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<!DOCTYPE html>
<html>
<head>
<title>Using OSF with lab and lecture projects</title>
<meta charset="utf-8">
<meta name="author" content="Chris Berndsen" />
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<textarea id="source">
class: center, middle, inverse, title-slide
# Using OSF with lab and lecture projects
### Chris Berndsen
---
# Using the Open Science Framework
- .Large[Research lab project and data management]
- .Large[Lecture-based research experience for undergraduates]
- .Large[Project management of the CGEMS site]
.pull-left[
]
.pull-right[
]
---
## Research Project Management with undergraduate students
### Problems:
.large[
- Lots of turnover --> Issues with continuity
- Inexperienced --> Need to be shown hows and whys of data management
]
<br/>
<br/>
.center[.content-box-purple[.large[Open Science Framework can mitigate these issues!]]]
---
# General setup for lab projects
.Large[Each project has a site]
- Students are added as contributors with "read + write" access
- Components delineate experiments or research areas
- *Makes it easier to make specific parts of a project public later*
.Large[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
.Large[*Mendeley/Zotero* reference area]
.Large[Link in other resources like *Github* or *Dropbox* as needed]
---
class: center, middle
# Examples from the Berndsen lab
<br/>
<br/>
.Large[
Publicly available project:
[Tetherin SNP modeling](https://osf.io/hwkj4/)
]
---
## Summary
.large[
**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
]
---
class: center, inverse, middle
# Lecture-based research experience for undergraduates
---
## How to get students to apply and retain knowledge?
.large[
- Active learning or engaging the student to participate in the learning process aids in understanding and retention
+ Lab courses are often use to supplement learning from the lecture
+ 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
]
---
## Course-embedded Undergraduate Research Experience
.large[
- Research project that integrates into the course curriculum to reinforce learning objectives
- Examples at JMU:
+ Intro Biology Lab sequence
+ Organic Chemistry Lab for Chemistry majors
]
<br/>
.center[.full-width[.content-box-gold[.Large[What about for a lecture course?]]]]
---
## Biochemistry (CHEM361) at JMU
.large[
- Lecture of 55 to 130 students with one/two instructor(s)
- ~70% students have no prior research experience
+ *Ranges from 50 to 95%*
- Mostly non-chemistry majors
+ *Biology, Health Science, Biotechnology*
- Diverse professional goals
+ *~1/3 to professional school, 1/3 graduate school, 1/3 job or other*
]
---
## Problems to solve when I started...
.large[
- **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!**
]
---
## My solutions
.large[
- Large lecture section with no associated lab course
+ **POGIL-stylebased classroom activities and used Socrative to monitor students in real time and give feedback**
- Materials and infrastructure to facilitate student interactions and active learning
+ **Used Canvas to facilitate peer groups, Socrative to check answers, in-class activities**
- Diverse student backgrounds, abilities, and interests
+ **By lecturing less, I spent more time talking to students in small groups or one-on-one**
]
---
## My solutions continued
.large[
- Management of the student data
+ **Word --> Sharepoint/OneNote --> Open Science Framework**
- Wanted students to think about biochemistry!
+ **Course-based project connecting DNA sequence to protein structure/function**
]
---
## Published results from the course-based activity
.pull-left[
.footnote[
[Berndsen, et al., 2016](https://iubmb.onlinelibrary.wiley.com/doi/abs/10.1002/bmb.20976)
]
]
.pull-right[
.footnote[
[Hossain, et al., 2018](http://www.molvis.org/molvis/v24/218/)
]
]
---
## General setup of the CURE project
.pull-left[
.large[**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
]
.pull-right[
.large[**Students then:**]
- Predict changes in weak interactions, pK<sub>A</sub> 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
]
---
## Open Science Framework
.large[
- Tried asking students to keep a notebook using **Word/Docs** --> .Large[:(]
- Used JMU's access to Sharepoint and **OneNote** --> .Large[:(]
- ~10% of students could not get access to OneNote
- Was a good solution otherwise
- Present solution is the **Open Science Framework**
]
---
## Two ways to manage student notebooks
.large[**1. Fork and go do Science (2016-2018)**]
.large[**2. Research Community (going forward)**]
---
## Fork and go do Science (2016-2018)
<img src="CGEMSOSFX_files/figure-html/fork-1.png" style="display: block; margin: auto;" />
---
## Fork and go do Science (2016-2018)
- Instructor creates a public base notebook and populates with necessary materials
- Students "fork" project and give the instructor access
.pull-left[
.bold[.large[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
]
.pull-right[
.bold[.large[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
]
---
## Research Community
<img src="CGEMSOSFX_files/figure-html/collab-1.png" style="display: block; margin: auto;" />
---
## Research Community
- Instructor creates a project and populates with necessary materials
- Students ask to be contributors
.pull-left[
.bold[.large[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
]
.pull-right[
.bold[.large[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
]
---
## Summary
.large[
**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.
]
---
class: center, inverse, middle
# Making the CGEMS workshop site
---
## Using the Wiki and Markdown language
.large[**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*
.large[**OSF** uses an interface that contains features known to uses of Word/Docs to make wiki easier to write in markdown]
.center[<img src="./img/markdown.PNG" width = "700">]
.footnote[(This entire presentation was written in a version of markdown)]
---
## OSF interface for the Wiki
.center[]
'##' 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
.large[While you type, you can preview the result of the markdown to HTML conversion]
---
class: center, middle
# Let's make a wiki page
---
## Group work
.large[
In groups we will:
1. Create a component for each part of the workshop
2. Begin to fill in the wiki using markdown language
]
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