this must be very important and hence left it there”. He had a way of making people feel special.

2016: In November of 2016, when the presidential election results were announced. As an immigrant - and because of my own political beliefs, I was keen to know how much America had changed. I reached out to JJ and other friends and talking with JJ calmed me down. For those who were aware of JJ’s political leanings - this should come as no surprise.

The lightning talk in Norwich: JJ was invited to give a five minute lightning talk on ‘how to improve your text life’. The crowd loved the talk and I think the moderator conveniently delayed pressing the buzzer.

Rockstar: As mentioned earlier, JJ was an excellent software developer and we are all in awe to watch him make the magic happen. I never forgot to mention to him that given that he was an English teacher he was a rock star just like Gordon Sumner (also known as Sting). One of the little known facts is that both Sting and JJ - were primary school English teachers and both went on to create magic with their respective art forms.

JJ was not only great at his work - but most importantly he was a great human being. Be it while making young researchers welcome to the Galaxy community, being a support in trying times, with his sense of humor or as a rockstar that created magic through software tools and workflows. JJ - thank you for all the moments spent together - we will miss you!

Pratik Jagtap
University of Minnesota

When I first became a part of the Galaxy-P team, I found myself confused and unsure during our initial team meeting. Amidst the discussions, I remained silent, feeling unsure of what was going on. By the end of the meeting, I felt disheartened as I had not contributed anything. It was then that JJ, perceptive as ever, noticed the weight of my expression and offered words of encouragement: "There will come a day, not too distant- when you will be the one contributing the most." Those words of encouragement made my day, and I can't express how grateful I felt.

I believe JJ's commitment to his craft was unparalleled, matched only by the boundless generosity of his spirit. Whether offering a sympathetic ear, extending a helping hand, or infusing the room with his infectious laughter (mainly joking about himself), JJ had a remarkable gift for lifting those around him. He was more than just a colleague; he was an integral part of our Galaxy-P team, and an excellent software developer, his insights and contributions shaped the very fabric of our weekly meetings.

Today, as I reflect on JJ's legacy, I recognize that it extends far beyond the tools he developed, the workflows he perfected, or the scientific papers he authored in the field of genomics and proteomics. His impact is imprinted in the lives he touched, the minds he inspired, and the countless moments of encouragement he shared. Though he may no longer walk among us, his spirit endures, a guiding light for all who had the privilege of knowing him.

Thank you JJ for being a part of our lives! We will miss you!

Subina Mehta
University of Minnesota

I was fortunate enough to know JJ for a few years through school and research. While I did not work closely with JJ for very long, I'd like to share my deepest condolences and sympathy to all his family, friends, and colleagues. He was a very kind-hearted man and an invaluable member of the Galaxy community. My most impactful memory is actually my first email from him back in the summer of 2021.

Back then, I was an undergraduate student who was transferring to the University of Minnesota to finish my bachelor’s degree. I had been accepted into a research program for summer 2021 and was set to join Dr. Timothy Griffin’s lab. I was incredibly nervous as I had zero bioinformatics experience or knowledge, meeting new people, (at the time) many things were remote, and so on. A few days before virtually meeting everyone, I sent an email to Dr. Griffin and other lab members to introduce myself. I got many polite and friendly replies, including one from Dr. Griffin, who added two more people to the email exchange. Dr. Griffin said that these two new people were MSI members, JJ and Reid Wagner and that I may work with them that summer. Unsurprisingly, all the replies created a very long email chain, which was overwhelming to a newcomer. Of course, JJ sent an email as well, introducing himself and welcomed me as the latest member of the Griffin lab.

To be frank, that email from JJ is quite ordinary, but there was only one thing that was different about JJ’s email. And it is that he sent it directly to me, separate from the very long email exchange. I don’t know the exact reason he did so or why this makes it “different” in my head. Maybe it was convenience on his end, or maybe he knew I’d already be getting a ton of emails besides his. I actually searched for it to see what it says. It reads:

“Hi Katherine,

I'm Jim Johnson, but usually known as JJ. I'm a software developer with MSI, Minnesota Supercomputing Institute. I've had the pleasure of working with Tim and members of his research group for many years. I look forward to working with you as the latest new member.


I replied and thanked JJ for welcoming me. And that was it. In the years since, I had forgotten about his email, and as time went on, I grew to greatly respect JJ for how much of a crucial role he plays in the Galaxy-P community with his expertise, skill, and countless contributions. To this day, I’m still learning about bioinformatics, and I know that the work I do wouldn’t be possible without JJ.

I remembered his email when I heard JJ had passed. And I remembered being a very, very nervous college student, who had no idea if she was the right fit for a new lab and if she could handle doing research about things she had no idea about. I remembered being welcomed by a wave of kind-hearted and helpful individuals in Dr. Griffin’s lab and feeling grateful but overwhelmed with keeping track of who was who and who did what. And I remembered the one email that was separate from the rest from a kind and gentle man named JJ, who just wanted to make sure the newest member felt welcomed. He could not have known who I was as a person or how anxious I was or that his simple email would mean a lot to me. He was one of the many who were kind to me when I needed kindness. I’m very glad to have known JJ. His memory will live on in many hearts.

Katherine Do
University of Minnesota

JJ was my primary mentor at the University of Minnesota, and what a lasting impression he left on me. He was a prolific, talented, and committed researcher, great at seeing the forest for the trees and finding the right approach past difficult roadblocks. He had so much wisdom that was invaluable to myself and others. For this, I learned that he often needed no introduction.

In equal part to his technical acumen, his character was so full of kind-heartedness, humor, and sincerity. His advocacy was constant, and in turn it was sometimes difficult to give him due credit as he was keen to give it away! I’m sure he knew his many years of work spoke for themselves - he just wanted to encourage others.

I remember that I was excited to introduce my wife to JJ - she had heard a lot about him already - after my first conference here in Minneapolis. This was only my second or third time meeting with JJ in-person, and I remember being pleasantly surprised that he invited us to visit him in Grand Marais. That’s who he was. Warm and welcoming.

JJ always comes to mind when Grand Marais comes up. He was of course known for his appreciation of the town, but I also see his calm introspectiveness in the peaceful nature there. He will be missed. Thank you, JJ!

Reid Wagner
University of Minnesota

JJ has brought the true spirit of community tool development into Galaxy. His insights were essential for the early development of Galaxy’s ToolShed, evolution of the Intergalactic Tools Commission (IUC), workflow development and many many other aspects of this complex system. JJ was also a person who everyone was seeking out during the Galaxy Community Conferences. We will miss him terribly!

Anton Nekrutenko
Penn State

I met JJ in the very early GalaxyP days, as usual in our community, on GitHub. We have been working on Proteomic tools a lot and dropped PRs and reviewed them, using the timezone difference very efficiently. I enjoyed working with him, discussing science and politics and learning from him so much. I remember his great talk in Norwich and the incredible evenings, gosh we had a lot of fun. I tried to persuade him to visit us in Freiburg at GCC 2019, but this was not possible so I was very happy to visit him in 2022 in Minneapolis - where he worked. As kind as he was, he offered me a bike, so I did not need to rent one every day to get to the venue. He cleaned the bike, put it into his care, and we assembled it at the venue. Long story short, it was stolen pretty quickly. I felt so bad, but he assured me 100 times that it was not a problem and that no one was using this bike. He was so good-hearted. I will miss you JJ and I still owe you a bike!

Björn Grüning
University of Freiburg