Each year, the LTER Information Management (IM) committee gathers updates from sites across the network related to IM system and personnel changes over the past year, compiling them into a series of ‘Site Bytes’, or site summaries. This November, the first 2020 Site Bytes that started rolling into the editors’ (virtual) office were all from coastal LTER sites, so welcome to the 2020 Site Bytes Coastal Edition!
Credit: John Porter
Florida Coastal Everglades LTER – Kristin Vanderbilt
Credit: John Porter
FCE LTER launched a new website prior to submitting a renewal proposal to NSF in March 2020. The old FCE website was hand-coded and laboriously maintained by FCE Project Manager Mike Rugge. The new website takes advantage of Cascade, the content management system used by FIU, to make website updates easier. Migrating the website into Cascade enables other FCE staff besides Mike to have permissions to sections of the website in order to update their own content. The information on the new website has been refreshed and reorganized for ease of navigation with input from PIs, staff, and students. Cascade facilitates integration with social media and newsfeeds, and offers website search functionality. The new website significantly improves on the old one by being mobile device friendly and resolving to a size appropriate to the device on which it is being viewed.
Unfortunately, Cascade does not support dynamic web pages, such as the popular custom query interfaces to data, bibliography, and personnel databases found on the old FCE website. The Foundation Framework, a responsive front-end software framework for web design, was therefore used to produce a template mimicking the Cascade FCE website to use when displaying dynamic content. Mike rewrote in PHP all the query scripts from the old website in order to replace near-obsolete Embperl scripts. He preserved the many options from the old website for filtering datasets, publications, personnel and photographs for ease of discovery, while offering the new look and feel of the Cascade website. This new, hybrid FCE website has improved the experience of web visitors seeking data or information about the FCE LTER.
FCE has also updated its approach to generating and querying the FCE website’s Data Catalog. The new method takes advantage of RESTful web services provided by Environmental Data Initiative (EDI) PASTA+ data repository software. Previously, the FCE IM had submitted EML documents to the EDI Data Repository and then captured a subset of that metadata in a local Oracle database to drive the FCE Data Catalog. With the new system, the IM submits EML to the EDI Data Repository as before, but then the EDI Repository becomes the source of metadata to populate the FCE Data Catalog. This new approach for generating and querying the FCE Data Catalog expedites updates of FCE datasets.
Beaufort Lagoon Ecosystem LTER – An T. Nguyen
It was a very hot and long summer here in Austin, TX, where the BLE IM team is based (far from the icy Arctic site itself). Actually, the above assertion is evidenced mostly by the AC bills my 426 sq ft studio has been commanding, since I didn’t step outside much. There’s no couch — I didn’t have any furniture — and moving in April meant that a desk setup was slated to claim a good portion of the prime estate budget. Tim appears on Zoom always from a certain angle in his office, where I listen in on life snippets courtesy of the resident notables, his two children and two dogs.
Back in the initial BLE field season of 2018, our scientists collected water and sediment samples from the Alaska North Slope lagoons, as well as deployed continuous observing instruments. In the second, 2019, more samples followed, moorings were retrieved and re-deployed. Laboratory analysis ramped up and that autumn the very first BLE data sets started trickling in. We have been steadily working on publishing them to EDI: our data catalog now boasts seventeen data packages, with more to be ushered in. These numbers, naturally, break all BLE records to date!
Along the way, we have been putting our IM system to practice and smoothing out the crinkles. This ranges from author attribution in metadata — we decided on three distinct practices according to how BLE was involved — to figuring out what our role in the broader project is.
BLE cancelled field work this year out of caution, not only for our scientists, but also for the rural Alaska communities out of which we operate. Our grant cycle placed BLE’s first mid-term review this past summer; this has now moved to the summer of 2021. We will soon be turning our attention towards this critical review in hope of a strong IM showing and a smooth project renewal.
Virginia Coast Reserve LTER – John Porter
We’ve completed a slimmed-down, priority-driven field season at the VCR/LTER. We were able to complete our core sampling with trimmed-down research teams and a field station capacity reduced from 25 to 4 people at a time and boats limited to 2 researchers at a time. Needless to say, we’ve kept Zoom busy as well! Our old wireless ISP went out of business, so we now have fiber running directly to our lab.
