RESEARCH NOTEBOOK, FILES

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1 PERCSS Program for the Ethical and Responsible Conduct of Science and Scholarship DATA MANAGEMENT: KEEPING A RESEARCH NOTEBOOK, FILES AND RELATED ISSUES Steven Brody, MD Department of Internal Medicine Washington University School of Medicine 1

2 Good record keeping promotes accountability and integrity it in research Necessary for data analysis, publication, collaboration, peer review among others. Necessary to support intellectual ectua property claims. Can defend you against false allegations of research misconduct. 2

3 Good record keeping, continued Important for the care of human subjects. necessary for members of your group or any other researcher e to be able to duplicate your work, when needed. Required by NIH and other granting institutions to meet policies and standards for the conduct of good science 3

4 The lab notebook: Overview It is a record of both physical and mental activity. Good records are complete, accurate and understandable dab e to others. Each member of the research team is responsible for his/her records. The PI has the final responsibility for the laboratory records. 4

5 Curie s Notebook Ca

6 Prof. X s Notebook Ca

7 What is a Lab Notebook? Complete record of procedures, reagents, data, and thoughts to pass on to other researchers Why experiments were initiated, how performed, and results, comments Place to compile data/charts/photos/ideas Place of clues, to troubleshoot problems Place to observe whole picture and think Legal document, to prove patents Defense against accusations of fraud or lawsuits 7

8 TpeandFomat Type Format Ultimately dictated by your PI Type Advantages Drawbacks Bound book (stitched) No lost sheets Proof against Fraud Entered as done No logical order Duplicate Bound Book (yellow sheets) Double record. Easy copies Diff. To Read. Not true duplicate Loose Leaf Order by expts Lost sheets (folders/notebooks) Easy recording Authenticity prob. Computer Easy to read Lost data (ELN) Easy calculations Authenticity prob 8

9 Physical Characteristics of a Good Notebook Large >= 8.5x11 at least Bound (stitched) pages to ensure integrity Numbered pages Number the book White gridded Acid free paper p (30 years) Name Dates PI Book No. Duplicate pages (differing opinions) Written in Pen (gel pens are good). Felt tip is bad. 9

10 What pen is best? Roller tip in this test: 10

11 Preparing a New Lab Notebook Create a table of contents in the first 2 pages List experiments by: Title Date Lab Book Number/Page Number 11

12 For Every Experiment, Record: Start Date: on all pages Title Why: Brief statement of purpose, rationale How: Description/protocol with ref to origin Calculations, concentrations, dilutions, etc., Include sketches, diagrams What Happened: All (protocol changes; on floor, kicked) Taped/stabled in Information Data Associated information: Samples, storage location, Data Files, Disks, Images What It means: Interpretation (and comments) What s Next 12

13 Attaching materials Computer generated data Photographic data Printed graphs (make as you go) Datasheet templates Product labels Who provided plasmids, etc. Notes (or pasted copies) of discussions, conversations, s, readings related to exp t design or goals Archive locations of plasmids, probes, etc. X-rays and other large items may be kept in a separate folder if they don t fit in the lab notebook. 13

14 Referencing attached data and samples Name Expt/Dates Book#/page# Name Expt/Dates Book#/page# Name Expt/Date es Book#/pag ge# Label Notebooks, Boxes with Lab Book Book#/Page# 14

15 Also record Discussions with others (time, names, issues). Good for future credit. Correspondence with colleagues (phone calls, s) mails). Names of individuals who have played any role in your research. Technicians in core laboratories are also important 15

16 Date Title Times Data Calculations Interpretation Future studies Correction 16 Taken from the online Linus Pauling Research Notebooks,

17 Frequently entl Forgotten Info Serum lot number Antibody titer Other people involved Centrifuge model, speed, temp Incubation time # washes Tube size and type Unexpected delays Growth medium used Buffer ph Calculations l Initial # cells Age/passage culture % Gel Growth stage Bact. Condition of cells used 17

