the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
| 25 Apr 2023
Overcoming barriers to enable convergence research by integrating ecological and climate sciences: The NCAR-NEON system Version 1
Abstract. Global change research demands a convergence among academic disciplines to understand complex changes in Earth system function. Limitations related to data usability and computing infrastructure, however, present barriers to effective use of the research tools needed for this cross-disciplinary collaboration. To address these barriers, we created a computational platform that pairs meteorological data and site-level ecosystem characterizations from the National Ecological Observatory Network (NEON) with the Community Terrestrial System Model (CTSM) that is developed with university partners at the National Center for Atmospheric Research (NCAR). This NCAR-NEON system features a simplified user interface that facilitates access to and use of NEON observations and NCAR models. We present preliminary results that compare observed NEON fluxes with CTSM simulations and describe how the collaboration between NCAR and NEON that can be used by the global change research community improves both the data and model. Beyond datasets and computing, the NCAR-NEON system includes tutorials and visualization tools that facilitate interaction with observational and model datasets and further enable opportunities for teaching and research. By expanding access to data, models, and computing, cyberinfrastructure tools like the NCAR-NEON system will accelerate integration across ecology and climate science disciplines to advance understanding in Earth system science and global change.
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The requested preprint has a corresponding peer-reviewed final revised paper. You are encouraged to refer to the final revised version.
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The requested preprint has a corresponding peer-reviewed final revised paper. You are encouraged to refer to the final revised version.
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Journal article(s) based on this preprint
Interactive discussion
Status: closed
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RC1: 'Comment on egusphere-2023-271', Manuel Acosta, 13 Jun 2023
Review to Manuscript Number: EGUsphere 2023-271
General comments:
The manuscript “Overcoming barriers to enable convergence research by integrating ecological and climate sciences: The NCAR-NEON system - Version 1” mainly reports the results of a computational platform that synergy meteorological data and site-level ecosystem characterizations from the National Ecological Observatory Network (NEON) with the Community Terrestrial System Model that was developed at the National Center for Atmospheric Research (NCAR), simplifying user interface that facilitates access to and use of NEON observations and NCAR models. The information brought up by the authors regarding the created computational platform is significant concerning the issues that are connected with the usability, operability and interpretation of acquired data at the ecosystem level and application of it to models or simulations in Earth system research. In general, I like the overall work, the combination of robust ecological data and the use of them to improve models to create multiple outputs. Moreover, and I found it very fruitful to improve data accessibility, facilitate research to scientists and provide data for educational opportunities.
Specific comments:
1) I suggest improving the information regarding the parameters measured by soil sensor assemblies in Line 121, similar to what was done in the meteorology part (lines 119-120).
2) I consider that the use of the term “Surface characteristics of soil properties and vegetation” (line 124) is not completely correct. I suggest using “Characteristics of soil properties and surface vegetation”, which is clear and concise. The same is in Table 1. Data Product Name: Soil physical and chemical properties, Megapit. It should be identified as Soil Characterization under the Data Product Use, instead of Surface characterization.
3) The use of any acronym must be stated even though is well known. In line 168 is stated netCDF, which stands for Network Common Data Format.
4) In Table 2. Four of the seven “URL” links mentioned in the Table are not working. Even though the authors stated that “Note we intend to provide permanent urls for these sites in the final published manuscript”, the links are not found. These are Tutorial, Interactive, Processing NEON data and NEON Prototype Data. I was disappointed I could not check the mentioned links and their operability. I hope the links will be active soon.
5) I suggest changing the name of the subchapter 2.1.2. to characteristics of soil properties and surface vegetation.
6) Perhaps will be good to bring a short explication for the statement “equilibrated” carbon, water, energy, and nitrogen states and fluxes, in line 263.
7) Again, the use of any acronym must be stated even though is well known. In line 362 is stated Data I/O, which stands for Data Input - Output.
8) In line 399 is stated “DEJU” that stands for? The official name of the site.
