--- Using the Open Tree of Life for your Research, SSB 2020: Jan 3, 2019

Using the Open Tree of Life for your Research, SSB 2020

Jan 3, 2019

1:30 pm - 5 pm

Instructors: Emily Jane McTavish, Mark Holder, Luna Luisa Sanchez Reyes

We have borrowed the Carpentries website template and installation instructions. This is not a Carpentries workshop (although we highly recommend them!). Learn more about the carpentries at https://carpentries.org/

Using the Open Tree of Life for your Research

The Open Tree of Life project is a phylogenetic resource that offers a synthetic tree summarizing evolutionary relationships across 2.6 million taxa. OpenTree (as of September 2019) also provides access to 4,168 published studies comprising 9,367 trees, and the database is growing weekly. The tips of these trees are mapped to taxonomic identifiers that link across taxonomic and informatics databases such as NCBI and The Global Biodiversity Information Facility (GBIF). The website also provides user-friendly resources for bulk reconciliation of taxonomic names to these standardized identifiers. Together these resources offer a formidable suite of tools and data for taxonomic name reconciliation and phylogenetic comparisons and analyses. This workshop will cover how to understand, access and apply these data resources from the Open Tree of Life project to your research questions. Topics will include accessing phylogenetic relationships for arbitrary sets of taxa, applying date estimates to these trees, linking phylogenetic and geographic information, assessing conflict between phylogenetic estimates, and incorporating your own phylogenetic estimates into the OpenTree of Life project. The workshop will include interactive browser based exercises, demonstrations of how to access OpenTree data through the API, and tutorials in R and Python. Experience using a command line interface, R or Python will be helpful, but is not required.

Requirements:

Accessibility: We are committed to making this workshop accessible to everybody. The workshop organizers have checked that:

Materials will be provided in advance of the workshop and large-print handouts are available if needed by notifying the organizers in advance. If we can help making learning easier for you (e.g. sign-language interpreters, lactation facilities) please get in touch (using contact details below) and we will attempt to provide them.

Contact: Please email ejmctavish@ucmerced.edu for more information.


Code of Conduct

Everyone who participates in SSB2020 is required to conform to the Code of Conduct.

Collaborative Notes Document

We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code. Please sign in!


Schedule

1:30 Intro to OpenTree
1:50 Supertree synthesis
2:10 Bulk TNRS, induced subtrees and study search in Python
2:45 Coffee break
3:00 Getting synthetic trees and dates in R
4:00 Adding trees to OpenTree
5:00 END

Setup

To participate in this workshop, you will need to be able to access RStudio, Python3 and Jupyter notebooks, and use git to clone repos. In addition, you will need an up-to-date web browser. If you already have these software installed and accessible on your laptop, please skip to the bottom and run the checks. Otherwise there are installation instructions listed below.

The Carpentries maintains a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.

The Bash Shell

Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.

Video Tutorial
  1. Download the Git for Windows installer.
  2. Run the installer and follow the steps below:
    1. Click on "Next" four times (two times if you've previously installed Git). You don't need to change anything in the Information, location, components, and start menu screens.
    2. From the dropdown menu select "Use the nano editor by default" and click on "Next".
    3. Ensure that "Git from the command line and also from 3rd-party software" is selected and click on "Next". (If you don't do this Git Bash will not work properly, requiring you to remove the Git Bash installation, re-run the installer and to select the "Git from the command line and also from 3rd-party software" option.)
    4. Ensure that "Use the native Windows Secure Channel library" is selected and click on "Next".
    5. Ensure that "Checkout Windows-style, commit Unix-style line endings" is selected and click on "Next".
    6. Ensure that "Use Windows' default console window" is selected and click on "Next".
    7. Ensure that "Enable file system caching" and "Enable Git Credential Manager" are selected and click on "Next".
    8. Click on "Install".
    9. Click on "Finish".
  3. If your "HOME" environment variable is not set (or you don't know what this is):
    1. Open command prompt (Open Start Menu then type cmd and press [Enter])
    2. Type the following line into the command prompt window exactly as shown:

      setx HOME "%USERPROFILE%"

    3. Press [Enter], you should see SUCCESS: Specified value was saved.
    4. Quit command prompt by typing exit then pressing [Enter]

This will provide you with both Git and Bash in the Git Bash program.

The default shell in some versions of macOS is Bash, and Bash is available in all versions, so no need to install anything. You access Bash from the Terminal (found in /Applications/Utilities). See the Git installation video tutorial for an example on how to open the Terminal. You may want to keep Terminal in your dock for this workshop.

To see if your default shell is Bash type echo $SHELL in Terminal and press the enter/return key. If the message printed does not end with '/bash' then your default is something else and you can run Bash by typing bash.

The default shell is usually Bash and there is usually no need to install anything.

To see if your default shell is Bash type echo $SHELL in a terminal and press the enter/return key. If the message printed does not end with '/bash' then your default is something else and you can run Bash by typing bash.

Git

Git is a version control system that lets you track who made changes to what when and has options for easily updating a shared or public version of your code on github.com. You will need a supported web browser.

