Posts Tagged: science

Takeaways from Posit::Conf 2024

R and Python together at last, the AI takeover, and Quarto ups its game.

Posit::Conf, Posit's annual conference, was held last week in Seattle, WA. While the name might be unfamiliar, many of you might recognize Posit's previous iteration, RStudio. Posit has produced many products R users know and love, including RStudio, Shiny and the Tidyverse. After a whirlwind three days, here are some takeaways from the conference!

A New All-in-One IDE

Togetherness was a key theme, with Posit rolling out the beta version of Positron, an IDE that combines elements of RStudio, VS Code, and introduces its own unique features. While switching IDEs is generally not at the top of any coder's to-do list, Positron is multilingual, enabling users to code in R, Python, and Julia within a single project. It also introduces new ways to interact with your data, such as readily available summary statistics, the ability to filter or sort data by multiple fields while retaining the active query in the window at all times, and the option to resize graphs and figures in the plots pane through a simple user interface. Positron also leverages many new and existing VS Code extensions, offering a wealth of customization and additional capabilities. Rstudio is by no means leaving the picture– Positron is still in beta, and Rstudio will continue to be supported for a good, long time. However, if you (like me) crave a unified interface for your R and Python coding, Positron may be worth trying out.

Helping R Users Learn Python

For Py-curious R coders, a session on “Python Rgonomics” suggested some packages to make the transition easier for those of us spoiled by the tidyverse.

• Polars for exceptionally fast data wrangling and dplyr-like syntax

• Plotnine and seaborn for ggplot-like syntax when making graphs and figures

• Great tables for producing functional, readable tables (also available in R as the gt package).

• Pyenv for environment management.

• Pins (for R and Python!) publishes objects to “boards” that allows users (or multiple users) to access them across projects. Boards can include shared/networked folders, like DropBox or Google Drive.

 

AI for All

Melissa Van Bussel provided practical tips for using generative AI. She highlighted some new capabilities of ChatGPT 4o, including the ability to transcribe handwritten notes and tables, preserving colors and formatting. GPT can even convert these into HTML or Quarto formats.

She shared insights on prompt engineering (i.e., how you ask questions to AI engines), noting, “Writing effective prompts goes hand in hand with your existing expertise.” Achieving correct and effective output requires providing specific prompts and making corrections when errors occur. She recommended structuring prompts in a way that mirrors coding practices. For example, to generate a graph, start by specifying the data, then define how to map each axis and assign colors. Next, specify the graph or chart type and indicate any grouping by other variables. Finish with aesthetic (eg palette, theme, title, legend) preferences.

While presenters were enthusiastic about the possibilities of generative AI, a recurring theme was the necessity for users to provide clear direction and verify the results. One presenter compared AI to hiring a new human assistant—AI can assist with tasks effectively when given proper guidance but will make mistakes and requires careful supervision. Generative AI performs best when used to quickly accomplish tasks that users already have the knowledge and skills to handle themselves.

One of the most prevalent use cases for generative AI was in combination with Shiny. Joe Cheng's presentation demonstrated integrating AI into Shiny apps, specifically into Shiny dashboards. Users could request modifications to the data displayed on the dashboard using plain language, which the AI translated into SQL queries to adjust the output based on the request. This is particularly noteworthy as the AI accessed only the schema, not the actual data, to apply the filters.

Winston Chang developed an AI assistant to help people build Shiny apps and did a live demonstration. Although still experimental, Shiny for R is widely used, and the assistant showed promising outputs.

Quarto Expands its Horizons

Quarto is a relatively new version of R Markdown (a publishing tool) that allows users to knit together code into documents, dashboards, web pages, PDFs, and even eBooks. An added advantage of Quarto is its multilingual capability– it, like Positron, supports both R and Python. Some new capabilities were highlighted at the conference:

• Dashboards: Easily build dashboards using the Quarto extension in RStudio or Positron. Each visualization (graphs, maps, tables, and even just text boxes) can be arranged like tiles or cards. Dashboards can also include sidebars and toolbars, and can support interactivity, including cards that use  jupyter widgets, leaflet, and shiny.

