GRAD 521, Research Data Management Winter 2014 – Lecture 4 Amanda L. Whitmire, Asst. Professor

1. Organizing Your Data GRAD 521, Research Data Management Winter 2014 – Lecture 4 Amanda L. Whitmire, Asst. Professor

2. Lesson 4 Outline File-naming conventions Data organization Standard operating procedures: keeping a [lab] notebook

3. File naming conventions

4. File-naming strategies (1) • BE CONSISTENT • Have conventions for naming: • (1) Directory structure • (2) Folder names • (3) File names • Always include the same information • (e.g. date and time) • Retain the order of information • (e.g. YYYYMMDD, not MMDDYYY )

5. File-naming strategies (2) • BE DESCRIPTIVE • Try to keep file and folder names under 32 characters • Within reason, Include relevant information such as: • Unique identifier (ie. Project Name or Grant # in folder name) • Project or research data name • Conditions (Lab instrument, Solvent, Temperature, etc.) • Run of experiment (sequential) • Date (in file properties too) • When using sequential numbering, make sure to use leading zeros to allow for multi-digit versions. For example, a sequence of 1-10 should be numbered 01-10; a sequence of 1-100 should be numbered 001-010-100. • No special characters: & , * % # ; * ( ) ! @$ ^ ~ ' { } [ ] ? < > - + / • Use only one period and before the file extension • (e.g. name_paper.doc NOT name.paper.doc OR name_paper..doc)

6. File naming conventions s/n, variable Retain order Project_instrument_location_YYYYMMDDhhmmss_extra.ext Index/grant conditions Leading zero!

7. File naming strategies • Order by date: 19550412_notes_MassObs.docx 19550412_questionnaire_MassObs.pdf 19631215_notes_Gorer.docx 19631215_questionnaire_Gorer.pdf • Order by subject: Gorer_notes_19631215.docx Gorer_questionnaire_19631215.pdf MassObs_notes_19550412.docx MassObs_questionnaire_19550412.pdf • Order by type: Notes_Gorer_19631215.docx Notes_MassObs_19550412.docx Questionnaire_Gorer_19631215.pdf Questionnaire_MassObs_19550412.pdf • Forced order with numbering: 01_MassObs_questionnaire_19550412.pdf 02_MassObs_notes_19550412.docx 03_Gorer_questionnaire_19631215.pdf 04_Gorer_notes_19631215.docx

8. On using number orderin file names… Dates listed in order of collection

9. On using number orderin file names… If we sort by MM/DD/YY, dates are out of order.

10. On using number orderin file names… If we sort by DD/MM/YY, dates are out of order.

11. On using number orderin file names… If we sort by YY/MM/DD, dates are in order.

12. On usingleading zeroes in file names…

14. Pair & share – 10 minutes 5 minutes: generate potential file names for your data & document your strategy 3 minutes: share your strategy with a partner & hear what they came up with 2 minutes: volunteer to share your idea with the class s/n, variable Retain order Index/grant conditions Leading zero! Project_instrument_location_YYYYMMDDhhmmss_extra.ext

15. FileOrganization

16. Data organization AGU presentation Class presentation OS presentation Presentations Ocean Sciences AGU Class

26. When naming& organizing your files and folders… be thoughtful be consistent documentyour approach

27. Documenting your process

28. Why keep a notebook? To provide yourself with a recordof how your data were collected, organized and processed. Yes, you will forget if you don’t write it down. To provide yourself with a central & physical locationfor protocols, results, and general happenings. To encourage a thoughtful process. The act of writing things out forces you to explore and clarify ideas. To enable continuityin the face of unexpected events. To establish a legal and scientific provenance (historical record) of your work

29. What to use as a notebook? A notebook with a stitched binding. Don’t be temped by the “carbon copy” types. A larger size is generally better, but preferences vary. Better quality paper is more expensive, but is worth it. A notebook with pre-numbered pages is also worth it. The kind that lays flat when open is nice to have. Electronic notebooks (ELNs) are hugely variable and often discipline-specific. Do your homework if you want to go that route.

30. What to write with? PEN

31. What should go into it? Everything that is directly relevant to your work. You tell me.

32. Suggested notebook content • Notes on all discussions and thoughts on the experimental/research goals • Protocols for experiments or for acquiring data (if using 2ndary data). Tape in printed versions if you want to. • Provide justifications for method, source of data (how did they generate the data?). • Annotate all calculations so that anyone could understand what you did. Remember units! • Provide full details on experimental/research organisms/subjects. • If performing lab experiments w/reagents, list details like manufacturer, batch, etc. • Record equipment details. • Capture field, laboratory, or interview conditions.

33. Suggested notebook content • Your personal description may be relevant. Maybe. If it could be, write it down. • Write the names of people who have assisted you, for future acknowledgement. • Make quick drawings set-ups, locations, etc. • Take photos and paste them in. • Record file names of data, where they are stored and backed up. • Get into the habit of making daily entries – ALWAYS date your entries, including YEAR. • If you record log data into a digital spreadsheet, record the event in your notebook. • Detail your mistakes. • Use military time, or at least AM/PM

34. Suggested notebook content • All entries should be un-obscured by attached graphs, data sheets, photographs, etc. • When you include photographs, graphs, product labels, etc., use glue to cleanly and permanently attach all edges. Do not use tape. • Avoid making entries that are unrelated to your project. • Include the full names and contact information for all collaborators • At the conclusion of your experiment, write or print out a full directory of all electronic files that relate to your experiment. • Describe the locations of all computer media, data binders, seeds, samples, etc.. • Typically, the laboratory notebook should stay in the laboratory where the experiments were conducted (i.e., with your mentor or employer). • Digital cameras are really cheap, so if you do expensive, important science I recommend that you have 1 camera per project. At the end of each work day the researcher should take a photograph of each page.

35. In summary: Write down All The Things

36. Homework will be posted on Blackboard after class Due before class Tuesday Write a summary (1-2 paragraphs) describing your current or expected approach for documenting and organizing your research activities.

37. Here’s our brainstorm photo