2021-sasi

2021 SASI Openscapes Champions Cohort

Welcome to the 2021 SASI Openscapes Champions Cohort! This is a Cohort for the Symbiosis in Aquatic Systems Initiative (SASI), funded by the Gordon and Betty Moore Foundation and co-led with protocols.io. Learn more about Openscapes and the Champions Program: https://openscapes.org.

Cohort Agendas

We will meet as a Cohort via Zoom eight times over four months for 1.5 hours, on alternating Thursdays in September through December 2021. Additionally, we will schedule several skillbuilding Clinics.

Agenda links below are only accessible to Cohort participants, as they are also an archive of our live notes.
Please see https://openscapes.org/series for more detail and to view blank versions of the agendas.

Date Cohort Call Topics Resources
09/09 1. Openscapes mindset and better science in less time mindset, better science in less time
9/13, 9/14 > GitHub Clinics < publishing, project management
09/23 2. Team culture and protocols for future us team culture
10/07 3. The art of writing methods and protocols communities  
10/11, 10/12 > protocols.io Clinics <  
10/21 4. Pathways share  
11/04 5. Troubleshooting & sharing negative results  
11/18 6. Workflows to save time: from protocols to publishing  
12/02 7. Data and coding strategies for future us data strategies, coding strategies
12/16 8. Pathways share reprise  

Participating teams

These are the teams participating: please add any edits directly (we’ll learn how in our GitHub Clinic!)

The Gladfelter Lab at the University of North Carolina is interested in how cells are organized in time and space.  They study how cytoplasm is spatially patterned and how cells sense their own shape.  They also investigate how timing in the cell division cycle can be highly variable yet still accurate. For their work, we combine quantitative live cell microscopy and computational, genetic and biochemical approaches in fungal and mammalian cells. GitHub/Protocols.io: https://github.com/GladLab/GladLab / https://www.protocols.io/workspaces/gladfelterlab

The Frederickson Lab at the University of Toronto focuses on the ecology and evolution of mutualism, or cooperation between species. Mutualisms are extremely common in nature—so common, in fact, that every plant and animal on Earth may be involved in at least one mutualism. The Frederickson Lab uses field, molecular, and computational approaches to study diverse plant-animal and host-microbe mutualisms, with the goal of understanding how and why species cooperate. GitHub/Protocols.io:

The Bolnick Lab at the University of Connecticut seeks to understand how ecological interactions affect the evolution of within-species trait variation. Research in the lab touches on a wide variety of species interactions, and combines theoretical models, natural history, field and lab experiments, and meta-analyses. Currently evolution of vertebrate immunity to parasites is a major, but not exclusive, focus of the lab. GitHub/Protocols.io:

The Milligan-Myhre Lab at the University of Connecticut focuses on how host genetic background contributes to the balance between the immune response to microbiota in the gut and intestinal microbial membership. While some disease phenotypes are controlled by one or two genes, other diseases, like inflammatory bowel diseases, have many genes involved that each have a small effect. We developed the genetically variable threespine stickleback (Gasterosteus aculeatus) as a model to examine how host genetic background influences immune response to microbiota in the gut and gut microbial community membership, and use it with the hopes that these mechanisms will elucidate genetic contribution to human diseases like inflammatory bowel diseases. GitHub/Protocols.io:

The Zheng Lab at the Carnegie Institution for Science has a long-standing interest in cell division and cytoskeleton. In recent years, the findings they made have broadened their research scope to include three research areas: 1. The mechanism of cell division. 2. The mechanism of genome organization in development, homeostasis, and aging. 3. The mechanism of endosymbiosis in cnidaria. They use a wide range of tools and systems, including genetics in model organisms and creating new model organisms, cell culture, biochemistry, proteomics, genomics, in their research. GitHub/Protocols.io:

The Amend Lab at the University of Hawaii examines the causes and consequences of microbial composition at the population and community scales. Their research includes Diversity and Evolution of Fungal Endophytes in Native Hawaiian Plants; Biogeography of Small Organisms; Habit Connectivity and Microbial Resevoirs; and Diversity and Distribution of Marine Fungi. GitHub/Protocols.io:

The Patel Lab at the Marine Biological Laboratory are beginning to explore the degree to which developmental pathways have been conserved or altered between various arthropods. Insights into the nature of developmental and molecular alterations will help to understand the evolutionary changes in the mechanisms of pattern formation and provide a molecular basis for analyzing the diversification of body morphologies and developmental mechanisms. The current work in the Patel Lab can be divided into three main project areas: The role of homeotic (Hox) genes in the evolution of body morphology; Germ line regeneration in Parhyale hawaiensis; and Structural color in Butterflies. GitHub/Protocols.io:

Openscapes Team

Julie Lowndes, Openscapes Co-Director, NCEAS, UCSB, is co-leading

Erin Robinson, Openscapes Co-Director, Metadata Game Changers, is co-leading

Lenny Teytelman, protocols.io CEO, is co-leading

Emma Ganley, protocols.io Director of Strategic Initiatives, is co-leading

More Background on Openscapes and the Champions program:

This opportunity is supported by the Symbiosis in Aquatic Systems Initiative (SASI), funded by the Gordon and Betty Moore Foundation.