Introducing the TE Hub, a platform for researchers in Transposable Elements

The TE Hub Consortium recently authored a commentary for Mobile DNA on the TE Hub, an open and collaborative platform, providing an entry point and reference site for researchers interested in Transposable Element (TE) diversity, identification, and annotation. While we eagerly await the publication in our journal, the authors participated in a sneak preview Q & A about the project.

Can you tell us a bit about the background and initiation of TE Hub?

Hadi Quesneville: In May 2019, during the FASEB Mobile DNA Conference, several of us met informally and started to discuss the overload we face with people asking for our help in annotating TEs, and storing TE annotations and their reference sequences. We realized that we have arrived at a point where none of us are able to reply comprehensively to this increasing demand. We needed to do something for the community to cope with the bottleneck of TE annotation and bioinformatic analysis. We proposed to engage the TE bioinformatic community in organizing their expertise, knowledge, and tools on a collaborative platform that would help the TE community to find their way in the expanding maze of tools, methods, and resources. After sending some emails, Slack messages, and Tweets, a first video meeting was organized to discuss how we could build it.

When and why did you compile lists of repeat databases and repeat tools?

Tyler A. Elliott: I’ve had a long-standing interest in the existing resources for TEs, and like many others I’m sure, have had the thought that it would be useful to have a single point of reference for all of this information. The first step though was just understanding what databases and tools are available. Some of my team members at the CBG helped compile an initial list, which I then expanded greatly during my spare time. Most of this work happened during 2019, when I first shared the lists in a publicly-accessible document.

I also wanted to compile information on the various systems used to classify TEs, as well as the references for these systems, in addition to a list of various named elements and when researchers proposed larger groupings of elements. I wanted people to be more aware of these, in the hope that when new elements are discovered they can be placed within this greater context.

What have been key milestones and obstacles in setting up TE Hub?

Travis J. Wheeler: After kicking off bi-monthly meetings in June 2020, we quickly locked in a vision and laid out a concrete plan for developing and populating the website. This required setting up the technology stack (a heavily augmented version of the wiki.js package), followed by extensive content contributions to prepare the site for its initial release. We’ve finally reached the part that motivated the work: inviting others to get involved!

A central challenge has been establishing the scope of TE Hub – what role will it serve (and importantly, not serve) in the TE community. It’s really easy for the scope of a project to expand beyond supportable limits; we’ve worked hard to clearly define the purpose of TE Hub as supporting the access to TE resources, tools, and annotation methods.

How can I stay updated on news and announcements in TE Hub?

Alexander Suh: Please follow us on Twitter @hub_te for TE Hub announcements, join the #te-hub channel on TransposonsWorldwide Slack for written news, and we also have our ‘Hub Updates’ (announced via the aforementioned channels) which are bi-monthly video calls for news and open discussions.

How can experts and novices get involved in contributing to TE Hub?

Robert Hubley: The implementation of TE Hub as a wiki-based site serves two central goals: it supports decentralized community-directed growth, and provides opportunities for contributors with a wide diversity of expertise.  The current topic areas are simply a starting point from which the site will evolve with the interests of individual contributors.  In addition, many of the resources currently residing on the site benefit directly from the ongoing assistance of novice and expert editors alike.  If someone is unsure of how they can best assist the effort, please get in touch.

Where do you see TE Hub going in the short, medium, and long term?

Tony Heitkam: Currently, we are communicating TE Hub’s mission and are inviting researchers to join our effort. One of our communication efforts is the upcoming Mobile DNA commentary; another is a poster at the FASEB conference.

In the short to medium term, we aim to broadly expand the wiki. To ensure secure and dependable maintenance, we are planning secure baseline funding for the scaling of TE Hub. In the long term, we wish to put forward a framework for the translation and integration of tools and databases. Ideally, we hope to step past the listing of databases and tools, and to provide translations from one system/tool/classification scheme towards the other. We foresee that this will open the TE field further, making it easier for both novices and experts to procure TE annotations.

Tyler A. Elliott, Tony Heitkam, Robert Hubley, Hadi Quesneville, Alexander Suh, & Travis J. Wheeler

Tyler A. Elliott is the Data Management Lead (Informatics Unit) at the Centre for Biodiversity Genomics at the University of Guelph, Canada. His interests include the origin and evolution of TEs across the Tree of Life, including their patterns of diversity and abundance within and across genomes

Tony Heitkam is a scientist at the Technische Universität Dresden (Germany). She aims to understand the biology and evolutionary history of plant genomes as well as the genome's organization into chromosomes -- all with a focus on the role of repetitive DNA and transposable elements.

Robert Hubley co-leads the Dfam project at the Institute for Systems Biology. His research focuses on generating new computational methods for modeling and annotating TE families.

Hadi Quesneville is research director at INRAE, the France's National Research Institute for Agriculture, Food and Environment, for which he is Chief Data Officer. His research encompasses tools and methods development for data annotation, data integration, and information system federation.

Alexander Suh is a lecturer at University of East Anglia (UK) and social media editor for Mobile DNA. His research group focuses on understanding evolution of animal genomes from the perspective of transposable elements, endogenous viruses, and germline-restricted chromosomes.

Travis J. Wheeler is an Associate Professor in the University of Montana Computer Science department. His research touches on statistical models, algorithms, and visualization for biosequence annotation.
Tyler A. Elliott, Tony Heitkam, Robert Hubley, Hadi Quesneville, Alexander Suh, & Travis J. Wheeler

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