TITLE: Checklist for organizing and managing data
AUTHORS: Chris Berndsen

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">When planning an experiment, making a plan for data organization is a key step. Data are the currency of science and allow for confirmation of results. Moreover, your data may aid others in their work. </div><br/><div class = "text-block">This protocol is a recommended checklist for planning (OR organizing data in hindsight) for students in Biochemistry lecture or labs at James Madison University. It was designed to help new scientists make their data accessible. </div><br/><div class = "text-block"><a href="https://osf.io/5jxe3/wiki/Data%20Management%20guide%20and%20tips/" style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;">A starting guide to data management</span></a></div></div>

[STEPS]
?. [Data organization]
Create a separate folder for each type of experiment. Data should be sorted to keep data from the same experiment together.
?. [Data organization]
Create separate sub-folders for distinct trials or data collection times within each experiment folder.
?. [Data organization]
Keep analysis files separate from the raw data files
?. [File naming]
Files names should be clear as to the experiment and avoid computer added versioning (i.e. the (1) that computers add when saving a file with the same name).
?. [File naming]
Experiment titles should contain information including type (NMR, SAXS), initials of scientist (if known), and type of data (intensity, counts, etc.)
?. [File naming]
If known, raw data files should have a collection date or experiment data in YYYYMMDD format OR YYMMDD format.
?. [File naming]
Files that are collected from iterations of the same experiment like multiple reads of the same sample should have leading numbers in 0001, 0002, 0003 so that they sort in order.
?. [File naming]
Avoid punctuation marks in file names (except - (dash) and _ (underscore)) in file names.
?. [Tables/spreadsheets]
Tables or spreadsheet data should be tidy, specific, and clearly indicate units. An example of a reasonable table is shown below.
?. [File formatting]
File extensions should be non-proprietary and accessible.  Table below shows suggested formats.File typeSuggested File extensionspreadsheet.csvbiomolecule coordinates/structure.pdb or mmCIFsequence file.FASTA or .FASTQ or .txtwords/text.txtimage.tff or .pngvideo.mov
File typeSuggested File extensionspreadsheet.csvbiomolecule coordinates/structure.pdb or mmCIFsequence file.FASTA or .FASTQ or .txtwords/text.txtimage.tff or .pngvideo.mov
?. [File formatting]
To convert a file, most programs offer a Save As functionality with a File Format option.
?. [README file]
Write a text file or a wiki entitled as README or file guide to describe the contents of each folder. The descriptions should include information on how the files are internally organized and how the data were generated in enough detail that an interested observer can read this file and easily find which files they need, understand how to access them, and have an idea of the contents.
?. [Saving checklist]
For class projects, this completed checklist should be turned in.  The easiest way is to export to a PDF via MORE>Export>PDF>to your computer.  Then upload the project to your team folder.