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

Outline

• Case Study Methodology

• Developing Case Study

• NECDMC Research Case Study

• Teaching NECDMC

Teaching Case for Data

Management

“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/

Case Study Method

• Present problems

• Focus on a topic or “teachable moment”

• Prepare users http://blog.tradeshift.com/tradeshift-case-study-broadway-design-company/

Creating a Case Study

• Background Research

• Data Interview

• Case Narrative

• Discussion Questions

• Data Management Plan

http://amitkaps.com/bring-the-right-brain-at-work/

Research Life Cycle

http://data.library.virginia.edu/data-management/

Down-stream

Upstream

New England Collaborative Data Management Curriculum

BackgroundModel organism

neuroscience research lab

Researcher

• Third year graduate student

• Areas of focus : neurotrauma, neurological disorders, gene therapy

https://ngsp.osu.edu/

http://medicine.osu.edu/neuroscience/Pages/index.aspxhttp://columbusneighborhoods.org/

Ohio State University

https://u.osu.edu/beattie.24/

Beattie Lab

Using Zebrafish as a Model System for Studying Motor

Axon Guidance & Motoneuron Disease

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?

Data InterviewModel organism

neuroscience research lab

Data Interview• Draw out information about project

• Questions focus on the data story

https://www.youtube.com/user/nealsciencebootcamp/feed

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/

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

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?

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?

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?

Final Suggestions

http://neilpatel.com/2015/05/12/how-to-attract-clients-as-a-part-time-content-marketer/

Case NarrativeModel organism

neuroscience research lab

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

Funding • NIH grant:

research project grant (r01)

• Other private funding

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

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

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

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

Motor Axons

http://zfin.org/ZDB-FIG-130516-36

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

http://biobide.es

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

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

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™

Programs• SPSS® : statistics software

• ImageJ™ : public domain, Java™-based image processing program developed by NIH

• Adobe® Photoshop® : photo editing

• Microsoft® Office : Word™, Excel™,

PowerPoint™

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/

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

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

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

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/

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/

• Nature

• Science

• PubMed

• Any one can ask for reagents, antibodies, enzymes, and/or fish that

• OSU: get anything pre-publication

Zebrafish Resources

http://www.nih.gov/science/models/zebrafish/

http://zfin.org/

http://www.zf-health.org/

http://zgc.nci.nih.gov/

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/

Research Case Study

Model organism neuroscience research lab

Case Study Example

• Teaching Points

• Case Narrative

• Discussion Questions

http://phys.org/news/2011-02-why-do-we-sleep.html

DMPModel organism

neuroscience research lab

New England Collaborative Data Management Curriculum

Data Management Plan

• Breakout Activity

• Use SDMP

• Create DMP

http://www.ru.nl/library/services/research/researchdata/dmp/

Creating a Case Study

• Background Research

• Data Interview

• Case Narrative

• Discussion Questions

• Data Management Plan

http://amitkaps.com/bring-the-right-brain-at-work/

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

Next Up…• Research Case Study

• Identify Data Management Needs

• Create Data Management Plan

• Teaching with NECDMC

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/

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