Yesterday at around noon I was on a conference call for a large-scale disease genomics project. In the middle of the call, a NCBI database that we use to exchange data — dbGaP — went offline. The shutdown had apparently taken effect.
To say that dbGaP is important for the day-to-day operations of a large-scale sequencing center is a great understatement. This database is vital to what we do. It’s not only where we submit grant-funded sequencing data, but also the controlled-access exchange portal for GWAS (SNP array) data, phenotype data, and other information for most of our collaborative projects.
Once it went down, there wasn’t really much to talk about, so we ended the call. Through the course of the day, I quickly came to recognize how essential U.S. government operations are to our research activities. It seemed to merit a blog post here on MassGenomics.
I won’t get into the ridiculous and embarrassing political ridiculousness that got us here. There’s no single person or party to blame; our elected officials simply aren’t doing their jobs. And the shutdown, I’m sorry to say, is already hampering our ability to conduct research.
NCBI Resources at Risk
The National Center for Biotechnology Information (NCBI) provides many resources that a lot of us take for granted. As Erika Check Hayden wrote yesterday in Nature, the NIH has already warned that it may not be able to sustain online resources such as PubMed and GenBank. Presumably, NCBI’s repository of sequence variation (dbSNP) and sequencing/genotype/phenotype data (dbGaP) are also affected. The top of every page reads, “Due to the lapse in government funding, the information on this web site may not be up to date, transactions submitted via the web site may not be processed, and the agency may not be able to respond to inquiries until appropriations are enacted.”
Large online databases, believe it or not, require considerable technical resources (servers, hard drives) as well as support and repair personnel to stay online. Most of those personnel are currently on furlough, so a hardware failure might render these resources inaccessible. Similarly, most of them aren’t accepting new data. Secure, controlled-access exchanges like dbGaP exist to facilitate the essential exchange of data and to protect the privacy of those individuals who participate in research.
With dbGaP essentially offline, we have no way to exchange data. So it truly puts the brakes on many areas of genomic research.
Government Employees on Furlough
The NIH employs about 18,646 employees, of which 73% are currently forbidden to work and without pay. This includes the administrators who manage the application, review, and funding of grants. Our program officers are incommunicado, which leaves many large, important research projects “in irons”. Most researchers are, of course, capable of moving forward on their own, but it sure helps to have leadership at the top. Otherwise it’s like a lab meeting without the P.I. We feel very badly for our colleagues. And we miss them.
NIH’s 27 institutes also fund many intramural researchers, many of whom are among the top investigators in their fields. I guess they had to quickly freeze their cell lines, feed the mice, and lock the door on their way out. Who knows how many fragile experiments were ruined by this unnecessary interruption? “Save early, save often” is a good rule for computers but unfortunately can’t always be done in science.
I hope someone remembers to feed the mice. We have enough problems with the animal rights activists already!
Ending the Shutdown and Preventing Future Ones
It is incredibly frustrating, and internationally quite embarrassing, that our government cannot function. This shutdown has hindered or halted U.S. biomedical research, whose ultimate goal is to improve human health. So even those who might not immediately feel the harm of the shutdown are going to eventually be affected. Drugs aren’t being approved. New disease genes aren’t being found. We all suffer the consequences when elected officials are unable or unwilling to do their fricking jobs, compromise, and work together like they taught you in kindergarten.