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. 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. Outline • Case Study Methodology • Developing Case Study • NECDMC Research Case Study • Teaching NECDMC
- 3. Teaching Case for Data Management
- 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. 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. Creating a Case Study • Background Research • Data Interview • Case Narrative • Discussion Questions • Data Management Plan http://amitkaps.com/bring-the-right-brain-at-work/
- 8. New England Collaborative Data Management Curriculum
- 10. Researcher • Third year graduate student • Areas of focus : neurotrauma, neurological disorders, gene therapy https://ngsp.osu.edu/
- 13. Using Zebrafish as a Model System for Studying Motor Axon Guidance & Motoneuron Disease
- 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. Data Interview Model organism neuroscience research lab
- 16. Data Interview • Draw out information about project • Questions focus on the data story https://www.youtube.com/user/nealsciencebootcamp/feed
- 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. 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. 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. 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. 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?
- 23. Case Narrative Model organism neuroscience research lab
- 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. Funding • NIH grant: research project grant (r01) • Other private funding
- 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. 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. 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. 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
- 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. • Nature • Science • PubMed • Any one can ask for reagents, antibodies, enzymes, and/or fish that • OSU: get anything pre-publication
- 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. Research Case Study Model organism neuroscience research lab
- 47. Case Study Example • Teaching Points • Case Narrative • Discussion Questions http://phys.org/news/2011-02-why-do-we-sleep.html
- 49. New England Collaborative Data Management Curriculum
- 53. Data Management Plan • Breakout Activity • Use SDMP • Create DMP http://www.ru.nl/library/services/research/researchdata/dmp/
- 54. Creating a Case Study • Background Research • Data Interview • Case Narrative • Discussion Questions • Data Management Plan http://amitkaps.com/bring-the-right-brain-at-work/
- 55. 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
- 56. Next Up… • Research Case Study • Identify Data Management Needs • Create Data Management Plan • Teaching with NECDMC
- 57. 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/
- 58. 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
Notas del editor
- Current library fellow Graduate of Simmons – took scientific research data management taught by UMMS Contributed to the curriculum – biological lab case study Joined NECDMC teaching team
- Methodology – what is it and how it works for NECMDC Developing – background, interview, narrative, discussion questions, DMP Case Study – zebrafish developed case study which will be used for the breakout activity Teaching – Donna will then expand on the case study method and how it relates to data management education and teaching using NCDMC case studies and materials
- A large part of the NECDMC curriculum uses case studies to teach best practices in data management for many different science disciplines
- Used for education in many areas – science, business, law
- Present problems users must attempt to solve within acceptable practices Teachable moment useful for educating others highlights specific data management practices or needs of a specific discipline or type of research builds an understanding of scientific research Prepare users for similar situations in the future
- First step is to identify the environment: background information on institution, researcher, research project (who, what, when, where, why) Hold a data interview with a researcher Write narrative of research project NECMDC case studies include the narrative, questions and highlight data management issues Develop discussion questions Craft a mock DMP
- Typical research lifecycle through a project – data flow in the in center Librarians typically downstream – collecting books/journals/datasets – data discovery/archiving Should be more involved upstream at the iteration/project start – project planning with data collection/organization/description
- Case study example in NECDMC
- Research project using model organisms in a neuroscience research lab
- My researcher (at the time) was a graduate student in the neuroscience program at OS Specifically interested in neurological disorders and gene therapy
- Research lab at the Ohio State University
- The Beattie Lab at OS Use zebrafish as model organism for research
- Using zebrafish as a model organism for studying motor axons in motoneuron diseases
- Research Questions: Biological basis of SMA Modeling ALS in zebrafish for drug and genetic screening Identifying genes for motor axon growth
- Go through the steps in setting up, conducting and analyzing a data interview
- Use this information so the librarian can address data lifecycle issues and begin to implement a data management plan Acquire as much information as possible from the researcher Questions on data story, purpose, and life span Great resource from New England Science Boot Camp – videos featuring UMMS librarians discussing “how to talk to researchers”
- Homework on researcher and their research – impress them with your knowledge Follow up during and after the interview – ask more questions to fully understand the project workflow Make the meeting about the researcher – not about the library and what the library can do (yet) Establishes relationships with institutional researchers Researchers will see that librarians are interested in the research process and understanding research needs/issues/challenges Associates the library with data – once the librarian understands the research project – make recommendations more how the library can help with the data needs…
