Why WorkFlowy and Latex make the perfect partnership for Academic Writing.

Introduction

I have just handed in my thesis. Yes, it was tough, but not as tough as it could have been. Why? Mostly because of a little web app called WorkFlowy which isn’t supposed to be for writing at all, let alone for a piece of writing as big and formal as a doctoral thesis. But it works. By god, it works. This post is firstly going to try convince you to adopt a combination of WorkFlowy and Latex for your academic writing, and then guide you through setting them both up with tips, tricks, add-ons and advice galore. This is going to be a long post, and is not necessarily devised to be read in order. Below is a table of contents to give you an idea of the layout. If you know nothing about WorkFlowy or Latex, I do suggest you start from the beginning. If you use both of these but want to know more about the best way to integrate them and use them to write a thesis, just skip to any section that grabs your attention. Throughout the post there will also be links to shared WorkFlowy lists and one particularly important one containing a load of Latex code and tips, so look out for those.

Here’s what’s to come:

  • The Power of WorkFlowy
  • Latex
  • WorkFlowy – Latex’s Best Friend
  • Writing Academic Papers in WorkFlowy
    • Tagging
  • Writing Latex in WorkFlowy
    • Phrase Express
    • Keeping your .bib file in WorkFlowy, a drop down list of references and citing papers
    • Miscellaneous tips
  • Comments, thoughts, ideas …
  • Keyboard shortcuts, Navigating and Bookmarks
  • When you are struggling
  • Compiling
  • Conclusion

The Power of WorkFlowy
WorkFlowy is an ‘outliner’, and it is at first sight a simple-looking program. When you first open a WorkFlowy account you are pretty much just presented with a single bullet point, like below, which can be a bit ‘Err, OK’.

Figure 1. The Humble Beginnings of your grand WorkFlowy document.

But this reductionism is in fact WorkFlowy’s greatest strength. Hidden behind this simplicity, it has a few core features that combine to make it a phenomenally powerful tool for a surprisingly vast range of activities:

  • Every ‘item’ in WorkFlowy is either a bullet point or a note attached to that bullet point. Bullet points are therefore simultaneously content and ‘folders’ for other bullet points.
  • You can nest bullet points within other bullet points to infinite levels (see below)
  • Figure 2. A Basic WorkFlowy Structure. It’s bullet points all the way down.

The best advert I can give is for you to just try it out yourself. Here is a link to a ‘shared’ list on my account which you can play around with. It is a ‘demo’ list so it will revert back to its original form the next time you click on it (or anyone else does), so feel free to go wild.

https://workflowy.com/s/XrFn8F2h1C?demo

Link 1. A demo WorkFlowy list to play around with.

  • You can ‘zoom in’ to bullet points by clicking on them to make that bullet point the ‘header’ and everything nested under it the only content on the screen – you can keeping zooming in as deeply as you like. When zoomed in you can see the ‘breadcrumb’ navigation at the top showing all the ‘levels’ above your current. Click on any of these to return to those levels / zoom out. Alternatively, alt + left will zoom you out, and alt + right will zoom you in.

Figure 3. WorkFlowy, zoomed mode!

  • WorkFlowy has a full tagging system with intelligent search function and logical operators using # and @ tags.
  • It is entirely plain text with the sole exception of bold and italic functions and so extremely lightweight and fast.
  • It has a raft of keyboard shortcuts to help you get around at rapid speed.
  • You can customise almost everything. Because it is web-based and simple, add-ons are super easy to make, and there are a vast range of excellent third party CSS additions which add colour, functions and a load of extra features – as you have access to the CSS code these are easy to customise to your heart’s content. These provide further functionality while keeping your actual document lightweight. For example you can add colour, like below:

Figure 4. WorkFlowy, in technicolour!

There are endless debates on various blogs and forums about whether hierarchical (e.g. OneNote) or tag-based (e.g. Evernote – if you’re doing it right) structures are best for digital organisation. In truth (as always) they both have their strengths, and are useful in different circumstances. The ideal of course is to have both at your disposal when needed. With the invention of infinite zoomable bullets, WorkFlowy has in my opinion created the perfect hierarchical system (I may be wrong but I honestly don’t really see how it can be improved upon other than with further ease of navigation) – navigating around something like One Note after a few days with WorkFlowy is hell itself – the differentiations between ‘different levels’ like ‘Notebook’, ‘Page’, ‘Sub-page’ etc have come to seem to me so pointless, dated and even quaint. Why make the distinction? Just allow the user to decide. With its version of a tagging system WorkFlowy has some advantages and some disadvantages over Evernote’s approach, but overall the same power to completely construct almost any organisation system you want that tagging systems afford. If I could make an analogy, I would describe WorkFlowy as a ‘sandbox’ digital organizer. Just as Minecraft removes the constraints on how you ‘should’ play a computer game and encourages you to explore your own way of doing things, so too does WorkFlowy remove the constraints on how you should organize your life. Once you absorb WorkFlowy into your life, other programs come to feel horribly restrictive. After around a year of use I have slowly come to use it as calendar, project and task manager, journal, life logger, finance and budgeting tool, and yes, thesis writer. None of these things came as templates or anything like it, I have ‘built’ them myself (with a lot of help from the WorkFlowy blogger Frank Degenaar’s great book), There is no compromise here – I am very aware of the popular products for these functions and WorkFlowy surpasses all of them if only because of sheer customisability and of course perfect integration / a single search box for my entire life. But this post is about thesis writing – I do intend to detail my life organisation approach with WorkFlowy at some point but that will have to wait for a later post (I should probably do some science posts in between to maintain the charade of this as a science blog too!).

