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FOSS test website for ACMEE team

Name: Institution: Job/Research: Favorite RomCom:

Test github website for team E (Wednesdays)

Clara Qin

University of California, Santa Cruz

PhD Student

Advisor: Kai Zhu

GitHub (here)

Clara is an ecologist, statistician, and sociologist of science with a broad interest in soil microbiota. Her ecological research examines how changing climates influence soil microbial communities, plant-soil feedbacks, and ecosystem processes in North American forests and grasslands. Her sociological research explores the “probiotic turn” in the agronomic sciences as a site of ontological politics for soil.

Favorite romcom: Happiest Season

Capstone II responses:

  • Which tool could you apply right away and why? For me, the GitHub Pages demo and associated GitHub Website tutorial were the most immediately applicable. So I created one GitHub Page and an alternative GitHub Website to host the documentation for my new R package, neonMicrobe.
  • What is your greatest barrier to these tools? A lack of relevant projects. I'm not currently working on anything that I think would need the tools offered in Apps. And I already use my institution's cluster for most tasks that would be offered by Atmosphere. The CyVerse Data Store and a data management plan could be useful for an upcoming project, though.
  • What tools would you wish we covered more in depth? Building containers! I know there's a separate course on this entirely, but I found myself wanting to build my own container for the final project, and at a loss about how to do so.

Final project: GitHub website for neonMicrobe R package documentation (here)

Emily Quach

San Mateo County Community College District

Adjunct Faculty

GitHub here

Capstone Statement: Emily's background is in molecular biology, microbiology, and parasitology. Currently, Emily is a first year adjunct intructor at community college. As a life long learner, she hopes to implement FOSS knowledge in her classes. Her plan is to learn all she can about open science, bioinfomatics, and the wolrd of coding over the next 2 years. After gaining all this in silico world, she will provide her students with data collected over the years so she may pass on the knowledge. This webpage is to her refresh the class in the future. My greatest barrier to the tools is new to coding and using new languages. Using R markdown is a tool I will try to apply right away, its a fast way to type and create pages.

Favorite romcom: How to Lose a Guy in 10 Days

Amy Schuler

Cary Institute of Ecosystem Studies

Director of Information Services, Library & Data Management

GitHub here

Amy is attempting to become Mother Nature's hacker (joke!) In real life, she supports research data management, library and information services at Cary.

Favorite romcom: Chungking Express

Capstone questions: Which tool can I apply right away and why? I can make use of GitHub repositories now because everyone I work with (including myself) has some data project to share. Other tools like containers, Jupyter notebooks, and others are still hazy but I can slowly help others at Cary use them, even as I improve my skills. What is your greatest barrier to these tools? TIME is my single greatest barrier! Learning on the job, while getting the "real work" done, is hard.
What tools would you wish we covered more in depth? I think we could have spent less time on the data management resources (DS Wizard) and more time on the data tools; diving into those more quickly so we had 1-2 extra sessions using Git in the command line, Jupyter notebooks, Docker.

Mery Touceda-Suárez

University of Arizona, Tucson

PhD Student

Website: (My web)

GitHub (here)

Research: Microbial Ecology / Sustainability / Data Science

Favorite romcom: "Imagine you and me"

Questions:

  • Which tool could you apply right away and why?

Git/GitHub to collaborate with team mates and other scientists. Docker to use software created by others.

  • What is your greatest barrier to these tools?

The system where I work, the HPC, uses a Singularity instead of docker, it is not as straight forward to implement as I thought.

  • What tools would you wish we covered more in depth?

NC

Emily Dart

Clark University

PhD Student

Emily is a viral and microbial ecologist. Her work focuses on using time series to study predator-prey dynamics between phage and bacterial host communities in marine and freshwater ecosystems.

Rom Com: "Howl’s Moving Castle"

Capstone Response: Which tool could you apply right away and why?What is your greatest barrier to these tools?

Git/GitHub to facilitate easier collaboration and problem solving within the lab and with outside collaborators. This is a tool that is relatively easy to learn how to use and use well. Some of the other tools have steep learning curves that makes the buy-in a much harder sell.

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