Wrap up on the Hopland Bioblitz 2016

This text excerpted from the Hopland Newsletter:

Over 70 scientists and naturalists descended upon HREC from  April 8-10th in our first Hopland Bioblitz. During the weekend over 400 species from the recently discovered blind silverfish to the characterful kangaroo rat were observed and recorded on the HREC iNaturalist page. 

You can still get involved with our bioblitz efforts by logging onto our iNatualist page and seeing if you can help to identify any unknown species. Enjoy more of our discoveries by taking a look through our photography competition entries.

This bioblitz was supported by a grant from the University of California Agriculture and Natural Resources and was organized by Kip Will, Maggi Kelly, George Roderick, Rosemary Gillespie. IGIS's Shane Feirer helped set up the IT infrastructure for the day.

Another rad lidar music video

https://www.youtube.com/watch?v=XBUdCBxrhZo

From NZ no less. 

Wall-E was right

Landsats - active and decommissioned

Used in my MDP lecture today, and so posting so I can find it easily later! 

http://apps.agi.com/SatelliteViewer/

Great web app for viewing current satellite orbits.

More detailed info here:  http://qz.com/296941/interactive-graphic-every-active-satellite-orbiting-earth/

Hopland Bioblitz is on!

Our big Hopland scientific bioblitz is this weekend (9-10 April, with some events on the 8th) and I look forward to seeing many of you there. If you can't make it to HREC, there are many ways you can remotely help us and check out what is happening all weekend long.

HELP US OUT. http://www.inaturalist.org/ Many people will be using iNaturalist to make and share observations. Helping out the effort is easy. Look for observations at the iNaturalist site by searching for "Hopland" in the "Projects" pulldown menu and choose "Hopland Research Extension Center". Once there, you can browse the plants and animals needing identification and needing confirmation. Every identification counts toward our goal of massively increasing the knowledge of the HREC's flora and fauna.

VOTE ON IMAGES.  http://www.hoplandbioblitz.org/ We are hosting an image contest for the plants and animals of HREC. Great prizes will be given  for images that get the most votes(REI gift cards and a GoPro grand prize!). Please visit the site and vote for your favorites frequently during the weekend and share them and then sit back and what the slide show.  

CHECK US OUT. http://geoportal.ucanr.edu/# Our new app will graphically show you our progress for the bioblitz observations. Results will be updated every 15 minutes. See how your favorite groups are doing in the challenge to document as many species as possible.

Look for #HoplandBioblitz on Twitter and Instagram

Follow along on Facebook https://www.facebook.com/HoplandREC/

AAG 2016 wrap up

1870s-ish map of SFAside from all the sunshine, architecture, maps, and food, at the 2016 AAG conference Kelly and I participated in four organized sessions on Historical Ecology. On Saturday, we heard from a number of fantastic researchers, and here is my wrap-up.  (Alas, these sessions overlapped with sessions on CyberGIS, Who says you can't be interestd in both? cyber-historical-environmental-spatial-data-science.)

• History: We heard from researchers working on data from the Holocene, to pre-history, to the 20th century.
• Focus: Ecosystems included prairie, forests (Maryland, New York, California, Florida, Ohio); and Wetlands (China, California, etc.); Land Use and Agriculture (Mexico, Brazil); Fire (Arizona); and biological collections. 
• Data included inventory (PLS system: land appraisal value; Cadastral surveys); Imagery (Landsat, aerial imagery); and biological (paleo; tree ring; resurveys; pollen records; bird census; and PLS system: witness trees, survey lines, FIA data). 
• Methods: Comparison between past and present from existing inventory data, as well as comparison between historic and modern resurveys; digitization of multiple data sources; narrative analysis; ecological modeling; ecosystem services modeling; fire behavior modeling; OBIA of historic imagery; and some really neat modeling work. 
• Emerging Themes from the sessions included: 
  • Data. Most people used digital data from an existing source - websites, clearinghouse, existing digital source. Many digitized their data. One person used an API. 
  • Accuracy. About half of speakers have thought about, or incorporated understanding of data quality or uncertainty in your work; but this is difficult to do quantitatively. Some people use the 'Multiple lines of evidence' from diverse datasets to increase confidence in results. 
  • Tools. We heard about a number of tools, including GIS as desktop tool, Open tools, Backcasting with landcover models, Complex modeling approaches, One paper used OBIA methods, and one paper discussed Big historic data (maybe moving toward the cyberGIS overlap). 
  • Theoretical frameworks: A few papers used resilience as a framework, social, ecological and coupled; and several papers used a landscape ecology framework. 
  • New terms: I learned a new term: “Terrageny”: a record of how a landscape became fragmented through time, containing information on the ‘ancestry’ of fragments and showing how an initially continuous landscape was progressively divided into fragments of decreasing size. Ewers et al. 2013. Gorgeous word. Must incorporate into cocktail party discussion. 

