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Virtual Training for Collaboration in Environmental Data Science

Welcome to the HackPad notepad for today's workshop. This notepad supports Markdown and HTML. We'll use this notepad to introduce ourselves, share helpful links and code, and provide other feedback and communication. We'll also post a link to the hackpad on KIStorm after the trainings for future access. Glad to have you here!!

Roll Call

Use this space to introduce youself. Be sure to include the following information:

• Name, Affiliation; optional: contact info, something interesting about yourself, land acknowledgement

Note: You can use an asterisk * or dash - followed by a space to create an item in a bulleted list. Create new lines to add your own information in the HackPad

• Nate Quarderer; ESIIL/Earth Lab/CIRES/CU Boulder; naqu1888@colorado.edu; I like turtles

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• Andrea Garcia; Researcher at Amazon Environmental Research Institute; asgarciaaa@gmail.com

• Test student goes here; email; affiliation

• Mike Binford, University of Florida and National Science Foundation. mbinford@ufl.edu or mbinford@nsf.gov. Observing and Trying to learn new data science!

• Jeff Weber; Scientific Project Manager Unidata Program Center UCAR/NCAR, jweber@ucar.edu, building Sovereign Network for Earth System Science Data, I acknowledge that the land I live and work on is the Traditional Territory of the Arapaho, Cheyenne, and Ute. Colorado's Front Range is a contemporary and traditional site of trade and gathering for many Indigenous people.

• Levi Simons; Postdoc with UC Santa Cruz. I'm working on building a global eDNA database. I've been rejected by Taco Bell Quarterly twice and accepted by Ecological Applications three times.

• Alicia Foxx: https://aliciafoxx.github.io/ Conservation Scientist at the Chicago Botanic Garden, Adjunct Northwestern University. Syntheses on plant ecology; afoxx@chicagobotanic.org

• Tyson L. Swetnam, University of Arizona / CyVerse / ESIIL, tswetnam@arizona.edu; Tucson is home to the O'odham and the Yaqui.

• Ty Tuff (He/Him), Friendly Neighborhood data scientist at the Environmental Data Science Innovation and Inclusion Lab (ESIIL), I like to dance and harmonize math with data!

• Erick Verleye, University of Colorado, Environmental Data Science Innovation and Inclusion Lab (ESIIL)

• Michele Cosi, University of Arizona / CyVerse. The University of Arizona is on the land and territories of Indigenous peoples, and only recently we have decided to acknowledge it. One step at the time, leading by example!

• Nathan Korinek, nathan.korinek@colorado.edu, Earth Lab, University of Colorado, Boulder. I am an earth data scientist, my work focuses around open source, Python, machine learning, UAS, and post fire vegetation recovery. Happy to help with coding and earth data science quesions!

• Nick Lyon (they/them), Data scientist at NCEAS (National Center for Ecological Analysis and Synthesis) / LTER (Long Term Ecological Research) Network Office. lyon@nceas.ucsb.edu

• [Ralph Apeaning] Research Fellow at American University

• Frannie Monasterio Water Fellow, Getches-Wilkinson Center for Natural Resources, Energy, and the Environment, University of Colorado Law School. I work on water accessibility for tribes in the Colorado River Basin. frmo7278@colorado.edu.

• Grant Foster (he/him). PhD student at the University of South Carolina, member of the Dallas Lab. I study ecological networks and disease ecology. I'm also very interested in undergraduate Ecology education! fostergt@email.sc.edu.

• Renée Brown (she/her), Information Manager at McMurdo Dry Valleys Long Term Ecological Research (LTER) Project. I'm also an dryland ecosystem ecologist. rfbrown@unm.edu

• Kimberly Cook University of Kentucky, PhD Student of biogeography and macroecology in the Burger Lab. Using mammals of the modern and paleo sort, I study how life history and other functional traits at the local scale determine large-scale biodiversity patterns. I love shrews, like so much.

• Alex Barth Ph.D. Student at University of South Carolina

• Halina Do-Linh (my website is very much a WIP - just converted to Quarto!), National Center for Ecological Analysis and Synthesis (NCEAS); dolinh@nceas.ucsb.edu; NCEAS is on the unceded land of the Chumash; I once camped for 100 days straight.