Now, pricing. WorkFlowy uses a freemium model, and the free version is absolutely fine to get a feel for the program and even for casual to medium usage. The main restriction on a free account is the number of items (bullet points) you can create per month: 250 with a basic free account, but, magically, 500, if you sign up via this link: https://workflowy.com/invite/3604d08c. This is actually less of a restriction for thesis writing than general task-type use, as you would tend to be making less, but longer (i.e. paragraphs) items, than a typical to do list for example. So I think you can definitely get a very good feel for everything in this post entirely for free. I suspect however, that once you get going with WorkFlowy, you will shortly be hooked, and the ~£5 a month for the level of life-organisation and peace of mind it provides.

Latex

Latex is of course much more well-known than WorkFlowy and is used throughout the world by academics to write their papers, so I am not going to spend much time introducing it. Basically, it is a relatively simple coding language for producing academic papers (and books etc.) It has a relatively steep learning curve (it’s really not that steep, but compared to a classic word processor…), which is presumably what puts some people off. However, not for you. Below is a WorkFlowy shared link with all the instructions you need to get set up with Latex, and all the snippets of code I (and therefore hopefully you) needed (/ will need) for your thesis or academic paper. This is a live and on-going list which I will also be sharing through other means, and as it says in that link, if there is anything academic-related you want to know (or perhaps even a tip you have that should be added) please let me know and I will endeavour to include it.

https://workflowy.com/s/0W0rIAQ3By

Link 2. A guide to using Latex (particularly but not exclusively with WorkFlowy).

WorkFlowy – Latex’s Best Friend

One thing a lot of people love about Latex is that you can write it in any text program – even in a .txt file. It is therefore lightweight (unlike Microsoft Word), unlikely to crash (unlike Microsoft Word) and it doesn’t intentionally format things like tables or figures in insane ways just to irritate you (I have a very healthy distaste for Microsoft Word). The other thing of course is that with all the packages out there (Latex is open source) you can format / layout a write up any way you like, with confidence, and, at the flick of a switch (function), have it formatted in a completely different way (say, for a different journal, or to transform a part of a thesis into a paper, as I am doing now). Now, there are some great Latex editors out there, like Tex Studio, which provide some nice features to help you write a big piece of work, such as a section navigation pane. However, none of them comes close to the power of WorkFlowy for helping you focus on exactly what you want, whether that is a single small section, full screen, with no distractions, or multiple sections from different parts of your report at the same time. And none of them has a full tagging structure to keep track of the state of every section of your work, or the ability to make endless notes on any section of work, or to have \subsubsubsubsubsubsubsubsubsubsubsubsections which don’t even have to show up in the final output, or allow you to see the structure of your document not only as an outline, but inherently, in the main body of the text, or to have keyboard shortcuts to take you back and forth between different sections, or the ability to edit perfectly well on a mobile device, without any fuss or worry. So. We are going to see how by combining WorkFlowy and Latex we can overcome the weakness of both (a lack of formal formatting capabilities in WorkFlowy’s case, and a lack of … well, WorkFlowy features, in Latex’s case) and harness each other’s strengths.

Writing Academic Papers in WorkFlowy

As I’ve said, WorkFlowy is an outliner: a set of nested bullet points. These nested bullets can be infinitely deep and each bullet point can also have an attached ‘note’ (shift + enter to edit the note of a bullet). When I write serious things with WorkFlowy the bullets become the section headings and the notes contain my prose. You can see a real example from my thesis below.

Figure 5. A depiction of a series of sections of my thesis.