9) It seems is a mistake in the interpretation of Figure 3b-c. In lines, 407-408 is stated “At BART we see that CTSM tends to underestimate sensible heat fluxes, while overestimating latent heat fluxes, especially during the summer months (Fig. 3b-c). The graphs showed different trends compared to those stated in the text.
10) I suggest deleting the word “Democratizing”, is too constitutional, perhaps use “Improving”.
Technical corrections
1) in line 201, a closing bracket is missing.
Citation: https://doi.org/10.5194/egusphere-2023-271-RC1 -
RC2: 'Comment on egusphere-2023-271', Anonymous Referee #2, 01 Jul 2023
I read with interest the manuscript titled "Overcoming barriers to enable convergence research by integrating ecological and climate sciences: The NCAR-NEON system Version 1" and feel like it makes a timely and relevant contribution to the scientific literature. The manuscript was really well written too, which made it easy to read and understand the science being presented. The specific comments I provide below should help clarify a couple of minor items.
Specific comments:
Line 68: I would have thought appropriate references here would be Novick et al. (2018) and Beringer et al. (2022), which describe Ameriflux and OzFlux, respectively.
Line 77-79: There are also numerous agricultural sites either in regional flux networks, or not affiliated at all, that represent a barrier for ESM development/parameterization, and ESM use. The authors might consider broadening their discipline scope here
Table 2: Nice table, and good to see the authors are already thinking about url permanency for the final m/s version
Lines 190-193: Yes, because this approach would not work so well for ecosystems where two plant functional types exist, such as tropical savannas that make up a large portion (20-25 % depending on definition) of the terrestrial land surface. Perhaps the authors could comment on when the CTSM is likely to include more than one PFT
Line 205: Is this method appropriate across all NEON sites? I realise its out of the scope for this manuscript, but would be somthing to consider whether the daytime approach is more applicable at some sites. Also, do any of the sites have a profile system? Can the authors comment on CO2 storage at low u* and what effect this might have on gap filling and flux uncertainty across sites?
Table 3: I know it can make tables messy, but adding a value for some level of variance/range/uncertainty would be useful for MAT, MAP and GPP to give the reader an idea of annual variability in these parameters. Can ET also be included? Would be useful to see alongside MAP
Line 429: Typo, either due to or related to
Line 499: Ah, good to see storage mentioned here. While this does somewhat address my earlier comment, I do think storage should be briefly mentioned in the methods too.
Lines 655-658: Talking of flux forecasting, the authors fail to mention project EDDIE, funded by the NSF. I believe a few papers have been published relating to this project (see: https://serc.carleton.edu/eddie/about/publications_presentations.html), and suggest the authors cite one or two here to be inclusive.
Line 622 (end of section): The NCAR-NEON tool seems like an excellent tool, especially for processing NEON data. However, at this point I'm left wondering how useful this tool might be for sites and users not in NEON, as there hasn't been much discussion about third-party non-NEON sites. There has also been little mention of other EC data processing tools that are already available, such as PyFluxPro used by the OzFlux community or commercial products such as TOVI from LICOR. Indeed, the ONEFLUX processing tool was designed with the purpose of standardising flux processing at a global scale. So, I'm left wondering what place the NCAR-NEON system has amongst these other options. Is it to seamlessly process NEON data quickly or can it be used more widely by other non-NEON sites? I think a little more discussion on these points would be helpful in this section.
Line 714-716: Ahh, here's the first mention of how another network could use the NCAR-NEON system, and its in the conclusion. This supports my point from earlier that some discussion around this is needed before this final point. And there are other networks beyond the US that could benefit from this, such as those that are still establishing or do not have the level of data management sophistication like NEON, OzFlux and ICOS.
References: There seems to be a lot of self-citing in this reference list, i.e. 7 Bonan first author papers. While it is somewhat understandable given the topic and focus of the manuscript, the authors could be more inclusive of other networks and groups who have already made significant progress towards observational data-model integration and in standardising EC processing protocols. By being more inclusive with citations throughout, the manuscript will be more relevant for a global audience and more likely to be cited widely.
