Tag Archives: funding

Participate in an NSF “IDEAS LAB” (generate research agendas and proposals)

Greetings!
The short link: IUSE IDEAS LAB: http://www.nsf.gov/pubs/2014/nsf14033/nsf14033.jsp

IUSE:
NSF’s education directorate has a funding opportunity called “Improving Undergraduate STEM Education” (IUSE).

The IUSE program description [PD 14-7513] http://www.nsf.gov/funding/pgm_summ.jsp?pims_id=504976 outlines a broad funding opportunity to support projects that address immediate challenges and opportunities facing undergraduate science, technology, engineering, and math (STEM) education,
To generate research agendas and proposals for this, NSF is holding an… 

Ideas Lab:
Ideas labs are meetings that bring together researchers, educators and others in an “intensive, interactive and free-thinking environment, where participants immerse themselves in a collaborative dialog in order to construct bold and innovative approaches and develop research projects.” MOre often than not, these “Ideas Labs” produce new collaborations and research projects proposals that often go on to be funded. The Ideas Lab is patterned after the Ideas Factory process.
“to make new connections, which are frequently cross disciplinary, and also generate novel research projects coupled with real-time peer review.”
This NSF Ideas lab has several purposes, but the one most pertinent to this community is finding new ways, and develop research proposals, to infuse computational thinking, literacy and competency into the core curriculum for undergraduate education.
Individuals apply to the Ideas lab, it’s a 2 page proposal and is DUE FEBRUARY 4 (Next Tuesday). Funding is provided for the trip. These ideas labs are excellent ways to meet and discuss genomics, biology and education, build new collaborations and to develop new research proposals.
The letter and more information (read the link):
A Dear Colleague Letter on the topic of ³Preparing Applications to
Participate in Phase I Ideas Labs on Undergraduate STEM Education² [NSF
14-033] has been posted on the NSF web site.
If you have any questions, you can ask here or by email (wlathe AT openhelix.com ). I am _not_ a project officer at NSF and don’t have all the answers, but I can direct you to the places you might find answers.
PLEASE feel free to disseminate!

Friday SNPpets

Welcome to our Friday feature link dump: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment…

(re)Funding Databases II

ResearchBlogging.orgSo, I wrote about defunding resources and briefly mentioned a paper in Database about funding (or ‘re’funding) databases and resources. I’d like to discuss this a bit further. The paper, by Chandras et. al, discusses how databases and, to use their term, Biological Resource Centers (BRCs) are to maintain financial viability.

Let me state first, I completely agree with their premise, that databases and resources have become imperative. The earlier model of “publication of experimental results and sharing of the reated research materials” needs to be extended. As they state:

It is however no longer adequate to share data through traditional modes of publication, and, particularly with high throughput (‘-omics) technologies, sharing of datasets requires submission to public databases as has long been the case with nucleic acid and protein sequence data.

The authors state, factually, that the financial model for most biological databases (we are talking the thousands that exist), has often been a 3-5 year development funding, that once runs out, the infrastructure needs to be supported by another source. In fact, this has lead to the defunding of databases such as TAIR and VBRC (and many others), excellent resources with irreplaceable data and tools, that then must struggle to find funding to maintain the considerable costs of funding infrastructure and continued development.

The demands of scientific research, open, shared data, require a funding model that maintains the publicly available nature of these databases. And thus the problem as they state:

If, for financial reasons, BRCs are unable to perform their tasks under conditions that meet the requirements of sceintfic research and the deamnds of industry, scientists will either see valuable information lost or being transferred into strictly commercial environment with at east two consequences: (i) blockade of access to this information and/or high costs and (ii) loss of data and potentioal for technology transfer for the foreseeable future. In either case the effect on both the scientific and broader community will be detrimental.

Again, I agree.

They discuss several possible solutions to maintaining the viability of publicly available databases including a private-public dual tier system where for-profits paid an annual fee and academic researchers have free access. They mention Uniprot, which underwent a funding crisis over a decade ago, as an example. Uniprot (then Swissprot) went back to complete public funding in 2002. There are still several other databases that are attempting to fund themselves by such a model. BioBase is one where several databases have been folded. TransFac is one. There is a free, reduced functionality, version that is available to academics through gene-regulation.com and the fuller version for a subscription at BioBase. This former version allows some data to be shared, as one could see at VISTA or UCSC. I am not privy to the financials of BioBase and other similar models, and I assume that will work for some, but I agree with the authors that many useful databases and resources would be hard-pressed to be maintained this way.

