Research lab project and data management
Lecture-based research experience for undergraduates
Project management of the CGEMS site
Lots of turnover --> Issues with continuity
Inexperienced --> Need to be shown hows and whys of data management
Handwriting in notebooks
Open Science Framework can mitigate these issues!
Each project has a site
Students are added as contributors with "read + write" access
Components delineate experiments or research areas
Procedures and Final results are displayed in the wiki
Intermediate or other results are included in component folders with data/experiment titles
Try to keep analysis and results files in distinct folders
Mendeley/Zotero reference area
Link in other resources like Github or Dropbox as needed
Publicly available project:
OSF provides a flexible framework for project management
Provides data storage and management
Continuity of techniques and project knowledge
Wiki panes are useful as notebooks for describing data and protocols
Reference panes make important papers part of the project
Active learning or engaging the student to participate in the learning process aids in understanding and retention
Lab courses
POGIL or flipped classrooms: students work on a project to apply knowledge and content to demonstrate concept
Promote critical thinking and adaptability --> Scientific process
Teach students to communicate scientific material effectively
Research project that integrates into the course curriculum to reinforce learning objectives
Examples at JMU:
Intro Biology Lab sequence
Bacterial Discovery
Organic Chemistry Lab for Chemistry majors
What about for a lecture course?
~70% students have no prior research experience
Mostly non-chemistry majors
Diverse professional goals
Large lecture section with no associated lab course
Materials and infrastructure to facilitate student interactions and active learning
Diverse student backgrounds, abilities, and interests
Management of the student data
Wanted students to think about biochemistry!
Large lecture section with no associated lab course
Materials and infrastructure to facilitate student interactions and active learning
Diverse student backgrounds, abilities, and interests
Management of the student data
Wanted students to think about biochemistry!
Instructor assigns:
A part of a target protein to analyze
Templates for online notebook and final report
Brief review of field, question, and direction to follow
List of possible online tools to use
Access to Open Science Framework project folder
Students then:
Predict changes in weak interactions, pKA values, broader changes in protein structure or active site
Rationalize why the change could occur based on biochemical knowledge
Connect to protein function/human disease
Propose how the conclusions could be supported with “real” experiments
Tried asking students to keep a notebook using Word/Docs --> :(
Used JMU's access to Sharepoint and OneNote --> :(
~10% of students could not get access to OneNote
Was a good solution otherwise
Present solution is the Open Science Framework
1. Fork and go do Science (2016-2018)
2. Research Community (going forward)
Instructor creates a public base notebook and populates with necessary materials
Students "fork" project and give the instructor access
What works:
All the data can be kept in a central place
Easy to see when students did the work
No access problems
Students have freedom to manage project as they wish
What needed improvement:
Creates a lot of divergent notebooks
Hard to distribute new information to all the projects
Students have freedom to manage project as they wish
Instructor creates a project and populates with necessary materials
Students ask to be contributors
Group Project:
Students in groups create component
research background on target gene/protein
Use wiki to illustrate the known aspects of gene/protein
Learn to use OSF and visualization software together
Individual Project:
Within group component, students create research component for their part of the research
Data repository for individual project and notebook
Use wiki to highlight results like a notebook
Students see how others solved similar problems
Lecture based research project for biochemistry
OSF facilitates data management and storage
In the future, OSF will be the hub for the students working to learn and collaborate on their research project.
Compare assessment on students who have taken BIO140/150 experience to those who have not.
What is Markdown language?
plain-text syntax that can be converted simply to HTML or other formats quickly
can be read easily with minimal tags or code to indicate formats such as Bold or Italic
OSF uses an interface that contains features known to uses of Word/Docs to make wiki easier to write in markdown
(This entire presentation was written in a version of markdown)
'##' indicates a header
'*' on either side of a word or phrase converts to italics
'**' on either side of a word or phrase converts to bold
While you type, you can preview the result of the markdown to HTML conversion
In groups we will:
Create a component for the data for each team in the Salmonella Isolate Data and Analysis Files component
Within the new component, modify the home wiki page with basic information on your isolate
Throughout the workshop:
Fill in additional components for new experiments and data
Fork the notebook template to create a group notebook for methods and data
Wikis can (should?) be used to indicate what is in each component section and highlight major findings
Research lab project and data management
Lecture-based research experience for undergraduates
Project management of the CGEMS site
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