There Is an Internet in Space

In a recent blog, Dr. Brennan correctly identified a future issue: access to medical information from a Mars colony, should one be established. In her summary, she said there was no Internet in space.

Actually, there is.

It uses a protocol suite other than the terrestrial TCP/IP originally designed by Bob Kahn and me beginning in 1973 and which has evolved over time thanks to the work of the Internet Engineering Task Force and many researchers and Internet practitioners around the world.

The Interplanetary Internet (sometimes called the Solar System Internet by the UN’s Consultative Committee on Space Data Systems) adopted a suite of protocols known generally as the Bundle Protocols. The prototypes of these protocols are on board the Mars rovers, Spirit and Opportunity, the Mars Science Laboratory, and the International Space Station.

The rovers and Science Laboratory use the Bundle Protocols to deliver their data to Earth by way of re-programmed orbiters initially sent to Mars to map the surface of the planet. In essence, the rovers and Science Laboratory capture sensor data, which they beam to the orbiter(s) as the orbiter(s) become visible. The orbiters then hold that data until they can be transmitted to Earth by way of the Deep Space Network (DSN), which was put into operation in the early 1960s to support manned and robotic space exploration. This transmit-and-hold approach of the Bundle Protocols is representative of Delay and Disruption Tolerant Networking (DTN).

The Deep Space Network has three 70-meter dishes located at Canberra, Australia; Madrid, Spain; and Goldstone, California. There are also several 34-meter dishes at these same locations. The DSN is operated by the Jet Propulsion Laboratory  in Pasadena, California, under the oversight of the California Institute of Technology. These large dishes allow the Jet Propulsion Laboratory to receive very weak signals from spacecraft very distant from Earth. The Voyager spacecraft, Voyager 1 and Voyager 2, are now respectively 20.7 billion kilometers and 17 billion kilometers away from Earth and into interstellar space. The DSN can still read the very, very weak signals from both spacecraft.

If a plan does indeed emerge to assure that relevant information from the National Library of Medicine is available to Mars astronauts and perhaps colonists, the natural preparatory step would be to outfit the NLM online systems with Bundle Protocol capability. But don’t expect any kind of real-time, interactive World Wide Web-like service for Mars residents. The light speed round-trip times between Earth and Mars vary from 7 minutes to 40 minutes, and the data rates between Earth and Mars currently run less than 1 Mb/s using conventional radio communications. Experiments have been conducted using laser communications between Earth and the Moon at 600 Mb/s, so one might hope for significant data rate improvements in the future.

If humanity is to become a space-faring species, it will need continuing access to the scientific and medical advances cataloged in the NLM’s systems. We can certainly imagine putting up local data servers on Mars for rapid local interaction while updating these local archives from Earth NLM periodically.

More Information
InterPlanetary Networking Special Interest Group

Image source (top): NASA: Mars Explorers Wanted Posters | modified

Is NLM Building a Library on Mars?

Safe, productive human space travel requires more than sophisticated spacecraft. From environmental conditions to the physiological and psychosocial impacts, NASA’s astronauts face unique challenges while living in space.

To help address those challenges, NIH and NASA established a research partnership in January 2016. The research opportunities arising from this partnership and through NASA’s Human Research Program are expected to improve health both for the population on Earth and for those who travel to Mars and beyond.

What’s the Library’s role?

Well, we’re not getting ready to build an NLM outreach-to-Mars program (yet!), but we are involved in issues related to informatics and health information technology.

We’re expanding our collections and the standard health care terminologies (MeSH, SNOMED, LOINC, RxNorm) to address new environments (i.e., space) and the health concerns faced there (e.g., long-term muscle wasting, bone loss, space radiation exposure). MeSH, for example, already includes terms related to space flight, such as hypogravity and weightlessness; PubMed offers a subset of content focused on space life sciences; PubMed Central houses peer-reviewed papers resulting from NASA-funded research; and our History of Medicine Division holds a unique collection of scientific studies, technical reports, books, and pamphlets received from NASA in 2015.

