Rework the chapters.

[grabear]

• The chapters could be more generalized by removing the protocols and putting them in their own chapter per protocol or putting them in the Appendix.

• The chapters need to be renamed to include more general terms like:

chapter_3: 
  filename: "03-molecular-isolation.Rmd"
  text: "Molecular: Isolation"
chapter_4:
  filename: "04-molecular-pcr.Rmd"
  text: "Molecular: PCR"

[sdhutchins]

@grabear I like the way ogawa had her chapters organized. I do agree on keeping things more general as well.

I think we could reserve the appendix for protocols that we didn't edit or modify to fit our use cases.

[grabear]

Nice. I'll keep that in mind. I am making some sweeping changes, as far as organization goes right now. I didn't have time today, but this is where I'm going (not taking into account internal vs external):

• Preface
• CH1 - Lab Management
• CH2 - Noteworthy Techniques
• CH3 - Molecular: Isolation
• CH4 - Molecular: Genotyping
• Ch5 - Molecular: Gene Expression
• ChN1 - Cellular: XXXXXX
  ....
• ChNN1 - Bioinformatics Overview
• ChNN2 - Modified Protocols
• Appendix A: Troubleshooting
• Appendix B: Scaling Tables
• Appendix C: Equipment and Manuals
• Appendix D: Kit Protocols
• Appendix E: Experimental Templates
• Appendix F: Safety Information
• Appendix G: Projects

I've currently removed all of the step-by-step protocols, and put them in their own file/directory. I know you've also done a ton of .md protocol conversions in the older repository, so this will be helpful too.

[sdhutchins]

I think that's a good start. I don't even think we need CH2.

I'm still thinking and brainstorming on structure, but I do think this is the right direction for us.

[sdhutchins]

Looking at CH2 (https://github.com/vallenderlab/protocols/blob/master/inst/bookdown-project/03-noteworthy-molecular-techniques.Rmd) again, I think we could turn it into a Best Practices chapter and break that into some subsections for Cell Culture/Molecular Bio/Bioinformatics/Miscellaneous.

Also, it's worth having a Common Lab Math/Formulas Chapter as well. I think of a lot of just basic formulas that newbies aren't too familiar with.

[grabear]

I like that. I'm working on doing some stuff with babun and git subrepo to give us help with #8.
https://github.com/ingydotnet/git-subrepo