nick brown

A prototype field-to-publication data system for a multi-variable permafrost observation network.

A prototype field-to-publication data system for a multi-variable permafrost observation network.
Blog post by Nick Brown, NSERC PermafrostNet Data Scientist

Analysis and prediction of permafrost change are hampered by lack of observational data. In collaboration with Stephan Gruber, Peter Pulsifer, and Amos Hayes, we developed a permafrost data management system to support permafrost observation networks that involve many different kinds of permafrost data.

We identify five broad challenges for permafrost data management and publication: (1) existing data management strategies do not scale well, (2) data users have different skills and needs, (3) permafrost data are varied, (4) resources for permafrost data management are limited, and (5) existing permafrost data sources are difficult to integrate. Our prototype system supports a permafrost data workflow from observation to the distribution of interoperable data. The system simplifies data publication and management, although we identify and discuss several hurdles in adapting the CF conventions and ERDDAP for permafrost data. Our learning can inform organizations who collect, manage, or distribute permafrost data or those who manage large observation networks.

In summary:

  • Five broad challenges limit permafrost data management and publication.
  • We frame these challenges as requirements, and identify similarities with the FAIR principles.
  • We developed a prototype a permafrost data system to support field-to-publication workflows.
  • In this project, we use an “adopt and adapt” approach for standards and software.
  • Our data system supports more FAIR permafrost data.

Nicholas Brown, Stephan Gruber, Peter Pulsifer, Amos Hayes, A prototype field-to-publication data system for a multi-variable permafrost observation network, Environmental Modelling & Software, Volume 175, 2024, 106006, ISSN 1364-8152, doi:10.1016/j.envsoft.2024.106006

This research was enabled in part by support provided by Compute Ontario and the Digital Research Alliance of Canada.

By nick brown, ago

Formats and variables – making permafrost data more useful

by Nick Brown, NSERC PermafrostNet Data Scientist

Students in NSERC PermafrostNet’s Theme 1, led by postdocs Michel Paquette and Samuel Gagnon, have digitized 2 historic reports (Hodgson, 1982 and Hodgson, & Nixon 1998) containing profile data from more than 250 boreholes in polar desert environments. Information on ground ice content, ground ice descriptions, soil type, grain size and more, is now available for re-use in a variety of formats using the PermafrostNet ERDDAP data server. Data can be accessed and searched from a single borehole, or from the entire report. Both the data and metadata can be downloaded as a csv.

These data take advantage of the new additions to the CF standard name list to make the data more interoperable and reuseable. Nick Brown has also documented a set of standardized variable names and their associated CF Names – Standardized permafrost variable names and equivalent CF Names. This technical note document describes the variables that are on the NSERC PermafrostNet ERDDAP and their associated metadata. It can also be used as a guide to connect commonly-used permafrost variables to the recommended CF standard_name.

One of the steps involved in redistributing these data on the ERDDAP server is converting them into the NetCDF data format. This is a way of distributing scientific data that is gaining popularity because it is self-documenting and uses a several well-established community-built standards to increase data interoperability. These include the CF conventions and the Attribute Convention for Data Discovery (ACDD). There are a number of data distribution platforms (ERDDAP, THREDDS, HYRAX) that can be used to easily distribute NetCDF files using a standardized API and web interface. NSERC PermafrostNet uses ERDDAP as a data distribution platform for these reasons and because it offers a graphical web interface for those who want to access data interactively. It also makes it possible to adopt the associated data standards as one way to increase the interoperability of permafrost data generated by and used within the network.

The NetCDF format and associated standards were originally developed for atmospheric, oceanographic and climatic data, so there are few examples of these files being used to represent observed soil profiles or geotechnical borehole data, and the CF standard_name table lacks many variables that are relevant to permafrost science. A new technical document – Representing geotechnical borehole profile data with netCDF and ERDDAP provides considerations and recommendations for structuring observed borehole profile data in a way that complies with existing standards, is distributable on ERDDAP, and useable by permafrost scientists.

These new documents are available on the PermafrosNet Data Standard Recommendations page.