We’ll also work to fully identify the information and resources needed to support biomedical research and to deliver health services to humans who may be light years away. We can potentially build upon NLM’s current work with machine learning and image recognition to speed diagnosis, and enhance our telemedicine efforts to account for an interplanetary communications delay approaching 42 minutes between Earth and Mars. We’ll further refine our emerging data science methodologies to accelerate discoveries in real time during manned missions. And perhaps most important to me, we’ll imagine—and plan for—a future without the internet.

No internet?!

Astronaut and moon reflected in the window of the space stationCurrently the internet is essential for the delivery of NLM’s most-used services, but there is no internet in space. We need to anticipate an independent technological infrastructure that will allow us to support research and medical care without it.

Such foresight, planning, and commitment can yield great results. Indeed, because of NLM’s leadership of the High Performance Communication and Computing Program 24 years ago (1992), we had satellite communication services in place to support the long-distance conversation between NIH Director Francis Collins and Astronaut Kate Rubins last October (2016).

But thinking systematically about how to deliver scientific knowledge in space will yield benefits long before the Orion spacecraft sets course for Mars.

While we don’t expect the internet here on Earth to go away, we must be prepared to deliver 24/7 access to NLM resources in the event of an interruption in internet service, whether due to natural disasters, construction failures, cyberterrorism, or even solar flares.

So, the next time you hear that NLM is working on human space exploration, remember that, while we’re planning for an information-rich future, we’re also ensuring an information-available present.

The library on Mars will come later.

Co-authored by Dianne Babski, Deputy Associate Director for Library Operations, who serves as the NLM representative to the NIH/NASA Biomedical Research Partnership.

Photo credit (Mars in space, top): Composite NASA Hubble Space Telescope Image (October 19, 2014) | cropped

Sharing Small Data Files for More Analysis Power

Guest post by Ashley Hintz, curator for NLM NCBI’s Sequence Read Archive.

Imagine the rows upon rows of books in the stacks of a research library. Then imagine how much information is stored in those books.

An organism’s entire genome is the equivalent of that large library with its multiple floors of loaded shelves. It is densely packed with information.

Just as reference librarians specialize in locating specific information within the library, bioinformaticians specialize in working through, analyzing, and understanding genomes.

And as librarians determine how best to search the online catalog to locate a specific item within the library, bioinformaticians write computer scripts to filter the massive amount of genomic data and identify the parts most relevant to particular research questions. Such filtering creates smaller data files that are easier to analyze, visualize, and share with colleagues.

Unfortunately, many researchers don’t start with the smaller, filtered genomic data sets.

These researchers are stuck believing they must always begin their analysis from the full genome, even though most of the genome’s elements have nothing to do with their research questions.

The idea that you must have the original raw sequence data to analyze the data correctly means that large amounts of data (sometimes terabytes) get moved on a regular basis, or, given the data’s large size, they never move, so access to them is limited.

It’s the equivalent of checking out the whole library when a couple books will answer your questions.

Genomes can be filtered by SNPs (or single nucleotide polymorphisms) from a vcf file, collections of genes, or read counts for gene expression data. All of these smaller data files have practical-use cases and deliver what researchers are commonly interested in.

Current technology also makes sharing these filtered data files incredibly easy. Given their small size (mere gigabytes), it’s more on the scale of sharing pictures of your children or pets.

Sounds good, but what can one accomplish with these filtered genome datasets?

One example: perinatal screening for genes and/or SNPs that can potentially cause disease. Once the entire genome or exome is sequenced, the doctor can examine a vcf file of SNPs, filter that file further using data about the family’s medical history or the infant’s clinical symptoms, and then transfer the data files easily to a specialist for a second opinion. In these cases, the smaller data file becomes a powerful diagnostic tool.

A second example: gene expression data used in research. Instead of each scientist recalculating read counts (such as FPKMs), one researcher can share smaller analysis files with others. The smaller files can then be used to identify and visualize meaningful differences in expression between genes or samples. This sharing is not only more efficient; it also facilitates the collaboration necessary to tackle such significant and complex medical issues as obesity, Alzheimer’s, and autoimmune diseases, all of which show differences in the expression levels of certain genes.