- Create an interview instrument – lots of options for templates Digital Curation Centre’s Checklist for a Data Management Plan Purdue Data Information Literacy Interview Instruments University of Virginia Data Interview Initiative John Hopkins
- In addition to using a template – create own questions related to specific researcher/research One question at a time Avoid yes/no questions – open ended (#12 & 17 bad) Limit questions to CORE aspects (I might have had too many questions…) Set up interview – I asked for 30 minutes of her time to talk about her research Skype interview and recorded Use follow-up questions – #10 (You have a lot of digital files being created, what file formats are those generated in? → Is there non-digital data?) Offer check-ins/copy of interview transcript
- More follow up – multiple meetings I sent very specific questions via email
- More follow-up Make sure you fully understand the research – shows your dedication to the project but do not become overbearing/disruptive Questions really tailored to the research projects
- This is what I learned: could have done more investigation beforehand! Who what when where why
- Construct narrative from the data interview transcript Telling the story of the research project and the research data lifecycle Include as many details as possible and point out missing pieces/challenges researcher expresses Now share my research case…
- Neuroscience research lab Investigating the biological basis of motoneuron diseases SMA and ALS Genetic and molecular cues that guide motor axons to their target muscle Using zebrafish as a genetic model for these diseases (click) Research project since 1996 – multiple grants
- NIH ro1 – award made to support a discrete, specified, circumscribed project Government is strict about data keeping and can ask to see data and notebooks any time NIH has the legal right to audit and examine record relevant to any research grant award Private funding: SMA & ALA families, foundations/organizations and private companies
- Overview of SMA helps to understand the research experiments and data collected Low levels of “survival of motor neuron” (SMN) protein leads to muscle atrophy and weakness Occurs early in life - is the leading genetic cause of death in infants and toddlers
- How zebrafish serve as genetic model of SMA Protein knockdown technology in zebrafish development Cell death in SMA caused by motor neuron defects during early development Use scoring system on florescent microscope images to determine conditions and development of motor neurons (severe, moderate, mild, no defect)
- Overview of ALS to understand experiments and data collection Muscle weakness and atrophy throughout the body due to degeneration of the upper and lower motor neurons Superoxide disumates 1, soluble (or SOD1) is a gene responsible for the enzyme on chromosome 21 that protects the body from free radicals Free radical accumulation can damage DNA and proteins produced within cells
- Looking at 2 specific gene mutations – correcting the effects of the mutant SOD1 gene Use zebrafish larva to understand defects in the early stages of neuron development
- Example of zebrafish microscopy images: Optineurin (OPTN) is a 577 amino acid protein of versatile functions which interacts with a variety of proteins Mutations in OPTN gene have been associated with ALS OPTN interacts with aggregating proteins (SOD1 and G93A) involved in ALS OPTN depletion in zebrafish causes motor axonopathy and mutant SOD1 increases motor axonopathy Images shows: Zebrafish injected with OPTN-specific translation blocking (OPTN ATG-AMO) morpholino showed a phenotype (curved tail indicated by the arrow) This research project is just focusing on SOD1 The overexpressing SOD1 G93A at 48 hours after fertilization in comparison with non-injected zebrafish or zebrafish injected with control morpholino (control AMO) Looking at the interaction of these proteins in motor axon development – causing axonopathy or axon degradation – curved spinal cord and loss of mobility
- From the previous image you can see that zebrafish larva are easy to use as an experimental model organism – easy to grow and see through Used for many kids of research
- Why zebrafish? Model established Genome fully sequenced Well-understood, easily observable Testable developmental behaviors Rapid embryonic development Large, robust, transparent embryos Develop outside mother Similar to mammalian models and humans
- Important factor in this research project is the zebrafish facility Facility supports three research labs – 10-12 people using fish for different projects Each person has their own fish – labeled accordingly Common stock for breeding and controls Facility manager over sees breeding, facility and IACUC compliance (institutional animal care and use control) Google Drive database for logging information and updates on fish/experiments – used to have a paper log book in the facility
- Researcher described “general lab work”: PCR: polymerase chain reaction amplifies copies of a particular DNA sequence Running agarose gel electrophoresis - DNA manipulation/separation Western blots to detect protein levels Microscope imaging
- Bio-Rad (RT)-qPCR machine – amplifies a single or a few copies of a piece of DNA across several orders of magnitude, produce Microsoft™ Excel™ files Thermo Scientific™ NanoDrop™ spectrophotometer – measures light transmittance or reflection intensity as a function of the light source wavelength Western blot images developed are scanned Agarose gels are read on a gel box and images are scanned and printed for densitometry quantification, the measure of light absorption through the medium Microscopes produce Tagged Image File Format (TIFF) and JPEG (.jpeg) files The team uses Excel™ and SPSS™ for data analysis
- SPSS™ statistical software for data analysis Edits image files in ImageJ™ - Java™-based image processing program developed by the NIH - or Adobe™ Photoshop™ Uses Portable Document Format (PDF) (.pdf) and PowerPoint™ (.pptx) files for figures and publications.