• Brian Knight, Ph.D. Student in Applied Mathematics at University of California, Davis. I study computational harmonic analysis; looking for useful ways to decompose your data :)

• Wai Ho CHAK, wchak@ucdavis.edu, Ph.D. Candidate in Applied Mathematics at University of California, Davis

• Alison Post, Program Manager, Earth Lab, University of Colorado, Boulder

• Kat Le, kat@bren.ucsb.edu, University of California, Santa Barbara

• Sumanta Chatterjee, chatterjeesumanta65@gmail.com, USDA-ARS postdoc, USDA Hydrology and Remote Sensing Lab, Maryland

• Mohammad Ahmadi Gharehtoragh, mahmadig@purdue.edu, Phd Student at Purdue University, Department of Industrial Engineering

• Elizabeth Joyner; Elizabeth.r.joyner@nasa.gov; NASA Earth Science Data Systems, Community Coordinator, I am a mom of two kids and a rescue Pit/Lab mix named Minnie Pearl, I live on a tributary of Virginia's James River, home of Nansemond Indian Nation.

• Dana Gehring, Chair of Math, Science, and Technology at Oglala Lakota College, Kyle, SD; I have 13 dachshunds; I live on the Rosebud reservation and teach on the Pine Ridge reservation.

• Tait Weicht; PhD student in applied math at University of California, Davis; I'm one of quadruplets

• Dylan Simpson; PhD candidate in Ecology at Rutgers University; I study wild bees; outside academia I like contra dancing

• Marie Faust, Science Outreach Specialist, National Ecological Observatory Network

• Sara Paull, Disease Ecologist, National Ecological Observatory Network

• Eric R Sokol, Senior Ecologist, National Ecological Observatory Network, Boulder, CO

• Ana M. Tarano, Data Scientist at University of Miami; ana.m.tarano@miami.edu, I am super excited to watch the Perseids meteor shower this year because it'll be during a New Moon (and it's my birthday!)., I live and am part of the land that belongs to the Tequesta, Miccosukee, Seminole, Mascogo, Taíno nations.

• Anna Boser (annaboser@ucsb.edu) I’m a PhD student at the Bren School of Environmental Science and Management at the University of California, Santa Barbara, located on unceded Indigenous Chumash ancestral lands and waters. I study water use and scarcity in agriculture using remote sensing and machine learning. I’m a fan of rock climbing and backcountry skiing!

• Marina Wolowski, Professor, Federal University of Alfenas; marina.wolowski@gmail.com, I like to cook. My research focus on pollination in natural and agricultural ecosystems, from field and natural hystory studies to synsthesis projects and database standards for plant-pollinators interactions.

• Ruben Remelgado Researcher at TU Dresden, Germany, dealing with Global Ecosystem mapping and associated data biases

• Sally Wang, Data Scientist at Pacific Northwest National Laboratory, using explainable AI/ML to predict and explain extreme weather events, including wildfires and mesoscale convective systems

• Katherine Siegel (ksiegel@ucar.edu) postdoc at CU Boulder + starting as an assistant prof at University of Toronto in January. Currently living on Cheyenne, Arapaho, and Ute land. Interested in forest conservation, social-ecological systems, and causal inference. (she/her/hers)

• Valentin Stefan; valentin.stefan@ufz.de; Helmholtz Centre for Environmental Research (UFZ) & German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig. LinkedIn

• Robert (Bob) Newman. robert.newman@und.edu Professor, University of North Dakota, Biology/Wildlife Biology. Most of us are on somebody else's land: https://und.edu/student-life/diversity/multicultural/land-acknowledgement.html I do field and remote sensing studies on a variety of wildlife on the northern plains: how do they make a living on a landscape dominated by ag and energy. I work with the TEK section in Ecological Society of America and the Native Peoples' Working Group in The Wildlife Society. Non-native myself.

• Brian Yandell, UW-Madison, Department of Statistics, Professor. brian.yandell@wisc.edu. Proficient in R and Rstudio, conversant in github.