By nick brown, ago

Take your permafrost metadata to the next level

by Nick Brown, NSERC PermafrostNet Data Scientist

Everyone’s been there. You are about to publish your dataset, but you’ve just spent the last half-hour trying to decide on the best formatting and naming conventions. Should that column be named “ground temperature”, “soil_temperature”, or just “Tg”? Maybe you should include units too; “ground_temperature_degree_C” has a ring to it. But how will other people know exactly what your dataset represents? Good metadata is the answer.

You may not realize it, but there are resources to help you in this situation. The CF Standard name table is a curated list of terms used to unambiguously identify the kinds of measurements in a dataset. For self-describing formats like netcdf, you can include these attributes directly in your data file, following the CF standards. Or, if you are publishing your data in a text file, like a CSV, you can include the information about each column in your dataset in a separate metadata file. This way, the name of your data column doesn’t have to do so much work describing itself.

Michel Paquette, Theme 1 Post-doctoral Fellow (Université de Montréal, NSERC PermafrostNet) and I have coordinated the inclusion of 12 additional permafrost-related terms (see table below) in the latest release of the Standard Names vocabulary (version 78). These terms will be particularly useful for field scientists wanting to make their published datasets more interoperable and for data publishers who host permafrost-related data. An additional 14 terms relevant to permafrost science have since been requested. The addition of permafrost-related terms contributes to improved data interoperability with the atmospheric science and modelling communities, where the CF terms are widely used.

For an up-to-date list of permafrost-related terms added to the CF names list by NSERC PermafrostNet, visit the Data Standard Recommendations page.

Common nameCF NameStatus
Ground temperaturetemperature_in_groundAdded (v78)
Excess iceice_volume_in_frozen_ground_
in_excess_of_pore_volume_in_unfrozen_ground_
expressed_as_fraction_of_frozen_ground_volume		Added (v78)
Ice saturation indexratio_of_ice_volume_in_frozen_ground_
to_pore_volume_in_unfrozen_ground		Added (v78)
Thaw depthdepth_at_base_of_unfrozen_groundAdded (v78)
Frozen thermal conductivitythermal_conductivity_of_frozen_groundAdded (v78)
Frozen heat capacityspecific_heat_capacity_of_frozen_groundAdded (v78)
Gravel content by massmass_fraction_of_gravel_in_soilAdded (v78)
Sand content by massmass_fraction_of_sand_in_soilAdded (v78)
Silt content by massmass_fraction_of_silt_in_soilAdded (v78)
Clay content by massmass_fraction_of_clay_in_soilAdded (v78)
Organic matter content by massmass_fraction_of_organic_matter_in_soilAdded (v78)
Soil water pHsoil_water_phAdded (v78)

Permafrost related terms added to v78 of the CF Standard Name vocabulary by NSERC PermafrostNet

By nick brown, ago

RCOP 2021 Data Systems Workshop Final Report

NSERC PermafrostNet hosted a data systems workshop at the 2021 Regional Conference on Permafrost, held online in October 2021. The workshop featured invited speakers Ashley Rudy from the Northwest Territories Geological Survey and Jeanette Nötzli from the Swiss Permafrost Monitoring Network (PERMOS). Attendees participated in breakout rooms and plenary discussion to identify current problems and limitations with permafrost data systems and to recommend how efforts can be better connected or coordinated. The final report summarizes the conclusions and provides a record of the interactions and discussions that occurred.

The workshop follows the 2020 Permafrost Data Workshop, which highlighted the importance of a community of practice and ongoing communication to improve the interoperability of permafrost data. In addition to the concrete objectives of identifying challenges and recommendations, the 2021 workshop was a way for members of the permafrost community to share ideas, and to cross-pollinate knowledge between sectors and disciplines of permafrost science.

Data Systems Workshop ReportDownload
By nick brown, ago

MSc in sustainable culvert design over degrading permafrost, Hudson Bay railway

Full description (PDF)

Posted: September 10, 2019
Anticipated start:  September 2021 (flexible)
Supervisory team: Dr. Shawn Kenny and Dr. Ryley Beddoe

The performance and integrity of northern linear infrastructure, such as railway lines and road networks, may be affected by ground deformation geohazards (e.g. subsidence, slope instability, permafrost degradation), which may be influenced by hydrology and climate change effects.