Citation: https://doi.org/10.5194/egusphere-2023-271-RC2 -
AC1: 'Author Response to Reviewers: egusphere-2023-271', Danica Lombardozzi, 06 Aug 2023
The comment was uploaded in the form of a supplement: https://egusphere.copernicus.org/preprints/2023/egusphere-2023-271/egusphere-2023-271-AC1-supplement.pdf
Interactive discussion
Status: closed
-
RC1: 'Comment on egusphere-2023-271', Manuel Acosta, 13 Jun 2023
Review to Manuscript Number: EGUsphere 2023-271
General comments:
The manuscript “Overcoming barriers to enable convergence research by integrating ecological and climate sciences: The NCAR-NEON system - Version 1” mainly reports the results of a computational platform that synergy meteorological data and site-level ecosystem characterizations from the National Ecological Observatory Network (NEON) with the Community Terrestrial System Model that was developed at the National Center for Atmospheric Research (NCAR), simplifying user interface that facilitates access to and use of NEON observations and NCAR models. The information brought up by the authors regarding the created computational platform is significant concerning the issues that are connected with the usability, operability and interpretation of acquired data at the ecosystem level and application of it to models or simulations in Earth system research. In general, I like the overall work, the combination of robust ecological data and the use of them to improve models to create multiple outputs. Moreover, and I found it very fruitful to improve data accessibility, facilitate research to scientists and provide data for educational opportunities.
Specific comments:
1) I suggest improving the information regarding the parameters measured by soil sensor assemblies in Line 121, similar to what was done in the meteorology part (lines 119-120).
2) I consider that the use of the term “Surface characteristics of soil properties and vegetation” (line 124) is not completely correct. I suggest using “Characteristics of soil properties and surface vegetation”, which is clear and concise. The same is in Table 1. Data Product Name: Soil physical and chemical properties, Megapit. It should be identified as Soil Characterization under the Data Product Use, instead of Surface characterization.
3) The use of any acronym must be stated even though is well known. In line 168 is stated netCDF, which stands for Network Common Data Format.
4) In Table 2. Four of the seven “URL” links mentioned in the Table are not working. Even though the authors stated that “Note we intend to provide permanent urls for these sites in the final published manuscript”, the links are not found. These are Tutorial, Interactive, Processing NEON data and NEON Prototype Data. I was disappointed I could not check the mentioned links and their operability. I hope the links will be active soon.
5) I suggest changing the name of the subchapter 2.1.2. to characteristics of soil properties and surface vegetation.
6) Perhaps will be good to bring a short explication for the statement “equilibrated” carbon, water, energy, and nitrogen states and fluxes, in line 263.
7) Again, the use of any acronym must be stated even though is well known. In line 362 is stated Data I/O, which stands for Data Input - Output.
8) In line 399 is stated “DEJU” that stands for? The official name of the site.
9) It seems is a mistake in the interpretation of Figure 3b-c. In lines, 407-408 is stated “At BART we see that CTSM tends to underestimate sensible heat fluxes, while overestimating latent heat fluxes, especially during the summer months (Fig. 3b-c). The graphs showed different trends compared to those stated in the text.
10) I suggest deleting the word “Democratizing”, is too constitutional, perhaps use “Improving”.
Technical corrections
1) in line 201, a closing bracket is missing.
Citation: https://doi.org/10.5194/egusphere-2023-271-RC1 -
RC2: 'Comment on egusphere-2023-271', Anonymous Referee #2, 01 Jul 2023
I read with interest the manuscript titled "Overcoming barriers to enable convergence research by integrating ecological and climate sciences: The NCAR-NEON system Version 1" and feel like it makes a timely and relevant contribution to the scientific literature. The manuscript was really well written too, which made it easy to read and understand the science being presented. The specific comments I provide below should help clarify a couple of minor items.
Specific comments:
Line 68: I would have thought appropriate references here would be Novick et al. (2018) and Beringer et al. (2022), which describe Ameriflux and OzFlux, respectively.
