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Developing a Research
Case Study
Julie Goldman, MLIS
@jgolds2
Library Fellow
Lamar Soutter Library
UMass Medical School
Ne...
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 Busines...
Case Study Method
• Present problems
• Focus on a topic or
“teachable moment”
• Prepare users
http://blog.tradeshift.com/t...
Creating a Case Study
• Background Research
• Data Interview
• Case Narrative
• Discussion Questions
• Data Management Pla...
Research Life Cycle
http://data.library.virginia.edu/data-management/
DownstreamUpstream
New England Collaborative
Data Management Curriculum
Background
Model organism
neuroscience research lab
Researcher
• Third year graduate student
• Areas of focus : neurotrauma,
neurological disorders, gene therapy
https://ngsp...
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
us...
Data Interview
Model organism
neuroscience research lab
Data Interview
• Draw out information about project
• Questions focus on the data story
https://www.youtube.com/user/neals...
Tips and Reminders
• Do your homework
• Use follow-up questions
• Make the meeting about the
researcher not the library
• ...
Interview Instrument
http://dmp.data.jhu.edu/sites/default/files/Questionnaire.doc
JHU Data Management Services of
the She...
Initial Interview
1. As a research focused university
what kind of NIH grant do you have?
2. What other funding sources do...
Follow up Email
1. What lab instruments you use?
2. You mentioned .TIFF files, what
other file formats do these
instrument...
Second Interview
1. When you collect data about your fish,
how do you make sure that information is
linked to that fish?
2...
Final Suggestions
http://neilpatel.com/2015/05/12/how-to-attract-clients-as-a-part-time-content-marketer/
Case Narrative
Model organism
neuroscience research lab
Research
• Motoneuron diseases SMA and ALS
• Genetic and molecular cues
• Genetic models of zebrafish
• Research since 199...
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...
SMA
• Protein knockdown technology
• What function of SMN leads to motoneuron dysfunction
• Cell death in SMA caused by mo...
ALS
• Amyotrophic lateral sclerosis
or Lou Gehrig’s disease
• Muscle weakness and atrophy
• Defect on chromosome 21
which ...
ALS
• Genetic mutation :
SOD1 gene to
generate SOD G93A
and G85R transgenic
zebrafish
• Drug screens with
zebrafish larva
...
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.ga...
http://biobide.es
Zebrafish Facility
• Facility supports three labs
• 1200 sq ft
• 1234 tanks & 40,000 fish
• Tank labels : research’s name,...
General Lab Work
• PCR : polymerase chain reaction
• Agarose gel electrophoresis: separate DNA
• Western Blot : detect pro...
Equipment and Products
• Bio-Rad (RT)-qPCR : Microsoft™ Excel™ files
• Thermo Scientific™ NanoDrop™ : Excel™ files
• Weste...
Programs
• SPSS® : statistics software
• ImageJ™ : public domain, Java™-based image
processing program developed by NIH
• ...
Data Flow
• Data produced on old computers attached to equipment
• Transferred to the big (old) lab computer for processin...
File Naming Conventions
• No standardization
• Personal
• Become more professional when sent
to the PI and goes to publica...
Lab Notebooks
• Paper lab notebooks for non-digital data
• Personal data keeping techniques
• Records detailed description...
Backup and Security
• Use personal computers
• Responsible for keeping
external hard drives
• Security: passwords and
key ...
Sharing
• Sharing via Dropbox™ and Google Drive™
• Data from previous graduate students
passed down through the use of CDs...
Access
• Once published: public access to data
• Anyone can ask for reagents and animals
• Fish genetic lines are submitte...
• Nature
• Science
• PubMed
• Any one can ask for reagents,
antibodies, enzymes, and/or fish that
• OSU: get anything pre-...
Zebrafish Resources
http://www.nih.gov/science/models/zebrafish/
http://zfin.org/
http://www.zf-health.org/
http://zgc.nci...
Preservation
• Archive: duration of the grant
• NIH: 3 years to have access to it
https://grants.nih.gov/grants/policy/dat...
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....
DMP
Model 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/d...
Creating a Case Study
• Background Research
• Data Interview
• Case Narrative
• Discussion Questions
• Data Management Pla...
Develop Your Own
• Use the case study methodology
• Understand the process and steps involved
• Follow this format: teachi...
Next Up…
• Research Case Study
• Identify Data Management Needs
• Create Data Management Plan
• Teaching with NECDMC
References
Ferguson (2012) Lurking in the Lab: Analysis of Data from Molecular Biology Laboratory Instruments:
http://esch...
Developing a Research
Case Study
Julie Goldman, MLIS
@jgolds2
Library Fellow
Lamar Soutter Library
UMass Medical School
Ne...
Developing a Research Case Study
Developing a Research Case Study
Developing a Research Case Study
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Developing a Research Case Study

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A large part of the NECDMC curriculum uses case studies to teach best practices in data management for many different science disciplines. This presentation goes through the methodology of a case study, how to develop a case study, and presents an actual example of a research case study.

