profile

Some personal profile and metrics

View the Project on GitHub

Professional Profile

"You're like a celebrity that isn't famous"
- E.M.; The 2nd best compliment I've ever received
"Pull back three curtains and there's Jason"
- C.T.B.; The 5th best compliment I've ever received
"You are an NBC sitcom but the writers room has the good cocaine"
- C.K.; The 17th best compliment I've ever received

An incomplete list of things I do and have done, if you have to know for some reason.

I’ve worked at Cold Spring Harbor Laboratory since 2004, first at the bench in the Plant Science group and currently as Assistant Director, External Collaborations of the lab’s DNA Learning Center. I also get to teach my own science course a few hours a week at Yeshiva University High School for Girls. I think helping scientists keep up with changing technology is one of the most important things we can do to accelerate research. Moreover I think this can be sustainably achieved by building, supporting, and promoting the people who do this training - hence my founding of the group Life Science Trainers, a global community of practice for short-format training in the life sciences ( open to anyone who provides training for life scientists).

Workshops, Talks, Teaching, and Presentations

This list mainly reflects my work with CyVerse (formerly iPlant Collaborative), a project I work on that brings cyberinfrastructure to biologists. I am their Education, Outreach, and Training lead, so I get to help lots of biologists use computation in their teaching and research. Workshops are mainly multi-day training events.

2019

(includes scheduled events)

Venue Presentation Location Notes
International Plant and Animal Genome Meeting (PAG XXVII) Session Chair/Organizer - Advanced Computational Methods – Machine Learning, Containers, and Clouds San Diego, CA  
International Plant and Animal Genome Meeting (PAG XXVII) Session Chair/Organizer - CyVerse - Software, Tools, and Services for Data-Driven Discovery, Data Science, and Education San Diego, CA  
International Plant and Animal Genome Meeting (PAG XXVII) Session Chair - Resources and Programs for Undergraduate Education in Genomics San Diego, CA  
International Plant and Animal Genome Meeting (PAG XXVII) Session Organizer - Pragmatic solutions for scaling your analysis: Machine Learning, Imaging, Containers, Clouds and APIs San Diego, CA  
5th Annual Meeting of the Arkansas Bioinformatics Consortium Invited Workshop: Extensible Cyberinfrastructure for Life Science Little Rock, AR  
Environmental Data Science Inclusion Network Lightning Talk: Broadening Participation with Bioinformatics, Big Data, and Data Science Boulder, CO  
CyVerse Foundational Open Source Skills Camp Workshop developer Tucson, AZ Course materials
Genomics Data Carpentry - Genomics 2.0 Lesson Release Workshop Workshop organizer/instructor Tucson, AZ  
Cold Spring Harbor Laboratory Frontiers in Plant Science Course, Invited Instructor: Introduction to R Cold Spring Harbor, NY  
International Society for Computational Biology: Joint Annual meeting - 27th Intelligent Systems for Molecular Biology/ 18th European Conference on Computational Biology Invited Opening Keynote: Education COSI - “Training, Teaching, Technology, Togetherness – Promoting Knowledge Exchange in Life Sciences Through Communities of Practice” Basel, CH slides
International Society for Computational Biology: Joint Annual meeting - 27th Intelligent Systems for Molecular Biology/ 18th European Conference on Computational Biology Invited Speaker: Scalable Plant-Research in Cloud Environments - “Overview of CyVerse tools and services: introduction to data/metadata management and sharing with CyVerse” Basel, CH  
International Society for Computational Biology: Joint Annual meeting - 27th Intelligent Systems for Molecular Biology/ 18th European Conference on Computational Biology Lightning Talk: The Data Carpentry Genomics Curriculum: Overview and Impact” Basel, CH  
Swiss Institute of Bioinformatics Invited Seminar: “Cyberinfrastructure for Scaling Research, Education, and People” Lausanne, CH  
GOBLET Annual Meeting LifeSciTrainers.org A global community of practice for short-format training in the life sciences Jakarta, ID (Virtual) slides
CyVerse Foundational Open Science Skills: Practical Data and Software Skills for Reproducible Research Workshop organizer/instructor Rome, IT Announcement and materials

