organizing research documentation

My Current Scheme:

Research

• Papers
  • downloaded PDFs, a Mendeley ‘watched folder’
• Paperwork
  • list of suppliers,
  • order forms for equipment,
  • reimbursement forms,
  • applications for grants / fellowships etc
• Protocols
  • a github hosted repo of Markdown files
• Presentations
  • conference talks / advisor chats / lab meeting talks
  • currently being moved to GoogleDocs Presentations
• Projects
  • Docs
  • Results (stuff for figures)
  • Data (analyzed data files)
  • Code
    • Functions (project specific functions. e.g. parsing Kc data or polymer sim
    • Scripts (all playing around)
    • FigureCode (finalized script to produce particular figures on particular day)
• Data (stored separately on drives)
  • folders organized by date:
  • YYYY-MM-DD_shortdescriptor

Problems

• would like to have both private and public protocols
• Scripts should be backed up github
  • (most are currently not on github)
• Better function sharing
• Make it more obvious where functions are
• Repositories with published URLs
  • Image_Analysis (cited in Cell Reports 2013 and PNAS 2011 papers)
  • Shadow-Enhancers (cited in PNAS 2011 paper)

New Scheme

• Protocols
  • Maybe these should be google-docs?
  • StackEdit.io can sync & modify the documents in google-docs
  • StackEdit.io can sync these documents to github for publication (the folder is just to create sub-folders in github).
  • see if we can link the google-docs for editing / private viewing of unpublished files
• Code: New matlab-functions folder
  • contains lots of subfolders for very specific function tasks
  • BLAST
  • NextGenSeq
  • OligoArray
  • qPCR