Recent flooding events caused an extensive disruption to service on the Hudson Bay rail line, with damage to bridges and culverts, and failure of the rail bed due to washout. A significant effort was undertaken to restore railway operations that included the installation of several culverts. The significance of climate change effects, such as future flood events and permafrost degradation, on the future performance of the railway culvert infrastructure requires further assessment. From this perspective, the research study will assess the resilience of current design standards and practices for railway culverts located in permafrost environments.  Supported by the research effort of other team members in the PermafrostNet network, site characterization (e.g. topographic, meteorological, hydrological, geotechnical, geophysical, permafrost attributes) of several culvert locations, for both original and recent installations, will be established. Centrifuge physical modelling and numerical simulation techniques may be used to assess these failure events, based on available knowledge, and estimate future performance, based on climate scenarios developed within the PermafrostNet research activities

We are seeking a highly motivated and engaged MSc candidate, to be enrolled in a civil engineering graduate studies program, with academic interests in the fields of geotechnical and permafrost sciences, site or field investigations, physical modelling and numerical simulation. The MSc candidate will be an integral team member of a multi-disciplinary supervisory committee and collaborate with other team members within the PermafrostNet network. All applications will be reviewed by the selection committee with respect to academic qualifications and integration within the network through the PermafrostNet lens on equity, diversity and inclusion. For more information on this project, please contact shawn.kenny@carleton.ca.

By nick brown, ago

MSc in sustainable culvert design over degrading permafrost, Hudson Bay railway

Full description (PDF)

Posted: September 10, 2019
Anticipated start:  September 2021 (flexible)
Supervisory team: Dr. Shawn Kenny and Dr. Ryley Beddoe

The performance and integrity of northern linear infrastructure, such as railway lines and road networks, may be affected by ground deformation geohazards (e.g. subsidence, slope instability, permafrost degradation), which may be influenced by hydrology and climate change effects.

Recent flooding events caused an extensive disruption to service on the Hudson Bay rail line, with damage to bridges and culverts, and failure of the rail bed due to washout. A significant effort was undertaken to restore railway operations that included the installation of several culverts. The significance of climate change effects, such as future flood events and permafrost degradation, on the future performance of the railway culvert infrastructure requires further assessment. From this perspective, the research study will assess the resilience of current design standards and practices for railway culverts located in permafrost environments.  Supported by the research effort of other team members in the PermafrostNet network, site characterization (e.g. topographic, meteorological, hydrological, geotechnical, geophysical, permafrost attributes) of several culvert locations, for both original and recent installations, will be established. Centrifuge physical modelling and numerical simulation techniques may be used to assess these failure events, based on available knowledge, and estimate future performance, based on climate scenarios developed within the PermafrostNet research activities

We are seeking a highly motivated and engaged MSc candidate, to be enrolled in a civil engineering graduate studies program, with academic interests in the fields of geotechnical and permafrost sciences, site or field investigations, physical modelling and numerical simulation. The MSc candidate will be an integral team member of a multi-disciplinary supervisory committee and collaborate with other team members within the PermafrostNet network. All applications will be reviewed by the selection committee with respect to academic qualifications and integration within the network through the PermafrostNet lens on equity, diversity and inclusion. For more information on this project, please contact shawn.kenny@carleton.ca.

By nick brown, ago

PhD in simulation of permafrost change and quantification of confidence in resulting data products

Full description (PDF)

Posted: April 27, 2020 (update)
Anticipated start: Fall (September) term 2020, with flexibility in responding to COVID-19 related travel restrictions.   
Supervisory team: Stephan Gruber (Carleton University), Joe Melton (University of Victoria / Environment and Climate Change Canada), Trevor Lantz (University of Victoria) and Steve Kokelj (Northwest Territories Geological Survey).