These examples just scratch the surface of the power behind filtering genome data for data analysis, visualization, and sharing.

With genome sequencing growing more affordable, the amount of sequence data is expected to grow more rapidly, so we need to change the mindset that we must start with the whole library to see results. Think “focused” instead of “complete,” or, as the librarians like to say, “precision over recall.”

It’s one more example of where less, most definitely, can be more.

Channeling My Inner Betsy

A few of the lessons she imparted to me

In just a few days Betsy Humphreys, MLS, will officially retire from the National Library of Medicine after 44 years of outstanding service.

Over the past two weeks we have been celebrating her and acknowledging her incredible contributions to the nation’s health through her many roles at NLM. Currently NLM’s deputy director, Betsy served as the first woman and first librarian to lead the Library (2015-2016 Acting Director) after many, many years in various leadership positions here, including as associate director of Library Operations. Over the years, Betsy received many accolades for her work, including the Medical Library Association’s Carla J. Funk Award, the Morris F. Collen Award from AMIA, and even an honorary LOINC code, 86466-0: Maestro of scalable info infrastructure. And though I could go on at length about Betsy’s accomplishments and all that she has done to advance access to medical information—for the good of NLM and the country—I’ve been pondering instead how I’m going to keep Betsy with us after she retires by channeling my “inner Betsy” as I lead NLM toward its third century.

Humphreys holds a plaque while standing next to Vreeman
Betsy Humphreys accepts a plaque from Dr. Daniel Vreeman of the Regenstrief Institute acknowledging her enduring contributions to health data standards.

First, I will draw on the amazing storehouse of knowledge Betsy developed over decades about how best to deliver the scientific literature to researchers, clinicians, and the public. That knowledge significantly exceeds what she managed to transfer to me over the 10 months we worked together, but fortunately, it exists in the work processes and practices of the 1,700 women and men at NLM and in the national bodies shaped by Betsy’s influence. Whether it’s an efficient and effective way to apply the MeSH terminology to citations or the importance of making SNOMED CT freely available, Betsy not only knew what to do but made sure it was done in a sustainable manner.

Next, I will conduct myself with generosity, grace, and good will. Betsy can discern the best talents within everyone, and she consistently noted those talents when she introduced someone or described his/her work to a new colleague. More than once I heard Betsy say, “You know, we have just the best person for handling…” whatever task needed to be handled. Obviously, she knew the players, but it was her ability to hold her colleagues in unquestioning positive regard that enabled the most effective partnerships to flourish and got the best people to address complex tasks.

I will channel a commitment to accountability—to science, to society, to patients, to partners, and to the authors who entrusted their works to NLM for archiving and distribution. Betsy didn’t wait for someone to ask for follow-up; she provided it as part of the workplace discourse. Maintaining accountability to our diverse stakeholders sometimes meant describing to one set of stakeholders why a decision apparently in support of a different set of priorities needed to be made and was most likely the best course. Betsy took that on and did it with tact and skill.

I will try to channel Betsy’s loyalty to her colleagues, to NLM, and to NIH. Betsy’s sense of accountability arose from this loyalty—her commitment to make possible a scientist’s research, a work team’s new process, a colleague’s investment in one of NLM’s services. Betsy didn’t often speak of loyalty; she simply demonstrated it.

Still from the video of a smiling Betsy Humphreys
Click to watch the tribute video to Betsy Humphreys.

Finally I will channel Betsy’s commitment to personal health and work-life balance. While many of us are sipping that second cup of coffee as we peruse the Sunday paper, Betsy and her husband/hiking partner, Glenn, are out traversing some trail, whether somewhere in the mid-Atlantic region or across the globe in the Italian Dolomites. Many a Monday was enriched by Betsy’s enthusiastic, bright-eyed description of how she and Glenn enjoyed a vista or found new flowers on a familiar path.

