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Repbase to Adopt Non-Profit Subscription Funding Model

Sep 9, 2018

If you've been keeping up with genetic research, you'll know that genome sequence information is expanding at an exponential pace. This is exciting and phenomenally important for further studies, but there is a downside. Catching up with this increasing pace is one of the major challenges for many bioinformatics databases, including Repbase1. As a database of fundamental genome sequence information, Repbase needs to be able to match its curation pace to the rapid acceleration of this genome data, all while maintaining the high-quality standards you have come to expect. This massive amount of data curation and technical upkeep requires financial resources that have not been forthcoming from government funding agencies. Despite this, we want to make sure that we are able to keep Repbase as current and high-quality as possible. Therefore, we plan to transition Repbase to a community-supported subscription model in the coming months.

Why are we switching to a subscription-based funding model?

Like many other life science databases, Repbase had been supported by government funding for its development from 1992 until 2014. This enabled us to provide our database free of charge for academic users. However, this funding alone was not enough to sustain the database in a longer run. Even before its government funding expired, Repbase was categorized as a vital but "endangered" database in a 2012 news article in Nature2. We attempted to continue free access for academic users via commercial licenses and private funds after the governmental support ended in 2014. Unfortunately, we could not rely on this model exclusively, so we reached the conclusion that we needed to move forward toward sustainable financial support for consistent service.

How it Will Work and How You Can Support Repbase?

Repbase/GIRI is developing our community-supported subscription model with the partnership of Phoenix Bioinformatics. Phoenix is a US-based 501(c)(3) non-profit organization that manages community financial support for TAIR (The Arabidopsis Information Resource), which was previously funded by the National Science Foundation (NSF) and is now fully supported by users3. Recently, BioCyc, a database collection of microbial metabolic pathways, successfully moved to the subscription-based model with support from Phoenix. Repbase is following the example of these two successfully transitioned databases. Subscription revenues will be invested into curation, operation, and outreach for Repbase.

Subscription prices will be based on usage level, and our goal is to keep them as low as possible so that anyone who needs these data will still be able to access them. We will be offering subscriptions at both the individual and academic institutional level, and are currently finalizing these prices. We will soon be providing you with more information, including details on how to sign up.

How to maintain access?

  1. Email your librarian. The best way to ensure continued access to Repbase is to send an email in support of an institutional subscription to your librarian. In most cases the library will pay for the subscription if they are able, meaning you wouldn't have to pay for it with your own funding. If you're unsure of what to write, feel free to use or modify the following template:

    Dear (Librarian), I would like to request an institutional subscription to Repbase (www.girinst.org/repbase). Repbase is a fundamental database for eukaryotic genome studies. It is essential to my work and that of my colleagues. Further subscription information can be found by emailing subscriptions@phoenixbioinformatics.org. Thank you for your consideration.

  2. Encourage your colleagues to add their voices. Very often, libraries don't decide to subscribe to a resource until they get enough support from researchers at their institution, particularly faculty members. The more people you have petitioning your library, the more likely it will be that they will consider a subscription if they are able.
  3. If your institution can't subscribe, subscribe individually. We will be offering individual subscriptions when we begin requiring a subscription for access. These are a good alternative if your institution is unable to subscribe.

The Future of Repbase

With your support, we can continue to provide the high-quality data and tools you expect from Repbase, and we will be improving! We heard you - last year's survey indicated that you'd like Repbase to cover more genomes. New species to be analyzed will be selected based on their medical and agricultural importance, the genome sizes and abundance of TEs, biodiversity, and the quality of genome sequences.

Please spread the word to your colleagues and friends -- the more supporters we have, the more useful we can make Repbase for the scientific community.

References

  1. Bao W. et al. (2015) Repbase Update, a database of repetitive elements in eukaryotic genomes. Mob DNA. 2015;6:11.
  2. Baker M. (2012) Databases fight funding cuts. Nature 489: 19
  3. Reiser L. et al. (2016) Sustainable funding for biocuration: The Arabidopsis Information Resource (TAIR) as a case study of a subscription-based funding model. Database 2016: bav018
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