Lab Operations - TREC-Agroecology/lab-wiki GitHub Wiki

TREC Agroecology Standard Operating Procedures

Most organizations have standard operating procedures for complex routine tasks for training and consistency. Our lab SOP includes computational tasks and field work. This page compiles SOP for tasks common across the lab, while SOP related to specific projects should be reported in project repositories.

File Management

New File

1. Generate new file in desired program.
2. Save file to appropriate folder in a shared folder using naming best practices (e.g., Zack-manuscript.docx)
3. • If appropriate text-based file type (e.g., data, code), commit to data repository.
   • Or else, generate or revise companion metadata/changes .txt file. The file should have a similar name to the file it references (e.g., Zack-manuscript-changes.txt).
4. Communicate your progress to your project collaborators. This is not necessary if the project is version controlled.

Revise File

1. Revise file.
2. Save file to appropriate folder in shared folder.
3. • If appropriate file type (e.g., data, code), commit changes to data repository.
   • Or else, revise companion metadata/changes .txt file to reflect changes.
4. Communicate your progress to your project collaborators. This is not necessary if the project is version controlled.

Data Management

• File naming and data formatting as per Karl Broman's Data Organization
• Database structure as per Data Carpentry for Biologists

Document Management

We all do a LOT of writing in the lab and most of it gets my attention, especially if we are working on something formal for submission. It is important to me that we communicate effectively throughout the writing process.

Include track changes and comments to revisions of formal manuscripts (e.g., proposal, thesis/dissertation, research manuscript, fact sheets). Just like a rebuttal letter for a peer-reviewed manuscript, I want to know what I asked to be changed and how you addressed those requests. You may not have made a revision to a comment or simply incorporated my changes. That is OK. Help me keep track.

Here's a list of things that are most important to me when it comes to writing:

• Organize your writing clearly with appropriate headings and topic sentences.
• Use summary paragraphs to communicate your primary message and supporting ideas.
• Write direct sentences.
• Take a top-down approach to writing. Topic sentences and clear messaging is critical.
• Avoid unnecessary linking words/phrases (i.e. however). Consider revising/reorganizing the sentence structure for more direct flow.
• Align left, not justify.
• Single space between sentences.
• Do not name a citation as the subject of a sentence.
• Do not cite the same source multiple times in consecutive sentences.