developing a research case study
TRANSCRIPT
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Developing a Research
Case StudyJulie Goldman, MLIS@jgolds2Library FellowLamar Soutter LibraryUMass Medical School
New England Collaborative Data
Management Curriculum
Scientific Research Data Management by Lamar Soutter Library, University of Massachusetts Medical School is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License
#teach-ingNECDMC
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Outline
• Case Study Methodology
• Developing Case Study
• NECDMC Research Case Study
• Teaching NECDMC
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Teaching Case for Data
Management
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“The case method packs more experience into every hour of learning than any other
instructional approach.”Harvard Business Publishing,
Hints for Case Teaching
http://www.expand2web.com/blog/marketing-case-study-how-weight-watchers-dominated-the-weight-loss-industry/
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Case Study Method
• Present problems
• Focus on a topic or “teachable moment”
• Prepare users http://blog.tradeshift.com/tradeshift-case-study-broadway-design-company/
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Creating a Case Study
• Background Research
• Data Interview
• Case Narrative
• Discussion Questions
• Data Management Plan
http://amitkaps.com/bring-the-right-brain-at-work/
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Research Life Cycle
http://data.library.virginia.edu/data-management/
Down-stream
Upstream
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New England Collaborative Data Management Curriculum
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BackgroundModel organism
neuroscience research lab
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Researcher
• Third year graduate student
• Areas of focus : neurotrauma, neurological disorders, gene therapy
https://ngsp.osu.edu/
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http://medicine.osu.edu/neuroscience/Pages/index.aspxhttp://columbusneighborhoods.org/
Ohio State University
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https://u.osu.edu/beattie.24/
Beattie Lab
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Using Zebrafish as a Model System for Studying Motor
Axon Guidance & Motoneuron Disease
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Research Questions
• What is the biological basis of the motoneuron disease SMA?
• How can modeling ALS in zebrafish be useful as a tool for drug and genetic screening?
• What genes define motor axon outgrowth?
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Data InterviewModel organism
neuroscience research lab
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Data Interview• Draw out information about project
• Questions focus on the data story
https://www.youtube.com/user/nealsciencebootcamp/feed
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Tips and Reminders
• Do your homework
• Use follow-up questions
• Make the meeting about the researcher not the library
• Establishes relationships
• Associates the library with data
https://yellowdoggraphics.wordpress.com/page/3/
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Interview Instrument
http://dmp.data.jhu.edu/sites/default/files/Questionnaire.doc
JHU Data Management Services of the Sheridan
Libraries : Questionnaire to Help with the
Creation of a Data Management Plan
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Initial Interview1. As a research focused university what kind of NIH grant do you have?
2. What other funding sources do you have?
3. How long has this research project been going on?
4. What is the overarching purpose of this research?
5. What is your role in the research process?
6. What kinds of experiments are you doing with the zebrafish?
7. Who else works on this
project?
8. What types of data products are being produced?
9. What file formats are your data produced in?
10. How is data analyzed?
11. How is the data managed?
12. Does your lab have naming conventions for files/data?
13. Where and how long is data and notebooks stored?
14. What kind of backup and security protocols does your lab have?
15. What is shared publicly and with the neuroscience community?
16. Who is allowed access to the data?
17. Are there security concerns within the lab?
18. Who owns and is responsible for the research data?
19. With a long research project, there is personnel turnover within the lab. How is data passed down among the research team?
20. How is you lab ensuring long term preservation of your research and data?
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Follow up Email1. What lab instruments you use?
2. You mentioned .TIFF files, what other file formats do these instruments create?
3. Do you have to change file formats to make them accessible to everyone?
4. Any idea how many files are being produced daily?
5. In terms of metadata, is there are a data dictionary to go along with it?
6. Who exactly is reusing the research data? Other OS labs? US labs? International?
7. You told me about your lab notebook and I am aware your lab is very low tech, but has the university or the lab thought about implementing electronic lab notebooks?
8. How much interaction is there between your PI and you and everyone else working in the lab?
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Second Interview1. When you collect data about your fish, how do you make sure that information is linked to that fish?
2. Where do all of the image files you are collecting end up? Only in your lab notebook and on your personal computer?
3. Can you explain the scoring system you use to quantify the defect in the motor neurons that are imaged on the florescent microscope?
4. Do you know how often the programs you use are updated for new versions?
5. Only zebrafish genetic lines are sent to the international registry. What happens with all the other data about the fish?
6. Does your lab submit data or publications to Ohio State University’s institutional repository?
7. Do you know if Ohio State has policies for data sharing or data preservation?
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Final Suggestions
http://neilpatel.com/2015/05/12/how-to-attract-clients-as-a-part-time-content-marketer/
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Case NarrativeModel organism
neuroscience research lab
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Research
• Motoneuron diseases SMA and ALS
• Genetic and molecular cues
• Genetic models of zebrafish
• Research since 1996https://science.nichd.nih.gov/confluence/display/
zfig/Home
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Funding • NIH grant:
research project grant (r01)
• Other private funding
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SMA• Spinal muscular atrophy
• Caused by mutations in the survival motoneuron gene (SMN)
• SMN protein is critical to the health and survival of nerve cells in the spinal cord responsible for muscle contraction
• Occurs early in lifehttp://en.wikipedia.org/wiki/
Spinal_muscular_atrophy
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SMA
• Protein knockdown technology
• What function of SMN leads to motoneuron dysfunction
• Cell death in SMA caused by motor neuron defects
• Use scoring system on florescent microscope images
http://www.smasupportuk.org.uk/blog/research/sma-support-uk-at-the-cure-sma-conference-2013
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ALS• Amyotrophic lateral
sclerosis or Lou Gehrig’s disease
• Muscle weakness and atrophy
• Defect on chromosome 21 which codes for superoxide dismutase (SOD1) enzyme
http://en.academic.ru/dic.nsf/enwiki/17085
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ALS• Genetic mutation :
SOD1 gene to generate SOD G93A and G85R transgenic zebrafish
• Drug screens with zebrafish larva
• Rescue motor neurons early in development
http://oncampus.osu.edu/article.php?id=1645
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Motor Axons
http://zfin.org/ZDB-FIG-130516-36
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Why Zebrafish?