18 The importance of timing Always record, update, review Record as you go Input paper towel and post-it info ASAP! At the LATEST, insert data the next day! Do a weekly checkup 1 hour to review Make sure everything is attached securely, all summaries written, future directions written, record in table of contents Retractions have been associated with untimely record keeping 18

19 If you make a mistake They should be marked through with a single line and a full explanation of the error provided. Never e obliterate mistakes with ink or cover them with corrective fluid. To a casual observer these actions may suggest improper reasons. 19

20 Characteristics Helpful for Filing a Patent t Patents on intellectual property p are awarded not by the first to file, but first to invent first to record! Sign and date each entry Have an independent d witness sign and date each entry Witness cannot be co-inventor and must understand data Do not change entries (make a new entry and cross-reference to prior entry) Use past tense Never remove original pages or attachments Record all discussions/meetings/ideas i /id relevant to the project Record as much detail as possible

21 Paper vs. Electronic Lab Notebook: Paper notebooks have limited capacity Raw data is massive Data capture is archaic Raw printouts t can no longer be stored Data formats are restricted 2-D gels, photomicrographs Record-keeping is tedious Repetitive protocols lost, require manual entries Searching is difficult Context of work is often lost No connection to other people, projects, labs Paper records no longer legally required Electronic records are legal 21

22 Data Flow in the Laboratory Lab Automation & Robotics Chromatography Data Systems Data Analysis Equipment Interfacing Data Warehousing Electronic Laboratory Notebooks Laboratory Information Laboratory Management Data Instruments t Systems (LIMS) Miningi Data Acquisition Information Processing Knowledge Management 22

23 Collaborative ati ELN clinician research specialist nurse scientist data encoder writer lab technician statistician lab manager 23

24 Demands for ELN: 21 CFR part 11* FDA rule initiated August 1997 Sets standards for electronic submission Electronic records Thoroughly validated Automatic audit trails Results can be recreated Electronic signatures Unique identity Linked to e-record No grandfather clause *Code of Federal regulations Title 21, Part 11, Electronic Signatures 24

25 Software for ELN 25

26 How long to keep notebooks and records? NIH policy mandates 3 years after the end of the project (grant funding period) FDA policy mandates 10 years after use Patent t t policy mandates 23 years after issue of the patent. The organization with the longest policy has priority 26

27 Who owns notebooks and data? When NIH awards a research grant to a university, any and all data collected as part of that funded project are owned by the grantee institution. Data books of all investigators (PI, postdocs, grad students, ts, technicians) c are the property of the institution. 27

28 Who owns notebooks and data? The principal investigator is the steward. If the PI resigns or moves to another institution: tut Equipment and all data belong to the initial institution. Permission can be obtained to transfer the award, equipment and data. 28

29 Research data do not include: Preliminary analyses Drafts of papers Plans for future research Peer reviews Physical objects (samples, tapes) Trade secrets or commercial information 29

30 Applicability of rules Data produced with Federal support that are cited publicly and officially. Data collected by institutions of higher education, hospitals, and non-profit institutions Does not apply to state and local l govt Does not apply to commercial organizations Applies to new and competing awards made after the effective date of the amendment (11/8/1999) 30

31 Public Access to Data The Office of Management and Budget (OMB) revised the regulations regarding public access to experimental data in 1999 The public can obtain access to experimental data through the Freedom of Information Act (FOIA) 31

32 What happens if the PI refuses to comply? This is view as a material failure to comply with the terms of the award NIH would initiate appropriate enforcement e acto action This could include withholding future support to the institution 32

33 Consequences of Research Misconduct Debarment from eligibility to receive Federal funds Prohibition from service on advisory committees, peer review committees, or as consultants Certification of information sources that is forwarded by the institution Certification of data by the institution Supervision by the institution Submission of a correction or retraction of a published article 33

34 Best practice principles for leaders of research groups: Set standards and provide examples of good record keeping practices for the group Provide tools for good record keeping Provide training for the group and review records Clarify data and research ownership and access rights 34