We also sent out a survey to the speakers prior to the talks, and here are some preliminary results. 

Question: What are the three top challenges that you see for historical ecology research?

• Data/Logistical/Availability
  • The further back in time we look, the more sparse the data. 

• Technical 
  • Lack of metadata: Current data deluge may attract attention/urgency away from the discovery and digitization of historical data;
  • Few models capable of incorporating human and environment interactions over long time scales. 
• Theoretical
  • Maintaining perceived relevance in the context of the novel ecosystem/no-analog system conversation - not having historical ecology be the baby that is thrown out with the bathwater.
• Operational 
  • Many respondants mentioned issues with funding - these projects are by nature interdisciplinary, often require large programs to fund at achievable levels, and not many funding sources exist.
• Communication
  • We need to focus on communicating the importance of understanding past conditions to inspire and guide current design proposals. 

Question: What exciting future directions do you envision for historical ecology research?

• The importance of historical data and analysis:
  • Historical data is essential: Multi- Inter-disciplinary research needs historical research, particularly so that we can understand 1) historical reference conditions, but also so that we can understand 2) when we might have novel interactions between species and ecosphere. 
• Practicality of historical data and analysis: 
  • Historical ecology is critical for restoration projects and for studying climate change, and for its power to communicate through environmental education with the public.
• New data/Big data/Data Fusion: 
  • Increase in digitally available historical sources (longer ecological and climate records and reconstructions), plus the availability of large, high-resolution datasets to assess change (thinking LiDAR, government reports, survey data...)  
  • There is also increasing sophistication of analysis and visualization tools.
  • But, the current data deluge may attract attention/urgency away from the discovery and digitization of historical data.

A fantastic time was had by all!

Spatial Data Science Bootcamp 2016!

Last week we held another bootcamp on Spatial Data Science. We had three packed days learning about the concepts, tools and workflow associated with spatial databases, analysis and visualizations. Our goal was not to teach a specific suite of tools but rather to teach participants how to develop and refine repeatable and testable workflows for spatial data using common standard programming practices.

2016 Bootcamp participants

On Day 1 we focused on setting up a collaborative virtual data environment through virtual machines, spatial databases (PostgreSQL/PostGIS) with multi-user editing and versioning (GeoGig). We also talked about open data and open standards, and moderndata formats and tools (GeoJSON, GDAL).  On Day 2 we focused on open analytical tools for spatial data. We focused on Python (i.e. PySAL, NumPy, PyCharm, iPython Notebook), and R tools.  Day 3 was dedicated to the web stack, and visualization via ESRI Online, CartoDB, and Leaflet. Web mapping is great, and as OpenGeo.org says: “Internet maps appear magical: portals into infinitely large, infinitely deep pools of data. But they aren't magical, they are built of a few standard pieces of technology, and the pieces can be re-arranged and sourced from different places.…Anyone can build an internet map."

All-in-all it was a great time spent with a collection of very interesting mapping professionals from around the country. Thanks to everyone!

ASTER Data Open - No April Fools!

We know about the amazing success for science, education, government, and business that has resulted from the opening of the Landsat archive in 2008. Now more encouraging news about open data:

On April 1, 2016, NASA's Land Processes Distributed Active Archive Center (LP DAAC) began distributing ASTER Level 1 Precision Terrain Corrected Registered At-Sensor Radiance (AST_L1T) data products over the entire globe at no charge. Global distribution of these data at no charge is a result of a policy change made by NASA and Japan.