• PDFs: Quarto now uses typst instead of LaTeX, enabling users to create customized PDF outputs with a more intuitive language.

• HTML (Websites): Quarto (like R Markdown) can produce HTML outputs. However, now it also supports more flexible HTML code chunks, and allows for HTML/CSS/JavaScript integration.

• Quarto live: A quarto extension that allows users to embed code blocks and exercises for R and Python into Quarto documents. This has lots of teaching applications, and can be used to generate exercises similar to those you find in DataCamp and other online coding courses.

• Closeread: A scrollytelling extension for quarto that enables interactive storytelling similar to that seen in fancy New York Times articles or Esri Storymaps. The gallery has some example outputs, while the guide can walk you through the process of creating your own scrollytelling page.

Finally, one of my favorite quality-of-life take homes was simply that it is possible to include emoji in your R or Python code, either using unicode or simply pasting them in. While the demonstrated use case was to make specific messages stand out in your log or printed statements, sometimes a picture can convey what 1000 characters cannot and help you enjoy coding just a little bit more.

If you love (or begrudgingly engage in) data science, I encourage you to check it out next year– virtual registration for educators and academics in 2024 was free, and hopefully will be next year too!

 

Science-to-Practice Grant Program 2024-25 request for proposals

UC Agriculture and Natural Resources (UC ANR) invites proposals to the Science-to-Practice (S2P) Grant Program for new projects that integrate research and extension. The S2P program provides funding to support the formation and development of teams proposing to explore innovative methods, structures, and projects that foster the translation of research into programs and outputs for dissemination and implementation.

Interdisciplinary teams of eligible participants can apply for grants up to $10,000 for one year, renewable as funding permits for up to three years. In addition, UC ANR's Research and Extension Center System will match funding levels awarded, up to $10, 000 per year, to offset the cost of any research and extension conducted at one of its nine Research and Extension Centers.

The S2P program's purpose is to foster integrated research and extension teams to address pressing, complex challenges requiring multiple perspectives and modes of knowledge. The S2P supports applied research-based activities that prioritize the development of collaborative networks in the UC ANR system across research and extension faculty, specialists and/or advisors as well as engaging partners beyond, such as practitioners, decisionmakers and thought leaders in the field.

Eligibility

The team must be composed of a research leader and an extension leader, both of whom will serve as the principal investigators co-leading the project. Team leadership must meet the following criteria:

1.    Research PI must be a faulty member (tenured, tenure-track, or non-tenure-track)with a research appointment in one of the Agricultural Experiment Station (AES) designated campuses and have an active Hatch or USDA multistate project.

2.    Extension PI must be a Cooperative Extension specialist or advisor.

Additional participants are encouraged and may be from UC ANR, from other UC-affiliated campuses or from outside the university. All funds must be used to directly support UC ANR activities and personnel. Funds cannot be used to support graduate students, employees or other persons not employed by or not enrolled in a UC ANR program.

Proposal Requirements

The full proposal will be submitted online as a PDF. The required components are outlined below with page limits and guidelines.

Proposal information:

A.    Project Participants

1. Designate only the research and extension principal investigators who will co-lead the project. Refer to the eligibility requirements stated above.

           i. Applicant may be either research or extension lead; include the other project lead in the “Co-Applicant” field.

           ii. Include the two project leads and all other team participants in the Team Roles section.

B.    Summary (300 words maximum)

1. Summarize the integrated project, including the primary stakeholders or clientele standing to benefit by the project, a brief statement of the goal(s) and the integrative strategy.

C.    Total Research and Extension Budgets

Unified PDF must contain all the following components:

D.    Title and Project Narrative (90 points)

Three pages maximum for new proposals does not include team roles, budget and justification or references.

