Phase II Quick Outline of Work
- Present progress and respond to Phase I feedback
- Read and adjust project based on reviewer feedback
- Create high level overview presentation of project goals and
progress
- Identify project adjustments and concerns for discussion
- Obtain and explore core analysis dataset
- Download, extract, and examine the contents of your code
dataset
- Decide on and describe a data selection or exclusion strategy
- Calculate summary statistics (counts, averages, ranges, percentages,
etc) for important variables or subpopulations in your likely
analysis
- Investigate and formalize your analysis plan
- Update literature reviews with more investigation to appropriate
analysis methods and benchmarks
- Describe individual steps of proposed analysis workflow
- Identify compute, software, and packages intended to complete
analysis
- Identify project risks and potential alternatives strategies
- Submit and review Phase II reports
Phase II Submissions and Deadlines [year-long
overview]
- Phase II Progress Presentation/Discussion (18 min
present & discuss): 5 pts, May 6 - Jun 14 @ [Zoom]
- Phase II Report and Proposal (around 4 pg team
report): 15pts, Fri, Jun 21 @ [form]
- Phase II Peer Evaluations (3 report evals): 9pts,
Wed, July 3 @ [link tbd]
Progress Presentation Sessions
Phase Objectives
- PP-1. Present your project importance and progress
quickly to a generalized audience
- PP-2. Prepare responses to written reviews and
respond to feedback and questions from a live audience
- PP-3. Identify project risks and weaknesses and
solicit assistance from other scientists/researchers
- PP-4. Participate in and provide valuable
contributions to data-related scientific discussions science
Updated and Revised Phase II Report
Phase Objectives
- P2-1. Produce a concise, clear, and well documented
written proposal for a data analysis that will be relevant to an
important clinical problem and demonstrate that the primary dataset(s)
are available and sufficient.
Phase II Report:
- At the end of Phase II, all teams are expected to revise and update
their previous submissions into a more complete report. By the end of
Phase II, the report should contain at least the following sections:
- Project Title & Authors (Revised)
- Proposal Abstract (New) - short paragraph conveying the high level
background, goal, and plan for how your data analysis will address an
important clinical or medical issue
- Introduction -
- Literature review of clinical relevance of issue (Revised)
- Background about primary dataset(s) (Revised)
- Literature review of analysis methods and benchmarks
(New) - Evidence from medical literature about the
types of analysis methods, their advantages and disadvantages, and any
previous benchmark values that have been applied and set in similar
prior studies
- Methods
- Methods for Basic Dataset Characterization
(New)
- Methods for downloading, extracting, and pre-processing primary
dataset
- Description and figure of data selection inclusion or exclusion
steps
- Results
- Results for Basic Dataset Characterization
(New)
- Initial description of important summary values observed in selected
data
- Table with summary statistics for key sample populations (cohorts)
and important variables related to the proposed data analysis
- Proposed Analysis Plan (New)
- Step-by-step description of multi-phase approach to answer clinical
question with data analysis of selected data set
- Indicating choice of analysis methods and evaluation criteria for
each analysis step
- Figure diagram to summarize that high-level analysis approach
- Description of analysis requirements: computing environments,
software applications and packages, other project needs or expenses
- Discussion on risks and weaknesses of analysis plan (what will be
the biggest challenges, where will the most time be spent, what are the
greatest uncertainties) and possible approaches or alternatives that
minimize those risks
- References - cited throughout and listed at the end (Revised)
- The length of this report is expected to be equivalent to around 4
pages of 12 pt single-spaced text, not counting any figures, tables, or
bibliography sections. As always, it is expected to conform to a medical
journal or technical report style and be submitted as a pdf following
the team number and shortened title naming convention, e.g. “Team 01 -
Analysis of Breast Cancer Readmission.pdf”. Additional material can be
included as a single (or zipped directory) supplementary file.
Report Evaluation:
- Submissions will be evaluated by faculty and peers on the following:
- Previous content (clinical review, dataset background) appropriately
updated
- Clear and concise proposal abstract
- Organization and clarity of the flow of thought, especially with
integration of previous and revised materials
- Tables and figures are numbered with titles and descriptions and
cited in the text
- Correct usage of grammar, punctuation, and spelling
- Adhering to professional journal/report formatting and style
Basic Dataset Characterization
…more details and evaluation criteria coming soon.
Methods and Benchmarks Literature Review
…more details and evaluation criteria coming soon.
Project Proposal and Analysis Plan
…more details and evaluation criteria coming soon.
Critical Evaluation
Phase Objectives
- E-1. Read, understand, and think critically about
data analysis reports.
- E-2. Corroborate and assess the soundness of
proposed and reported research in domains outside your expertise.
- E-3. Provide meaningful and professional peer
review feedback.
Phase Peer Evaluations:
We will assign every student to review three submitted reports each
phase and provide valuable feedback to their peers. The purpose of this
exercise is to give reviewers exposure to the efforts and outputs of
other teams and exercise the ability to read and think critically about
analyses in other domains presented to them and practice communicating
their questions or suggestions. For the teams reviewed, this provides
additional outside perspectives on the presentation and direction of
their project that they have the chance to consider and respond to. We
expect peer reviews to contain Meaningful Feedback, defined as
- advice for fixing content errors (not grammatical errors) in the
presentation, organizing the information in different ways to make it
easier for the audience to follow, or suggestions for alternative
methodology, research questions, or interpretation of findings which may
constitute a future improvement to the work.
Some resources for how to perform and write a meaningful review can
be found at the paper, How
to Review a Clinical Research Paper or the JEE
reviewer guidelines