SORTEE members organise workshops and webinars. Details will be announced to SORTEE members closer to the events.
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Title: Integrating SQL into R analytical workflows using dbplyr
Panelists: Julien Brun and Greg Janée (University of California, Santa Barbara)
Date and Time: 7th Mar 2024, 17:00:18:30 UTC
Duration: 1.5 hrs
Summary: In this workshop, we will discuss why you might consider a relational database to store environmental data. We will go over how to insert data in and retrieve data from a database using R and duckDB. We will focus on how to use the R dbplyr package to integrate databases into tidyverse focused analytical workflows.
This workshop will cover these main points:
- Introduce concepts of a database and discuss why you might want to have/want to use one
- How to integrate the use of a database into an R analytical workflow
- Hands-on exercise using dbplyr and how it can be used to learn some SQL basics
The event is open to all, and will be of value to scientists across career stages working with large databases. It will be held via Zoom. The link is emailed after registration.
Title: A Panel Discussion with Data Editors
Panelists: Paula Lemos-Costa (American Naturalist), Sebastian Lequime (Journal of Evolutionary Biology), Bethany Allen (Proceedings B) & Tad Dallas (Ecology Letters)
Type: Panel Discussion
Date and Time: 25th January 2024, 16:00 UTC
Duration: 1 hr
Summary: In recent years, a handful of journals within Ecology, Evolutionary Biology and related fields have been trialing a “Data Editor” role within the peer-review process. Data editors focus their review on the data associated with a potential publication, with the goal to improve the reliability and transparency of publications. But how does/should the data review process work? Has it been a success? Should all journals adopt such a step in their peer-review process? What should authors do to ensure their data passes a data review? To explore these questions and more, we have invited three data editors from three different evo/eco journals to take part in a panel discussion. We aim to facilitate a lively discussion that draws on the experience of the panel, and the interest and questions from the audience.
Title: How to prepare and publish research data in open access repositories
Presenters: Dr Michael Oellermann
Date and Time: November 28 2023 at 16:00 UTC
Duration: 2 hrs
Summary: This webinar will cover the benefits of publishing your research data open-access. Attendees will learn about how to select suitable open-access data repositories to ensure their data are accessible, reusable, and citable. We will discuss best practices for preparing and submitting tabular data to repositories, including data collection templates, metadata requirements and how to ensure data is accessible, reusable, and citable. By the end of the webinar, attendees will have a clear understanding of how to publish their research data in open access repositories, which can increase the visibility and impact of their research.
Logistics: The webinar will take place online using Zoom (link provided after signup). Attendees will be able to use their camera and microphone to interact with the speaker and other attendees. Attendance will be capped at around 25 participants.
Title: Dashboards: Using R to Create Actionable Science
Presenters: Ben Best and Marcus Beck, in collaboration with Enrique Montes and Tylar Murray
Date and Time: September 28 2023 at 15:00 UTC
Duration: 1 hrs
Summary: The Shiny R package is now ten years old and is a popular tool to create immersive, web-based content. Although many researchers have experience with R, expertise in dashboards is uncommon. This workshop will include a mix of instructor-led demonstrations, discussion, and exercises that will empower attendees to create their own Shiny applications. We will begin by showing what’s possible with the Quarto publishing system and Shiny by demoing existing applications from the Marine Biological Observation Network and the National Estuary Program. We will then transition to instructional material on the fundamentals of reactive programming with Shiny. Recent additions and improvements to Shiny (e.g., drag and drop user interface development, Python integration) will also be demonstrated. The remainder of the workshop will involve hands-on exercises that will allow attendees to develop their own applications using data from the examples above.
Anyone interested in learning how to expand existing R skills for dashboard development will benefit from this workshop. This includes students, early career, and advanced professionals from any employment sector and field of expertise.
Presenters: Sam Csik and An Bui
Date and Time: May 23 2023 at 16:00 UTC
Title: The UNESCO Recommendation on Open Science
Presenters: Ana Persic (Chief of Science Policy and Partnerships, UNESCO), Eleanor Haine (Canadian Commission for UNESCO)
Date and Time: April 27 2023 at 13:00 UTC
Summary: In 2019, 193 Members States tasked UNESCO with the development of an international standard-setting instrument on Open Science. Two years later, the UNESCO Recommendation on Open Science was adopted. The Recommendation defines shared values and principles for Open Science, and identifies concrete measures on Open Access and Open Data, with proposals to bring citizens closer to science and commitments to facilitate the production and dissemination of scientific knowledge around the world.
This webinar will explore how the UNESCO Recommendation on Open Science provides an international framework for open science policy and practice, and an overview of how it is being used to support policymaking in a Canadian context.
Recording: A recording of the webinar is available on OSF
Title: UK ambassadors for life sciences data stewardship
Presenters: Gabriela Lopez-Gonzalez (University of Leeds), Richard Ostler (Rothamsted Research), Xenia Perez Sitja (University of Bradford/ELIXIR-UK)
Date and Time: March 30 2023 at 16:00 UTC
Duration: 1h 30 minutes (max)
Summary: Data Stewardship has grown over the last years as an emerging key role for high-performing research. Stewards are not only crucial to managing research data but also building capacity and advocating for institutional, national and international policy changes. Yet, steps need to be taken to professionalise this critical role of data stewards beyond the go-to person in a team who knows about data.