The AST_L1T product provides a quick turn-around of consistent GIS-ready data as a multi-file product, which includes a HDF-EOS data file, full-resolution composite images (FRI) as GeoTIFFs for tasked telescopes (e.g., VNIR/SWIR and TIR ), and associated metadata files. In addition, each AST_L1T granule contains related products including low-resolution browse and, when applicable, a Quality Assurance (QA) browse and QA text report.

More than 2.95 million scenes of archived data are now available for direct download through the LP DAAC Data Pool and for search and download through NASA‘s Earthdata Search Client and also through USGS‘ GloVis , and USGS‘ EarthExplorer . New scenes will be added as they are acquired and archived.

ASTER is a partnership between NASA, Japan‘s Ministry of Economy, Trade and Industry (METI), the National Institute of Advanced Industrial Science and Technology (AIST) in Japan, and Japan Space Systems (J-spacesystems ).

Visit the LP DAAC ASTER Policy Change Page to learn more about ASTER. Subscribe to the LP DAAC listserv for future announcements.

It's AAG time again!

The annual AAG conference is rolling into town next week, and several of us will be there. 

• Kelly and Jenny will be presenting; 
  • Kelly: Disentangling drivers of change in California Forests: management and climate 
  • Jenny: Spatial Data Science for Collaborative Geospatial Research
• Alice is a discussant on THREE panels; and 
• I am a discussant on the Historical Ecology session. 

Former kellylabbers will also be in force: 

• John Connors is presenting (and organizing, and morderating, and all kinds of things): 
  • Disentangling Diversity: Agrobiodiversity, Livelihoods, and Food Security in the Kilombero Valley, Tanzania
• Desheng Liu will be there: 
  • Reconstructing Land Cover Trajectories from Dense MODIS Time Series
• Ellen Kersten will be presenting:
  • Got health? Using spatial and temporal analysis to achieve health equity for children 

 Have a great time everyone! (If I have missed anyone, let me know!)

Bootcamp is here! Spatial Data Science 2016

Spatial Data Science for Professionals

We live in a world where the importance of spatial data is ever increasing. Many of the societal challenges we face today — fire response, energy distribution, efficient resource allocation, land use, food scarcity, invasive species, climate change, privacy and safety — are associated with big spatial data.  Addressing these challenges will require trained analysts fluent in:

• integrating disparate data, from aircraft, satellites, mobile phones, historic collections, public records, the internet;
• using easily available and open technology for robust data analysis, sharing, and publication;
• understanding and applying core spatial analysis methods;
• and applying visualization tools to communicate with project managers, policy-makers, scientists and the public.

Mastering these challenges requires Spatial Data Science: big data tools, geospatial analytics, and visualization. Today’s marketplace needs trained analysts who know how to find, evaluate, manage, analyze and publish spatial data in a variety of environments. With this hands-on Spatial Data Science Bootcamp for professionals, you can expand your GIS skill level and learn how to integrate open source and web-based solutions into your GIS toolkit by gaining an understanding of spatial data science techniques.

The goal of this Spatial Data Science Bootcamp is to familiarize participants with the modern spatial data workflow and explore open source and cloud/web based options for spatial data management, analysis, visualization and publication. We’ll use hands-on exercises that leverage open source and cloud/web based technologies for a variety of spatial data applications.

https://iep.berkeley.edu/spatial/iep-spatial-bootcamp-overview

LandFire is looking for field data! Add yours now.

I wanted to send out a friendly reminder that the data submission deadline for the current data call is March 31, 2016.  Data submitted before March 31 are evaluated for inclusion in the appropriate update cycle, and submissions after March 31 are typically considered in subsequent updates.  

This is the last call for vegetation/fuel plot data that can be used for the upcoming LANDFIRE Remap. If you have any plot data you would like to contribute please submit the data by March 31 in order to guarantee the data will be evaluated for inclusion in the LF2015 Remap. LANDFIRE is also accepting contributions of polygon data from 2015/2016 for disturbance and treatment activities. Please see the attached data call letter for more information.

Brenda Lundberg, Senior Scientist

Stinger Ghaffarian Technologies (SGT, Inc.)

