Workflow for thesis, any recommend softwares

Hi, i’m currently working on my master program right now. I just switched from PC to Mac, love my new mac. I hate M$S word, abandon it. Well anyhow, the point of this discussion go like this:
I’m currently using Mellel and Bookend to do my research paper, i’m currently experiencing with Scrivener becuase i’m the type of person who read alittle bit and write a little bit, but i want to know from the expert here how to incorporate following software for the research workflow:
I bought:

  1. Deventhink Pro
  2. Scrivener
  3. Bookends
  4. Mellel (use it as my final format from scrivener)

I have difficult incorporating these software into my research workflow: what app would i use first? any suggestion of the workflow, i really need help, or do i need all of these app for research? thanks in advance

My approach to this is to drop Devonthink from the list of tools, and store everything right in SCR instead. I have used SCR for dozens of projects like this (both big and small) and so far have not felt the need to go back to using DTP. My understanding is that DTP is much preferred for web links but I use Webstractor (now defunct I think) or Google Notebook for that.

Then, do all your writing in SCR (of course) in the same project that stores your notes, pdfs, graphs, etc. When you are finished writing, export to Mellel and do all the Bookends stuff there. While it might be nice to integrate Bookends functions within SCR, I used to find (using Nisus, or Word) that this was just another (unnecessary) distraction. Now I just use a Bookends Group to store all refs for each manuscript, then export the ref list in the correct format when I am done, never bothering with the in-text Bookends linking. If you really like the in-text linking, that can be readily done after you export to Mellel.

For me doing all the DTP stuff right in SCR greatly improves my workflow, especially because I no longer have to jump back and forth between apps to see stuff.

FWIW, my experience has been just the opposite. I keep a master database in DT, and only pull references into Scriv on an as-needed basis. I’ve found that DT’s tools for managing large amounts of data are vastly superior to anything Scriv offers. (Not surprising, since that’s DT’s whole reason for being.)


I think it depends on how much research information you are trying to keep in Scr. There have been several discussions about using Mellel, DTPro, Scrivener and Bookends. This seems to be a popular combination! If you do a search for Mellel, for example, you’ll find those threads where a lot of folks, including myself, weigh in on how they use these programs (or don’t use them).


I do want to incorporate Devonthink into the work flow, what i’m interesting is when dong the research in the devonthink, do i need to outline the stuff in Devonthink and mimic the outline to scrivener?
if i was to use devonthink with scrivener.

Commend from above is if i drop Devonthink completely, when doing research, do i outline the research in the research binder of the scrivener and mimic it’s outline to what i am going to write. thanks a lot

Really real questions is, what is the use of research binder in scrivener? let say i want to do a research on a topic, i know that i outline stuff int he draft of what i want to write about, what about the research binder, do i need to outline it too to mimic the outline of the draft? thank you

Just as a quick note, I am hoping to add a little better support for BookEnds in Scrivener, thanks to the very helpful BookEnds developer. This is on the sooner-rather-than later list of things to do… It certainly won’t be the same integration as Mellel offers, though.

Vanternator, like you I’ve recently switched from a PC to a Mac, so I’m relatively new to this also.

But I’ve found so far that what works best is to keep most of my research in my Home folders. For me this research consists mainly of PDFs of news clippings; I’ve destroyed the originals and so I want easy access to the PDFs. I’ve indexed the PDFs (which I’ve previously OCR’ed) with DevonThink Pro, so that I can use the DevonThink search and collation tools. Then I copy the small number of key documents I need at any particular time into Scrivener on a temporary basis, having dug the references out of DevonThink with its search.

In essence, DevonThink Pro is my databank, and Scrivener acts as my data-wallet. For me, the research binder in Scrivener is purely a holder, not a structural outline.

It’s possible that I’m failing to exploit the full capabilities of DevonThink and could dispense with it by using Spotlight (or that I should use DevonThink more effectively by importing rather than indexing my PDFs.)

But at the moment I believe that as my databank grows, DevonThink’s usefulness will grow also.

Using Scrivener to write University and College level assignments.

This may help. It provides a simple form template you can build on and it

Currently being edited

Sorry the last post went up twice - the server showed up as busy so I accidentally hit send a second time.

You “need” to do whatever works best for you. That may not be what works best for anyone else.

Like Hugh, I use DT as a databank, and only drag references to Scrivener as I need them.

