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applications:diy [2022/03/02 21:10] – joetulenkoapplications:diy [2023/02/16 19:14] (current) – joetulenko
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 Please find links and descriptions to tutorials for 1) getting set up with ICE-D (ie connecting to the database from your own personal computer through various desktop applications like MySQL, ArcGIS, QGIS and Matlab), and 2) using ICE-D for some interesting visualization and analysis applications. Please email any of us on the project [[balcs@bgc.org|Greg Balco]], [[benjamin.laabs@ndsu.edu|Ben Laabs]], and/or [[jtulenko@bgc.org|Joe Tulenko]] if you have further questions. Please find links and descriptions to tutorials for 1) getting set up with ICE-D (ie connecting to the database from your own personal computer through various desktop applications like MySQL, ArcGIS, QGIS and Matlab), and 2) using ICE-D for some interesting visualization and analysis applications. Please email any of us on the project [[balcs@bgc.org|Greg Balco]], [[benjamin.laabs@ndsu.edu|Ben Laabs]], and/or [[jtulenko@bgc.org|Joe Tulenko]] if you have further questions.
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 === GETTING SET UP WITH ICE-D === === GETTING SET UP WITH ICE-D ===
-Please find descriptions and links to tutorials here for connecting with ICE-D from your personal desktop on various applications. Whether you use Mac or prefer the Windows darkside like myself (J. Tulenko speaking here), we've got you covered. 
  
-**1) Connecting to the database using a MySQL client** +**[[applications:connect|CONNECT TO ICE-D PAGE]]**
-ICE-D is hosted in a MySQL server, and there are free desktop applications that one can download from the internet and set up to connect with the actual database itself. This section may eventually get archived, but for now, set up directions are linked below.+
  
-Please find the tutorial for **Windows** computers using the MySQL application **HeidiSQL** {{ :applications:heidisql_set_up.pdf |here}}. +On this page you will find descriptions and links to tutorials for connecting to the database though various software products like Matlab, MySQL and in the future, ArcGIS and QGIS.
  
 {{:applications:heidisql_logo.jpg?nolink&200|}} {{:applications:heidisql_logo.jpg?nolink&200|}}
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-Please find the tutorial for **Mac** computers using the MySQL application **Sequel Pro** {{ :applications:sequel_pro_set_up.pdf |here}}. 
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-{{:applications:sequelpro_logo.jpg?nolink&200|}} 
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-**2) Connecting to the database using Matlab** 
-Making queries directly in the database and adding new data to the database is excellent, but for the queries that you make in your MySQL client, the output then has to be copied over into either a geospatial application (ie ArcGIS/QGIS) or a plotting/data analysis application (ie Matlab/Python GUI). However, there is a way to connect with the database directly in Matlab so that you don't need to make static copies of what is already in the database and instead interact with the live data! Cool. 
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-Please find the tutorial to connect with ICE-D through Matlab {{ :applications:connect_through_matlab_windows_.pdf |for Windows here}}. 
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-Please find the tutorial to connect with ICE-D through Matlab for Mac here. 
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 {{:applications:matlab_logo.png?nolink&200|}} {{:applications:matlab_logo.png?nolink&200|}}
 +{{:applications:qgis_logo.png?nolink&200|}}
  