Some might prefer to just use bullets and sub bullets for both section headings and content, and you could, but I find my approach easier for formatting (more freedom within a note), and simply for taking in the structure of my document visually at a glance (because bullets and notes look different). Now before you get writing in WorkFlowy you are going to need a few add-ons. To get started you need to install the ‘Stylish’ extension (available at the least for chrome, Firefox and Safari with a quick internet search) which allows you to make visual user-end modifications to web-pages. The first and perhaps most important of these for writing is an add-on that allows you to have all the notes attached to your bullets ‘open’ or ‘expanded’. This option is not a native feature of WorkFlowy unfortunately, but this add on works perfectly so do not worry. To get this add-on, once you have stylish installed, open WorkFlowy, click on the ‘Stylish’ button that has now appeared on your browser bar and click (right at the bottom) ‘Write Style for Workflowy.com.’ Copy and paste the below code in, give it a name (e.g. ‘Open All Notes’) and save.

div.notes div.content {display: block !important; height: auto !important; overflow: visible !important;}

Now click on the Stylish button again and there will be a check box with the name you used. You can choose to flick the ‘Open All Notes’ style on or off. Flick ‘Open All Notes’ off to get an overview of your document and for quicker navigation, or flick it back on to have a full-prose format (like in my thesis screenshot above). Don’t forget if you really want to focus on a specific section to use the ‘zoom’ functionality to make it full screen.

Tagging

WorkFlowy has two types of tags, the @ tag, and the # tag. You can of course use them how you like – my preference is to use @ tags for structure e.g. @Thesis, @Chapter1, @Introduction, @Method and # tags to indicate the status of things such as #todo, #reviseddraft, #finaldraft # wip (work in progress, to allow you to easily move between sections of your document you are currently engaged with – kudos to Frank for this invention). This nice thing about maintaining a rigid distinction like this is that sometimes you want two tags called the same thing but with different functions. For example, you might want to use the @Introduction tag for structural searches, but you might also want to tag a note, comment or thought (see further down for more on this) with #introduction to bring all thoughts (wherever they are) about your introduction together with a search. When you come to write each day you can use your tags to decide what to work on. Finding sections that are marked #todo and zooming in on them is far less daunting and easy to get into first thing in the morning than a huge word document with no obvious place to start. It is tricks like these that help ease you into writing each day and curb procrastination. The advantage of having structure tags is firstly for speed of navigation but secondly that you can easily see all of a certain type of section, for example all the discussion sections (if you have multiple experiments) with a simple search, all in a single pane. If you have several experiments with their own small discussions, and then a general discussion, this can be a great way to see if they flow / if you have repeated yourself, etc. If there are certain unrelated sections of your document you want to see all at once, just make up a new unique tag on the spot – at one point I wanted to look at all the sections which were to do with #NestedSetsvsNatFreqs (don’t ask) – so I simply tagged them all with this then searched for that and bingo, there they all are, neat and organised. Things like this, which require so much effort in other programs are child’s play in WorkFlowy.

Writing Latex in Workflowy

Phrase Express

Now, I want to briefly introduce another application into the mix (and again thank Frank for the introduction to it). Phrase Express is one of many, but I believe a particularly good / easy to use, keyboard shortcut / macro program. It is perfectly functional in its free version and it’s up to you if you think you get enough value from it to support them (I certainly get enough). It is also extremely easy to use and can be incredibly powerful. One problem with writing in Latex is human error. If you write out all the code necessary for an entire thesis, there will be mistakes, a lot of them, and they can be hard to find (however, see the section in the Latex link on debugging). I recommend putting every single Latex command (yes even the simple ones) into Phrase Express. This not only allows you to access them with a keyboard shortcut (increasing speed for large things like figures), but also ensures you never, ever make a mistake. This will save you so much frustration at the end. Shift and alt and f provides me instantly with all the code needed for a figure. Shift and alt and 1 turns any selected text into a perfectly formatted chapter heading (and so on for shift and alt and 2, 3, 4, etc). Shift and alt and p opens up a parentheses citation (more on this shortly) and shift and alt and t, a text citation. It really is wonderful once you get it going. Here’s a link to the phrase express download page: http://www.phraseexpress.com/

Keeping your .bib file in WorkFlowy, a drop down list of references and citing papers.

The one thing that completely sold me on Latex was the citation management and the one thing some people might have raised an eyebrow at in leaving something like Tex Studio is the ability to open up a citation command and get a drop down list of all the papers in your .bib file. You are right that this is of course not an innate function of WorkFlowy and would be sorely missed. However, the exact same function can be achieved through @ tags, which also come with a drop down menu. I must confess to being quite excited right now: this is the best thing in this post. Firstly, I would wholly recommend using WorkFlowy as a place to keep your bibtex database, even if you didn’t use WorkFlowy for your writing at all. I recommend a setup like the image below.

Figure 6. My .bib file in WorkFlowy.

