University of California
Informatics and GIS Program

Posts Tagged: class

The Why, How, What, and Who of GIS Fall 2017

Every fall I ask my GIS students to answer the big questions in advance of their class projects. This year climate change, wildlife conservation, land use and water quality are important, as well as a number of other topics. Remote sensing continues to be important to GISers. Scientists, government and communities need to work together to solve problems. 


  • What does the proposed project hope to accomplish?
  • What is the problem that needs to be addressed?
  • What do you expect to happen?


  • What analysis approach will be used?
  • Why was this approach selected?
  • What are alternative methods?
  • Is the analysis reproducible?


  • What are the datasets that are needed?
  • Where will they come from?
  • Have you downloaded and checked this dataset?
  • Do you have a backup dataset?


  • Who will care about this? And why?
  • How will they use the results?
  • Will they be involved in the entire workflow?

Here are the responses from Fall 2017:

Posted on Sunday, August 27, 2017 at 10:33 PM
Tags: class (29)

Distillation from the NEON Data Institute

So much to learn! Here is my distillation of the main take-homes from last week. 

Notes about the workshop in general:

NEON data and resources:

Other misc. tools:

Posted on Monday, June 26, 2017 at 9:33 PM
Tags: class (29), conferences (8), programming (5), remote sensing (5)

Day 2 Wrap Up from the NEON Data Institute 2017

First of all, Pearl Street Mall is just as lovely as I remember, but OMG it is so crowded, with so many new stores and chains. Still, good food, good views, hot weather, lovely walk.

Welcome to Day 2!
Our morning session focused on reproducibility and workflows with the great Naupaka Zimmerman. Remember the characteristics of reproducibility - organization, automation, documentation, and dissemination. We focused on organization, and spent an enjoyable hour sorting through an example messy directory of misc data files and code. The directory looked a bit like many of my directories. Lesson learned. We then moved to working with new data and git to reinforce yesterday's lessons. Git was super confusing to me 2 weeks ago, but now I think I love it. We also went back and forth between Jupyter and python stand alone scripts, and abstracted variables, and lo and behold I got my script to run.

The afternoon focused on Lidar (yay!) and prior to coding we talked about discrete and waveform data and collection, and the opentopography ( project with Benjamin Gross. The opentopography talk was really interesting. They are not just a data distributor any more, they also provide a HPC framework (mostly TauDEM for now) on their servers at SDSC ( They are going to roll out a user-initiated HPC functionality soon, so stay tuned for their new "pluggable assets" program. This is well worth checking into. We also spent some time live coding with Python with Bridget Hass working with a CHM from the SERC site in California, and had a nerve-wracking code challenge to wrap up the day.

Fun additional take-home messages/resources:

Thanks for everyone today! Megan Jones (our fearless leader), Naupaka Zimmerman (Reproducibility), Tristan Goulden (Discrete Lidar), Keith Krause (Waveform Lidar), Benjamin Gross (OpenTopography), Bridget Hass (coding lidar products).

Our home for the week

Posted on Tuesday, June 20, 2017 at 10:59 PM
Tags: class (29), cloud (2), coding (5), collaboration (6), conferences (8), learning (1), lidar (1), open source (3), programming (5), remote sensing (5), tools (3), training (3)

Day 1 Wrap Up from the NEON Data Institute 2017

I left Boulder 20 years ago on a wing and a prayer with a PhD in hand, overwhelmed with bittersweet emotions. I was sad to leave such a beautiful city, nervous about what was to come, but excited to start something new in North Carolina. My future was uncertain, and as I took off from DIA that final time I basically had Tom Petty's Free Fallin' and Learning to Fly on repeat on my walkman. Now I am back, and summer in Boulder is just as breathtaking as I remember it: clear blue skies, the stunning flatirons making a play at outshining the snow-dusted Rockies behind them, and crisp fragrant mountain breezes acting as my Madeleine. I'm back to visit the National Ecological Observatory Network (NEON) headquarters and attend their 2017 Data Institute, and re-invest in my skillset for open reproducible workflows in remote sensing. 