In 2021, ELIXIR-UK was granted a UKRI award for the ELIXIR-UK Fellowship, building capacity and professionalising data stewardship. It leverages local expertise with a community of Fellows from diverse research-performing organisations in the UK – creating a data management culture change from within the institutions.
This webinar will explore the model of this Fellowship and its current outputs. Attendees will also hear first-hand experiences from two of the Fellows: Gabriela Lopez Gonzalez (long-term monitoring of peatland data, working with ecologists, conservation organisations and volunteers) and Richard Ostler (crop traits, soil chemistry and physics, environmental/sensor datasets, agroecological and agronomic data).
Title: Equitability in data reuse in microbial ecology
Presenter: Dr. Stephanie Jurburg
Date and time: Feb 20 2023 at 14:00 UTC
Duration: 1 hour
Summary: Data collection, management, and reuse are increasingly important in ecology and biodiversity research. In microbial ecology, sequencing has altered our relationship to the hidden microbial world and created massive amounts of reusable microbiome data. These data can now be used to integrate bacteria into macroecology and to fill major gaps in the field through synthesis. However, ~50% of archived sequence data is not reusable, and biodiversity blind spots remain, especially in regions where the lack of access to scientific resources precludes the generation, archiving, and reuse of sequence data. This webinar will explore the current limitations to sequence data reuse in microbial ecology, and explore how promoting equitability in research through dedicated database creation and outreach can overcome them. Though we will discuss these issues through the lens of microbial ecology, this webinar is relevant to anyone interested in issues of open data and equity.
Title: Using and contributing open data to the Global Biodiversity Information Facility (GBIF)
Presenter: Carole Sinou
Date and time: Jan 24 2023 at 10:00 EST (UTC 15:00)
Duration: 1.5 hour
Summary: GBIF is an international network and data infrastructure funded by the world’s governments and aimed at providing anyone, anywhere, open access to data about all types of life on Earth. Many countries and organizations have deployed infrastructures aimed at facilitating publication of biodiversity data on GBIF.
During this workshop, you will learn how you can contribute different types of data to GBIF, providing visibility to your institution/project and allowing others to use data you collected.
You will also discover how you can use GBIF mediated data in your own research and projects. Filtering data from GBIF allows users to generate fit-for-purpose datasets that can then be used for different types of analyses, such as ecological niche modeling and species distributions.
Title: Open Educational Resources as a Tool for More Inclusive Teaching in E&E
Presenter: Natasha Gownaris
Date and time: Dec 5 2022 at 9:00 EST (UTC 14:00)
Duration: 1 hour
Summary: Motivation for using OER in E&E classes and how to find and implement these resources.
Objective 1: Describe some of the benefits of implementing OER in E&E classes.
Objective 2: Find OER resources, with a focus on open textbooks, of relevance to your courses.
Objective 3: Learn the basics of using Libretexts to remix OER and create content fine-tuned to your courses.
Objective 4: Learn how to use Hypothesis.io for community commenting on OER.
Title: An Ecologist’s Introduction to Transitioning into Data Science
Presenter: Alessandro Filazzola and Sophie Breitbart
Date and time: Nov 2nd 2022 at 10:00 EDT (UTC 14:00)
Duration: 2 hours
Summary: Ecological researchers have skills that are highly transferable, especially in data science. We provide suggestions on why data science may be a suitable alternative to a career in ecology and steps towards becoming a data scientist.
Objective 1: Contextualize data science for ecologists including defining what is data science, the overlaps with ecology, and what a career in data science may look like,
Objective 2: Provide a brief introduction to SQL, one of the most frequently used tools by data scientists,
Objective 3: Detail actions and strategies for transitioning into data science.
Title: Creating reproducible workflows in R with the targets:: package
Presenter: Elliot Gould
Date and time: Oct 20 2022 at 4:00 pm AEDT (UTC 05:00)
Timezone(s): Australasia Duration: 2 hours
Summary: Using the targets R package to create reproducible data analysis pipelines.
Objective 1: Appreciate the need for establishing reproducible, make-like workflows and be aware of the basic components of setting up a reproducible analysis using the targets package.
Objective 2: Specify, run and query the outputs of a small data analysis pipeline using the targets infrastructure.
Objective 3: Scale up a targets pipeline to incorporate more complicated analysis pipelines by:
- using the the outputs of a targets pipeline in literate programming documents,
- incorporating literate programming documents into the targets pipeline, and
- batching and iterating tasks using branching in targets
Objective 4: Troubleshoot and debug a targets pipeline so you can apply this knowledge to synthesise targets workflows for your own data analyses.
Title: Authoring documents, websites, presentations, and more with Markdown
Presenter: Alexa Fredston
Date and time: Sept 14 2022 at 1:00 pm EDT
Duration: 2 hours
Summary: Using Markdown, including from R, to generate well-formatted and easily readable notes, slides, reports, manuscripts, web pages, PDFs, etc. from code.
Objective 1: Understand Markdown and how it can be applied to generate visually appealing materials.
Objective 2: Build Markdown files with multiple content types (text, plots, images, etc).
Objective 3: Explore Markdown applications to various use cases.
Workshop materials: here