Use a blank bullet point, with the bibtex entry in the note. Of course, if you wanted to arrange your bibtex entries in some hierarchical format according to subject, this would be easy to achieve, and I probably haven’t explored everything you could do with this. However, right now we are going to take this to the next level. For each bibtex reference ‘code’ e.g. Turner2015, put a space and an @ tag in front of it (you need the space – see image above). So Turner2015 would just become @Turner2015. It has just become a tag. When you come to compile, Latex has no issue with either the space or the @ sign, so don’t worry about that. However, you now have two great new features. Firstly, you can search your .bib file in an instant with a drop down menu of codes from the search box (say, if there’s an error with a particular reference). Secondly, when you want to cite a paper from your .bib file in your document, when you type \citep{ @ a drop down list of tags appears, with all your .bib codes, just like in Tex Studio or similar. This admittedly only apes that same functionality, and doesn’t better it, but the ability to manage your actual database in WorkFlowy is far better I think than even the professional citation management systems can offer. You can utilise WorkFlowy’s hierarchical and full tagging system to sort entries by topic, you can easy add additional information such as links to the appropriate pdf or, perhaps, to your Evernote summary page on that paper (See my post on a system for using Evernote for academic literature reviews). When you want to export your .bib file it takes four clicks: alt and click on the title (copy all – alternatively click anywhere and press ctrl a twice), copy, open target .bib file, paste. Done.

Now, for actually citing papers while writing I have a set of phrase express macros which make life far easier.

First, to get a paranthetical cite just use ‘/citep[][]{ @’ without apostrophes and for one which gives the text cite ‘\citet{ @’. For these you literally just copy that text into phrase express and when you press the keyboard shortcut it will just spit out the text.

Then, I have one which tidies up the previous citation (removes the spaces) and adds another citation (if you are citing multiple authors), like this: \citep[][]{@Gigerenzer1996, @

This is a bit trickier. To get this working, copy the following into phrase express:  x{#CTRL {#LEFT -count 2}}{#LEFT -count 2}{#DEL}{#CTRL {#RIGHT -count 2}}{#DEL}{#BKSP}{#BKSP}, @

Then we have another macro that tidies up and closes a citation off (when you are finished citing), like this: \citep[][]{@Gigerenzer1995,@Macchi2000}

To get this working, copy the following into phrase express:  x{#CTRL {#LEFT -count 2}}{#LEFT -count 2}{#DEL}{#CTRL {#RIGHT -count 2}}{#DEL}{#BKSP}{#BKSP}}

I do recommend you explore Phrase Express. While the above may look complicated in written form this can all be achieved by using the drop down menus found in the ‘Macro’ menu – it can all be done through the far more friendly button-and-menu-based user interface rather than pasting ugly bits of code and really is quite easy to build your own macros through trial and error.

For those less familiar with what I am on about in this section, below you can see the before and after for both ‘paranthetical’ citations and ‘text’ citations below:

citetopdf

 

Miscellaneous tips

I would now like just to give a range of miscellaneous tips for writing with WorkFlowy and latex.