- Typical data flow involves analysis of direct microscope images of manipulated fish samples, or gel images of DNA/protein analysis These image files are produced on computers attached to the lab equipment Files are analyzed on a computer and/or sent to the experimenter’s personal computer The researcher always prints out a hard copy of any images and pastes them in her paper lab notebook
- Lab does not have any standardized way to document its data No naming conventions for saving and locating documents and images No data dictionary Files usually just involve the person’s name and a title or description meaningful to that person These files are re-named for the PI and/or publication
- Pastes hard copy images (gels, microscope) in notebook Graduate student feels her notebook is comprehensible and easy to follow/better than post doc
- Team uses their personal computers for lab work She feels each person is responsible for his or her own data management She backs up the lab files on her computer to an external hard drive Security: passwords and key access to building and lab
- When the graduate student began working in the lab - given CDs with pervious data CDs containing images and data analysis Now the lab team shares its data with each other using Google Drive and Dropbox on university server Ultimately PI: responsible for data
- Graduate student feels she can get any data she needs pre-publication The graduate student feels that once the research is published, then anyone who wants it has access to the relevant data in the article Anyone can ask for reagents and animals used in published study
- Places of publication – science/nature/pubmed Any one can ask for reagents, antibodies, enzymes, and/or fish that were used in any published study
- Share and use data via repositories that house data on genetically modified zebrafish ZFIN – NIH-funded zebrafish model organism database Zebrafish Gene Collection (ZGC) – NIH initiative supports the production of cDNA libraries, clones and sequences of expressed genes for zebrafish – publicly accessible to the biomedical research community – all ZGC sequences are deposited in GenBan ZF-HEALTH – is a Large-scale Integrating Project funded by the European Commission
- Publications are considered the primary “electronic” form of data conservation in her lab At the time – NIH’s Data Sharing Policy – no formal data management plan beyond sharing Expected to archive for the duration of the project/grant as the NIH could ask for data/lab notebooks/ect
- Case study on site Teaching points Case narrative Discussion Questions
- Teaching points – integrate the data story into the simplified data management plan & highlight where the researcher is doing something well, not doing something, or doing something that is not of best practice Narrative – overview of research project (background, researcher) & data flow (collection, storage, sharing, preservation) Discussion questions – highlight the data management topics and needs within a research case, help when teaching with the case study, prompt people to identify the data flow within a project, understand the components of a SDMP and what areas librarians can help researchers
- Case study example in NECDMC
- Breakout activity after lunch Create a data management plan using the case study (case narrative, teaching points, discussion questions) and the SDMP that Donna will expand on in her presentation
- First step is to identify the environment: background information on institution, researcher, research project (who, what, when, where, why) Hold a data interview with a researcher Write narrative Develop discussion questions Craft a mock DMP NECMDC case studies include the narrative, questions and highlight data management issues
- Now that you have the methodology for why case studies are useful, and the steps to create one – create your own As you can see this case is not long Go through the process –identify a researcher at your institution or other place, understand the institution or environment, conduct an interview, create a narrative, create discussion questions to highlight the data management needs and challenges We can add your research case to our list of examples on the NECDMC site – we are always looking for new areas of science and disciplines
- After the research story and understanding the data flow throughout the project… Librarians can identify the data management flaws/challenges and needs Make recommendations for fixing/avoiding problems Use the Simplified Data Management Plan to develop a formalized plan for the research team to follow Donna will work though another research case study and talk about how to identify the data management needs, then how to develop a DMP, and how to teach with NECDMC…