Rubrics and Advice for Final Group Projects

Presentations (1 per group): 20 pts

• Time: 30 minutes total/group for presentation & questions/discussion from the audience

• Group Dynamic:

  • Give approximately even time for each student in your group to talk about the background/methods/results that they spearheaded
  • OK if the presentation goes back and forth between different presenters as your work through the content
  • Presentation should be practiced and flow well

• Motivation: Be sure to provide the biological context for your study. Include relevant background information demonstrating your knowledge of the study system and SSW

• Hypotheses: Formally state the hypotheses or questions you tested, and their predictions.

• Methods: Demonstrated understanding of the experimental design and the analysis pipeline and its components.

  • Give brief overview of the parts of the analysis shared by everyone that are pertinent to producing the data you've analyzed (library type, sequencing, read cleaning, assembley, mapping, annotation, SNP calling, 16S clustering and taxonomy assignment, etc)
  • Provide detailed methods on the analyses specific to your project. Include relevant details about what type of input data the analysis required, any processing you had to do to prepare the input, and any specific options chosen that affects interpretation of your specific analyses.
  • The level of detail here should be more than the usual scientific talk, since it reflects much of the effort unique to each project.

• Results & Discussion: Are the results presented well and interpreted with a biological understanding?

  • Include clear, legible figures or tables that demonstrate the result.
  • Critical evaluation of the results in terms of the biology of the study species and what is known about SSW.

• Conclusions: Take homes and nuggests of wisdom gained. Emphasize the biological insights gained; include any technical/methodological issues encountered or

• Future Directions: Where would you take this study next? Other analyses with these data, additional sampling, or followup experiments?

Papers (Group effort, but individual write-up): 100 pts

• Style of Molecular Ecology

• Max length of 4500 words in the main text (not including abstract, references, figure/table legends)

• Combined total of 5 Tables and/or Figures

• Incorporate feedback from homework assignments, including:

  • emphasize reporting results with the biology up front rather than the statistics
  • be careful not to over-interpret your results, particularly with PCA
  • understand and motivate the biological motivation for each analysis

• Rubric follows the formal structure of a scientific article, including:

  • Title and Abstract (5 pts)

    • Title should be informative, but not overly wordy
    • Abstract should have all the major parts of the paper represented, in-brief

  • Introduction (15 pts)

    • Start out with a paragraph that gives the broad motivation for the big picture problem
    • Use subsequent paragraphs to provide some background on what is already known, and identify an important unaswered question in the context of the big picture problem
    • Conclude with your specific hypotheses/questions/objectives, and any predictions you have a priori about specific results

  • Methods (20 pts)

    • Include a summary of the "shared" methods leading up to your specific data analysis that demonstrates your basic understanding of how the data were produced. This should include a succinct description of the following: library type, sequencing strategy, cleaning/trimming, assembly, read mapping, SNP calling, and gene annotation.
    • Provide a more detailed description of the specific analyses you performed, including your motivation for running these, any specific processing steps necessary, and any options specified or assumptions made. Don't forget to cite sources of the analysis routines you use.

  • Results (15 pts)

    • Discuss the most important biological findings, providing reference to supporting statistics or figures/tables to back them up. Don't forget the biology!
    • Use topic sentences to structure the start of each paragraph. The remaining sentences in that paragraph should fill in additional details/findings that build upon the theme in the topic sentence.
    • Avoid interpreting the data here (that's for the Discussion); rather present the results

  • Discussion (20 pts)

    • Discuss your most important/critical/interesting biological results first, and leave the caveats and more technical discussion points for later in the Discussion
    • Interpret your results in light of the biology of the study system. This is your opportunity to suggest what biological processes you think are responsible for producing your results, what implications they have for SSW and future studies in similar systems, and how your findings fit into the context of other similar research (are your findinds consistent with others' work; do they suggest a novel direction?).
    • This is also your opportunity to raise any caveats or technical issues that you feel are important to properly interpreting the data without bias, and to suggest any future modifications, improvements, or critical experiments that should be considered for the future.

  • References (5 pts) — style of Molecular Ecology. Use of a Reference Manager (Mendeley, EndNote, etc. is highly recommended)

  • Figures and Tables, with well annotated legends (15 pts)

  • Overall Organization and Flow (5 pts)

    • Are the sections well organized, and present a clear, cogent understanding of the study and a well reasoned hypothesis?
    • Does the writing flow well between paragraphs and develop the ideas smoothly?