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-**3) Connecting to the database using Geospatial software (ArcGIS/QGIS)** 
-At the moment, we are still working on how to figure this out, but we believe the best way to do this might be to set up a Web Feature Service (WFS) directly on the ICE-D webpage. The WFS would create one large file (probably something in a shapefile format or a geojson format) that can be essentially copied over into your GIS application. The link would be live, and continuously updated as the database updates so you would once again circumvent the need to download and store static copies of whatever subset you want to extract from the database. 
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-For now, please see this example of what a WFS looks like on a webpage and how to open the {{ :applications:connect_through_wfs_in_qgis.pdf |WFS in QGIS here}}.  
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-I am currently showing examples using QGIS but I know you can do it in ArcGIS as well. QGIS is a FREE alternative to ArcGIS that has a lot of the same functionality. 
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-{{:applications:qgis_logo.png?nolink&200|}} 
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-{{:applications:arcgis_logo.png?nolink&200|}} 
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-=== ANALYSIS AND APPLICATIONS EXAMPLES === 
-Here are some examples we have come up with so far. Please email any of us on the project [[balcs@bgc.org|Greg Balco]], [[benjamin.laabs@ndsu.edu|Ben Laabs]], and/or [[jtulenko@bgc.org|Joe Tulenko]] with your ideas so we can add them to the list! 
- 
-**1) Analysis layer examples: the ICE-D X OCTOPUS web application** 
-The [[http://octopus.x.ice-d.org|ICE-D X OCTOPUS]] web application is not very much like the rest of the ICE-D focus area applications because it doesn't rely on an ICE-D-maintained back end database. Instead, its data layer is the [[https://earth.uow.edu.au|OCTOPUS database of cosmogenic-nuclide data used for erosion rate estimates]]. Also, the web application accesses those data by interacting with a Geoserver web feature server rather than a MySQL database. However, it does use ICE-D middle layer applications (the web service implementation of the online erosion rate calculator), so it's a good example of an analysis-layer application that uses both data-layer and middle-layer services. Also, it highlights the idea that you can mix and match data- and middle-layer servives from various places to do what you need to do. Finally, it's a pretty simple web application with a fairly minimal amount of code.  
- 
-The source code for the ICE-D X OCTOPUS web app can be viewed [[https://github.com/balcs/ice-d-x-octopus|here]]. It is written in Python 2.7, uses the [[https://webapp2.readthedocs.io/en/latest/|webapp2]] application framework, and runs on Google App Engine. Unfortuately this is kind of obsolete because GAE has been migrating to Python 3 and different web app frameworks (so I am not sure if you could install and run it on a newly created GAE project), but it is a nice simple example of how a transparent-middle-layer application can work.  
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-**2) Data-model comparison between LGM and penultimate moraine ages, and model output from simulations over multiple glaciations** (ie the ice sheet influence on regional climate example). **Hypothesis:** if the impact from ice sheets on re-arranging large-scale atmospheric circulation and thus modulating regional climate is actually significant, we should be able to use climate model output to predict the geospatial patterns of moraine preservation over multiple glacial cycles. This could be tested by comparing moraine ages and geospatial patterns from the database with model output to see where there is good fit between model output and data and where there isn't. +=== ADDING DATA TO ICE-D ===
  
-See the example output figure below and {{ :applications:ice_sheet_influence_exercise.pdf |find a link to the tutorial here.}}+**[[applications:add| DATA ENTRY PAGE]]**
  
-{{ :applications:ages_vs_model_output.jpg?nolink |}} 
  
----- +We have recently updated the data entry process for ICE-D such that community contributors can now add data through an admin page directly on the website! Users can import excel spreadsheets of new and pre-existing data that will instantly populate on the webpage and in the database
  
-**3) Testing global expression of Younger Dryas** +{{ :applications:admin_pic.png?nolink |}}
-Please find a tutorial and some matlab scripts used to generate some of the plots found in a recent paper from Greg Balco ([[https://www.annualreviews.org/doi/abs/10.1146/annurev-earth-081619-052609|Balco, 2021]]) in this example.+
  
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-Tutorial here. 
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-Matlab scripts here in this zipped folder. 
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-**4) Post-Glacial Greenland ice-sheet retreat time-distance diagram** following up on a workshop at the University at Buffalo, we attempted to generate a time-distance diagram of SW Greenland Ice Sheet retreat and you can find the matlab script here. 
  
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-**5) Determining if measurement precision has gotten better through time** 
-This is a somewhat simple and fun exercise to investigate whether or not we as a community have been making progressively better measurements (ie improvements to field sample techniques, lab extraction procedures, AMS measurements, etc that should hopefully be leading to more precise cosmo measurements). 
  