http://blog.investis.com/en/2011/11/the-hope-tank-go-on-jump-in/#axzz3anEBzkb2
http://www.devbio.biology.gatech.edu/?page_id=6534
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http://biobide.es
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Zebrafish Facility• Facility supports three
labs
• 1200 sq ft
• 1234 tanks & 40,000 fish
• Tank labels : research’s name, fish name, DOB, stock number
http://medicine.osu.edu/neuroscience/neuroscience-core-services/core-b-genetics/ii-zebrafish-and-
genome-manipulation-facility/pages/index.aspx
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General Lab Work• PCR : polymerase chain reaction
• Agarose gel electrophoresis: separate DNA
• Western Blot : detect protein levels in tissue
• Microscopy : scoring system (axon morphology)
doi: 10.1083/jcb.200303168
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Equipment and Products
• Bio-Rad (RT)-qPCR : Microsoft™ Excel™ files
• Thermo Scientific™ NanoDrop™ : Excel™ files
• Western Blots : film developed in a dark room
• Agarose gels : read on a gel box and printed/scanned for densitometry quantification
• Microscopes : TIFF and JPEG files
• Data analysis : Excel™ or SPSS™
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Programs• SPSS® : statistics software
• ImageJ™ : public domain, Java™-based image processing program developed by NIH
• Adobe® Photoshop® : photo editing
• Microsoft® Office : Word™, Excel™,
PowerPoint™
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Data Flow• Data produced on old computers attached
to equipment
• Transferred to the big (old) lab computer for processing and data analysis
Example: florescent microscopy images are saved on the computer attached to the microscope which are then printed out and sent to other computerswww.labx.com
https://u.osu.edu/beattie.24/
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File Naming Conventions
• No standardization
• Personal
• Become more professional when sent to the PI and goes to publication
http://dilbert.com/strip/2011-04-23
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Lab Notebooks
• Paper lab notebooks for non-digital data
• Personal data keeping techniques
• Records detailed descriptions of experiments
• Notebooks stay in the lab
http://2012.igem.org/Team:LMU-Munich/Lab_Notebook
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Backup and Security
• Use personal computers
• Responsible for keeping external hard drives
• Security: passwords and key access to lab
http://d7.library.gatech.edu/research-data/home
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Sharing• Sharing via Dropbox™ and
Google Drive™
• Data from previous graduate students passed down through the use of CDs
http://www.creativewomenscircle.com.au/social-media-using-dropbox/
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Access
• Once published: public access to data
• Anyone can ask for reagents and animals
• Fish genetic lines are submitted to international database for zebrafish
http://www.ru.nl/library/services/research/researchdata/finding/
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• Nature
• Science
• PubMed
• Any one can ask for reagents, antibodies, enzymes, and/or fish that
• OSU: get anything pre-publication
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Zebrafish Resources
http://www.nih.gov/science/models/zebrafish/
http://zfin.org/
http://www.zf-health.org/
http://zgc.nci.nih.gov/
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Preservation• Archive: duration of the
grant
• NIH: 3 years to have access to it
https://grants.nih.gov/grants/policy/data_sharing/data_sharing_guidance.htm
NIH Data Sharing Policy and Implementation Guidance
http://wiki.dpconline.org/
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Research Case Study
Model organism neuroscience research lab
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Case Study Example
• Teaching Points
• Case Narrative
• Discussion Questions
http://phys.org/news/2011-02-why-do-we-sleep.html
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DMPModel organism
neuroscience research lab
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New England Collaborative Data Management Curriculum
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Data Management Plan
• Breakout Activity
• Use SDMP
• Create DMP
http://www.ru.nl/library/services/research/researchdata/dmp/
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Creating a Case Study
• Background Research
• Data Interview
• Case Narrative
• Discussion Questions
• Data Management Plan
http://amitkaps.com/bring-the-right-brain-at-work/
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Develop Your Own
• Use the case study methodology
• Understand the process and steps involved
• Follow this format: teaching points, narrative and discussion questions
• NECDMC research case
http://www.dtpli.vic.gov.au/planning/urban-design-and-development/design-case-studies
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Next Up…• Research Case Study
• Identify Data Management Needs
• Create Data Management Plan
• Teaching with NECDMC
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ReferencesFerguson (2012) Lurking in the Lab: Analysis of Data from Molecular Biology Laboratory
Instruments: http://escholarship.umassmed.edu/jeslib/vol1/iss3/5/
The Beattie Lab at OSU, Department of Neuroscience:
https://u.osu.edu/beattie.24/
Ohio State University Neuroscience Graduate Program:
http://ngsp.osu.edu/
Ohio State University Library:
http://library.osu.edu/staff/admin-plus/AdminPlusNotes_20110427.pdf
Johns Hopkins University Data Management Services:
http://dmp.data.jhu.edu/sites/default/files/Questionnaire.doc
National Institute of Environmental Health Sciences:
http://www.niehs.nih.gov/news/newsletter/2013/9/science-ntptalk/
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Developing a Research
Case StudyJulie Goldman, MLIS@jgolds2Library FellowLamar Soutter LibraryUMass Medical School
New England Collaborative Data
Management Curriculum
Scientific Research Data Management by Lamar Soutter Library, University of Massachusetts Medical School is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License
#teach-ingNECDMC