Other possibilities include fully  including databases under a single public institution funding mechanism. The many databases of NCBI and EBI fit this model. In fact, there is even a recent case of a resource being folded into this model at NCBI. Again, this works for some, but not all useful resources.

Most will have to find variable methods for funding their databases. Considering the importance of doing so, it is imperative that viable models are found. The authors reject, out of hand, advertising. As they mention, most advertisers will not be drawn to website advertising without a visibility of at least 10,000 visitors per month. There might be some truth to this (and I need to read the reference they cite that use to back that up).

But the next model they suggest seems to me to have the same drawback. In this model, the database or resource would have a ‘partnership of core competencies.’ An example they cite is MMdb (not to be confused with MMDB). This virtual mutant mouse repository provides direct trial links to Invitrogen from it’s gene information to the product page. They mention that though 6 companies were approached, only one responded. It would seem that this model has the same issues as directly selling advertising.

They also mention that, at least for their research community of mouse functional genomics, “Institutional Funding” seems the best solution for long-term viability and open access. Unfortunately, until institutions like NIH and EMBL are willing or able to fund these databases, I’m not sure that’s thats a solution.

As they mention in the paper, the rate of growth of the amounts and types of data that is being generated is exponential. I am not sure that government or institutional funding can financially keep up with housing the infrastructure needed to maintain and further develop these databases so that all the data generated can remain publicly and freely accessible.

Information is should be free, but unfortunately it is not without cost. It will be interesting to see how funding of databases and resources evolves in this fast growing genomics world (and imperative we figure out solutions).

PS: On a personal note, the authors use their resource, EMMA (European Mouse Mutant Archive), as an example in the paper. I like the name since it’s the name of my daughter, but it just goes to prove that names come in waves. We named our daughter thinking few would name their daughter the same. When even databases name the same name, you know that’s not the case.

Chandras, C., Weaver, T., Zouberakis, M., Smedley, D., Schughart, K., Rosenthal, N., Hancock, J., Kollias, G., Schofield, P., & Aidinis, V. (2009). Models for financial sustainability of biological databases and resources Database, 2009 DOI: 10.1093/database/bap017

(re)Funding Databases I

I blogged recently about (de)funding databases and lo and behold, a new paper was just published in Database (which is a new journal I just blogged about earlier this year) on that very subject:

Models for financial sustainability of biological databases and resources — Chandras et al. 2009 (0): bap017 — Database.

I will be writing up a longer review and some thoughts about the article. I’m having a bad blog week, and kind of lost some stuff I was writing. But I would like to point out the article for now, post my thoughts soon (later this evening?)

(de)Funding Databases


From Deepak Singh:

Scientists spend years collecting and generating increasing amounts data. The data ranges from raw instrument data, “finished” data (e.g. a

crisis_newbanner_correctsize1_flattenedgenome sequence which is constructed after aligning all the short reads from a next-gen sequencer), and annotated data, which has been marked up to add additional information. We have repositories where a lot of this data goes, RCSB, NCBI, etc. In many cases there is clarity in these

destinations and for the better part, resources like RCSB and NCBI are well funded and long lived (although I am always nervous about RCSB). However, many data repositories are dependent on funding, with no guarantees that the funding will be renewed. Given the size of some of these data resources, shouldn’t we be thinking of a more sustainable model for funding? This is a general problem for infrastructure resources, given the cost and the fact that you shouldn’t be looking at these from a 3-5 year perspective. This especially baffles me when libraries come into play. Shouldn’t the timescale there be in the 10’s of years?mndoci.com, The disconnect in funding data resources, Oct 2009

You should read the whole article.

A recent example of this is the arabidopsis resource, TAIR.

Continue reading

SBIR and STTR Funding Bill Extension Being Considered this Week

SBIR Funding ImageThe Office of Technology administers the Small Business Innovation Research (SBIR) Program and the Small Business Technology Transfer (STTR) Program to provide funding to small and fledgling biotechnology and genomics businesses. These programs are currently scheduled to sunset in September, but this week an extension is being considered that would take the programs through September 2012, according to the article I just saw in the GenomeWeb News email that I just received. You can read more about the program here.

Now you may be wondering “Who Cares?”… Continue reading