• Steve Goldstein University of Madison-Wisconsin, Data Science Institute, Emeritus Scientist. stevenjaygoldstein@gmail.com

• Kelly Aho, assistant prof at Michigan State; kellyaho@msu.edu. Michigan State University occupies the ancestral, traditional, and contemporary Lands of the Anishinaabeg–Three Fires Confederacy of Ojibwe, Odawa, and Potawatomi peoples. The University resides on Land ceded in the 1819 Treaty of Saginaw.

• Cathleen Torres Parisian, ctorresp@umn.edu, Polar Geospatial Center at University of Minnesota, Geospatial Engagement Lead. University of Minnesota - Twin Cities stands on Mnisóta Makhóčhe, the homelands of the Dakhóta Oyáte.

• Charles Jason Tinant (jtinant@olc.edu), Water Resources Engineering, Earth Science, GIS, Tidyverse enthusiast, aspiring horticulturalist

• Tad Dallas. Assistant professor. University of South Carolina, Biological Sciences.

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• Joe Miller GBIF Global Biodiversity Information
  Facility

• [Lizbeth Amador], University Maine Orono graduate student; lizbeth.amador@maine.edu, Modeling flowering sensitivities to climate change & land use, I live in the historical and territory of the Penobscot people whom are currently battling land rights.

• Ronit Purian, purianro@tauex.tau.ac.il and more info here: https://roniturban.wixsite.com/urbanit

• [Lise St. Denis] CIRES, Earthlab, lise.st.denis@colorado.edu, avid baker!

• Andrea S. Garcia, Amazon Environmental Research Institute; asgarciaaa@gmail.com; I am a researcher working on land use dynamics and mechanisms to avoid deforestation; I love basketball

• Lilly Jones, lijo8146@colodo.edu. CU-Boulder CIRES Earth Lab post doc. I live in the traditional homeland of the Oceti Sakowin.

• Mike Packard, United States Forest Service (michael.packard@usda.gov). I am a data analyst with a masters degree in computational social science, working to improve the data governance, architecture, and analytics capabilities for a large government agency. Excited to be here!

• John Musinsky, Research Scientist, Airborne Remote Sensing Group, National Ecological Observatory Network. Avid hiker, sailor, squasher. Occupy a small sliver of the ancestral homelands of the Ute, Arapaho, and Cheyenne people

• Jess Logan - United Tribes Technical College, Computer Information Technology Instructor, ESIIL Stars Faculty Mentor

• Diego Brizuela. PhD student at Helmholtz Centre for Environmental Research & German Centre for Integrative Biodiversity Research (iDiv) (diego.brizuela-torres@ufz.de). My PhD is on socio-economic drivers of deforestation in the Amazon.

• Katherine Halama- Education Program Coordinator, Earth Lab/ESIIL/CU Boulder, katherine.halama@colorado.edu

• Emily Biggane - United Tribes Technical College, Intertribal Research and Resource Center, UTTC ESIIL Stars Faculty Mentor, I was a missing person lost in woods of Alaska for 24 hours

• Khum Thapa-Magar, Postdoc, INSTAAR, University of Colorado.

• Elizabeth (Lizzie) Lombardi (she/her); Postdoc at University of New Mexico, Museum of Southwestern Biology (emlombardi@unm.edu).

• Garrett Knowlton, Graduate Student @ University of Wisconsin-Madison in Ecology. I research forests, disturbance, and climate change.

• Lin Xiong, lxiong@umd.edu, assitant research professor, university of maryland, college par

• Betsy von Holle, National Science Foundation, bvonholle401@gmail.com. I am a program director on LTPD (aka sabbatical), learning new programming skills.

• Foster Sawyer, jfsawyer@olc.edu, Faculty-Research Scientist at Oglala Lakota College

• Darian Sorenson, dsorenson@ucdavis.edu, PhD student in Applied Mathematics at University of California, Davis

• Amanda Richey, amandaleighrichey@gmail.com, MS student in Biology at Florida International University in Miami

• Erin Polka (polkaen@bu.edu). Research Data Analyst and incoming PhD Student at Boston University School of Public Health in the Environemntal Health Department. Stuyding the health impacts of oil and gas activites.