Contractor to the U.S. Geological Survey (USGS)

Earth Resources Observation & Science (EROS) Center

Phone: 406.329.3405

Email: blundberg@usgs.gov

IGIS exploring applications of drones for UC Agriculture and Natural Resources

IGIS is excited to be working with 3D Robotics (3DR) to explore new applications of small unmanned aerial systems (sUAS) for monitoring agriculture and natural resources.  This technology has never been more practical for scientific exploration; however, there is still much to be learned about how to best utilize sUAS in this way.

DEM from drone flightIGIS is now developing protocols for safe and efficient deployment of a 3DR Solo sUAS.  Equipped with a common 12 megapixel GoPro Hero camera, this platform can survey up to 75 acres, at 3 inches of spatial resolution in less than 20 minutes, while flying a pre-defined flight path at 23 miles per hour, at 300 feet above ground level.  Then thanks to Pix4D mapping software, which is used to combine the pictures collected by the sUAS's GoPro into a single image mosaic, automated photogrammetric processes can render a digital terrain model from the images with a vertical accuracy close to the same 3 inches spatial resolution found in the original image collection.

IGIS has introduced sUAS and remote sensing training into our workshop schedule for this year.  Please check out our IGIS training calendar by Clicking Here for more information.

New IGIS Academic Coordinator: Andy Lyons

I would like to welcome Andy Lyons as Academic Coordinator III in the ANR Informatics and GIS (IGIS) Statewide Program. Andy comes to ANR from Stanford and before that Berkeley, where he completed his PhD in ESPM. He has an exceptionally broad academic training, bridging both the social and natural sciences, with considerable experience within both academic and not-for-profit business environments. He has a strong combination of ecology, social science, data science, and computer applications (programming, data management, multimedia, web, modeling), and grant/report writing skills. He is also a gifted teacher, won awards for his teaching at Cal including an Outstanding Graduate Instructor Award in 2004, and has been one of our instructors at the GIF's Spatial Data Science Bootcamp.

Data Science for the 21st Century - External Partners Invited!

Developing data-driven solutions in the face of rapid global change

Global environmental change poses critical environmental and societal needs, and the next generation of students are part of the future solutions.  This National Science Foundation Research Traineeship (NRT) in Data Science for the 21st Century prepares graduate students at the University of California Berkeley with the skills and knowledge needed to evaluate how rapid environmental change impacts human and natural systems and to develop and evaluate data-driven solutions in public policy, resource management, and environmental design that will mitigate negative effects on human well-being and the natural world.  Trainees will research topics such as management of water resources, regional land use, and responses of agricultural systems to economic and climate change, and develop skills in data visualization, informatics, software development, and science communication.

In a final semester innovative team-based problem-solving course, trainees will collaborate with an external partner organization to tackle a challenge in global environmental change that includes a significant problem in data analysis and interpretation of impacts and solutions. This collaboration is a fundamental and distinguishing component of the NRT program. We hope this collaboration will not only advance progress on the grand challenges of national and global importance, but also be memorable and useful for the trainees, and for the partners.

An Invitation to Collaborate

We are inviting collaboration with external partners to work with our students on their Team Research Project in 2016-17. Our students would greatly benefit from working with research agencies, non-profits, and industry.

• Our first cohort of 14 students come from seven different schools across campus, each bringing new skillsets, backgrounds, and perspectives.
• Team projects will be designed and executed in the spring of 2017.
• Partners are welcome to visit campus, engage with students and take part in our project activities.
  • Join us at our first annual symposium on May 6th 4-7 pm.
  • Participate in workplace/ campus exchange.
  • Contact the program coordinator at hconstable@berkeley.edu
  • Visit us at http://ds421.berkeley.edu/ for more information.

This new NSF funded DS421 program is in the first of 5 years. We look forward to building ongoing collaborations with partners and UC Berkeley.

With Drought Comes Disease

You’ve heard that millions of California’s trees have died from drought and bark beetles. Weakened by lack of water due to four consecutive years of drought, over 29 million conifers and hardwood trees were unable to fight off attacks from bark beetles and died. Check out where and when these trees have died across California using the new Tree Mortality Viewer from FRAP, CalFire, and USFS

Tree Mortality Viewer: Mortality at Point Reyes National Seashore

Overlayed on a map of California, the Viewer visibility layers show:

• Tree Mortality — Results of 2012-2015 aerial tree-mortality surveys. See how the situation has dramatically worsened over the years

You can download the original data  here too!

