Keeping a laboratory notebook

1. Keeping a laboratory notebook good ^ A laboratory notebook is a record of both physical and mental activity. Laboratory data include tangible data such as gels, scans of peaks, photographs, and computer printouts as well as intangibles such as quantitation, observations and conclusions. All of this data are important to preserve and organize!

2. Why is it important to keep a good notebook? • Good record keeping is necessary for data analysis, publication, collaboration, peer review, and preserving data for other research activities. • Good record keeping permits the conduct of good science: accountability and reproducibility. • Good records are necessary to support intellectual property claims. • Good records can help defend you against false allegations of research misconduct. • Build your lab cred (and your legacy!). Good records build confidence in your work. & the more confidence people have in your work, the more likely they are to use it • Source for mentorship & tutelage (ensures your PI is reviewing the raw data and methodology) • Statement of your acquired skill sets

3. A Lab Notebook is not… • A journal • A record of communications • A place to compile and store lab protocols/manuals • Yours to keep

4. NOTEBOOK FORMS Paper vs. Digital -accessibility -searchability -transparency -data storage potential -organization Installed vs. Online

5. What goes in a notebook? • Notebook identifiers: • Your Name • Year • General project name • Contact information for lab • Table of Contents: • Date • Subject/Experiment • Page number • Body of notebook: • Complete, Dated entries • Tasks performed and details to perform the tasks • Accurate, Reliable, and Clear - understandable for any reader • Written in English

6. General Aspects of Dated Entries: Date Title Hypothesis or Goal: Brief statement of purpose Background How: Protocols, calculations, reagents, equipment Observations: All that happens (planned or unplanned) Raw experimental data (primary data) Pasted in information or reference to data location Sample storage Data analysis: Processing of raw data, graphs, Interpretations (secondary data) Ideas for future experiments Date Purpose Method Parameter Data Results/Analysis Conclusions Page#

7. The devil is in the details • Reagents: source, product number, lot number, expiration date, how and where stored • Solutions and how they were made (from 10X stock, from powder, etc.) • Type of water used (Milli-Q, distilled, RO, sterile, RNase-free) • Cells used: type, source, passage number, growth medium • Instruments: type/model, name, location, serial number, settings (temperature, laser power, etc) • Number and volume of washes (and duration) • Reaction size (volume) • Centrifuge speeds and duration of spins • Heating rates and levels of agitation • Time between and during steps • Gel percentages • Kit names and deviations from standard protocols • Sample description, date stored, condition, source, collection details

8. 07-Feb-2012 Study: Comparative Genomics of wild vs. genetically-modified strawberries Wild Strawberry DNA extraction weight of strawberry extracted = 3 g Materials: heavy duty ziploc bag 1 strawberry 10 mL DNA extraction buffer (soapy, salty water) cheesecloth funnel 50 mL tube glass rod 20 mL ethanol One wild strawberry was manually mashed in a ziploc bag. 10mL of extraction buffer was added to the bag and again the strawberry was mashed for 1 min. Collected supernatant and measured DNA. Nanodrop estimate = 12 ng of DNA Sample stored in DNA extracts box at -20 deg C until all samples to be analyzed are obtained Pg 15 Q & A (Think-Pair-Share) Was all information recorded? What is missing? Why should it be included? How confident are you in using this material? How confident are you in repeating the extraction for the GM strawberry?

9. Notebook Ethics “Notethics?” • All data go in to the notebook • Even “bad” data points or “outliers” • Failed experiments or contradictory experiments • Include images, analysis, printouts whenever possible, or refer to where it is • Refer back to repeated procedures, samples from another entry • “See Notebook 4, page 62 for procedure on isolating membrane proteins” • -OR- • “See entry from 03/19/11 for DNA extraction protocol.” • Nothing comes out of the notebook • Do not remove any data or delete entries • Do not remove or skip pages in physical notebooks & cross out any unused parts of a page • Correct mistakes, do not remove them • Make note of previous entries’ mistakes by referring to them in a present entry • Cross out mistakes with a single line/ paste in corrections without covering anything • Sign and date all corrections

10. Do a search for “Electronic Lab Notebook,”“ELN,” or “Digital Lab Notebook” and you will be flooded with options Word- notebook layout OneNote eCAT Lab track Labware Lab Archives Evernote Word- notebook layout mode OneNote Wordpress and other blog sites…. OpenWetWare LabGuru Syapse iLabber

12. Notebook Checklist* • Did you: • Keep up with the table of contents or use continuation notes? • Date each entry? • Make entry/post promptly? • Properly introduce and summarize each experiment? • Include complete details of all first-time procedures? • Enter all information directly into the notebook or link to external files? • Include calculations? • *IN PROGRESS- I will post this on the 299 blog. • Let’s work on building this checklist throughout the semester- comment freely!!

13. Resources: Guidelines For Recordkeeping in the Intramural Research Program at the NIH, 2008 Writing the Laboratory Notebook, Kanare, ACS 1985 Linus Pauling Research Notebooks, http://osulibrary.orst.edu/specialcollections/rnb/index.html http://gemsclub.org/yahoo_site_admin/assets/docs/StrawberryDNAExtra.4395135.pdf http://sciencecareers.sciencemag.org/career_magazine/previous_issues/articles/2012_09_14/caredit.a1200103 http://www.ruf.rice.edu/~bioslabs/tools/notebook/notebook.html