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Beagle Investigations Return with Darwinian Data

BioQUEST 2018

Welcome to the Serenity Session Start Page

Goals: We are going to cover a lot of ground here.

  • Get a sense of BIRDD as an example of a problem space.
  • Orient to the Galapagos as a ecological / evolutionary system (Activity 1).
  • Work with some finch morphology data and generate a reproducible research report using Serenity (Activity 2). 
  • Launch a longer term project using some of these (and other) resources (Activity 3). 

We will be using Serenity on QUBESHub so you will need to join the BIRDD Group - [Link here].

Schedule

10 min. - Introductions and overview of the session.  

15 min. - Activity 1: A table top activity to orient to Galapagos as an ecological / evolutionary system.

  • Use the information packet to connect different types of data from the Galapagos and explore patterns that might be interesting to try to explain. 
    • Do you see different types of patterns when you look at different scales or resolutions? For example, try dividing the archipelago into 4 quadrants and looking at the distributions within each. Or, try mapping genera instead of species.
    • What does it look like if you make island categories of small, medium and large?
    • Are there features that seem to correlate with the presence or absence of particular species?
    • Which species are most likely to be found together? Find a phylogeny of the finches and see if that information is useful in explaining what you have observed.
  • You might want to consider information about the evolutionary relationships between the finch species. 
  • Want more geographical detail? Try Google Maps of the Galapagos.
  • You can get the raw materials for this activity at the Tree of Life Project and at the BioQUEST BIRDD site.

30 min. - Activity 2: Exploratory analysis of finch morphology data

Work with morphology data using Serenity

Description - this is a set of 3 morphology datasets. Give them some info about how to think about measurements. The task is very similar to the previous one in the sense that they first need to orient to the data and context, then they will explore the data actively by interacting with it. Keep notes and build your report. Participant Tasks Generate a report with BIRDD *BQ report template Share findings with others Discuss potential of this approach

(30 min) Activity 3: User choice

Pursue more BIRDD data May not involve Serenity? Work with an existing report and open / modify it. Work with your own data - What data management skills are you working on? Look at examples of what others do with MarkDown. Dig into the tech.

A link to the Workshop Session Project - a place where we can directly access files using Serenity.

Resources

Tips and tricks for working with Serenity

Tool areas

  • Data - this is where you will be able to see and work with your data. When you choose this tool area you will see a series of tabs that give you different functionalities. 
  • R - this is where the "reporting" functions reside. When you choose this tool area you will see the Activity 2 Report Template on the left (in R markdown) and the rendered version of that file on the right (use the "knit" button to render the markdown). 
  • Save- this is where you can save your reproducible research product. Use the "save state" option to download a file ( .rda) that contains the data and the markdown version of your report. 
  • Power - this is where you can end your session. Clicking "Stop" will close the tab you are working in. Sometimes, the session is not stopped this way and continues to hang. It is a good idea to check your dashboard (https://qubeshub.org/members/myaccount) when you finish working with a tool to terminate any hanging sessions. 

Other functions

  • Edit the report markdown file. 
    • Go to the "R" tool area.
    • Place your cursor in the markdown document (left hand pane) and start typing. 
    • Markdown syntax - learn more here.