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Keeping a lab notebook

Keeping an updated lab notebook is required to get a “Satisfactory” grade for your research units.

The main goal in keeping and maintaining a lab notebook is for you to be able to look at your look at your entries / data several years from now (which is probably around when we will be trying to publish this experiment) and know everything you need to know about the data because the associated notebook entry is complete.

Maintaining an up-to-date lab notebook is essential for:

  • Data integrity, -ensuring that all data records must be:are:
    • Attributable - Who recorded the measurement or performed the experiment? If changes were made to the data, who did it, when was it done, and why?
    • Legible - Will the data still be legible when you graduate in several years? What about 5 years later, or 15? Data must be permanently archived and readable in perpetuity - not just for the duration of the project.
    • Contemporaneous - Was the data collected at the time of the experiment? Data should include date and time stamps, leaving no room for ambiguity.
    • Original - Is the record an original or approved copy? Even if a paper printout is transcribed into electronic format, the original copy must be retained.
    • Accurate - Does the record reflect what was accurately measured? Workflows should be designed to eliminate any potential for data to be changed from its true value.

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  • Reproducibility, allowing others (and your future self) to makereplicate experiments based on detailed records.
  • Accountability, providing a transparent trail of research activities.

What should go into your ELN entries:

  • Start making dated entryentries into your electronic lab notebook (ELN) at elab.richhartman.com every day:

    • Even if you have nothing, just type "nothing new to report" or “just checked on the flies – they’re doing well!” in the dated description.
    • Record all info that you need to "perfectly" reconstruct data collection at any time in the future (years from now).
    • At the end, include a very brief plain English summary of the day’s events.

    The main goal is for you to be able to look at your look at your notebook entry / data several years from now (which is probably around when we will be trying to publish this experiment) and know everything you need to know about the data because the associated notebook entry is complete.

    An ELN like eLab allows lab notebook entries to be automated and customized… for example:
    • create customized Templates with specific Steps for common daily activities (Lit Review / Maintain Fly Colony / TBI experiment / Exercise protocols / Process EEG data / etc)
    • attach files (excel, pics, etc)
    • tag / link entries for easy searches / recall
    • schedule / reference lab Equipment ("tools"), Instruments ("things that provide a measurement of some sort"), and Expendables ("stuff that gets used up over time")
    • time stamp entries into an immutable worldwide blockchain (which may be important if you ever make an interesting "discovery")

    Please read through the User Documentation and start using it. Don't be afraid to try out the various features - as far as I know, you can't "break" anything :)