-See the summary plot below that shows the story is a bit more complicated and perhaps we as a collective community have room for improvement.+=== ANALYSIS AND APPLICATIONS EXAMPLES ===
  
-{{ :applications:precision_over_time_output.png?nolink |}}+**[[applications:applications|ANALYSIS AND APPLICATIONS PAGE]]**
  
-please find a script that you can copy into a new script editor written to produce this plot here (actually not sure how to upload atm.. the wiki takes photos and pdfs but not text files?). +On this page you will find examples we have come up with so far. Please email any of us on the project [[balcs@bgc.org|Greg Balco]], [[benjamin.laabs@ndsu.edu|Ben Laabs]], and/or [[jtulenko@bgc.org|Joe Tulenko]] with your ideas so we can add them to the list!
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-**6) Is there a correlation between Al/Be ratios and sample elevation?** +
-This example is based off a recent publication ([[https://www.mdpi.com/2076-3263/11/10/402|Halsted et al., 2021]]) that found there is a correlation between Al / Be ratios and elevation that likely needs to be taken into account. +
- +
-The resulting plot below demonstrates there is a negative correlation (ie the ratio decreases as elevation increases):+
  
 +{{ :applications:ages_vs_model_output.jpg?nolink |}}
 {{ :applications:ratio_v_elevation.png?nolink |}} {{ :applications:ratio_v_elevation.png?nolink |}}
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- 
-please find a script that you can copy into a new script editor written to produce this plot here (actually not sure how to upload atm.. the wiki takes photos and pdfs but not text files?). 
  
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-**7) Heinrich Stadials aridity drives glacier retreat in the Mediterranean?** 
-This example is a follow up to a paper recently published in Nature Geoscience ([[https://www.nature.com/articles/s41561-021-00703-6|Allard et al., 2021]]) that found that glaciers in the region may have been retreating during Heinrich Stadials due to more arid conditions.  
- 
-They compiled many moraine and erratic boulder ages from across the Mediterranean, found intervals of erratic boulder deposition //during// Heinrich events and suggested this as evidence of retreat during Heinrich Stadials.  
- 
-This is an example of an easily testable hypothesis using ICE-D: Do moraine ages across the Mediterranean more often lie outside of Heinrich Stadial events while erratic boulder ages more often line up within Heinrich Stadial events when compared to a random distribution of both moraine and erratic boulder ages? If yes, this would support the conclusions put forth in Allard et al., 2021. If no, it may bring into question some of the interpretations made in the paper. 
- 
-The set up would first be to compare a random distribution of both moraine and erratic boulder ages against a North Atlantic record (such as the NGRIP d18O curve) and see how frequently ages line up with Stadials and warm intervals (ie, what % of the time, from x-x ka, do moraine ages line up with Stadial events? What % of the time do random ages line up with warm intervals? And do the same exercise for erratic boulders). Then, run the same exercise for the actual observed ages from the Mediterranean and compare. Is there actual evidence to suggest that moraine ages occur a higher % of the time within warm intervals compared to a random distribution? Is there evidence to suggest that erratic boulder ages occur a higher % of the time within stadial intervals compared to a random distribution? Who knows? Let's find out. 
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-**8) Identifying regions of possible heavy moraine degradation** (using the moraine ages and land degradation models incorporated into the middle layer of calculations) and **comparing identified areas of high degradation to geohazards** (plate boundaries and areas of high seismic activity).  
-**Hypothesis:** if geohazards actually present a notable obstacle to moraine dating through moraine degradation, then we should be able to find instances of high moraine degradation coinciding with high seismic activity. 
- 
  
  
 +=== PRODUCTION RATE CALIBRATIONS AND CALCULATING EXPOSURE AGES IN V3 ONLINE CALCULATOR ===
  
 +**[[applications:calculate|CALCULATIONS INSTRUCTIONS PAGE]]**
  
-[[applications:connect|Connect to the database]] 
  
 +On this page please find a brief set of instructions for copying input data automatically formatted in ICE-D into **[[https://hess.ess.washington.edu/math/v3/v3_age_in.html|version 3 of the online exposure age calculator]]** to calculate both reference production rate calibration values and surface exposure ages.