• Miles Moore (miles.moore-1@colorado.edu). Research technician at the Institute of Arctic and Alpine Research, Data Synthesis intern for NASA's Arctic Boreal Vulnerability Experiment (ABoVE @ GFSC) and senior undergraduate at the University of Colorado Boulder. I am interested in researching vegetation change in time and space using modelling, remote sensing, and data synthesis via R/python, machine learning tools as well as high-performance computing!

• Nicole Hemming-Schroeder, PhD Candidate, Department of Earth System Science, University of California, Irvine

• Caitlin White (caitlin.t.white@colorado.edu), PhD student @ University of Colorado, Boulder. Affiliations: the Suding Lab, Dept of Ecol + EvoBio, Institute of Arctic and Alpine Research (INSTAAR), and Niwot Ridge LTER 🏔️. Living on the lands of the Arapaho, Ute, and Cheyenne.

• Mansi Shah; Data Science + Environmental Science. I am currently a software engineer at Planet on our DevRel team, working to make geospatial data actionable and accessible. (If there's an application of geospatial data you're passionate about, I'm excited to learn about it!) I am also a musician and love connecting with people through the arts.

• Hannah Haynie, University of Colorado Boulder, Department of Linguistics; hannah.haynie@colorado.edu My research centers on linguistic and cultural diversity and the ecological contexts in which these develop (biocultural diversity). I live and work on the unceded lands of Arapaho, Ute, and Cheyenne people. I recognize the devastating and lasting impacts of forced removal of peoples from this land and honor the contributions of many Indigenous cultures to this place.

• Patrisse Vasek. Oglala Lakota College, Department of Math, Science, and Technology; pvasek24220@olc.edu. Bachelor's Degree in Natural Science emphasis in Earth Science and Yankton/Oglala Sioux. Research in environmental health and an emphasis in water, soil, and plant uptake chemistry. Specifically contaminants either manmade or natural, and the mobility within ecosystems. Mapping and Krigging of these elements within the environment and approximation to residential or agricultural areas. Modeling of contaminant transportation and potent``ial risks to public health, especially tribal lands. Currently reside on the lands of the Oceti Sakowin, the Black Hills, SD.

• Hilary Brumberg, University of Colorado Boulder, PhD student in Environmental Studies. Researching tropical forest conservation and restoration, watershed conservation, sustainable agriculture, conservation finance and organizational management. Living on the lands of the Arapaho, Ute, and Cheyenne.

• Jada Daniels, Ecology PhD Student at Louisiana State University, Researching the effects of habitat fragmentation on plant-microbe interactions in aquatic ecosystems.

• Nayan Mallick, PhD Candidate at the University of South Carolina. email: nmallick@email.sc.edu. My research focuses on the impact of climate change on zooplankton dynamics in estuarine environment. I am also working with national estuarine research reserve (NERR) data to look for change in hydrodynamic properties in three NERR sites.

• Kimberly Thompson, Postdoctoral researcher at the German Centre for Integrative Biodiversity Research, kimberly.thompson@idiv.de

Day 1 (Weds, May 17): Collaborating with Other People Using Cloud Computing

Day 2 (Thurs, May 18): R & Python Bilingualism: How to Talk to Everyone

Day 3 (Friday, May 19): Tools for Reproducible and Open Science

Pre Assessment

If you see something you agree with, add a + next to the word/statement :)

• Reproducibility +++++++++++++++++++
• Shareability ++++++++++++
• Strong Metadata+++++++++++
• CARE Principles ++++++
• FAIR Principles +++++++
• Findable+++++++
• Well-documented Code++
• internet searchable+
• cloud-native
• accessible ++++

Assessment 1: Introduction to Open Science

• Open Access Publications+++++++

• Open Data++++++++++++++

• Open Educational Resources++++++++++

• Open Methodology ++++++++++

• Open Peer Review ++++

• Open Source Software++++++++++

Democratic++++++++++ - ++

Pragmatic++++++++

Infrastructure++++++++++

Public++++++++++

Measurement++++++++

Assessment 2 Documentation

Select (+) as many as you like

• Teams +++++++++++++
• SLACK +++++++++++++
• BaseCamp + - +
• GitHub ++++++++++++++++
• WhatsApp ++++
• SMS ++ -
• Trello ++++
• Asana ++
• listservs ++
• GitLab +
• Outlook +++++++
• Google Drive/Docs ++++++++++++
• Jira +
• Telephone ++
• Box +
• Monday.com++
• Signal +
• Facebook +
• Twitter ++
• Google Docs++++++++ -
• Airtable +
• Mattermost +
• Overleaf