2018

Venue Presentation Location Notes
NSF INCLUDES summit Broadening Participation with Bioinformatics, Big Data, and Data Science Alexandria, VA poster
International Plant and Animal Genome Meeting (PAG XXVI) Session Chair/Organizer - CyVerse Education: DNA Subway, Data Science, and Microbial Genomics - CyVerse - Software, Tools, and Services for Data-Driven Discovery; BOF-Organizer: Machine Learning, Imaging, Containers, Clouds and APIs San Diego, CA  
North Carolina State University Genomics Data Carpentry and CyVerse Tools and Services Workshops Raleigh, NC  
ASPB Southern Section Regional Meeting Symposium Keynote Speaker: “Data, Data Everywhere, Nor Any a Drop to Drink” New Orleans, LA slides
Chan-Zuckerberg Biohub Data Carpentry: Ecology San Francisco, CA  
University of New Orleans Genomics Data Carpentry and CyVerse Tools and Services Workshops New Orleans, LA  
Amazon Research Invited Seminar: “Scaling Science by Scaling People, Purpose-built Cyberinfrastructure for the Life Sciences” Cambridge, UK  
University College, Dublin Genomics Data Carpentry and Carpentry Con Dublin, IE  
Bioinformatics Open Source Conference/Galaxy Community Conference Joint Session Talk: “Improving the Undergraduate Bioinformatics Curriculum”, Panelist: Training and Documentation in Bioinformatics Portland, OR  
Cold Spring Harbor Laboratory Frontiers in Plant Science Course, Invited Instructor: Genomics Data Carpentry - Introduction to R Cold Spring Harbor, NY  
Cold Spring Harbor Laboratory Genomics Data Carpentry and Machine Learning Cold Spring Harbor, NY  
Plant Biology 2018 Poster: “The Next 10 Years of Data-Driven Plant Biology”/ Data Carpentry and RNA-Seq Workshop Montreal, CN  
Colorado State University Genomics Data Carpentry and CyVerse Tools and Services Workshops Ft. Collins, CO  
CSHL Biological Data Science Poster: “Improving the Bioinformatics Curriculum” Cold Spring Harbor, NY  
BioInfoSummer Invited Keynote:”Improving the Bioinformatics Curriculum” Invited Instructor: “Introduction to Kallisto and Sleuth RNA-Seq Workflows - Bulk and Single-cell RNA-Seq applications” Perth, AU  
Earlham Institute CyVerse UK Workshop Norwich, UK  

2017

Venue Presentation Location Notes
International Plant and Animal Genome Meeting (PAG XXV) Session Chair/Organizer: CyVerse Education: DNA Subway, Data Science, and Microbial Genomics - CyVerse - Software, Tools, and Services for Data-Driven Discovery San Diego, CA  
CyVerse UK Workshop University of York York, UK  
Plant Biology 2017 - American Society of Plant Biology Symposium Chair: Computation/Bioinformatics: CyVerse Resources for Enabling Data-driven Plant Biology; Panelist: Common Author Errors and How to Avoid Them; ASPB Journal Editor’s Session: Tools for Reproducible Plant Biology Honolulu, HI slides
Cold Spring Harbor Laboratory - Frontiers & Techniques in Plant Science Invited Instructor: Genomics Data Carpentry Cold Spring Harbor, NY  
Beyond the Bench 2017 Panelist: Careers in Education and Government Cold Spring Harbor Laboratory agenda
University of Arkansas Genomics Data Carpentry and CyVerse Tools and Services Workshops Fayetteville, AK  
James Madison University Genomics in Education and CyVerse Tools and Services Workshops Harrisonburg, VA  
Los Alamos National Laboratory Software Carpentry Los Alamos, NM  
New Mexico State University Genomics Data Carpentry and CyVerse Tools and Services Workshops Las Cruces, NM  
ASPB Conviron Scholars Panelist: Plantae Conviron Scholars Career Panel Online  
Toronto Bioinformatics User Group Invited Speaker: TorBUG Bioinformatics Seminar - “The Bioinformatics Training Landscape” Toronto, CN slides