  • WorkFlowy is a web app, so you are perfectly able to have two instances of the web browser up, split screen, and further to have as many tabs open on those two browsers as you like. Too many can get confusing, but for serious writing I often find this extremely useful.
  • The % Sign. Get in to the habit of putting a % sign after every section title (it can even be part of your phraseexpress macro). That way, if you want to add tags after section titles, like #firstdraft these won’t show up in Latex and ruin your compile.
  • WorkFlowy has intelligent search functions. You can use the OR operator to good effect for debugging your latex document. For example the search { OR } will highlight ALL curly brackets, making it super easy to spot any opener without a closer.
  • Search & Replace (Chrome). For the eternally-useful ‘search and replace’ function, there is a great chrome app called exactly that here. However there is a little (admittedly slightly annoying) trick you need to know to use it with WorkFlowy:
    • Once you have done your replacing, you need to click in every note that you changed (not on every change, just in every note, so if you have multiple changes in one note, just 1 click), otherwise when you refresh the page, the changes will revert – annoying I know, but it’s a 30 second job really.
    • Pro Tip: To make this a bit easier, first search in WorkFlowy for the thing you are going to replace. This will bring up only the notes with them in. THEN do the search and replace thing, and you won’t have to scroll through your whole document looking for the notes you have to click in – with this additional step, it’s really not so bad. An added advantage is that even after replacing the words, they will remain highlighted until you click on them, so it is easy to see where to click.
  • The WorkFlowy app on both android and iphone is fantastic. You can do serious work in this app on the go, on your thesis, seriously (it can even be a nice mental change). This is a tiny bullet point in a large post, but this is no small benefit to using WorkFlowy – the ability to zoom in to the section you want to work on takes on even greater power on a small screen. No more scrolling through endless reams of tiny text and feeling overwhelmed before giving up and checking Facebook. Use a tag search to go straight to sections which are still in #firstdraft or #todo status, edit them on the go (editing is a task I often intentionally left for phone time as it doesn’t need too much typing), change them to #reviseddraft, move on to the next. There is no better irritation-free text editor on mobile than WorkFlowy, I guarantee you.
    • For more advanced computer-like functionality on iphone and android, check out the excellent third-party HandyFlowy app (no offline mode though and relatively data intensive).
  • Here are some more great add-ons:
    • The highlighter tool. WorkFlowy has no highlight function, but do not fear. To create your own, make a new stylish style and enter the below code. By the way, this code turns underline into a highlighter, so if you love underlining, you’ll have to make a choice. I suppose you could alter the code to make bold or italic a highlighter instead, but unless you’re unusual they are probably more often used than underline.
      • span.contentUnderline {     background-color: #FFFF00 !important;     text-decoration: none !important; }
    • Customisable coloured tags (code below, just copy and paste it in to a new stylish style). You can modify these to your hearts content. Just change the tag name in the code and choose the colour hex code (the #FFA500 thing). Just internet search for hex colour codes.
      • .contentTag[title*=”#firstdraft”] { color: #FFA500 !important; } .contentTag[title*=”#reviseddraft”] { color: #FFD700 !important; } .contentTag[title*=”#finaldraft”] { color: #00ff00 !important; } .contentTag[title*=”#comment”] { color: #FFD700 !important; } .contentTag[title*=”#todo”] { color: #FF0000 !important; }
    • Rawbytz and the WorkFlowy Count
      bookmarklet / add-on:
      • ‘Rawbytz’, another key figure in the WorkFlowy community, has created a range of extremely useful ‘bookmarklets’ / browser add-ons which add extra functionality to WorkFlowy: see his webpage for a full list here.
      • If you want to log how long you spend on your write up, you can add time tags such a #1h #50m, etc. – these need the third party app WorkFlowy Count (See Frank’s post on this bookmarklet here) to be recognised – but if you want, the feature is there. If you do a bit of work just quickly throw the amount of time you spent in the section header (after a % sign, remember), and at the end you can click on the bookmarklet and it will give a pop up window which instantly adds them all up – a voila – you can even see which sections took you the longest by zooming into that section before pressing the button.
    • Tag Index Bookmarklet / add-on:
      • Another one by Rawbytz. This gives you a paste-able list of all the tags in the current list. Handy if you’ve gone wild with tags and forgotten them all: See Frank’s post on this here.
    • Collaborating & Tracking Changes. WorkFlowy is an incredibly intriguing collaboration platform, and I am only just beginning to explore the potential of this. Hover over the bullet point of a list and go to share – give someone the link that pops up and they can view / edit the list live along with you. The best thing is they don’t even need to have a WorkFlowy account, so you don’t have to convince your supervisor or collaborator to sign up to WorkFlowy or install anything at all in order to check over / comment on your work.
      • Because WorkFlowy is such a DIY program, you need to devise a collaboration ‘system’ or ‘code’ yourself: for a very well-considered one which has been through considerable testing, check out Frank’s offering here.
      • Also check out Frank’s system for tracking changes here.
        • By the way, as with all of these add-ons, if Frank’s specific choice of bold-italic-underline combinations don’t work for you (personally, I found Frank’s to be a bit too complicated to ask a WorkFlowy-naive supervisor to do) – you can easily change the code to suit your needs. I have had some success with simply asking people to underline text they want to remove, italicise text they want to add and bold any in-line comments). As we use these very rarely in academic writing, there isn’t much issue around clashing with content you actually wanted bold etc. (other than headings but you can just ignore these).
          • If you do want to change the style for this add on just click on the stylish button and go to the edit button next to it. At the top of each block of text you will see somethings saying e.g. ‘span.contentUnderline.contentBold’. That means the formatting beneath will apply when text is both underlined and bold. Delete / change that to whatever you want such as just ‘span.contentBold’ – now the formatting changes beneath will apply to anything bold.
  • Placeholders. Tags are great if you need a placeholder as you can search for them later. Common examples when I was writing up were @figure, @table, @reference, etc. When I was thrashing something out and didn’t want to take the time to insert a figure, OR I wanted to refer to a figure or table but it didn’t exist to refer to yet, I used these. When I came to the point where I wanted to fill these in, I didn’t have to trawl through the whole document to try and spot them, but just had to carry out a simple search – and of course, I didn’t miss any.

