(Estimated reading time: around 8 minutes).
I have been trying to establish an academic workflow for quite some time now. Writing about it helps me to organise my thoughts better. I’ll highlight what I have found useful. This list is by no means exhaustive. This is also in line with my idea of documenting everything as I hurtle towards the goal of academia. Its an ongoing struggle but I am hoping that someone more knowledgeable than me would take time out to point any obvious flaws. I also hope to spur on discussion about their own workflows.
Created in scapple; a basic mind map
Step 1: Creating a mind map.
I use Scapple for it. There are other alternatives available but I haven’t explored them. Stare at a blank canvas and start writing randomly. Identify the thoughts as they come to you. They help in brainstorming. This involves identifying the parameters that I have to use/cover, all the ideas I have to write about and how I need to be able to distinguish my write up from other published ones.
That, I believe, is the most important part, since the first part of any research is identifying the question and being able to coherently frame it. This is followed by supportive evidence (if any) and the strength of the protocol that you are out to write. If you don’t want to use Scapple from the outset, you can always write it down; see all the ideas that form a feedback loop, if any, and then take it forward.
Key takeaway: Identify the idea first!
Step 2: Pubmed
Once I have done it, I hit Pubmed. The search on Pubmed has improved vastly although a compelling use case exists for Quertle as well. Previously, Quertle had a free tier but its a paid option now. I haven’t used it recently though. Nevertheless, I use advanced search and booleans to drill down to the specifics on pubmed. Once I have identified my key words that give me adequate results, the fun starts.
A specific keyword is likely to give a river of publications. Most of them are usually contextually related and Pubmed has complex algorithms to sort them out. I prefer to subscribe the whole list by RSS feeds (which I covered recently). These RSS feeds then pipe into Inoreader. Few people might prefer to get email for it but this is easily lost in the sea of email that we get (I hit on a specific actionable inbox zero protocol long time back and its serving me very well). Email is a bad idea.
Step 3: Inoreader for RSS feeds
Inoreader is a fantastic resource. Apart from the specific Twitter searches, I can filter out the feeds.
Lets say, if the feed is showing up keywords for canine oligodendroglioma (which is irrelevant for me), it can be filtered out. Once its done, I can set up several other rules in conjunction with IFTTT.
Inoreader and IFTTT (If This, Then That) allows you to create applets that links various services. For example, I pipe articles related to specific keywords, IFTTT can be triggered each time the article comes in. I add specific hashtags to it and viola! All articles that are of relevance (from specific keywords/filtered) are pushed out to Twitter. A bit of human curation also occurs in this river of articles. I usually “star” the articles (things I have to follow) and IFTTT appends separate hash tag to it and pushes out to Twitter.
In this, specific write ups that are relevant to my work (starred articles, for example), are saved and downloaded (usually from Sci-Hub or through institutional paywalls).
Step 4: HighlightsApp on Mac
I use Highlights App on Mac (I think it was created by a PhD student himself). The coolest thing about it is the annotations come as a note (which now happens in Bookends as well). These notes are exported as TextBundle and opened up via Ulysses. I add meaning to these notes (needed to learn a little Markdown; enough for me to get going) and Ulysses pushes it to my publishing website on word press.com
Step 5: Using Ulysses to craft your ideas
The beauty about Ulysses (apart from the simplicity, writing long form, ability to preview in various formats etc) is stellar customer support. I faced an issue with Highlights app and Ulysses and it was addressed by the developer himself. They moved towards a subscription based model and I think it was a wise sensible decision.
Step 6: Always use a Bibliography manager for your papers!
Nevertheless, I have found peace with using Bookends. It is (I think) a one man show (Sonny Software) and is one of the most comprehensive solutions. Sente/Papers 3 are gasping but Bookends has thrived on a payment model (upgrade every 2 years) with stellar support; both on forums and email. Bookends serves as a bibliography tool (this deserves another blog post some day).
Step 7: Scrivener for writing papers. A must have and a life saver!
After annotations/note taking, I prefer to write using Scrivener; especially the long form. I break up the article in several parts and I can work on them at different intervals. This also requires another blog post!
Scrivener pipes out the output in rtf (for example) where Bookends can scan it, add the citations which then requires some more formatting to be pushed to journals for submission (and then hope that the anonymous reviewer would be nice to you!)
Starting from Pubmed, this train of thought may sound complex (but it isn’t) and is straightforward. Each one of them serves a specific purpose.
Ulysses works perfectly to write these blog posts since I prefer to use a distraction free environment. I use Vivaldi browser as my preferred software; has tons of shortcuts and muscle thats absolutely amazing.
Don’t forget cups of tea/coffee and some Spotify lists to keep things interesting! (meditative music helps me :))
Disclosure: None of them are affiliate links and I have paid for the software in full. They deserve to be highlighted!