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Schwilk Lab Resources

Repository for lab resources for lab and field work, data management and analyses, and field methods and lab protocols. The Schwilk Lab at Texas Tech

Schwilk lab code

Code for various projects is stored in separate individual git repositories. A few that might be of most interest for re-use are

  • chiller: Code to run a temperature profile program on the Thermo-Fisher refrigerated bath.
  • serial-balance: Communicate with an analytical balance.
  • pandoc-build-system
  • skyisland-climate: Example of a fairly well documented and organized repository for a large project.
  • emacs-starter: Fairly lightweight emacs starter package (.emacs.d config files) for my students so you setup will be not too different from mine.

File organization in this repo

data-code

Information on lab data management, code and version control

  • Git and GitHub: Our lab guide to using git and GitHub for collaboration.
  • data-management: Our current lab best practices for managing lab data, setting up a project, organizing code and keeping the whole thing in version control

equipment

Equipment lists and maintenance histories

[TODO] - add history of balance repairs and calibration

[TODO] - Organize equipment list that has been started; organize into categories such as field equipment, plant phys, etc; correct names and give manufacturer; correct location information in more detail.

html

Holds script to build html version of these local markdown files.

[TODO] - remove or rename this? Is this necessary?

lab-org

This folder folder for information on lab business, scholarships and funding, data management, etc.

methods

Experimental methods and protocols. See individual files. Includes folder for plant identification tools:

plant-id

We'd like to add a key to plants of Lubbock County and that will be an ongoing project aided by collections students make in BIOL-3306.

safety

Lab safety plan and safety protocols

Instructions for editing

These files are all stored in markdown format (https://daringfireball.net/projects/markdown/ , see also https://help.github.com/articles/github-flavored-markdown)

If these are methods on which you are working, feel free to edit and commit changes or create an issue first to give folks a heads up on the proposed changes.

Although it is ok to commit to master, a good workflow on a shared repository is:

  1. Make a working branch for yourself. You can even push this branch to the repository, in that case, make sure to give it a descriptive name involving the planned work or perhaps your name.
  2. Do you work in this branch and commit often.
  3. Issue a pull request so others can review your work before it is merged into /master.

This may be overkill for the protocols repository, but may make sense for others.

Important Note:

The plan is to make this repository public. Because it is very difficult to actually delete anything from a git repository, it is important to never commit any private information we don't want shared. I don't think there is much chance of that, but I just wanted to warn everyone.

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Field and lab protocols, information on lab organization, and logistics

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