Help ensure BioGPS remains available

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 asuatscrippsdotedu and cwuatscrippsdotedu, 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.
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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!


7 Comments

  1. Ruirui Zhang

    for aim2: Expand MyGene.info data resources.
    thanks~

  2. Dear Madam/Sir,

    This letter is to provide my sincerely support to BioGPS for research studies of various areas.
    I, as faculty of the Department of Anesthesiology and Perioperative Medicine in the Medical College of Georgia at Augusta University, have been using BioGPS for my research projects for many years. BioGPS is extremely useful to understand in which tissues a gene is expressed at high levels in our body. Such information is particularly important to develop potential therapeutics for many types of disorders. Our research focuses on hematology and we visit BIoGPS so often to examine whether a gene is expressed in non-hematological tissues. The database of BioGPS include a variety of organs and tissues in humans and other animals, which makes BIoGPS so useful.

    I am hoping that BioGPS is further supported and, if possible, should be expanded to include multiple Aims that are listed in this web site. Also, I acknowledge the usefulness of BioGPS for many years.

  3. I love BioGPS, I use it to quickly look at the expression pattern of my genes of interest in tissues or cell lines

  4. Utsav Saxena

    Please keep BioGPS alive, it is an indispensable research tool.

  5. TO WHOM IT MAY CONCERN
    Lisardo Boscá (Spain, 1957) is Senior Research Professor at the Spanish Research Council (CSIC) and has been director of the Institute of Biochemistry (1999-2005; co-shared by CSIC and UCM) and of the Institute of Biomedical Research Alberto Sols, (2008-12; co-shared by CSIC and UAM). He has acted as NCP for the FP6, FP7 and CYTED, and responsible of the National Research Program in Biomedicine (2008-12) and of the Financing agency of the Instituto de Salud Carlos III (Spain; 2013-14). He is author of more than 200 original articles of research published in international journals in the field of biochemistry, molecular biology and immunology (J. Exp. Med; Nature Cell Biology, FASEB Journal, Gastroenterology, Blood, J. Clin. Invest., Proc. Natl. Acad. Sci. USA; J. Immunol; J. Biol. Chem; Hepatology, Biochem. J, Nature Medicine). He began his studies under the direction of Professor Alberto Sols investigating the effect of protein interactions in the regulation of carbohydrate metabolism. Later he continued his post-doctoral training at Oxford University, Louvain Medical School, Cancer UK (London) and Ottawa studying the role of protein kinase C on energy metabolism in tumor cells. From 1997 onwards he focuses on the study of the physiopathology of inflammatory processes investigating the contribution of inflammation to the onset of pathologies as diverse as myocarditis, septic shock, and to the liver regeneration processes. In this context, he studied the role of reactive oxygen and nitrogen species, in particular nitric oxide, on the regulation of liver regeneration after partial hepatectomy as well as in macrophage activation and in the heart after sepsis or myocardial ischemia/reperfusion, demonstrating its role in processes of remodeling of the extracellular matrix. Recently, he focused on the study of the metabolic control in macrophages as a primary regulator of the functional polarization and fate in the course of the inflammatory response.
    BioGPS has helped me in depth, providing cured information, and offering a platform of tremendous value to validate genomic information and suggesting new focus in the development of my work.
    I am happy to provide my help to this initiative for all actions intended to sustain continuity and improvement.

  6. James C. Fleet

    My apology for being late. I was unavailable until now.

    BioGPS has been a consistently useful resource for me and my research group. We use it regularly to understand where specific transcripts are expressed in mouse/rat/human tissues. This is critical for discovery based genetics and genomics studies. I strongly encourage continued funding for this valuable resource

  7. ginger

    To all of you who posted a comment in support of BioGPS–THANK YOU! We’ve submitted the grant renewal application and will keep the community posted when we hear back.

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