35 Institutional Best Practice Principles: WUSTL It is the policy of WUSTL to publish research results and to foster the use of University inventions, discoveries and and other works for the common good. Intellectual Property Policy 35

36 With care and attention to our work we should avoid RETRACTION We wish to retract our report (Science 2004; 303, 371) in which h we reported that β-n-acetylglucosamine-serine can be biosynthetically ti incorporated at a defined d site in myoglobin in E. coli. 36

37 RETRACTION Regrettably, through no fault of the authors, the lab notebooks are no longer available to replicate the original experimental conditions, and we are unable to introduce this amino acid into myoglobin with the information and reagents currently in hand Z. Zhang et al., UT at Austin. Science 2009; 326,

38 Notebook Ethics "Many people say that it is the intellect which makes a great scientist. They are wrong: it is character." -- Albert Einstein 38

39 Research Integrity The NIH Office of Research Integrity defines misconduct in science as: Fabrication, falsification, plagiarism, a or other practices that seriously deviate from those that are commonly accepted within the scientific community. This does not include honest error or honest differences in interpretations t ti or judgments of data. (Federal Register 54: , Aug 8, 1989) The integrity it of research depends d on accurate, detailed, organized, complete, and accessible data Office of Research Integrity 39

40 Tips to Preserve e Data Integrity Never, e ever, e remove e a page Fill consecutive pages Cross out unused parts of pages Record all info as accurately as possible. Do NOT omit any result, no matter how odd. Cross out mistakes lightly (might need to recover) Write legibly Put a full date (international date problems ) with month spelled out. 40

41 More Helpful l Tips The institution owns your notebook Do NOT remove your notebook from the lab (unless this is an acceptable lab practice) You may get permission to take copies at graduation, but do not take original pages Do NOT read another person s notebook without permission (even the PI won t look at advanced researcher s notebooks secretly). Should be kept for at least 5 years 41

42 Data manipulation Data may be excluded from the experimental results only if you have a sound reason to do so! Mother Nature 42

43 misleading presentation of data from data management errors Number of animals vs. number of determinations Non-standard normalization Not showing entire gel Varying exposures of images INSIST ON VIEWING THE RAW DATA! 43

44 As photographed Brightness- Contrast Adjustment 44

45 As photographed Erasing 45

46 The Journal of Cell Biology: revokes the acceptance of about 1% of its papers due to inappropriate image manipulation 25% of accepted papers p have at least 1 figure with undocumented manipulation If you misrepresent your data you are deceiving people. Rossner, M. (2006). The Scientist 20:24 :

47 47

48 What can I do? Nature, instructions to authors (2006) List all image acquisition and processing tools and software Document key image-gathering g g setting and manipulations in the Supplemental materials Clearly demarcate borders between images collected at different times Avoid use of touch up tools or deliberately obscuring parts of an image Processing is acceptable only if applied across the entire image Be prepared p to deliver the original, unprocessed images to the editor 48

49 Slide sources: Gail P. Taylor PhD and Angelina Hoefle, UT San Antonio Carmen S. Dence MS, Washington University Edward d Krug PhD Medical College of South Carolina Douglas Perry PhD, IU School of Informatics 49

50 Acknowledgements and Referencesences Kathy Barker, At the Bench: A laboratory Navigator. Cold Spring Harbor Laboratory ypress Guidelines for Keeping a Laboratory Record. David Caprette, Rice University. Guidelines for Keeping a Laboratory Notebook. Colin Purrington, Swarthmore Univ. Laboratory Record Keeping. Todd E. Garabedian, Nature Biotechnology v. 15 (August 1997) pp com/gi/dynamic/offsite htm Office of Research Integrity, U.S. Dept. of Health and Human Services Responsible Conduct of Research Online Study Guide. Julie Simpson, University it of New Hampshire Francis L. Macrina, Scientific Integrity: An Introductory Text with Cases. ASM Press Academic Research Record-keeping: Best Practices for Individuals, Group Leaders and Institutions. Academic Med. 81, 42-47; 2006, 50

51 Questions 51

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