My workflow for academic writing and editing: Bookend, Scrivener to Mellel 5



Finally, I integrate these three lethal weapons for academic writing: Bookend, Scrivener, and Mellel 5. I have done my master thesis and several journal articles these years with MS word. However, using Word to complete a thesis is really painful. The integration of Mendeley to MS word is quietly performed well. But MS Word in Mac is really annoyed. Besides, MS Word is a tool for word editing, not writing itself. Multiple buttons and functions distracted my focus.

Last month, after the vacation, I found a powerful weapon: Scrivener.


Scrivener is a proper tool for writing, not only academic writing but best in fiction writing. The design and the concept of Scrivener are all for writing itself.

After implementing Scrivener in my system, I enjoyed writing and put my thoughts section by section into Scrivener.

However, there is still some weakness. The weakest point to me is the integration between Scrivener and Reference management system, previously Mendeley. For this reason, I try to find some way to fix it.


I have compared Mendeley to other Reference Management systems before. The last decisions for several turns were all Mendeley. Mendeley is pretty a good reference manager. It kept a thousand articles for me in my Macs and on the cloud.

Since last November, Mendeley decided to stop the iOS version. That caused me some inconvenience, but it is not a big issue.

When I started to apply Scrivener in my system, some issues floated. In the process, I have to copy the LaTex form citation key to Scrivener and copy the full title at the same time. If I want to check which paper was cited, I must copy the title back to Mendeley and search it. That’s a frustrating process.

After several weeks of searching and testing, I finally decided to buy Bookend and terminate the PRO account of Mendeley.

Now, I can just copy the link in Bookend into Scrivener and the citation format to the place I want. I can just click the link in Scrivener, and it will bring to back to the reference in Bookend.

Not only in Scrivener, but I can also copy and paste the link everywhere. I use Scapple for brainstorming and making the structure of my studies. I can also paste the reference link to Scapple. That helps me to make my structure in Scapple more efficient and promising. 


When I decide to buy Bookend, I found an interesting software, Mellel. I downloaded it and tried it for a while, and these minutes changed my thought. The fluent Word processing in Mellel is not comparable to MS Word or LaTex. I just edited my document just in several hours.

That is the dream team of my writing.

After several hours of testing for Mellel, I decided to buy the bundle of Bookend and Mellel for 89 USD. Mellel has several pros to MS word and LaTex. Most PROS are good at academic writing, including cross-reference, citation and bibliography, and auto-title. It is also easier to learn and change the style than LaTex.

The final process of my writing

Now, my whole process was crafted. I started by capturing the reference article in Safari and saved then to Bookend. I brainstormed the idea and made a road map in Scapple. I built the structure and started to fill-in in Scrivener. Finally, I exported the draft to Mellel for final editing.

If you do not have a similar workflow, I suggest building one with the tools I described above. That will really help you with the dissertation or Ph.D. process. 


CQI365: My workflow with Scapple

 It is an accidence that I found this incredible app, Scapple, when I started my use of SCrivener. This application, fast and easy, is definitely not 'simple.' The way you use Scapple is user-oriented and free of style.

Here is the draft of my workflow. It is a draft, but I can wait to share it here. 

I will keep renewing this article after deeper use of Scapple. 


CQI365 Tools: The Scrivener Bookmark

The Inspector of Scrivener has a column of the bookmark.

Here, we can attach the internal bookmark of the document and the link to external files or websites.

This bookmark is single item-specific. That means it will attach a specific item in Scrivener, including group or text.

Therefore, I can link the project folder itself or the single file.

The example

In the graph below, I put the Scapple file link into the file's bookmark, named “key paper reading.” I can see the preview below the bookmark. 

I can also attach the bookmark in the project and manuscript folder. 

Furthermore, I can press “Space” on the bookmark to preview the linked file. 

Why do that?

We need tons of information and reference outside the Scrivener in academic writing. I permanently save the reference in dropbox and sync in Mendeley. If I move the file into Scrivener, I can not edit it quickly across the devices. Therefore, I prefer to save the links in the bookmark rather than transfer the files into Scrivener. For the example, I linked to Scapple file, and I can edit it separately without opening Scrivener.


Outliner 不僅做大綱,也可以寫日記

自從從Evernote搬家到Devonthink後,我已經徹底改用Markdown個是來做日記。這幾個月唯一有改變的是寫日記的介面,從typora 到Obsidian,最後回到Devonthink。


這幾天因為開始學習一些專案的拆解,找到了OmniOutliner這個軟體。雖然過去有一段時間曾經試用,但是當時出發點是要找Draft App的替代方案,相較之下Outliner與draft 確實不是同一種產品。因此這樣的比較,不意外的沒有正面的評價。參考這篇文章

這一次以尋找Project 拆解以及寫作的概念出發,還真的將outliner玩出一個新花樣,也真正的能夠在我的workflow中扮演一定的角色!



Outliner 格式

  • 較美麗且多種的格式,多種預設的主題可以改變。markdown只能整體改變呈現格式。
  • 所見及所得。markdow必須開兩個視窗!
  • 條列式較強
  • 可以使用outliner的URL 連結,進行快速切換。如: omnioutliner:///open?focus=oH_yt0FVDuw&row=oDCnPSfUH5x。(
  • 圖片可以直接貼上,不用分開存檔。(可以用照片呈現或者用icon呈現)
  • 打字順暢。在Devonthink容易lag。
  • 無法使用Latex模式(使用OmniOutliner解決方案:在Devonthink寫出latex 公式,在貼過來。)


  • 可以在devonthink 中應用 section-link。
  • 檔案較小 (以這個檔案為例:Markdown才2.2kb,但outliner檔高達467kb)
  • 可以直接在devonthink中編輯,不用另外開軟體。
  • 圖片可以使用markdown link的格式,比較省空間。
  • 可以使用Latex數學格式






我的GTD 流程MindMap版

使用GTD來作個人管理系統已經快要十年,從單純的task managmer(todoist) 到後來整合知識管理系統(Evernote),但後來使用omnifocus與Devonthink的整合。

下面我個人的管理系統,使用mind map來呈現,提供大家參考。