1. Research Component (20 points)
• What is the research problem, defined in the context of a field of research or discipline?
• What are the gaps in data or knowledge that make this project significant?
• What is this project's potential to impact knowledge advancement in a particular research field/discipline/area?
• Identify research-specific activities required to advance the integrative strategy outlined below, including defined research-related deliverables (e.g., publications, grant applications, etc.) and expected outcomes and impacts.
2. Extension Component (20 points)
• What are the learning objectives that will deliver the science-based knowledge generated through the research component?
• What is the significant public benefit of this project?
• Who will benefit from or be affected by this project?
• Identify education-specific activities required to advance the integrative strategy outlined below, including defined extension-related deliverables and expected outcomes and impacts.
3. Integrative Strategy (40 points)
• What is the strategy that combines the generation, translation, and transfer of technology and/or knowledge into practical applications or practices?
• How do the research and extension components complement one another?
• Why does this project require an integrated approach and interdisciplinary team to create societal value through research-based education relevant to identified stakeholders' needs?
• How will the identified stakeholders be engaged in the research and extension activities?
4. Project Timeline (10 points)
• Outline significant benchmarks along this project's timeline that can illustrate the team's vision and trajectory during and beyond this proposal's timeframe. The benchmarks should align with the objectives described above in the research, extension and integrative strategies.
• Identify all approvals required to complete the project (e.g., IRB, IACUC, etc.) and the timeline for obtaining them.
• This may be presented as a diagram or table.

E.     Team Member Roles (10 total points)

1. Briefly describe the roles and expertise of the research and extension PIs.
2. Include a coordination plan for integrating team members across UC ANR functions and units and university and external partners.
3. List all team members with their affiliations. Describe the role and responsibilities of each member, including how the expertise of each will contribute to the research, extension or integrated activities. A balanced team representing both research and extension is important.

F.     Budget and Justification

1. Provide a two-column budget, dividing research and extension expenses.
2. Successful projects will be awarded up to $10,000, with the funding period beginning on January 1, 2025.

          i. All budgets should be constructed so that up to $5,000 in expenses support research activities and up to $5,000 support extension activities.

          ii. If the project's research and/or extension will be conducted at a Research and Extension Center, a budget should be developed in collaboration with the specific REC Director to ensure funding levels requested are aligned with the Center's recharge rates and do not exceed $10,000 for the funding period.

          iii. Please note that submissions to this internal competition do not require the budget to be created through the UC ANR Office of Contracts & Grants (OGC).

     3. Include a detailed budget justification, providing a brief description and explanation of need for costs associated with project activities.

     4. Funds used to pay part-time wage-payroll must be for activities outside of any job description currently paid for by UC ANR, or it must support work on a new activity.

          i. Part-time wage-payroll must be paid through the UC ANR system (funds cannot be transferred to county systems).

     5. All other project costs typically allowed by federal extramural sponsors are allowed in this program.

     6. Funds cannot be used for the following:

          i. Faculty salaries (including supplemental) or standing appointment salaries

          ii. Travel to professional meetings

          iii. Out-of-country travel

          iv. Equipment purchases exceeding $5,000

          v. Support of non-UC ANR personnel

     7. Funds to support personnel outside the UC ANR must be obtained from other units and require a letter of commitment from the non-UC ANR unit, submitted with the proposal as a supplemental document.

     8. Budgets are constructed for a maximum of one year and must be expended by Dec. 31, 2025. No carryover is allowed.

     9. Funded projects can be competitively renewed up to two times, for three years of support; unexpended funds in one year will not carry over. Extensions for unexpended funds are not allowed for any projects.

Evaluation Criteria

Proposals will be evaluated and scored on the following criteria:

• Presents a clear plan for building or supporting an interdisciplinary team
• Demonstrates the potential for effective strategies to integrate research and extension activities
• Proposes activities that help to initiate, advance and strengthen teams and projects to obtain extramural support
• Defines both research and extension deliverables and provides clear benchmarks for achieving expected outcomes and impacts
• Incorporates audiences traditionally not targeted
• Projects that demonstrate considerable opportunities to achieve the UC ANR mission and our commitment to diversity, equity and inclusion are especially encouraged
• Identifies outcomes that are easily measurable and scalable
• Contributes to the knowledge base through distribution of results that benefit other efforts.

Submission and Review Process

Full proposals must be submitted as a single PDF by 11:59 p.m. on Sept. 30, 2024. Proposals are to be emailed to Brent Hales, Associate Vice President, at bdhales@ucanr.edu and to Kathryn Stein at kathryn.stein@ucop.edu.