Comments, thoughts, ideas …

While writing, one has many ideas which are not formal enough to include in the main text. There is no specific comment ‘function’ in WorkFlowy. However, what there is is better. Firstly, when writing in WorkFlowy I recommend breaking your document down into very small sections as a general rule – this makes it way easier to understand your structure, and when you really want to hash out a paragraph, being able to look only at this is just wonderful. Now, if you want to make a comment on the specific section you are working on, make another bullet point nested under it, start the bullet with a % so it will be ignored by any Latex compiler if you accidentally leave it in, use a tag like #comment and say what you need to say, then minimise it so it doesn’t get in the way during normal writing. Add any tags that make sense for you like #introduction #discussion if the thought relates to those sections. Avoid going overboard with tags as if you forget they exist, you can’t search for them and they serve no function. You can now easily search your document in an instant for every section which has outstanding comments. If you want to make inline comments, I firstly recommend you use the Coloured tags add on from the link above to give the #comment tag some colour that works for you (mine is yellow). Use the highlighter to highlight sections of the text which you want to refer to then either add a #comment nested bullet or in the body of the text add a comment and put your comment in between two square brackets (or whatever works for you of course). You might also want to highlight your comment, who knows. You can do the same thing with anything: a chunk of text from a pdf you think might be relevant, some scrap notes you wrote, just nest it under the relevant section and give it a #comment or #note or #todo tag, or whatever. If you have an idea about a different section, don’t bother navigating there – just tag it with #introduction or whatever and run a search for these later. Or, have a ‘thoughts’ section somewhere, with a keyboard shortcut (see below) to navigate there, then once you’re done, just press the back button on your browser to go back to exactly where you were.

Additional note, 01/12/16: I recently found a trick with comments in WorkFlowy which I thought I would add here. If you want to add the comment ‘this needs revision’, consider formatting it like this: #comment-this-needs-revision . The entire comment is now a single tag. Now, if you have configured stylish to make the #comment a certain colour, this will also be that colour, so the whole thing really pops out. Secondly, if you search for #comment, this and any others like it will show up in the search. Finally, if you want to get rid of the comment, you can hold down alt and left click on it with the mouse (alt and left click ‘explodes’ tags in WorkFlowy). So there you have it: searchable, coloured, one-click ‘explodable’ comments. The only downside is pressing – instead of space, but I don’t find this too bad personally.

Keyboard shortcuts, Navigating and Bookmarks

There are lots of extensions for every browser which allow you to assign keyboard shortcuts to bookmarks. One I use at the moment for chrome is called speed dial. What I like about this is it lets you have your bookmarks in a folder so keeps your bar neat. One very important and wonderful feature of WorkFlowy is that every bullet point has its own unique URL. When you have WorkFlowy open every word of your document is ‘loaded’ (even this doesn’t take long because it’s all just simple text). You can therefore type the URL of a bullet point (or list) into the address bar, press enter, and it will open instantaneously, without loading, even offline. This means that you can save WorkFlowy lists to your bookmarks bar, assign keyboard shortcuts and navigate back and forth between these different sections at the press of a button and without waiting for it to load – you can also re-assign these shortcuts extremely easily anytime you like. Even better, these bookmarks can be saved searches, so if you search for #comment, then bookmark the URL, every time you click that URL it will run that search from the same place you ran it when you bookmarked, not from your current location. This is a wonderful thing. I recommend for example a bookmark which displays the major sections of your document (this might be a search from the ‘top level’ of your document for “@Introduction OR @Method OR @Results OR @Discussion”. This will make it extremely easy for you to navigate to a new section whenever you like. A “#comment OR #todo OR #firstdraft” search from the top level might also be a good idea for when you want to know what to do next. Another nice search is the lastchanged:1 search. This shows every bullet you have altered in the last minute. The 1 can be changed to a different number and you can even use 1h or 1d etc to search for hours and days.

When you are struggling

When I am struggling with writing a section, the best approach for me (and I think for many others) is to break it down – and at breaking a section of text down to help you understand it’s structure, all programs bow to WorkFlowy. Just cut-and-paste (by the way if you ever use the mouse to cut, copy and paste, stop it right now and learn ctrl + x, ctrl + c, and ctrl + v) to break it up into smaller and smaller bullet-point-headed sections until you have a grasp on the argument being made. Use the actual bullet point to summarize each paragraph and the note to contain the actual text. A useful guide I teach my students is to use a single sentence to summarise a paragraph (write this sentence in the bullet point). Now, just read the bullet point sentences and you will be able to tell far more easily if the argument you’ve made makes sense, flows effectively, or where the logical flaws are, than if you tried to read the whole section in full. Maybe you need to delete a whole section. A neat way to do this without losing the section is to use ctrl + enter which in WorkFlowy ‘completes’ the bullet point. Use ctrl + o to toggle whether completed sections are visible or invisible. If you turn it to invisible you can ‘try’ deleting a section and easily bring it back if you regret it. Maybe you need to reorganize. Dragging different sections around by clicking and holding on the bullet point makes this child’s play. Maybe you need to tag different paragraphs according to how vital they are to the argument being made / how well written they are. It is times like this that I think WorkFlowy shows its greatest power. It makes the frustrating enjoyable, and the difficult easy. It makes writing fun.