Because DT is a databank, it contains many items unrelated to any particular project. Thus, it’s sort of pointless for me to try to mimic a project’s outline within DT. Instead, I use the Group functionality to classify items by topic. From there, I can use labels and smart groups to create temporary classifications as the situation demands.

Since Scrivener usually only contains a few references, I haven’t needed to impose a lot of organization on the Research folder. Larger projects would naturally demand more organization, but whether you accomplish that with links or an outline structure is really up to you.


So basically what you saying is that:

  1. Outline the topic in scrivener
  2. research stuff and put everything in Devonthink, (wouldn’t it cause problem if i just put everything in devonthink, what if i don’t know what to find. wouldn’t it be nice to mimic the outline and through stuff that is relate to that topic in the database, and when start reading, i can refer to that.
  3. what step does Bookends come to play, do i create references for everything that i find.

anyone have a sample workflow that want to share, i’m up for exploring, i’m stressing out, basically i’m not good at doing research, i need help that why i have all these tools and i want to make good use of it. thanks you

forgot to mention, how do i use group classify in devonthink

OK, the subject is workflow. Does anyone else think that’s an ugly word? I looked it up in Wikipedia and apparently it comes from IT, those folks who have no way with words and gave us such gems as input, output, throughput, and default, which used to mean no action taken, or not showing up to play, but in IT means the normal state, business as usual. Anyway, I suppose workflow is no worse than “process,” an earlier term for motion and change, which my thesis adviser hated because it reminded him of Velveeta.

To the point: I just wrote an 800-word book review for publication, using only Scrivener. In the Research section of the Binder, I set up an outline of the book’s chapters and sub-chapters. In each of those sections, I typed reading notes: paraphrase of action or idea, some with ** because important. In Document Notes, I entered critical thoughts: disagreement, agreement, eureka moments, and other insights. For once I made no use of Synopsis, since the structure of a review is quite standard: introduce, describe, evaluate, conclude. When I learn how to make a template, maybe I’ll set that up. I added a few links in References but did not use Key Words, again because of the brevity of the project.

In the Draft portion of the binder, I wrote a brief first draft and then a longer second draft. The first was actually a letter to my editors, to show them what I was going to say and get feedback. In both drafts, I used Split Vertically to see side-by-side views of the draft and the notes. That looks right to me, on an iMac 20" screen. After drafting, I exported in DOC and e-mailed that text to my writing partner. She and I did some tweaking in Word and I sent the file off before midnight. The whole process took about six hours. I’ve never done one that quickly nor felt better about the end result. The work flowed nicely, and I went along for the ride. :slight_smile:

Regarding DT Pro and Scrivener, I have two workflows in which they interact.

  1. Long term projects, or project-neutral readings: I type my reading notes directly into DT, per book. While doing this, if I have a project at hand that can benefit from what I’ve read, I drag and drop that DT note into Scrivener.

  2. Short term projects (i.e. current working projects): I type all ideas that I have, all brainstorming type of thoughts, into an “ideas” folder in the “research” folder that Scrivener provides. Furthermore, I jot down any notes from a book or article that I’m reading directly into Scrivener; I type these notes directly into the Synopsis pane, with the first line of the Synopsis being [Author’sLastName, ShortTitle, PageNumber], with the quotation or summary thereafter. I use the “notes” pane to type reminders to myself as what to do with this info, or where it might fit into the overall plan.

That being said, DT is still my long-term storage place. Thus, when I am done with my short-term Scrivener project (the essay, thesis, article, whatever) I export all the notes out, including the Synopses. I trash everything other than the synopses, and then import the synopses into DT, organizing them by book/article as I would have if I’d typed straight into DT (like method #1 above). It takes a tiny bit of work – since when typing into Scrivener I don’t type by work but by its relevance to the piece I am writing – but in the end I have saved all my research notes into DT in a way that they will be useful in the future.

It seems you have all the tools you could possible need. Suggestions for using them and possible alternatives IMO (which is not expert advice by any means) are …

  1. Information Management: DevonThink, Notebook, OmniOutliner
  2. Authoring and Editing: Scrivener, Notebook
  3. Citation Management: Bookends, BibDesk (free)
  4. Designing and Printing: Mellel, Scrivener, MSWord, Nisus Write, NeoOffice (free), LaTeX (free)

I do suggest that you focus FIRST on choosing and using (simultaneously) the first three tools for YOUR general convenience and that you subsequently determine the best tool for the fourth step on hand a) any restrictions that your university may place on their preferred submission format (especially if they do electronic publishing) and b) its ease of integration with the second and third tools.

Good luck!