Proposals will be evaluated by a panel of reviewers established by the Associate Vice President. Applicants will be notified of decisions by mid-November 2024.

Please direct any questions regarding your proposal to Brent Hales at bdhales@ucanr.edu.

Reporting Guidelines:

The period of performance for S2P grants will begin Jan. 1, 2025, and terminate Dec. 31, 2025. Projects may be renewed for up to three years of support. Proposals for renewal can

Be submitted in the next cycle for the S2P grants. An interim report for all awarded proposals will be due on July 15, 2025. Final reports will be due Jan. 15, 2026.

Lawn-pocalypse! Surviving Drought

Ah, summer! The season of sunburns, pool parties, and… lawn droughts. If your once lush, green carpet now looks like a crunchy brown doormat, you're not alone. Let's dive into why your yard is staging a dramatic death scene and what you can do to...

Bermuda grass and weeds overtaking drought stressed turf grass.

A patch of former lawn, mostly dead, with a few green weeds and Bermudagrass

Green Hall of Famer Oki retires after 29-year UC career

UCCE specialist's research prevents water pollution, reduces water use

When interviewed to become a University of California Cooperative Extension specialist in environmental horticulture, Lorence “Loren” Oki was asked what kind of research he wanted to conduct.

In response, he showed the hiring committee a photo of a residential gutter. “Water is a big concern, and I found very little research on runoff from homes,” said Oki, explaining that studying residential runoff is what “started his career” with UC Agriculture and Natural Resources back in 2002.

Although he remains active supporting growers and advising industry leaders, Oki retired from UC ANR in July 2023. Before joining ANR, Oki worked as a researcher for UC Davis' Department of Environmental Horticulture studying greenhouse irrigation in 1994, bringing his total time with the University of California to 29 years.

Oki, professor emeritus of Cooperative Extension at UC Davis, led many research projects that advanced the green industry which includes landscapes, nurseries and floriculture.

“Loren is the epitome of a specialist,” said Darren Haver, UC ANR's Research and Extension Center system director, who has worked with Oki for more than 20 years on projects that have  significantly improved urban water quality and water conservation efforts across California.

Research influences pesticide management statewide

With a $3 million grant funding a statewide study, Oki and Haver set out to characterize runoff from residential sources over a five-year period. They determined the volume of irrigation runoff from residential land use, as well as the pollutants in the runoff.

Oki and Haver, co-principal investigators, along with researchers from UC Davis and UC Riverside, discovered that the degradation products of the insecticide fipronil – commonly found in runoff water – were more toxic than its parent compound. The study led to an investigation of human pathogens and pathogen indicators in residential runoff, the first of its kind.

Another contribution was the early detection of a new pesticide used for ant control, enabling strategies to be put in place to prevent it from reaching local streams and creeks. Oki and Haver's work also persuaded the California Department of Pesticide Regulation to change pesticide labels to minimize the chances of pesticides moving off target during irrigation and rain events. 

These changes included preventing pesticide application before predicted rain and preventing irrigation after applications, keeping pesticides from impervious surfaces, and restricting applications on lawns and landscape beds within two feet of impervious surfaces and others.

Plant trials expand beyond California

Oki was also the principal investigator of the Climate-Ready Landscape Plants project, which may be the largest irrigation trial in the western U.S., and the UC Plant Landscape Irrigation Trials, the California component of that project. The UCPLIT trials originated in 2004 at UC Davis as a research project by Karrie Reid, retired UCCE environmental horticulture advisor for San Joaquin County, while she was pursuing her master's degree. In 2017, the irrigation trials were duplicated at the South Coast Research and Extension Center.

These projects evaluate landscape plants under varying irrigation levels to determine their optimal performance in regions requiring supplemental summer water. Throughout the trial, Oki identified many landscape plants, including rose cultivars, that remain aesthetically pleasing with little water.

Today, the trials have expanded beyond California as the Climate-Ready Landscape Plants Project at Oregon State University, University of Washington, University of Arizona and Utah State University.