Betsy imparted these and many other lessons I’m sure I can put to good use, and I hope to channel my inner Betsy throughout my entire tenure at the National Library of Medicine.

How you will channel your inner Betsy? Chime in below.

The Hōkūleʽa Worldwide Voyage Comes Full Circle: The NLM Connection

Guest post by Dr. Fred Wood, Outreach and Evaluation Scientist in the Office of Health Information Programs Development.

On June 17, the ocean-going, double-hulled canoe Hōkūleʽa (named for Arcturus, the Star of Gladness) successfully completed its historic Worldwide Voyage.  The Hōkūleʽa departed Honolulu, Hawaiʽi, on May 18, 2014 and over the last three years traveled more than 60,000 nautical miles, stopping at 150 ports in 27 nations, while completing its circumnavigation of the globe.

Launched in 1975, the Hōkūleʽa recreates the type of ocean-going canoes used by Polynesians for thousands of years to traverse the Pacific Ocean and to discover other Pacific islands, including Hawaiʽi.  Hōkūleʽa’s original mission was to prove that traditional double-hulled canoes “powered” only by native knowledge of the wind and swells, as well as the sun, moon, stars, and ocean wildlife, could voyage across the 2,500 miles each way between Hawaiʽi and Tahiti. Once accomplished, this initial mission expanded to include voyages to other islands throughout the Pacific, west to Asia, and east to the US mainland.

Building on this voyaging success, the Hōkūleʽa transformed into a symbol for a broader revitalization of Native Hawaiian culture, pride, ecological sustainability, and health, messages that remain at the heart of its global voyage.

When that voyage reached Washington, DC in May 2016, NLM hosted Nainoa Thompson, one of only a handful of Native Hawaiians trained in the traditional navigation methods referred to as wayfinding. Thompson spoke passionately about the history and role of the Hōkūleʽa in promoting Hawaiian culture and health, and in advocating for environmental protection, sustainability of the oceans, and world peace.

Even before the Worldwide Voyage and Thompson’s lecture, NLM had closely followed the Hōkūleʽa and honored its importance in NLM exhibitions and associated websites and apps.

model of a double-hulled sailing canoe
A scale model of the Hōkūleʻa graced the entrance to the Library from 2011-2015.

For the NLM exhibition Native Voices: Native Peoples Concepts of Health and Illness, the Library commissioned a one-sixth scale model of the Hōkūleʽa built by Hawaiian artisans to the exact specifications of the full-sized canoe. The model was on display for several years in the NLM rotunda. In addition, Native Voices included interviews with Thompson, and with several of Hōkūleʽa medical officers, including Drs. Ben Young, Ben Tamura, and Marjorie Mau, who served on various legs of the Hōkūleʽa’s 40+ years of ocean voyaging.

The Hōkūleʽa and the ancient arts of navigation and voyaging were also at the center of the NLM exhibition A Voyage to Health, which looked at how the resurgence of Native Hawaiian culture helped heal the soul of the community. When the canoe and her crew returned to Honolulu last week, A Voyage to Health was there as part of the welcoming celebration.

Both traveling exhibitions have visited dozens of venues across Hawaiʽi and the rest of the US. And NLM’s scale-model Hōkūleʽa is now on display at the Disney Aulani Resort, in West Oahu, under auspices of the Friends of the Hōkūleʽa and Hawaiʽiloa.

NLM celebrates the accomplishments of the Hōkūleʻa and the entire Hawaiian voyaging community that participated in the Mālama Honua (“Care for the Earth”) Worldwide Voyage.  As that voyage comes to a close, NLM acknowledges once again its significance as an icon of Hawaiian culture, values, and health.

More Information
Native Voices Exhibition: NLM Hōkūleʽa microsite
Video: Nainoa Thompson’s Special Lecture on the Hōkūle’a and Native Hawaiian Health (May 23, 2016)
NIH Record: “For Native Hawaiians, Canoe Instills Pride, Healing”