Compiling

Compiling from WorkFlowy is as easy as two copy + pastes. Open up your entire document (I recommend including every single word in WorkFlowy including the whole pre-amble, /begin{document}, etc.) by going to the top level and double clicking on the header (this ‘expands’ / ‘opens’ all nested lists, ensuring everything is copied. Alt and click on the title (or click anywhere and press ctrl a twice) to select it all, and copy and paste it over (I personally used Tex Studio for this compile but sharelatex is becoming very popular and has just introduced a track changes feature which is currently unique among Latex compilers. Then, do the same for your .bib file. Compile. Done. Well, actually you’ll undoubtedly have some errors to sort out, but that’s Latex life.

Conclusion

Without Latex, WorkFlowy wouldn’t be great for writing a thesis. It would still be nice for getting a first draft because it helps your mind flow and helps you understand the structure, argument flow, and nature of your document, which is the key to good writing. With Latex however, WorkFlowy is a thesis powerhouse, all the way up to the final compile and beyond. Reviewers come back with a raft of comments? No problem. Insert them all as sub-bullets under the appropriate section, tag them all up as #todo and perhaps according to how difficult they will be to deal with (allowing you to deal with the hardest when you are at your most cognitively able – first thing in the morning for me), deal with each in turn by zooming in (avoiding being overwhelmed), break difficult sections down, reorganize, tag, rewrite. It’s all just so much easier. I beg you, for your own sanity, never write another paper in anything but WorkFlowy with Latex again.

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The Right Way to use Evernote for Academic Literature Reviews

In this post I will be taking a rather major departure from the normal topics I cover to discuss something very dear to my heart: digital productivity! I will be presenting a system for digitally capturing, organizing and retrieving the key information from academic papers to ensure that you have the information you need exactly when you need it without tiresome searches.

I am in the 3rd year of my PhD now and I have spent far more time than I probably should have in developing digital systems to help my productivity. This has slowly led to a fairly sophisticated digital organization system, a part of which I want to share with you today. The main reason for this is that while I have stolen almost every digital productivity system I use from someone else, I actually developed this portion of it myself, with a lot of trial and error, and I think it finally works very well. Two final things to say are that I use Evernote on Windows but as far as I am aware everything I suggest here should translate over to mac (at least functionally if not button->button). Also I will be assuming you are already a user of Evernote so I won’t be introducing basic concepts – there are so many good guides elsewhere it isn’t even worth giving a link! – if you are new to the software and I suggest you read those first.

So, if you’re ready, let’s get going.

Firstly, you might be tempted to store your paper pdf’s in Evernote – don’t. Mendeley’s auto meta-data population (i.e. bringing in abstract, author, year, journal etc) and intelligent search function make it far more powerful for this.

No, Evernote is for your personal notes on those papers.

The rest of the post will be separated into three broad sections corresponding to the vital steps of any information processing system:

  1. Capturing
  2. Organizing
  3. Retrieval

There will also be some bonus material at the end in ‘Extra Tips’.

Capturing

Step 1: Create New Tag / Notebook

So when you start taking notes on a new paper, make a new tag for that paper. You could also make a new notebook for each paper (I used to do this) but there is a 250 notebook limit which doesn’t take long to hit in some fields (Ps. If you are interested in using a tag-only system in Evernote see the final section ‘Extra Tips’). I recommend naming the tag / notebook by ‘Year: Authors’ e.g. ‘2015: Jim Bob & Frank’ (oh by the way if you use tags you can’t include commas between authors names – Evernote will get very upset if you try). The reason the year needs to come first is so that once you have multiple tags / notebooks for your various papers in a list they will be automatically sorted by year.

Step 2: Go through paper taking screenshots / notes

The next step is just to start transferring the important stuff from the paper you are reading into notes in Evernote. For speed, I highly recommend screenshotting. Especially for the graphs in a paper, you are going to be want to be taking screenshots, but I am not talking about those old-fashioned whole-screen print-screen things. Find out how to take screenshots of only a portion of the screen. On my computer it is shift + win + s but I think I may have set that up in the far distant past so you might need to look up how to do it on yours.

Step 3: Paste them into notes – single ‘idea’

Paste these screenshots into a note in your tag / notebook and give it a meaningful title. Don’t be tempted to put loads in a single note – try to keep each one to a single ‘concept’ or ‘idea’ – it will make it easier to understand what is in each at a glance later, and will ensure you don’t overlook things ‘further down’ the note. Feel free of course to add your own notes above or below summarizing what is going on.

Step 4: Don’t forget the annotation tools!

Don’t forget the awesome attachment ‘Skitch’ which you might have to download separately but which allows you to add really eye-catching annotations to the notes you bring in very easily.

Step 5: Screenshot text in too!

I personally screenshot text in as well as graphics. You can of course copy it in as text, but I find this makes a nice division for me between the notes I have brought in from the paper and the notes I then make on those notes.
Also on a lot of pdf’s when you copy text over some of it becomes corrupted or is formatted weirdly etc.
I tend to highlight important sections within the paper itself before screenshotting so that I have those highlights in Mendeley too if I ever want to flick through the paper there.