2016

Venue Presentation Location Notes
International Plant and Animal Genome Meeting (PAG XXIV) Session Chair/Organizer: iPlant and Education: DNA Subway, Data Science, and Microbial Genomics - Cyberinfrastructure for Life Science and Beyond – Scaling your science with iPlant San Diego, CA  
Stony Brook University, Genomics Cluster Genomics Data Carpentry Stony Brook, NY  
University of Delaware Genomics in Education Workshop/CyVerse Tools and Services Workshop Newark, DE  
MidSouth Computational Biology and Bioinformatics (MCBIOS) Invited Workshop Organizer: CyVerse tools for Data Driven Discovery Memphis, TN  
Ohio State University CyVerse Tools and Services Workshop Wooster, OH  
iDigBio Webinar: Education and Outreach Webinar Series: iPlant’s DNA Subway Online slides
University of Melbourne Invited Lecture/Workshop Organizer: CyVerse Training Day Melbourne, AU  
National eResearch Collaboration Tools and Resources project (Nectar) CyVerse and Atmosphere Cloud Overview Melbourne, AU  
Jackson Laboratory Big Genomic Data Skills Training for Professors: Invited Lecture/Workshop Organizer: CyVerse Cloud for Research and Education Farmington, CT  
National Institutes of Health Genomics Data Carpentry/BD2K Bethesda, MD  
Langebio/Cinvistav Genomics Data Carpentry/CyVerse Tools and Services Irapuato, MX  
2016 National Academies Special Topics Summer Institute on Quantitative Biology/BioQUEST Guest Lecture/Workshop Organizer: CyVerse Overview/CyVerse Atmosphere for Education Raleigh, NC  
Plant Biology 2016 Bioinformatics Symposium: Symposium Speaker: Resources for Big Data Biology: The Evolution of iPlant Austin, TX  
Genetics Society of America/ Allied Genetics Conference Workshop Organizer: CyVerse Tools and Services Orlando, FL  
Network for Integrating Bioinformatics into Life Science Education (NIBLSE) NSF RCN Kick-off meeting Omaha, NE NIBLSE website
South African Genetics Society/South African Bioinformatics Society - Join Conference Keynote Speaker Leveraging Cyberinfrastructure to Scale Science and People Durban, ZA slides
NorthWest University Genomics Data Carpentry Workshop Potchefstroom, ZA  
CSHL Cereal Genomics Workshop Invited Instructor: Accelerating Plant Science with CyVerse Cold Spring Harbor, NY  
Biological Data Science Poster: Required Parameters - What Does it Take to Bring Bioinformatics into the Classroom at a National Level? Cold Spring Harbor, NY poster
EMBL-Australian Bioinformatics Resource Invited Lecture/Workshop Organizer: EMBL-ABR workshop on Open Source and Software Development Best Practice Melbourne, AU agenda
EMBL-Australian Bioinformatics Resource Invited Lecture/Workshop Organizer: EMBL-ABR Open and Scalable Training workshop Melbourne, AU agenda

