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 undergraduates ### Problems: .large[ - Lots of turnover --> Issues with continuity - Inexperienced --> Need to be shown hows and whys of data management - Handwriting in notebooks ] <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/) ] 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** + **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 + Bacterial Discovery + 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_A 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="index_files/figure-html/fork-1.png" width="70%" 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="index_files/figure-html/collab-1.png" width="70%" 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. *Compare assessment on students who have taken BIO140/150 experience to those who have not.* ] --- class: center, inverse, middle # Constructing and updating 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 the data for each team in the *Salmonella Isolate Data and Analysis Files* component - Name the component after your isolate (*example*: DG7) 2. Within the new component, modify the home wiki page with basic information on your isolate ] --- ## Continuing work .large[ **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 ]