Growing up in the nursery industry

In 2017, Oki obtained tenure, allowing him to expand his professional responsibilities to include production horticulture, specifically greenhouses and nurseries, an industry he was extremely familiar with. “I come from a nursery family,” Oki explained. “My grandfather started Oki Nursery in the early 1900s.”

During World War II, Oki's family was incarcerated in the Poston Relocation Center in Arizona and lost their homes and property. When they were released, they returned to the nursery industry to rebuild their lives. “After World War II, my father and uncle got more involved with my grandfather's work,” he said.

The Oki family played an instrumental role in technological development for nurseries in general. Oki Nursery, which was located in Sacramento, worked closely with IBM and was the first to use a computerized system in the industry.

Oki developed computerized scheduling for the bedding plants, poinsettias, chrysanthemums, bulbs and other crops.  He developed a method to calculate the cost of any crop grown by the nursery at any point in the crop cycle and computerized greenhouse environmental and irrigation controls. This may not sound impressive now, but that was in the 1980s.

“My father was known for being progressive and he also knew everyone at UC Davis,” said Oki. “He wanted to work with anyone who had an interest in doing something good for nurseries.”

Inducted into Green Industry Hall of Fame

In the 1950s, Oki Nursery partnered with researchers from UC Davis' agricultural engineering program and developed the overhead sprinklers commonly used in nurseries today. Until the 1980s, Oki Nursery was the largest nursery in Northern California. Before it shut down in 1993, Oki worked in the family business as a greenhouse manager when runoff became a growing concern.

“I remember getting served with a notice by the Regional Water Quality Control Board stating that we needed to prevent runoff because it was polluted with nitrate fertilizer, which was common in the nursery industry,” Oki said.

One of those efforts focused on using controlled-release fertilizer instead of applying fertilizer via irrigation as a liquid feed. “What we learned is that if we converted nurseries to controlled-release fertilizer, we could reduce the nitrate runoff,” he said. While a member of the Oki Lab, Bruno Pitton earned his Ph.D. studying nursery hydrology and the fate of nitrogen fertilizers in container crop production adding to the information on runoff and nitrate management. Pitton is now the environmental horticulture advisor for Placer and Nevada counties.  

In 2023, Oki was inducted into the Green Industry Hall of Fame, which recognizes individuals with a minimum of 20 years in the landscape, nursery or floriculture industry and who have made significant contributions to the field.

Having grown up in the industry, Oki said that his father taught him to never be afraid to try new things. “If you think you have an idea that might work, do the best you can to make it work. If it doesn't work out, then it doesn't work out. And that's OK,” he said.

Revitalizing space for greater impact

This mentality encouraged Oki whenever tackling new tasks, like rebranding the California Ornamental Research Federation, a space for education and collaboration, as UC Nursery and Floriculture Alliance.

In 2009, Oki and David Fujino, executive director of the California Center for Urban Horticulture, became co-directors of CORF, which catered to the cut flower industry. At that time, Oki and Fujino realized that nurseries generated much greater revenue in the state than cut flowers.

“It was a strategic decision to change CORF to UCNFA, which included floriculture and nurseries in the name,” Fujino said. Combined, nurseries and floriculture have consistently placed in the top five agricultural commodities in the state.

When reflecting on their partnership, Fujino said that working with Oki was a “natural fit.” “I couldn't have asked for a better partner, a better colleague and, ultimately, a better friend to have my back and work side by side,” he added.

Since UCNFA's launch, the two have worked to maintain the group's impact by hosting “Ask your Advisor” webinars to connect advisors to growers, as well as co-hosting large-scale events such as the annual conference for the International Plant Propagators' Society — an organization focused on greenhouse and nursery production education — for the Western Region, which Oki's father helped establish in the 1960s.

Encouraging a return to education

Gerry Spinelli, UC Cooperative Extension production horticulture advisor for San Diego County and member of UCNFA's administrative committee, described those who have learned from Oki as his sons and daughters. “When I meet someone that's learned from Loren or worked with him, that person instantly becomes my friend. That's the kind of effect Loren has on us,” Spinelli said.