Spring 2016 GIF Workshops

Spring 2016 GIF Workshops 

The Geospatial Innovation Facility is excited to announce that we will be offering our standard workshops series for FREE this spring to UC Berkeley students, faculty, and staff. Currently we still need to retain our pricing of $224 for all non-UC affiliates. However, space is limited and the workshops will be filled on a first-come first-served basis, so register today at to take advantage of these great training opportunities!

GIF workshops offer hands-on applications oriented training in a variety of geospatial topics. Our Introduction to Geographic Information Systems (GIS) and Introduction to Remote Sensing workshops are designed for participants with little to no experience in GIS, or those who would like to refresh their geospatial skills. Each workshop teaches core geospatial principals and techniques through a combination of lecture and hands-on interactive activities.  

We are currently accepting registration for our introductory series of workshops offered over the next several weeks. See more detailed descriptions and register for any of the upcoming trainings at: http://gif.berkeley.edu/support/workshops.html

January 29: Intro to GIS: Social Science Focus

The presentation will get you up to speed on what kind of analyses GIS may be used for, as well as the basic structures of spatial data. After the lecture you will follow an interactive exercise that has been designed to introduce you to ArcGIS Desktop software while analyzing street and census data around the City of Berkeley.

February 5: Intro to GIS: Environmental Science Focus

The presentation will get you up to speed on what kind of analyses GIS may be used for, as well as the basic structures of spatial data. After the lecture you will follow an interactive exercise that has been designed to introduce you to ArcGIS Desktop software while analyzing environmental data from around Lake Tahoe.

February 12: Intro to Open Source GIS: Using QGIS

QGIS is a free and open source geospatial desktop application that has been developing at a rapid pace. Its ease of use and accessibility (available for PC, Mac, and Linux platforms) has created a strong and active user community. In this workshop, we will explore the basic functionality of QGIS so that you may quickly learn how to load and format vector and raster data, edit shapefiles, and query attributes. 

February 19: Intro to GIS for Agriculture: Rangeland Focus

An introductory presentation will get you up to speed on what kind of analyses GIS may be used for, as well as the basic structures of spatial data. After this brief lecture you will follow an interactive exercise that will introduce you to using free and open source online data to analyze and map rangelands in the California Central Valley.

February 26: Intro to Remote Sensing: Understanding Digital Imagery

This workshop introduces basic principles of understanding digital imagery, both satellite and aerial. Through a combination of lecture and interactive activities, we will explore what makes up a multi-spectral image, where to find and download them, and how to view and manipulate imagery.

These workshops are held in 124 Mulford Hall and run from 1pm – 4:30pm. Sign-up now for this great opportunity for intensive, hands-on training in geospatial methods, tools, and analysis!

GIF & IGIS from space

Made this for fun for the GIF & IGIS from NASA's "abcs from space" site: http://earthobservatory.nasa.gov/Features/ABC/. Was going to do "Kellylab" but ran out of time.

• G: This image of Pinaki Island was captured by astronauts on the International Space Station in April 2001.
• I: On February 10, 2007, the Moderate Resolution Imaging Spectroradiometer (MODIS) on NASA’s Terra satellite captured this image of the Andaman Islands. The thin, bright rings surrounding several of the islands are coral reefs that were lifted up by a massive earthquake near Sumatra in 2004.
• F: The Operational Land Imager (OLI) on Landsat 8 acquired this false-color image of valleys and snow-covered mountain ranges in southeastern Tibet on August 4, 2014. Firn is a granular type of snow often found on the surface of a glacier before it has been compressed into ice.

• I: On February 10, 2007, the Moderate Resolution Imaging Spectroradiometer (MODIS) on NASA’s Terra satellite captured this image of the Andaman Islands. The thin, bright rings surrounding several of the islands are coral reefs that were lifted up by a massive earthquake near Sumatra in 2004.
• G: This image of Pinaki Island was captured by astronauts on the International Space Station in April 2001.
• S: On April 29, 2009, the Moderate Resolution Imaging Spectroradiometer (MODIS) on the Terra satellite acquired this image of clouds swirling over the Atlantic Ocean.