Assessment 3 Reproducibility

• The original repository does not include an environment file (~/.Renviron) and this causes difficulties with reproducing the code. ++ -
• Comments absent or insufficient detail to understand operations +++++
• Vague / "bad" commit messages (with projects on Git/GitHub) +
• Unclear or incomplete methods used +++
• missing packages/libraries ++
• no metadata ++++++++++
• Insufficient time - I'm working on my own project, not somebody else's.
• Absolute file paths or file paths that depend on OS +
• Use of proprietary software ++++++
• The original repository does not include all the neccessary data to make comparisons across sites +
• Source code poorly organized/documented making it hard to reproduce. +++
• Poor code readability ++
• Inconsistent coding style / formatting
• Contact authors data available upon request
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  +++
  • sometimes required by data sources

Choose (+) one:

• Replicability++
• Reproducibility+
• Repeatablity ++++++

• Replicability +++++
• Reproducibility+++
• Repeatablity+

Useful Links

Use this space to share helpful links:

NOTE: You can use the following syntax to add a link to this notepad using Markdown

[alt text](https://) - creates a hyperlink

• Course Webpage

• Earth Data Science Textbooks

• GitHub Pages instructions

• geemap is a powerful python library to integrate google earth engine code and data into your python workflows!

• R and Python Code Examples (This is the one you want! The link on the course website goes to a different document)

• CyVerse User Account Creation and Workshop Enrollment - Create your CyVerse account, use the email address that you enrolled for ESIIL summit. Important: Make sure to create a password when you create your account!!

• Innovation Summit JupyterHub: https://innovation-summit-training.esiil.org - use the email name you registered with w/o @xxx.xxx, the password will be revealed live over zoom

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• Jetstream2 intro: https://cu-esiil.github.io/pre-innovation-summit-training/1CollaborationonCloud/jetstream2lesson/jetstream2lesson/

• Innovation Summit Data Library: https://cu-esiil.github.io/data-library/

• Pre-summit survey [Please take before the summit!!]: https://cuboulder.qualtrics.com/jfe/form/SV0rA5ZykZoBx53Po

• CyVerse Intro Google Slides

• RGEE - R interface to the GEE Python API

• Resouces for R users interested in learning Python (from Melanie Kammerer):

  • https://jakevdp.github.io/WhirlwindTourOfPython/
  • https://jakevdp.github.io/PythonDataScienceHandbook/index.html

Open & Reproducible science (Day 3)

• From Leah Shanley in Zoom chat

  • There are a lot of legal issues related to indigenous data sovereignty that need to be considered (e.g., having an MOU and contract to protect the data may not be sufficient to protect indigenous data against federal FOIA requests for access to federally funded data that affect tribes). https://zenodo.org/record/4085173#.ZGe_Xy-B3AY
  • Our Data Working Group of the intenrational Group on Earth Observations has issued guidance on open data licensing https://earthobservations.org/article/9348185/geo_blog_obs.php?id=590

• White House OSTP Listening Sessions: https://www.whitehouse.gov/ostp/events-webinars/

• From Nick Lyon in Zoom chat

  • Quarto’s website creation tutorial is also really friendly to first-timers https://quarto.org/docs/websites/

• Carpentries (training for shell/bash and automation): https://software-carpentry.org/lessons/

Code

Use this space to share helpful code:

NOTE: You can wrap your text in three back quotes ``` to make it look like code as shown below

Here is some example code

Using GitHub within the JupyterHub

Go to the Innovation Summit Jupyter Hub and login with your username and password

Open a new Terminal by clicking on the + notebook icon, or open a Python notebook.

git clone https://github.com/cu-esiil/innovation-summit-utils.git