Line 77-79: There are also numerous agricultural sites either in regional flux networks, or not affiliated at all, that represent a barrier for ESM development/parameterization, and ESM use. The authors might consider broadening their discipline scope here
Table 2: Nice table, and good to see the authors are already thinking about url permanency for the final m/s version
Lines 190-193: Yes, because this approach would not work so well for ecosystems where two plant functional types exist, such as tropical savannas that make up a large portion (20-25 % depending on definition) of the terrestrial land surface. Perhaps the authors could comment on when the CTSM is likely to include more than one PFT
Line 205: Is this method appropriate across all NEON sites? I realise its out of the scope for this manuscript, but would be somthing to consider whether the daytime approach is more applicable at some sites. Also, do any of the sites have a profile system? Can the authors comment on CO2 storage at low u* and what effect this might have on gap filling and flux uncertainty across sites?
Table 3: I know it can make tables messy, but adding a value for some level of variance/range/uncertainty would be useful for MAT, MAP and GPP to give the reader an idea of annual variability in these parameters. Can ET also be included? Would be useful to see alongside MAP
Line 429: Typo, either due to or related to
Line 499: Ah, good to see storage mentioned here. While this does somewhat address my earlier comment, I do think storage should be briefly mentioned in the methods too.
Lines 655-658: Talking of flux forecasting, the authors fail to mention project EDDIE, funded by the NSF. I believe a few papers have been published relating to this project (see: https://serc.carleton.edu/eddie/about/publications_presentations.html), and suggest the authors cite one or two here to be inclusive.
Line 622 (end of section): The NCAR-NEON tool seems like an excellent tool, especially for processing NEON data. However, at this point I'm left wondering how useful this tool might be for sites and users not in NEON, as there hasn't been much discussion about third-party non-NEON sites. There has also been little mention of other EC data processing tools that are already available, such as PyFluxPro used by the OzFlux community or commercial products such as TOVI from LICOR. Indeed, the ONEFLUX processing tool was designed with the purpose of standardising flux processing at a global scale. So, I'm left wondering what place the NCAR-NEON system has amongst these other options. Is it to seamlessly process NEON data quickly or can it be used more widely by other non-NEON sites? I think a little more discussion on these points would be helpful in this section.
Line 714-716: Ahh, here's the first mention of how another network could use the NCAR-NEON system, and its in the conclusion. This supports my point from earlier that some discussion around this is needed before this final point. And there are other networks beyond the US that could benefit from this, such as those that are still establishing or do not have the level of data management sophistication like NEON, OzFlux and ICOS.
References: There seems to be a lot of self-citing in this reference list, i.e. 7 Bonan first author papers. While it is somewhat understandable given the topic and focus of the manuscript, the authors could be more inclusive of other networks and groups who have already made significant progress towards observational data-model integration and in standardising EC processing protocols. By being more inclusive with citations throughout, the manuscript will be more relevant for a global audience and more likely to be cited widely.
Citation: https://doi.org/10.5194/egusphere-2023-271-RC2 -
AC1: 'Author Response to Reviewers: egusphere-2023-271', Danica Lombardozzi, 06 Aug 2023
The comment was uploaded in the form of a supplement: https://egusphere.copernicus.org/preprints/2023/egusphere-2023-271/egusphere-2023-271-AC1-supplement.pdf
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Cited
1 citations as recorded by crossref.
Danica L. Lombardozzi
Negin Sobhani
Gordon B. Bonan
David Durden
Dawn Lenz
Michael SanClements
Samantha Weintraub-Leff
Edward Ayres
Christopher R. Florian
Kyla Dahlin
Sanjiv Kumar
Abigail L. S. Swann
Claire Zarakas
Charles Vardeman
Valerio Pascucci
The requested preprint has a corresponding peer-reviewed final revised paper. You are encouraged to refer to the final revised version.
- Preprint
(8062 KB) - Metadata XML
-
Supplement
(2096 KB) - BibTeX
- EndNote
- Final revised paper