ESRI @ GIF Open GeoDev Hacker Lab

We had a great day today exploring ESRI open tools in the GIF. ESRI is interested in incorporating more open tools into the GIS workflow. According to www.esri.com/software/open, this means working with:

1. Open Standards: OGC, etc.

2. Open Data formats: supporting open data standards, geojson, etc.

3. Open Systems: open APIs, etc.

We had a full class of 30 participants, and two great ESRI instructors (leaders? evangelists?) John Garvois and Allan Laframboise, and we worked through a range of great online mapping (data, design, analysis, and 3D) examples in the morning, and focused on using ESRI Leaflet API in the afternoon. Here are some of the key resources out there.

• Main ESRI Open Information: http://www.esri.com/software/open

• Slide deck from today: http://slides.com/alaframboise/geodev-hackerlabs#/

• Afternoon example using Leaflet: http://esri.github.io/esri-leaflet/

• ESRI's developer toolkits: https://developers.arcgis.com/en/, including

• ESRI's javascript API: https://developers.arcgis.com/javascript/beta/

Great Stuff! Thanks Allan and John

Spatial Data Science Bootcamp March 2016

Register now for the March 2016 Spatial Data Science Bootcamp at UC Berkeley!

We live in a world where the importance and availability of spatial data are ever increasing. Today’s marketplace needs trained spatial data analysts who can:

• compile disparate data from multiple sources;
• use easily available and open technology for robust data analysis, sharing, and publication;
• apply core spatial analysis methods;
• and utilize visualization tools to communicate with project managers, the public, and other stakeholders.

To help meet this demand, International and Executive Programs (IEP) and the Geospatial Innovation Facility (GIF) are hosting a 3-day intensive Bootcamp on Spatial Data Science on March 23-25, 2016 at UC Berkeley.

With this Spatial Data Science Bootcamp for professionals, you will learn how to integrate modern Spatial Data Science techniques into your workflow through hands-on exercises that leverage today's latest open source and cloud/web-based technologies. We look forward to seeing you here!

To apply and for more information, please visit the Spatial Data Science Bootcamp website.

Limited space available. Application due on February 19th, 2016.

California parcel data download

Parcel data for California summary and download here. http://egis3.lacounty.gov/dataportal/2015/09/11/california-statewide-parcel-boundaries/

The data are not complete. But downloadable in geodatabase format. 

"A geodatabase with parcel boundaries for 51 (out of 58) counties in the State of California. The original target was to collect data for the close of the 2013 fiscal year. As the collection progressed, it became clear that holding to that time standard was not practical. Out of expediency, the date requirement was relaxed, and the currently available dataset was collected for a majority of the counties. Most of these were distributed with minimal metadata."

SNAMP project wrap-up: relationships made and lessons learned

The Sierra Nevada Adaptive Management Project SNAMP

Word cloud from our 31 recommendationsThe Sierra Nevada Adaptive Management Project is a joint effort by the University of California, state and federal agencies, and the public to study management of forest lands in the Sierra Nevada. This 10-year project to investigate the effects of vegetation management treatments implemented by the Forest Service on fire risk, wildlife, forest health, and water in two areas in the Sierra Nevada, in the Sierra National Forest and the Tahoe National Forest. A lasting solution to forest management must engage stakeholders and promote active public participation in all phases of the process, including the development, interpretation, and incorporation of research-based information in the adaptive management decision making process.

My group was involved in both the spatial analysis work and public participation efforts. It has been a great honor to work on this project, as well as being a tremendous learning experience. Two wonderful dissertations from my lab have resulted from this research: Marek Jakubowski and Shufei Lei. So many students and staff worked on the project during its 10 year run: Qinghua Guo was instrumental to the project from UC Merced; Ken-ichi Ueda began work on the website in the early years of the project; Shasta Ferranto added years of insightful work on the public participation team; everyone in the lab participated in some way to the outcomes; and we all learned so much and made tremendous networks of expertise and knowledge across the state. 

For papers from the SNAMP project, see here. For papers from the SNAMP project at large, see here.  More Information: Please check out our website (we are also on Facebook): http://snamp.cnr.berkeley.edu/.