2015

Venue Presentation Location Notes
International Plant and Animal Genome Meeting (PAG XXIII) Session Chair/Organizer DNA Subway: Genomics, DNA Barcoding, and RNA-Seq Made Easy for the Undergraduate Classroom - iPlant Workshop: Why a Biology Cyberinfrastructure is the Best Way to Meet the Challenges of Large Datasets San Diego, CA  
Clemson University iPlant Tools and Services Workshop Clemson, SC  
Cold Spring Harbor Laboratory Data Carpentry Hackathon on Genomics Lesson Materials Cold Spring Harbor, NY wiki
Cold Spring Harbor Laboratory USDA-iPlant BigData Workshop on Genome Variation Cold Spring Harbor, NY  
University of Georgia, Athens iPlant Tools and Services Workshop Athens, GA  
Santa Fe Community College iPlant Tools and Services and Genomics in Education Workshop Santa Fe, NM  
Bowie State University RNA-Seq for the Next Generation Workshop Bowie, MD website
South Dakota State University iPlant Tools and Services and Genomics in Education Workshop Brookings, SD  
California State University, Long Beach RNA-Seq for the Next Generation Workshop Long Beach, CA website
The Genome Analysis Centre (Earlham Institute) iPlant Tools and Services Workshop Norwich, UK  
John Innes Centre Galaxy Community Conference Norwich, UK  
Bioinformatics Open Source Conference Invited Panelist: Open Source, Open Door: increasing diversity in the bioinformatics open source community Dublin, IE  
ISMB/European Conference on Computational Biology Workshop: Using Biological Cyberinfrastructure to Scale Science and People – Applications in Data Storage, HPC, Cloud Analysis, and Bioinformatics Training Dublin, IE agenda
Plant Biology 2015 Bioinformatics Symposium: Symposium Speaker: How to Scale Data, Science, and People using Biological Cyberinfrastructure - PUI workshop: Using iPlant Cyberinfrastructure To Support Diverse Research and Education Objectives Minneapolis, MN  
Plant Biology 2015 Data Carpentry Workshop at Plant Biology 2015 Minneapolis, MN  
USDA-ARS Meeting on Microbial genomics, Biomics, and Metagenomics Workshop Overview of iPlant Resources Cyberinfrastructure for Metagenomics Athens, GA  
Florida SouthWestern College iPlant Genomics in Education Workshop Ft. Myers, FL  
University of California, Davis iPlant Multiworkshop with Data-Intensive-Biology Lab Davis, CA  
Colorado State University Invited Speaker: MIP Seminar: How to Scale Data, Science, and People Using Biological Cyberinfrastructure Ft. Collins, CO  
National Ecological Observatory Network NEON/Data Carpentry Hackathon on Geospatial Data Boulder, CO  
Cold Spring Harbor Laboratory Half-day iPlant workshop at CSHL Plant Genomes and Biotechnology Meeting Cold Spring Harbor, NY  
Plant Genomes & Biotechnology: From Genes to Networks Invited Talk: Scaling plant science (and scientists) using Biological Cyberinfrastructure Cold Spring Harbor, NY  

2014

Venue Presentation Location Notes
International Plant and Animal Genome Meeting (PAG XXII) Session Chair/Organizer DNA Subway Workshop - iPlant Workshop: Cyberinfrastructure for All Life Sciences San Diego, CA  
Linfield College iPlant Tools and Services Workshop McMinnville, OR  
The Genome Analysis Centre (Currently: Earlham Institute) Invited Seminar: The iPlant Collaborative - A Unified Cyberinfrastructure for the New Life Science Norwich, UK  
Wageningen University The iPlant Collaborative and CoGe Wageningen, NL  
2014 Maize Meeting Workshop: Introduction to iPlant Collaborative Beijing, CN  
UC Davis iPlant Train-the-Trainers/Tools and Services Workshop Davis, CA  
University of Omaha NSF (RCN) Incubator: Network for Integrating Bioinformatics into Life Sciences Education (NIBLSE) Omaha, NE  
Cold Spring Harbor Laboratory Software Carpentry Workshop Cold Spring Harbor, NY  
Stony Brook University iPlant Tools and Services Workshop Stony Brook, NY  
University of Nebraska, Lincoln Understanding GWAS workshop Lincoln, NE  
Plant Biology 2014 Symposium Speaker: CyVerse Resources for Plant Science Portland, OR  
Plant Biology 2014 Software Carpentry Workshop Portland, OR  
Botany 2014 iPlant Tools and Services/Genomics in Education half-day workshops Boise, ID  
World Congress on Genetics Applied to Livestock Production Invited Talk: DNA Subway An Educational Bioinformatics Platform for Gene and Genome Analysis: DNA Barcoding, and RNA-Seq Vancouver, CA  
National Science Foundation Invited Talk NPGI Annual Awardee Meeting: The iPlant Collaborative: Computational Resources for Young Investigators - How Can We Help? Arlington, VA  
Cold Spring Harbor Laboratory (Banbury) High Performance Computing (HPC) in Undergraduate Biology Education Cold Spring Harbor Laboratory, NY  
European Conference on Computational Biology Invited Workshop: Dual Benefit of Bioinformatics Training Strasbourg, FR  
USDA-ARS ARS Arthropod Genomics Workshop Beltsville, MD  
Cold Spring Harbor Laboratory Meeting founder/organizer/session chair: Biological Data Science (Inaugural Meeting)/ Cold Spring Harbor, NY  
Cold Spring Harbor Laboratory iPlant Train-the-Trainers Cold Spring Harbor, NY  

