Projects

Curation of materials from Hopkins Marine Station's hydrobiological surveys, including the Hopkins CalCOFI Archive | 1929 - 1974
Background

In the Summer of 1928, Henry Bryant Bigelow from Harvard University – one of the preeminent oceanographers of the time – came to Hopkins Marine Station (HMS) for the summer. He taught Oceanic Biology, and led the students on a series of hydrobiological surveys of Monterey Bay. He was assisted by Eugene Scofield from California Division of Fish and Game (CDFG) and Tage Skogsberg from HMS, and the patrol boat Steelhead was used in the effort. They sampled for temperature, salinity, a range of nutrients (phosphate, silicate, nitrate, etc.), dissolved oxygen, phytoplankton and zooplankton at 31 stations over the month of July.

 

This summer collaboration led directly to a working partnership between Hopkins and CDFG to conduct regular hydrobiological surveys in Monterey Bay. Surveys were carried out as often as possible, but usually at least every other week, from 1929 – 1938 (Skogsberg, 1946). Surveys were interrupted from 1939 – 1945 due to World War II. The kind of work conducted by Skogsberg and Scofield was among the earliest of what eventually came to be known as fisheries oceanography. Previous approaches had focused on studying recruitment of fishes from year to year as a means to track the status of fish stocks. Partnership between a fisheries person (Scofield) and a biological oceanographer (Skogsberg) was novel.

In 1949, HMS professor Rolf Bolin resurrected the hydrobiological survey and began weekly hydrobiological surveys in Monterey Bay. Shortly thereafter, in 1951, Hopkins Marine Station became a partner in the California Cooperative Oceanic Fisheries Investigations (CalCOFI) program with a directive to collect oceanographic data in and near Monterey Bay. The aim of the program was to conduct joint fisheries-oceanographic cruises that would help researchers understand what contributed to observed fluctuations in the California sardine fishery. Hopkins conducted weekly sampling (more or less) continuously from March 1951 through June 1974.

 

What's the situation?

The raw and aggregated data for most of these cruises currently reside in analog form (handwritten data logs, annual reports, etc.) in the library at the Hopkins Marine Station. The dataset includes variables such as temperature, salinity, oxygen, phosphate, silicate, phytoplankton and zooplankton community structure and abundance, meteorological conditions, fish and marine mammal counts, and more. The collection includes forty-four 3-ring or loose-bound notebooks, twenty-two small, bound notebooks, minutes from annual meetings, annual data reports, and other ephemera. The Hopkins CalCOFI collection is large, completely analog, and very heterogeneous. My objectives for the collection are to digitize it, add metadata, convert sampling data to actionable formats, and make it all public. As of April 2018, most of the CalCOFI materials (1951 - 1974) have been digitized and made available via the Stanford Digital Repository.

Major challenges?

I have the wildly unrealistic goal of converting all of the data in digitized PDFs to actionable formats (like spreadsheets) so that the data can be used by people who need it. With respect to the data that have been typed into reports, this is not overly complicated. With hand-written data in field notes, this is currently only possible via manual labor. I could pay to have the materials triple-keyed, but that doesn't interest me nearly as much as solving the larger problem of liberating pre-digital data from the file cabinets and university archives of the world. Solving this problem will take time, collaboration across disciplines (looking at you, computer science and digital humanities folks!), and money. I am not afraid.

The Fabrication Space | Founded in 2017

In marine science, as with many other fields, the sensors or equipment needed to make novel observations do/does not exist. The ocean is a tricky place to do research, and it's a difficult environment to recreate in a lab. Ipso facto, in order to do research in this field, you very often have to be a maker (or engineer, or fabricator, or whatever label you want to put on it). Having access to fabrication equipment & supplies is not a luxury for this community. "Making" is not just a fun side interest for our students. Learning how to build sensors is absolutely critical to their development as scholars. This is something that I can't emphasize enough. Here is a short article about the development of our space.

What's the situation?

Discussions with faculty, graduate students and post-docs revealed a pervasive need for 3D printing technology across several research groups, even those conducting primarily laboratory work. Needs range from making custom field and laboratory equipment to replicating the shape of marine animals (in toto or their various parts) for testing hydrodynamics or biomechanics in the lab. I wrote an internal funding proposal to buy a 3D printer, which was granted. A year later I made the case for a second printer that works via a different technology to complement the capabilities of the first printer. I also discovered a need to support the development of skills around the use of microcontrollers (e.g. Arduinos and Raspberry Pis), and I was able to use some gift funds to build out supplies in that area. I need to do more (a soldering station, a laser cutter), but I am out of room at the moment.

Major challenges?

Space. I crammed the fabrication space into a corner at the front of the library, and we have already outgrown it. I badly need a purpose-built fabrication space. Luckily, this is not complicated. We just need to clear out some stacks to open up space and hack together some butcher block worktables. While our first capital budget request for a library remodel was declined,  I remain undeterred. We will implement a legit fabrication lab in the manner of pure academics - we'll cobble stuff together and make it work!

Other stuff I'm working on that I'll tell you about soon:

  • Planning a major library remodel
  • Stanford Oceanographic Expeditions (AKA, the Te Vega cruises) [a legacy data curation project]
  • Stanford@SEA [a born-digital curation project]
  • Hopkins Marine Station Student Papers [a digitization project]
  • Our new marine science children's books collection [honestly, so much fun - send me your favorites]
  • Digitizing the complete corpus of Hopkins Marine Station theses and dissertations [it's fair use, eh?]
 
(Did I mention that I am a librarian for only 60% of my job? I am Very Busy.)
To see more or discuss possible work let's talk >>

Background photograph by

jake faulstich on Unsplash

Follow me

© 2019 by Amanda L. Whitmire

  • Grey Facebook Icon
  • Grey Twitter Icon