organizing research documentation

My Current Scheme:


  • 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


  • 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?
    • can sync & modify the documents in google-docs
    • 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    • see if we can link the google-docs for editing / private viewing of unpublished files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
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