    • Note that the "model" for this ELN is not to have 1 entry that serves as your entire notebook, but rather that each time you do something lab-related, you make a separate time-stamped entry (ideally using predefined Templates).
    • Each individual entry is (unfortunately) called an "experiment" in eLab. If you click the "Create" button next to Experiment (in your Dashboard or in the upper tabs), that will bring you to a "generic" entry template with Goals, Procedures, and Results laid out already.
      • Note that you can change these as you see fit for each entry. If you click on the little Left Arrow on the side of the Create button you should see a list of Templates that I have made (feel free to modify / make more). You can also see them all and edit / make more under My Templates in your upper right profile icon.
    • Generally, try to use pre-defined templates - for example, one lab member’s entry ("experiment") might be a "Maintain fly colony" entry. When another lab member maintains their flies, the steps / procedures should be pretty much the same except for specific numbers / parameters, etc. So, if both use the same "Maintain fly colony" template for those entries, consistency between and within projects should be preserved.
      • There is also a "Brainstorming / connect the dots" Template for recording ideas / general notes etc.
      • There is also a "Data analysis" template for uploading graphs, data files, recording stats procedures / results, etc.
      • Other templates can be easily made (e.g., make a template for recording Python code)…
    What should go into your ELN entries:
    • For each entry, specify purpose and reference an experiment name. If you just wrote, "Recorded weights" for a particular date, you would not have a record of which experiment you recorded or what specific data you were collecting.
    • Detailed notes on all discussions, thoughts, etc. on experimental goals. Start making dated entries immediately, before the experiment(s) are started. Cut/paste emails, websites, PDFs, photos, etc. It should feel like you're scrapbookin' it.
      •  Include:
      • Detailed experimental protocols that could be easily followed by someone else. Give each experiment a name so that you can refer to it quickly in subsequent entries.
        • All
      • Detailed notes on all discussions, thoughts, etc. on experimental protocols should be accompanied with clearly-worded hypotheses and goals and indicate exactly what measurements are going to be taken and how.goals.
      • Full details for all experimental organisms (source, genetic background, delivery conditions, catalog #, etc).
      • Provide full justification of all experimental details (species used, temperature, reagents, etc.). Justification might be in the form of simple logic (stated in your own words) or references to other published research (with citations included).
      • PhotographsReagent/media/chemical/drug/etc. thatdetails, documentincluding keyvendor experimental(name, details.website, Makeemails) quickand drawingsproduct information (brand, product number, chemical structure, purity grade, lot number, date of experimentmixing/production, set-ups,expiration location of experiment in laboratory,date, etc.). TheseWhenever sketcheswater dois notused, havespecify todeionized, bedistilled, workstap, ofcold, art.hot, Takesterile, a pic and upload it to the notebook entry.etc.
      • Equipment details (brand, model number, sensitivity). In some circumstances it is important to record a serial number, just in case there was something unique about the item you used. For incubation chambers, always record bulb type / wattage / brand.
    • Reagent/media/chemical/drug/etc. details,
      Try includingto vendormake a dated entry every day:
      • Even if you have nothing, just type "nothing new to report" or “just checked on the flies – they’re doing well!” in the dated description.
      • Record all info that you need to "perfectly" reconstruct data collection at any time in the future (name,years website,from emails)now), including, but not limited to:
        • Name of the experiment. If you just wrote, "Recorded weights" for a particular date, you would not have a record of which experiment you recorded or what specific data you were collecting.
        • Time at which each procedure / test / trial started and productended.
          • information (brand, product number, chemical structure, purity grade, lot number, date
        • Purpose of mixing/production,the expirationday's date,activities and detailed experimental protocols that could be easily followed by someone else. All experimental protocols should be accompanied by clearly-worded hypotheses and goals that indicate exactly what measurements are going to be taken and how.
        • ID, group code, sex, etc.). Wheneverfor watereach issubject.
          • used,
        • Photographs specifythat deionized,document distilled,key tap,experimental cold,details. hot,Make sterile,quick drawings of experiment set-ups, location of experiment in laboratory, etc. These sketches do not have to be works of art. Take a pic and upload it to the notebook entry.
        • Laboratory and incubation chamber conditions such as temperature (in Celsius, ideally), humidity, barometric pressure, light levels, light/day cycle (hours of each, and when night starts), etc.
        • Annotate all calculations so that all numbers, concentrations, units, etc. are fully explained and would be interpretable by another researcher.
        • Either use military time or append AM/PM to all your times for all time entries.
        • Information about your experimental parameters - what you were wearing (white lab coat etc), where you were standing, etc.
        • Any anomalous events / observations (loud noises, caretakers coming into room, equipment issues, animals acting oddly, looking sick, falling off equipment, etc.).
        • All mistakes, problems with procedures, and lapses in data collection so that you can fully explain “odd” results at the end of the experiment.
        • Names / contact information of collaborators and people who assisted with data collection, techniques, statistical advice, equipment loans, stipend support, supplies funds. Write this information down immediately so that you remember to include it in your future acknowledgements sections when you publish your research. Keep notes about phone conversations and e-mail interactions.
          • If other people are asked to care for your organisms and/or collect data, ask that person to keep a detailed log of what they did and record it.
          • IDs
          (coded) for each subject.
        • Time at which each procedure / test / trial started and ended.
        • Upload / attach any associated data files and also list where the file is backed up (e.g., on laboratory computer in “Backup folder”, personal laptop, etc.). Give your file an informative name (e.g., “TBI_exp1_2018-12-25.xlsx”) rather than “experiment1.xlsx” and make sure to properly backup any such files.
      • At the end, include a very brief plain English summary of the day’s events.

    In 5 years, I should be able to ask you what you were doing in the lab today, and you should be able to tell me all the specifics about data collection, spreadsheet file names / locations, etc. that would be required to write a paper.

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