Selected Publications and Products

Academic and Community Service

Role Year  
Curriculum Advisory Board: Health Data Research UK 2019-  
Founder: LifeSciTrainers.org/LifeSciTrainer Slack 2018  
Science and Industry Advisory Board member: ELIXIR UK 2018-  
External Panel of Consultants: National Institutes of Health-NHLBI Data STAGE (Storage, Toolspace, Access and analytics for biG data Empowerment) 2018-  
Steering Committee member: Biodiversity Literacy in Undergraduate Education, NSF RCN-UBE 2018-  
External Panel of Consultants: National Institutes of Health Data Commons 2017-  
Steering Committee member: Plantae, American Society of Plant Biology/Global Plant Council 2017-  
Chair, International Science Advisory Group: EMBL-Australian Bioinformatics Resource 2016-  
Steering Committee Chair: Software Carpentry Foundation 2016-17  
Conference Review Committee member: Open Bioinformatics Foundation Bioinformatics Open Source Conference 2016-  
Steering Committee Treasurer: Software Carpentry Foundation- (Founding Committee) 2015-16  
Science Advisory Board member - NIBLSE Network for Integrating Bioinformatics into Life Science Education 2016-  
Trainer/Instructor/Maintainer: The Carpentries - Software and Data Carpentry 2014-  
Founder: CSHL Biological Data Science Meeting 2014  
Scientific Training Advisory Board member: The Genome Analysis Centre Currently - Earlham Institute, Norwich, UK 2013-15  

Things to Fund

Any takers?

Photo and Speaking Bio

An acceptable photo for your press releases

If you are introducing me at a talk, feel free to use (or not) the following:

Jason is Assistant Director, External Collaborations of Cold Spring Harbor Laboratory’s DNA Learning Center, and is the Education, Outreach, and Training lead for CyVerse (A U.S. national life science cyberinfrastructure funded by NSF). Jason organizes, instructs, and speaks at a variety of bioinformatics-related workshops, conferences, and meetings annually. He also serves in an advisory capacity on a variety of bioinformatics and open science projects including his service as Chair of the International Science Advisory Board for EMBL-Australian Bioinformatics Resource, and service on the National Institutes of Health (NIH) National Heart Lung and Blood Institute’s Data STAGE (Storage, Toolspace, Access and analytics for biG data Empowerment). He is an active Software and Data Carpentry instructor, and a former Chair of the Software Carpentry foundation (an international organization of researchers that promote training and education in software development, scientific data management, and open science). He is the founder of LifeSciTrainers.org, a global community of practice for short-format training in the life sciences. Jason is also a teacher at the Yeshiva University High School for Girls.

Other Things

Blood type: Ragù

Personal Catch Phrases, Quotes and sayings:

Kryptonite: Most pop music

Beverage: Gin and Tonic

Astronomical Phenomenon Eta Carinae

Subatomic Particle: Top quark

Special Powers (partial list):

Travel Tips and Recommendations

I travel a fair bit. Here are some of my favorite items for the road-warrior scientist

