As a research assistant, I need a better document filing and workflow system that can solve my current problems.


I mainly encounter these kinds of documents in my day-to-day work:

  • papers I need to read (prepare, excerpt)

  • essays, presentations & theses from students I need to read and grade

  • applications I need to comment on

  • administrative documents (travel costs, student exchange, applications, transcripts of records...)

  • various issues that reach me via email (that I need to solve)

  • websites I need to setup and maintain (html, css, js, content)

  • lessons I need to prepare

  • presentations I need to prepare

  • books (collections) & journal issues I need to prepare as an editor (corrections, proof reading, author communication, typesetting & layouting)

  • parts for applications I need to write

  • papers I need to write (including different long-hand drafts or collaborative documents online, feedback, corrections etc.)

  • the thesis I need to write (including long-hand drafts, feedback, corrections etc.)

My problems

Pretty much all of the abovementioned documents

  • exist either electronically or physically [e/ph], or both (but as e.g. different versions)

  • have additional documents, links, images, videos etc associated with them. Those also exist [e/ph].

  • are part of different "projects" - but since I cannot only work on one project at a time, I have to

(I tried scanning everything for a while but it takes a lot of extra time and the benefit sometimes is marginal.)

Some of these documents

  • appear in multiple contexts (for digital docs, I tried symlinks, labels, duplicates. Tagspaces was much too slow and clunky for me)

  • are time sensitive

  • are effort sensitive

  • are time sensitive and effort sensitive

  • have different milestones and deadlines associated with them

  • need constant follow-ups

  • need 2 or 3 rounds of re-reading, correction, re-checking & proof reading on my part

  • need to be sent out immediately to compensate for the delays of other people & then reread as soon as they arrive back

  • need to be linked to my own notes on them

what I feel I need

A system where

  • I can assign deadlines, follow up markers, effort markers to different documents or folders, digital and physical

  • I can keep track of "versions" of stuff in a human readable way

  • the digital and physical organization system are identical in structure and workflow, without having to have the 100% identical contentwise.

  • documents can appear in different contexts without being copies

  • the specific mixture of deadlines, time sensitivity and effort is automatically calculated across these different contexts or projects resulting in a "meta project" timeline (gantt chart, calendar etc) for myself.

  • I don't need to either print out everything and file it in huge binders, or to scan everything and put it in a folder. I will do this for the most important stuff, though.

  • not only structure but process and workflow is represented. I would need to be able to "archive" one context or project until in 10 months and so on.

my main issues with existing solutions

I've tried a couple of things. My main problem is that I feel like I don't produce any synergy because ideas, insights, results, good comments etc. are not stored centrally or not findable right away.

The systems I've tried require themselves a very high level of constant maintenance, otherwise they fill up quickly with "cruft" and become unusable.

I don't see right away where I need to invest the most time and effort right now, because the system has trouble anticipating causes and effects...

I've tried GTD to keep complete chaos at bay, but with that I am mainly focused on the immediate time scale. Long-term projects and the creation of personal knowledge across different projects, as well as logical filing etc. seems difficult to do.


I admit that this is probably an utopia and that a lot of it has to to with personality traits. I know colleagues who are somehow constantly calculating and recalculating all of their contexts and projects. They read and reread their emails, they recheck their digital and physical folders and boxes multiple times a day.

This stresses me out to no end and I just want to be able to concentrate on the stuff that will keep the sky from falling on my head - either tomorrow or in 2 years.

Maybe somebody has developed a working solution.

  • Have you searched this topic / question on here? academia.stackexchange.com/q/13230/72855
    – Solar Mike
    Mar 29, 2018 at 9:04
  • Possible duplicate of best practices for organizing digital and physical articles
    – Solar Mike
    Mar 29, 2018 at 9:05
  • @SolarMike yes, I have seen this question, but it is specific to literature management / references / pdfs. I need a solution that works for articles, word docs, emails, google docs, code files, printed stuff... of those, only a small part are research articles. Mar 29, 2018 at 9:47
  • 1
    What I feel I need: a TL;DR summary of the above. Or ideally just an edited version distilling your main problems without quite so much detail... Mar 29, 2018 at 10:42
  • @Bartholomaios Use the Dewey system... works for libraries...
    – Solar Mike
    Mar 29, 2018 at 12:03

1 Answer 1


Since you want to

assign deadlines, follow up markers, effort markers to different documents or folders, digital and physical,

you might be conflating project management and reference management. Better to keep them apart.

  • Use a project management tool to assign deadlines, resources (e.g. "effort"), and status (e.g. "follow up"). Various tools are available, from simple pen and paper todo-lists, to complex markup languages and software packages like Emacs Org-Mode or TaskJuggler. *
  • Use a reference management tool to collect documents, organize them according to projects, tag them according to subject, etc. This also satisfies your requirement of having documents appear in different contexts. Again, there is an embarrassment of riches. Among the free (as in free speech) software tools, let me mention Zotero and JabRef.

I can keep track of "versions" of stuff in a human readable way

There are various Q&As on this site on version control tools. If you work a lot with plain text, Git is something of a gold standard. But I hear even Word has some kind of version control built in these days, on the Mac there's Time Machine, and Cloud services like Dropbox also offer version control.

the digital and physical organization system are identical in structure and workflow, without having to have the 100% identical contentwise.

Use a reference manager to keep track of what documents you have and where they are stored, and separate the location from the semantics. Just like an Amazon storehouse:

...[T]here is no area just for books, or a place just for televisions (like you might expect in a retail store layout). The product’s characteristics and attributes are irrelevant. What’s important is the unique barcode associated with every product that enters the warehouse (Source).

Signatures are your "unique barcode". Use signatures for your hardcopies, and keep all digital files as attachment in your reference manager (or just in a digital folder, with files named according to the Author-Date scheme).

Finally, don't waste your productive time on chasing the One Productivity System to Rule them All. It's an elusive goal and probably has more to do with procrastination than productivity.

*(I like Tom's Planner for medium and long-term planning and KanbanFlow for the daily to weekly stuff.)

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