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Developing a Research Case Study

  1. 1. Developing a Research Case Study Julie Goldman, MLIS @jgolds2 Library Fellow Lamar Soutter Library UMass 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 #teachingNECDMC
  2. 2. Outline • Case Study Methodology • Developing Case Study • NECDMC Research Case Study • Teaching NECDMC
  3. 3. Teaching Case for Data Management
  4. 4. “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/
  5. 5. Case Study Method • Present problems • Focus on a topic or “teachable moment” • Prepare users http://blog.tradeshift.com/tradeshift-case-study-broadway-design-company/
  6. 6. Creating a Case Study • Background Research • Data Interview • Case Narrative • Discussion Questions • Data Management Plan http://amitkaps.com/bring-the-right-brain-at-work/
  7. 7. Research Life Cycle http://data.library.virginia.edu/data-management/ DownstreamUpstream
  8. 8. New England Collaborative Data Management Curriculum
  9. 9. Background Model organism neuroscience research lab
  10. 10. Researcher • Third year graduate student • Areas of focus : neurotrauma, neurological disorders, gene therapy https://ngsp.osu.edu/
  11. 11. http://medicine.osu.edu/neuroscience/Pages/index.aspxhttp://columbusneighborhoods.org/ Ohio State University
  12. 12. https://u.osu.edu/beattie.24/ Beattie Lab
  13. 13. Using Zebrafish as a Model System for Studying Motor Axon Guidance & Motoneuron Disease
  14. 14. 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?
  15. 15. Data Interview Model organism neuroscience research lab
  16. 16. Data Interview • Draw out information about project • Questions focus on the data story https://www.youtube.com/user/nealsciencebootcamp/feed
  17. 17. 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/
  18. 18. 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
  19. 19. Initial Interview 1. 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?
  20. 20. Follow up Email 1. 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?
  21. 21. Second Interview 1. 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?
  22. 22. Final Suggestions http://neilpatel.com/2015/05/12/how-to-attract-clients-as-a-part-time-content-marketer/
  23. 23. Case Narrative Model organism neuroscience research lab
  24. 24. Research • Motoneuron diseases SMA and ALS • Genetic and molecular cues • Genetic models of zebrafish • Research since 1996 https://science.nichd.nih.gov/confluence/display/zfig/Home
  25. 25. Funding • NIH grant: research project grant (r01) • Other private funding
  26. 26. 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
  27. 27. 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
  28. 28. 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
  29. 29. 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
  30. 30. Motor Axons http://zfin.org/ZDB-FIG-130516-36
  31. 31. 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
  32. 32. http://biobide.es
  33. 33. 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
  34. 34. 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
  35. 35. 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™
  36. 36. Programs • SPSS® : statistics software • ImageJ™ : public domain, Java™-based image processing program developed by NIH • Adobe® Photoshop® : photo editing • Microsoft® Office : Word™, Excel™, PowerPoint™
  37. 37. 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 computers www.labx.com https://u.osu.edu/beattie.24/
  38. 38. 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
  39. 39. 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
  40. 40. Backup and Security • Use personal computers • Responsible for keeping external hard drives • Security: passwords and key access to labhttp://d7.library.gatech.edu/research-data/home
  41. 41. 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/
  42. 42. 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/
  43. 43. • Nature • Science • PubMed • Any one can ask for reagents, antibodies, enzymes, and/or fish that • OSU: get anything pre-publication
  44. 44. Zebrafish Resources http://www.nih.gov/science/models/zebrafish/ http://zfin.org/ http://www.zf-health.org/ http://zgc.nci.nih.gov/
  45. 45. 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/
  46. 46. Research Case Study Model organism neuroscience research lab
  47. 47. Case Study Example • Teaching Points • Case Narrative • Discussion Questions http://phys.org/news/2011-02-why-do-we-sleep.html
  48. 48. DMP Model organism neuroscience research lab
  49. 49. New England Collaborative Data Management Curriculum
  50. 50. Data Management Plan • Breakout Activity • Use SDMP • Create DMP http://www.ru.nl/library/services/research/researchdata/dmp/
  51. 51. Creating a Case Study • Background Research • Data Interview • Case Narrative • Discussion Questions • Data Management Plan http://amitkaps.com/bring-the-right-brain-at-work/
  52. 52. 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
  53. 53. Next Up… • Research Case Study • Identify Data Management Needs • Create Data Management Plan • Teaching with NECDMC
  54. 54. References Ferguson (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/
  55. 55. Developing a Research Case Study Julie Goldman, MLIS @jgolds2 Library Fellow Lamar Soutter Library UMass 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 #teachingNECDMC

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