You will need an account at github.com for parts of the Git lesson. Basic GitHub accounts are free. We encourage you to create a GitHub account if you don't have one already. Please consider what personal information you'd like to reveal. For example, you may want to review these instructions for keeping your email address private provided at GitHub.

Git should be installed on your computer as part of your Bash install (described above).

Video Tutorial

For OS X 10.9 and higher, install Git for Mac by downloading and running the most recent "mavericks" installer from this list. Because this installer is not signed by the developer, you may have to right click (control click) on the .pkg file, click Open, and click Open on the pop up window. After installing Git, there will not be anything in your /Applications folder, as Git is a command line program. For older versions of OS X (10.5-10.8) use the most recent available installer labelled "snow-leopard" available here.

If Git is not already available on your machine you can try to install it via your distro's package manager. For Debian/Ubuntu run sudo apt-get install git and for Fedora run sudo dnf install git.

Text Editor

When you're writing code, it's nice to have a text editor that is optimized for writing code, with features like automatic color-coding of key words. The default text editor on macOS and Linux is usually set to Vim, which is not famous for being intuitive. If you accidentally find yourself stuck in it, hit the Esc key, followed by :+Q+! (colon, lower-case 'q', exclamation mark), then hitting Return to return to the shell.

nano is a basic editor and the default that instructors use in the workshop. It is installed along with Git.

Others editors that you can use are Notepad++ or Sublime Text. Be aware that you must add its installation directory to your system path. Please ask your instructor to help you do this.

nano is a basic editor and the default that instructors use in the workshop. See the Git installation video tutorial for an example on how to open nano. It should be pre-installed.

Others editors that you can use are BBEdit or Sublime Text.

nano is a basic editor and the default that instructors use in the workshop. It should be pre-installed.

Others editors that you can use are Gedit, Kate or Sublime Text.

Python

Python is a popular language for research computing, and great for general-purpose programming as well. Installing all of its research packages individually can be a bit difficult, so we recommend Anaconda, an all-in-one installer.

Regardless of how you choose to install it, please make sure you install Python version 3.x (e.g., 3.6 is fine).

We will teach Python using the Jupyter Notebook, a programming environment that runs in a web browser (Jupyter Notebook will be installed by Anaconda). For this to work you will need a reasonably up-to-date browser. The current versions of the Chrome, Safari and Firefox browsers are all supported (some older browsers, including Internet Explorer version 9 and below, are not).

Video Tutorial
  1. Open https://www.anaconda.com/distribution/#download-section with your web browser.
  2. Download the Anaconda for Windows installer with Python 3. (If you are not sure which version to choose, you probably want the 64-bit Graphical Installer Anaconda3-...-Windows-x86_64.exe)
  3. Install Python 3 by running the Anaconda Installer, using all of the defaults for installation except make sure to check Add Anaconda to my PATH environment variable.
  1. Open https://www.anaconda.com/distribution/#download-section with your web browser.
  2. Download the Anaconda Installer with Python 3 for Linux.
    (The installation requires using the shell. If you aren't comfortable doing the installation yourself stop here and request help at the workshop.)
  3. Open a terminal window and navigate to the directory where the executable is downloaded (e.g., `cd ~/Downloads`).
  4. Type
    bash Anaconda3-
    and then press Tab to autocomplete the full file name. The name of file you just downloaded should appear.
  5. Press Enter. You will follow the text-only prompts. To move through the text, press Spacebar. Type yes and press enter to approve the license. Press Enter to approve the default location for the files. Type yes and press Enter to prepend Anaconda to your PATH (this makes the Anaconda distribution the default Python).
  6. Close the terminal window.

R

R is a programming language that is especially powerful for data exploration, visualization, and statistical analysis. To interact with R, we use RStudio.

Video Tutorial

Install R by downloading and running this .exe file from CRAN. Also, please install the RStudio IDE. Note that if you have separate user and admin accounts, you should run the installers as administrator (right-click on .exe file and select "Run as administrator" instead of double-clicking). Otherwise problems may occur later, for example when installing R packages.

You can download the binary files for your distribution from CRAN. Or you can use your package manager (e.g. for Debian/Ubuntu run sudo apt-get install r-base and for Fedora run sudo dnf install R). Also, please install the RStudio IDE.

Installation checks (Please complete before the workshop starts)

Git check

You should be able to open a terminal window and run:
    git
This should print out some text that starts with "usage: git [--version] [--help] [-C ] [-c =]"

Jupyter check

    jupyter notebook
This should open up a browser window that says "jupyter" at the top. If you click on 'new' in the upper right, there should be an option to create a python3 notebook. (You can close this window and close the terminal.)

RStudio check

Open RStudio. Click in the 'console' window. (It's the one with the '>') Run:

    > version$version.string
    > install.packages("rotl")
    > install.packages(c("devtools", "ape", "stringr"))
    > devtools::install_github("phylotastic/datelife")
    
 
Make sure your version is at least 3.6.0 or higher. The r opentree installation output should end with "* DONE (rotl)"
If theses checks work, then you are all set! Otherwise, please follow the installation instructions above, and then try these tests again. Contact ejmctavish@ucmerced.edu if you are still having issues.