Day 1 Wrap Up from the NEON Data Institute 2017
What a day!
Attendees (about 30) included graduate students, old dogs (new tricks!) like me, and research scientists interested in developing reproducible workflows into their work. We are a mix of ages and genders. The morning session focused on learning about the NEON program ( its purpose, sites, sensors, data, and protocols. NEON, funded by NSF and managed by Battelle, was conceived in 2004 and will go online for a 30-year mission providing free and open data on the drivers of and responses to ecological change starting in Jan 2018. NEON data comes from IS (instrumented systems), OS (observation systems), and RS (remote sensing). We focused on the Airborne Observation Platform (AOP) which uses 2, soon to be 3 aircraft, each with a payload of a hyperspectral sensor (from JPL, 426, 5nm bands (380-2510 nm), 1 mRad IFOV, 1 m res at 1000m AGL) and lidar (Optech and soon to be Riegl, discrete and waveform) sensors and a RGB camera (PhaseOne D8900). These sensors produce co-registered raw data, are processed at NEON headquarters into various levels of data products. Flights are planned to cover each NEON site once, timed to capture 90% or higher peak greenness, which is pretty complicated when distance and weather are taken into account. Pilots and techs are on the road and in the air from March through October collecting these data. Data is processed at headquarters.

In the afternoon session, we got through a fairly immersive dunk into Jupyter notebooks for exploring hyperspectral imagery in HDF5 format. We did exploration, band stacking, widgets, and vegetation indices. We closed with a fast discussion about TGF (The Git Flow): the way to store, share, control versions of your data and code to ensure reproducibility. We forked, cloned, committed, pushed, and pulled. Not much more to write about, but the whole day was awesome!

Fun additional take-home messages:
- NEON is amazing. I should build some class labs around NEON data, and NEON classroom training materials are available:
- Making participants do organized homework is necessary for complicated workshop content:
- HDF5 as an possible alternative data format for Lidar - holding both discrete and waveform
- NEON imagery data is FEDExed daily to headquarters after collected
- I am a crap python coder
- #whofallsbehindstaysbehind
- Tabs are my friend

Thanks to everyone today, including: Megan Jones (Main leader), Nathan Leisso (AOP), Bill Gallery (RGB camera), Ted Haberman (HDF5 format), David Hulslander (AOP), Claire Lunch (Data), Cove Sturtevant (Towers), Tristan Goulden (Hyperspectral), Bridget Hass (HDF5), Paul Gader, Naupaka Zimmerman (GitHub flow).

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Posted on Monday, June 19, 2017 at 11:55 PM
Tags: class (29), coding (5), collaboration (6), conferences (8), data (2), open source (3), privacy (2), programming (5), remote sensing (5), tools (3), training (3)

DS421 Data Science for the 21st Century Program Wrap Up!

Today we had our 1st Data Science for the 21st Century Program Conference. Some cool things that I learned: 

  • Cathryn Carson updated us on the status of the Data Science program on campus - we are teaching 1200 freshman data science right now. Amazing. And a new Dean is coming. 
  • Phil Stark on the danger of being at the bleeding edge of computation - if you put all your computational power into your model, you have nothing left to evaluate uncertainty in your model. Let science guide data science. 
  • David Ackerly believes in social networking! 
  • Cheryl Schwab gave us an summary of her evaluation work. The program outcomes that we are looking for in the program are: Concepts, communication, interdisciplinary research
  • Trevor Houser from the Rhodian Group gave a very interesting and slightly optimistic view of climate change. 
  • Break out groups, led by faculty: 
    • (Boettiger) Data Science Grand Challenges: inference vs prediction; dealing with assumptions; quantifying uncertainty; reproducibility, communication, and collaboration; keeping science in data science; and keeping scientists in data science. 
    • (Hsiang) Civilization collapses through history: 
    • (Ackerly) Discussion on climate change and land use. 50% of the earth are either crops or rangelands; and there is a fundamental tradeoff between land for food and wildlands. How do we deal with the externalities of our love of open space (e.g. forcing housing into the central valley). 
  • Finally, we wrapped up with presentations from our wonderful 1st cohort of DS421 students and their mini-graduation ceremony. 
  • Plus WHAT A GREAT DAY! Berkeley was splendid today in the sun. 
Posted on Tuesday, May 2, 2017 at 12:00 AM
Tags: class (29), conferences (8), data (2)

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