Grant Johnson, UC Cooperative Extension urban agricultural technology advisor for Los Angeles and Orange counties, credits Oki for his master's degree in horticulture from UC Davis.

“Loren gave me a lot of direction as far as career choices and research interests. He instilled in me a dedication to life-long learning, just like he continues to do,” said Johnson. Before Oki became his professor, Johnson worked with Oki as a staff research associate at the South Coast Research and Extension Center in Irvine.

Another influential person in Oki's life is John Kabashima, emeritus environmental horticulture advisor for UCCE Orange and Los Angeles counties and fellow Green Hall of Fame inductee. Like Oki, Kabashima grew up in the nursery industry.

Oki, who earned a bachelor's degree in ornamental horticulture from Cal Poly San Luis Obispo and a master's degree in plant science from UC Riverside, decided to pursue a Ph.D. in ecology at UC Davis with Kabashima's encouragement.

While Oki was still working in his family's business, Kabashima said that Oki relied on UC ANR researchers for scientific information and felt like Oki wanted to be one of them. “I told him that he's a good nursery guy, but he's a better scientist,” said Kabashima. “His heart is in science.”

The two began working together as soon as Oki became a graduate student and have been colleagues and friends for nearly 40 years. “My favorite response from Loren whenever people ask him a question is, ‘It depends,'” Kabashima said. “It always leads to people opening up and giving more context. That's what Loren does, he gets you to think.”

Bohart Museum of Entomology: 'Be Curious'

It's Saturday, Feb. 10 and it's the 13th annual UC Davis Biodiversity Museum Day at the Bohart Museum of Entomology. It's a Super Science Day showcasing 10 museums or collections across campus.  Some 2000 visitors fan into the Academic Surge...

UC Davis professor Jason Bond, director of the Bohart Museum of Entomology, shows butterly specimens to Woodland residents Olive Smith, 8, and her mother Sarah Smith. (Photo by Kathy Keatley Garvey)

UC Davis professor Jason Bond, director of the Bohart Museum of Entomology, shows butterly specimens to Woodland residents Olive Smith, 8, and her mother Sarah Smith. (Photo by Kathy Keatley Garvey)

Doctoral student Iris Quayle of the Jason Bond lab answers questions about spiders at the Biodiversity Museum Day at the Bohart Museum of Entomology. (Photo by Kathy Keatley Garvey)

Doctoral student Iris Quayle of the Jason Bond lab answers questions about spiders at the Biodiversity Museum Day at the Bohart Museum of Entomology. (Photo by Kathy Keatley Garvey)

Forensic entomologist Robert Kimsey (left) of the Department of Entomology and Nematology and postdoctoral researcher Severyn Korneyev, a Ukrainian entomologist who studies flies, answer questions from visitors at the Bohart Museum open house. Korneyev holds a joint appointment with the UC Davis Department of Entomology and Nematology and the California Department of Food and Agriculture. (Photo by Kathy Keatley Garvey)

Forensic entomologist Robert Kimsey (left) of the Department of Entomology and Nematology and postdoctoral researcher Severyn Korneyev, a Ukrainian entomologist who studies flies, answer questions from visitors at the Bohart Museum open house. Korneyev holds a joint appointment with the UC Davis Department of Entomology and Nematology and the California Department of Food and Agriculture. (Photo by Kathy Keatley Garvey)

Professor and ant specialist Phil Ward and lab members answer question about ants. With him are doctoral candidate Ziv Lieberman and research assistant Brittany Kohler, who seeks to enroll as a doctoral student at UC Davis. (Photo by Kathy Keatley Garvey)

Professor and ant specialist Phil Ward and lab members answer question about ants. With him are doctoral candidate Ziv Lieberman and research assistant Brittany Kohler, who seeks to enroll as a doctoral student at UC Davis. (Photo by Kathy Keatley Garvey)

Margo Rubin, 5, squints to get a better look through the microscope. (Photo by Kathy Keatley Garvey)

Margo Rubin, 5, squints to get a better look through the microscope. (Photo by Kathy Keatley Garvey)

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