Help ensure BioGPS remains availablePosted by Andrew Su on Jun 20, 2016 in application, BioGPS, crowdsourcing, funding | 7 comments
2016.06.28 update- We need letters of support submitted by Friday, July 1st…please help!
In the last two months, we focused on encouraging the user community to add and review more plugins. Since its humble beginnings, BioGPS has been a product of an amazing community of users–users who have extended its functionality with plugins, and aided its development with their letters of support. The very first grant application for the development of BioGPS was funded, thanks to 60 compelling letters of support from the user community; and our renewal was again made possible by your support.
We still have a lot of improvements in store for BioGPS, but won’t be able to implement them let alone maintain this resource without community support. Once again, we are applying to renew funding for BioGPS, and will likely not succeed without your help. If you have used BioGPS or would like for BioGPS to continue to be available, please contribute a letter in support of BioGPS. Topics in your letter might include (but not be limited to):
- A little bit about yourself
- Why you use BioGPS and/or MyGene.info
- What impact BioPGS and/or MyGene.info have had on your research
- What you’re particularly excited about in our plan moving forward (more below!)
We would very much appreciate any letters in pdf format with official letterhead showcasing your institution or company. Email your letters directly to asuscrippsedu and cwuscrippsedu, and feel free to contact us with any comments or questions. Your letters of support are essential for us to continue providing innovative tools for biomedical research.
For those who are wondering what our plans are, here is a sneak peek of our proposal:
Aim 1: Integrate BioGPS with community tools for plugin, gene list, and data set management. The landscape of Big Data resources has drastically changed over the past four years. Specifically, there are many aspects of BioGPS that are now handled by other applications “as a service”. By technically integrating with these other specialized services, our users can benefit from additional features and greater stability. That move will in turn allow us to focus on building up the unique aspects of BioGPS — the customizable and integrated user interface to useful biomedical data.
Aim 2: Expand MyGene.info data resources. MyGene.info provides simple programmatic access to almost 250 gene and protein annotation fields via our high-performance API. And judging by our 10M hits per month from over 4000 users, this platform is a useful community resource. We’ve come up with a “short list” of ~20 new data resources to add, which includes some resources that are well-known in the field, as well as some other useful resources you probably didn’t know existed.
Aim 3: Generalize the MyGene.info software pattern to other biomedical entity types. As the MyGene.info users probably know, we have created a sister project called MyVariant.info, which provides the same high-performance API for integrated reports on annotations of human genetic variants. MyVariant.info is also getting quite a bit of traffic, which has convinced us that there may be many other applications of our infrastructure. In this aim, we generalize what we’ve learned in creating and maintaining MyGene and MyVariant into a Software Development Kit (SDK) called Biothings.io, and apply that the creation of a similar resource for diseases and chemical compounds.
Aim 4: Create BioReel, a new application for monitoring updates about any Biothings entity. We view BioGPS and MyGene.info as great tools to answer the question “Tell me everything that’s known about a new gene of interest” (candidates from some genome-scale experiment, for example). But for people who already know quite a bit about a given gene, there isn’t a great tool to get customizable and integrated notifications when something new is discovered or annotated. That is our vision for BioReel, a new application that will allow users to subscribe to update notifications for any Biothing entity.
We think that this proposal is a nice blend of building on existing products with an established user community (BioGPS and MyGene.info) and of building new applications that will appeal to a broader audience of researchers (Biothings and BioReel). If you agree, please send us your letter of support!