On the IM-side we’ve had the usual business of ingesting researcher datasets and building on existing long-term datasets. Fortunately, many of our sensor systems are connected via our wireless network, so data from our flux tower, meteorological and tide stations have been largely uninterrupted. Everyone has been working primarily from home. As one colleague put it “I’m not working at home, I’m living at work!”
We’ve been busy updating our Linux servers from Ubuntu 18.04 LTS to Ubuntu 20.04 LTS. As always, there are a few glitches, as the behavior of newer software changes, but so far, we’ve been able to remedy them rapidly. We continue to use WordPress for our websites and have had no problems with it during the upgrades.
UVA has been very active in working on diversity, equity and inclusion issues at all levels, with policy revisions and training activities at the University, School and Department, and Field Station levels. VCR investigator Matt Reidenbach has been playing a leading role in departmental efforts. For the field station, we’re revising online reservation forms to better support gender diversity, but that remains a work in progress.
Our Site Director and Educational Coordinator Cora Johnston Baird has been building out new WordPress websites to aid in education and outreach. Her new https://coastaleducation.virginia.edu website now features a multimedia experience that combines art and science to accompany the live “Ghosts of the Coast” exhibition (https://www.coastaleducation.virginia.edu/wp/?page_id=1389), which is about “ghost” forests caused by rising sea levels. A new “Shiny” app is under development to facilitate interactive visualization of VCR tide and meteorology datasets.
Santa Barbara Coastal LTER – Li Kui
In 2020, SBC LTER long-term time-series data collection was identified as critical research and was able to continue as planned during the time of COVID. Kaitlin Johnson joined us in August to help with data quality control and website maintenance.
SBC LTER launched our new website that incorporated recent technology and leverages LTER Network resources. Several primary improvements include: one, the frequently updated website content is stored and managed using a back-end database that allows centralized information management; two, the website hosts a local data catalog and its customized metadata viewer pages that mirror to the EDI repository; and three, the security and accessibility of the website have been greatly improved using Hypertext Transfer Protocol Secure (HTTPS) instead of HTTP.
The SBC IM, Li Kui, used SBC’s information system as a model to develop a compact data management system that is currently used by several small research groups as well as large organizations such as the Partnership for Interdisciplinary Studies of Coastal Oceans (PISCO). This “Excel-to-EML” tool (https://github.com/lkuiucsb/Excel-to-EML) uses the Excel workbook as a metadata storage database and R scripts to generate the XML document used for data publication.
Plum Island Ecosystem LTER – Hap Garritt
Field and lab work during the 2020 field season at the PIE LTER, a coastal site in Northeast Massachusetts, have certainly been an interesting endeavor during the COVID-19 pandemic. We have been following Massachusetts and Marine Biological Lab COVID-19 guidelines throughout the various phases of working in a pandemic environment. We used a scaled back field crew (2 – 3 people) of essential personnel to maintain some long-term sampling and various sensor logging networks including weather stations, water quality sondes and eddy covariance towers. Fortunately, our field stations provided enough space to ensure social distancing with one person per household. Field vehicle travel was limited to one person per vehicle and boat travel was limited to 2 – 3 people (socially distanced) in the boat and wearing masks. Lab work during the summer was scaled back as our focus was on maintaining long-term field studies. Lab analyses have resumed in a limited way during the Fall of 2020 following guidance for mask wearing and social distancing.
PIE LTER researchers have maintained their communication via Zoom meetings and participating in various scientific meetings including ESIP, ESA and NEERS. We are all looking forward to the day when we can resume normal activities, resume the spontaneous personal interactions that maintain our sanity and minimize “Zoom Butt” fatigue!
Plum Island Ecosystem LTER 2020 field season. Clockwise from top: Sam Kelsey collecting marsh porewater, October 2020; Sam Kelsey traveling to field sites, October 2020; Inke Forbrich at eddy covariance tower in short Spartina alterniflora marsh, September 2020.
Credit: Jane Tucker, PIE LTER
