We’ll engage in 5 team-based asynchronous lab exercises or Mini-projects that span 2-3 weeks of class. Teams will be randomly assigned before the beginning of each MP.

New MPs will be released on Thursdays with an MP project description (see links above under and our schedule page). These project descriptions begin with some background, a survey of some of the important concepts from class that we’ll invoke in the MP, and the question we’ll seek to answer. From there, you’ll move on to performing experiments or simulations and collect data to answer the MP’s question.

Report Guidelines

Report Content

After you’ve completed the experiments for an MP, you’ll be asked to analyze data and synthesize and contextualize your results in a report. The reports should be short (<1000 words), contain relevant figures and table, and be written in R Markdown. They are due on Wednesdays and should be uploaded to a directory specified in the MP description. The submission should include the markdown file (an .Rmd) and all the data associated with the analysis. Each MP is worth up to 50 points toward your final grade.

In the first AME, we’ll explore how to analyze data using R and how to synthesize analysis and text into a reproducible Markdown document. The following must be included in your .Rmd. How to implement each of these requirements will be discussed in AME1.

  1. A YAML header that specifies the author, title, date, output, and bibliography file.
  2. The following section headers that organize your text and includes 4-5 short relevant sentences:
    • Introduction: Include a brief background to the project (why are we studying this anyway?), what the main questions is, and how this question will be answered.
    • Methods: Briefly outline the specifics of how the question will be answered.
    • Results: Briefly summarize the results.
    • Discussion: Briefly discuss the importance of the results (i.e., how they relate to the main question and the field in a broader context).
    • Author Contributions: Briefly state the contributions made by each team member to the project.*
    • References: Populate a bibliography section that includes the works cited in the text.
  3. At least 1 relevant figure.
  4. All the code used in analysis and that produces figures. This should be included as code chunks.
  5. Citations to at least 2 relevant peer-reviewed papers.

*Author contributions statements are now almost universal in scientific publications. In fact, when submitting manuscripts, authors are often asked to list the contributions of each coauthor BEFORE the manuscritpt is considered by the the journal.

Author Contribution Evaluations

Before the deadline for each MP, EVERY group member of each team must submit an evaluation of their own and their teammates’ contributions to the project. These evaluations can be made using this form. Please check out our Author Contribution Evaluation page for more information.

Note: Team members who do not submit their peer evaluations before the deadline will be subject to a 5-point penalty for each 24-hour period the assessment is not submitted. For example, if an evaluation is submitted 12 hours late, this will mean a 5-point penalty; for one that is 36 hours late, this will mean a 10-point penalty.

Content Rubric

The following rubric describes how the content of each MP report will be evaluated.

Component Spot On Pretty Good Needs Work
Tasks and Outputs Completes all tasks fully; submits all required outputs and materials (including data) on time
(10 pts)		 Completes a majority but not all tasks fully; submission meets the deadline
(6 pts)		 Completes few required tasks or submits few required materials; submission misses the deadline
(2 pts)
Effort and Engagement Individual or team asks questions or seeks help regularly
(10 pts)		 Individual or team asks questions or seek help sometimes, but not regularly
(6 pts)		 Individual or team does not seem help
(2 pts)
Report Format Report contains all the appropriate headings and components (including a bibliography)
(5 pts)		 Report contains most of the appropriate headings and components (including a bibliography)
(3 pts)		 Report contains few of the appropriate headings and components
(1 pt)
Analysis and Code Report contains concisely written code chunks within the results or methods sections that produce the appropriate analyses, figures, and/or tables
(10 pts)		 One or a few code chunks are unneeded or produce analyses, figures, and/or tables not directly related to the project goals
(6 pts)		 No code chunks contained in report or all code chunks are unneeded or produce analyses, figures, and/or tables not directly related to the project goals
(2 pts)
Graphics and Tables Figures, tables, and images are clear, add much to the results in analysis, and have concise but descriptive captions
(5 pts)		 One or a few figures, tables, and images are unneeded or inappropriate or they lack captions that are concise or descriptive
(3 pts)		 Few figures, tables, and images are unneeded or inappropriate
(1 pt)
Writing and Style The writing is concise, clear, avoids passive constructions, and is in the past tense; grammar is appropriate
(5 pts)		 The writing is unclear or rambling in spots or uses passive constructions and future tense; grammar is shaky in spots
(3 pts)		 The writing is unclear, and/or uses passive constructions or future tense throughout; grammar is shaky for the most part
(1 pt)
Sources and References Statements of scientific findings and fact are supported by references; references are contained in a BibTex bibliography and inserted with @ tags.
(5 pts)		 Some statements of scientific findings and fact are not supported by references; some references are not contained in a BibTex bibliography or inserted with @ tags
(3 pts)		 Most statements of scientific findings and fact are not supported by references; references are not contained in a bibtex bibliography nor inserted with @ tags
(1 pt)

Writing Advice

Students often find writing such reports—which resemble scientific manuscripts—difficult, specifically how to formulate the report and what to include in each section. Although the format and structure of our MPs are outlined in detail above, some additional advice may help. The very prestigious Nature publishing group has released a series of articles on their “Scitable” site devoted to writing in science. You may find this article helpful in writing your MP reports.

In addition to the structural requirements of including important sections and relevant text and figures, the writing must be clear and free of distracting usage errors and spelling mistakes. Here’s some writing advice you might find helpful, complements of Prof. Kenaley’s graduate school advisor.

Report Assessment

All team members will receive a preliminary grade for each report according to the content rubric. Prof. K will then review the author contribution evaluations and adjust the preliminary grade accordingly.