This project will develop methods and tools for evaluating permafrost models with observational data. This is important because the lack of meaningful and quantitative evaluation of permafrost simulation results impedes the improvement of simulation tools and the use of their outputs for informing adaptation design or policy. This project will use the database compiled in NSERC PermafrostNet (PINGO) as a source of observational evidence to provide confidence in simulation-based permafrost climate services. With practical application of simulation results in mind, this project will comprehensively investigate how well ground temperature change and ground-ice loss can be predicted. For this, ensemble permafrost predictions will be analyzed in terms of error and uncertainty. Ensembles will use multiple re-analyses, downscaled heuristically, as driving climate, multiple models as well as multiple parameter and input data sets (e.g., estimated ground ice distribution, vegetation) for perturbed physics simulations in each model. Error and uncertainty will be statistically decomposed with respect to their likely origins to better inform model development and the use of model results. This quantitative evaluation will be complemented by investigating face validity, a concept developed to capture the trust that diverse experts, such as model developers, permafrost field scientists and northerners, place in simulation results based on subjective assessment. This will allow to better utilise the diverse expertise in the network for identifying and assessing known unknowns in simulations and to develop ways of communicating these to modelers and stakeholders. The combination of statistical evaluation with face validity will improve the dialogue between model developers and users of simulation results and thereby reduce barriers to the acceptance and uptake of simulation products.

This fully funded PhD studentship will be based at Carleton University in Ottawa, Canada. As part of NSERC PermafrostNet, the new Permafrost Partnership Network for Canada (permafrostnet.ca), it will have an outstanding training environment.

The successful candidate will have (1) a master’s degree in a relevant discipline (e.g., geography, Earth science, geophysics, soil physics, atmospheric science, environmental engineering or geotechnical engineering); (2) demonstrated skill in programming and data analysis; (3) previous experience (or a demonstrated interest) in cold regions; as well as (4) excellent written communication in English.

This PhD studentship is fully funded for twelve months per year, for up to four years. International students are eligible to receive a bursary that will reduce their tuition to the amount paid by domestic PhD students.

To apply, Send a cover letter, c.v., copies of transcripts, a writing sample, and contact details for three references to Stephan Gruber (stephan.gruber@carleton.ca). Applications will be received until the position is filled.

By nick brown, ago

PhD in thaw pond initiation and evolution pathways

Full description (PDF)

Posted: June 27, 2019
Anticipated start: September 2019 (or as soon as possible) 
Supervisory team: Dr. Pascale Roy-Léveillée, Dr. Merritt Turetsky, Dr. Trevor Lantz, Dr. Peter Morse

This position will elucidate controls on 1) the initiation of thaw lakes and ponds, 2) variation in rates of expansion, and 3) pathways of stabilization and permafrost recovery post stabilization. Field work will take place in thermokarst-affected lowlands between the Blackstone Uplands (YT) and Tuktoyuktuk (NWT). The position will develop predictive models based on the interacting effects of paleogeography (deposits and ice), climate, topography, snow cover, and vegetation growth within thaw ponds. This work will support the development of a lowland thermokarst hazard assessment framework to support the effective evaluation and management of risks associated with signs of thermokarst initiation near existing or planned infrastructure, traditional travel routes and areas of cultural significance, sensitive wildlife habitat, etc. For more info on the project contact proyleveillee@laurentian.ca.

By nick brown, ago

MSc in thaw-related landscape change in Weenusk Traditional Territory

Full description (PDF)

Posted: June 27, 2019
Anticipated start: September 2022 (flexible) 
Supervisory team: Dr. Pascale Roy-Léveillée, Dr. Maara Packalen, Dr. Trevor Lantz, Dr. Peter Pulsifier

In Weenusk First Nation’s traditional territory, near the Hudson Bay coast, local residents report widespread signs of permafrost degradation: degrading palsas and peat plateaus, widespread ground wetness, and changes in vegetation cover. These changes affect local access to country food by impeding overland travel and modifying the habitat of species key for local food security. This MSc will work in collaboration with community members and use remotely-sensed imagery and ground observations to map changes in moisture, vegetation, and extent of palsas and peat plateaus using object-based analysis. This work will support on-going community-based monitoring initiatives by creating maps of changing conditions at the territory scale that can be overlain with maps of trails, family areas, and sites of cultural significance. For more info on the project contact proyleveillee@laurentian.ca.

By nick brown, ago