Travel Essentials

Category Item Link Notes
Bag Arkiv Modular Backpack link This is my FAVORITE bag. I have the rucksack for everyday use, but this is a buy-it-for life quality travel bag. You can fully customize the bag for all your travel needs. I have the large 40L R6. I have compartments for my laptop, iPad/small electronics, and water bottle. You can add more accessories as needed. I have gone on a 10-day international trip including an clothes and an extra pair of shoes with just this bag. You will only need one.
Bag Adidas Rumble Sack link The Arkiv bag can split into smaller bags, but is too much for days on a trip when I am not flying. This bag is very light, sturdy, and good for carrying my laptop and few small supplies. Also nice if you are going shopping for a few small things.
AV equipment (airplane iPad holder) High View link This is perfect for watching movies on your iPad mini or other small tablet on a plane. Even when a TV is available, I usually am watching highbrow classical concerts not available even in first-class. This will secure your small tablet to the seat in front of you.
Bag Foldable Duffle Bag link You never know when a casual seminar will turn into a bank heist. This foldable duffle bag is helpful if you do a fair bit of shopping on your trip and need the extra room. Also on a longer trip, I will use this with my carry-on bag.
Suitcase/carry-on Zuca Flyer Business Bag link This really is the ULTIMATE suitcase. It is a carry-on size, but this plus the Arikiv are a month’s worth of clothes for me - especially if I also bring the duffle bag. This is an indestructible bag. If you need to make repairs you can find what you need at Home Depot. It also doubles as a seat when you are waiting at the gate.
Travel accessory Bag Bungie link I secure this to my carry-on and then can add a duffle bag on top
Travel accessory Jacket grip link Lets you easily hang a jacket from your bag. I haven’t tried, but I bet this would help with a poster tube as well
Travel accessory Travel vacuum bags link This is a must. You can compress all your clothes without a vacuum. Just roll the air out using these bags. This is one of several brands I have used. Cary an extra one to keep your worn dainty unmentionables separated.
Travel accessory Travel umbrella link A dependable, lightweight umbrella.
Travel accessory RFID neck stash wallet link If you will be visiting shady locales, this may help keep your valuables safe.
Travel accessory Sleep mask link Comfortable!
Travel accessory Ostrich Pillow link For when you must block the outside world out.
Travel accessory - electronic Bluetooth Speaker link I have to surround myself with music. This is very loud, compact, and holds a charge.
Travel accessory - electronic Lightning cables link These cables for Apple mobile products won’t crack.
Travel accessory - electronic External battery link Provides several charges for phone and iPad. Buy whatever you need but make sure that the mAh are not above TSA/FAA standards; some countries you travel to may also have local standards - I’ve lost batteries this way.
Travel accessory - electronic Travel adaptor link Perfect for foreign travel and has USB ports.
Travel accessory - electronic Parrot Headphone link My choice for noise-cancelling headphones. Make sure to get an extra battery.
Travel accessory - electronic Lapa Bluetooth tracker link I have a few that I can put in my bags. Besides the ability to help you find a lost item (in theory) via crowdsourced GPS; you can set a safety mode which will inform you if you (or your item) is more than a certain distance away.

Other Travel Items

Travel Pharmacopeia - liniments and snake oils

Drugs are an essential part of travel; conferences are germ cesspools. Be prepared. Also, anyone with a little MacGyver ingenuity and a first-year pharmacy degree will recognize the possibilities in my selections should they find themselves kidnapped by nefarious forces.

Travel Phrase Book

If you are going to a place where your language is not spoken, keep some kind of book (paper/electronic) with useful phrases. Most languages will have an App you can download with the more common phrases. Here are some phrases you might not find in an App, but which I have always found useful. I will be adding to this, and also some translations. I am grateful for additions or corrections to translations so please submit a pull request.

Phrase Translation: Chinese
“Either get this for me now, or find someone who can!” 要么现在得到这个给我,要么找到一个可以的人!
“What is it going to take to get the charges dismissed?” (helps to flash a $20) 如何解决这些指控呢?(给他们看100元)
“Do you know who I am?!” 你知道我是谁吗?!
“Are you out of your mind? I am a citizen of the United States of America!” 你疯了吗?我是美国公民!
“S/he’s not expected to survive, I did everything I could”😏 他/她没有预期的生存,我尽我所能😏
“I can’t be connected to(this)in any way” 跟(这个)一点关系我要都没有
“Send a message to our listening posts…” 发送消息给我们的聆听帖子
“I deserve the best!” 我应该得到最好的!
“I thought it would amuse me” 我认为这会让我愉快
“If I go down, you’ll lose everything” 如果我失败,你会失去一切
“I don’t have time for this nonsense” 这个废话我没有时间了
“I’ll have another (beverage)” 再一杯!
“I’m feeling attacked!” 我感觉到被攻击了!
“I find accusations that I stole the cake, insulting and provocative” 我觉得无礼的传闻我偷了蛋糕是完全辱骂的,挑衅的。
“By this time tomorrow, every cupcake within 1000 miles will be mine.” 明天这个时间,每一个1000英里以内的纸杯蛋糕都将是我的。
“Make it look like an accident” 使(它)看上去像一个事故了。