Organization

Now that we have got our stuff into Evernote it is time to organize it. These leads us to …

Step 6: Create (no ordinary) Table of Contents Note

and …

Step 7: Make it into a personalized summary note

So you make a table of contents note by selecting all your notes on that paper and clicking the ‘Table of Contents’ button that comes up. This creates a new note with green ‘links’ to all your other notes in it. But we won’t just leave it like that – oh no no. This will be our ‘summary’ note and it is where the real magic begins. Firstly title this note with exactly the same title as you gave the notebook / tag you used to group all your notes on this paper i.e. ‘Year: Authors’. Next at the top of the note give a brief description of the paper – like a personalized abstract – a few lines which will work with however your mind works to immediately remind you what paper this was from the dark recesses of your memory when you come across it again half a year down the line. Secondly add a little more detail to your ‘links’ to the other notes so that when you scan this ‘summary’ note it is clear what is in them. Now …

Step 8: Tag it with ‘PaperSummary’ (non-negotiable) and any other tags needed

Next, we tag this note only. Unless you have any particular reason, you don’t need to tag any of your other notes. Firstly this would take ages so you probably wouldn’t keep up the practise in the long run, and secondly all the ‘lesser notes’ are already linked in this note, so there is no need really.

Firstly we add the tag ‘PaperSummary’ or something similar. This is non-negotiable and you will see the benefit shortly. Then add other tags to describe the paper itself. When I first started this I added 10+ tags to each of my paper summaries, and soon found out that I was only actually using 2-3 of them. Think about the most important sub-categories of your academic life. For example, I am interested in the presentation of risk, and I am interested in which papers look at visual presentation vs verbal presentation so I always tag my summaries as ‘visual’ or ‘verbal’ – I am also interested in whether papers are about ‘Frequentist’ or ‘Bayesian’ statistics so I use those tags also. In some ways it is better to over-tag than under-tag, but also, if tagging becomes too much of a pain then there is a tendency to just stop doing it at all, and then your system really will fall apart. If you are really in a rush then you could add a ‘ToSort’ tag which you would need to review regularly to tag them up properly.

Retrieval

Ok so you have all your paper notes in Evernote, with summary notes which are tagged up. What did we do all that for?

Step 9: Filtering

Once you get beyond 10-20 papers organized in the way I have outlined above, you will really start to see the benefit. Now search for the tag ‘PaperSummary’ and all your summaries from all your papers will come up, in order of when they were published (because we put the Year at the start of the name of each one). Now depending on what you are looking for you can begin to sub-divide these by your descriptive tags – for example I might, as I said above be writing a paper about visual presentation, so I only want to look at those during my research – or perhaps I only want to look at those who looked at visual presentation of risk and at Bayesian statistics, or visual presentation and frequentist, or any other combination! Furthermore once you have found the papers you are interested in you have a personalized an organized summary with links to all the important information on that paper. I struggle to imagine an information retrieval system which could bring you what you want more quickly than this with current technology – if you know of one please tell me and I will put off my real work for another couple of weeks to implement it. This system is also helpful if I want to find a paper but can’t remember exactly who it was or the year – I probably know if it was, say visual or verbal risk presentation, and Bayesian or Frequentist statistics, so if I sub-divide by these then I have a much smaller list to scour through than if I were to search through all my papers one by one. You also of course have a powerful search function if you remember any snippets of text that might be in it. Further you don’t have to explore your papers through these summaries. You can just go to all your paper notebooks / tags (whichever one you chose) and search through them by year (or search for author names) to look at all your notes for that paper. If you click on notebooks/tags and search for a particular author’s name only also, it should bring up every paper they were author on, whether first, second, third, etc … lots of options!

Finally, another great thing you can do at this point is, if you are writing a literature review for a paper or an article you could make a new tag called ‘NewLitReview’ and then as you go through all your summary papers, filtering etc, and then tag the ones you think will be important to the write up with this tag so you can refer back to them anytime and have them all in one place. Once you are done with this review, just delete the tag!

If that isn’t enough to wet your appetite, wait until you see ..

Step 10: Areas Overviews!

So say you are writing a paper on visual presentation of risk, and you look at all your notes on this area and there are still loads – 30, say – way too many to get your head around simply by reading through one by one. How can Evernote help here? Summaries of your summaries, that’s how! Select all the papers you are interested in and make another Table of Contents note.

Step 11: Area Overviews continued …

So as you can see in this link I have a bunch of green titles: these are links to the paper summaries of each of those papers – just like the paper summaries above had links to the other notes about that specific paper. I then have a brief summary of each paper in this area written below the link for that paper – I tend to put them in chronological order (which should happen by default if your list of papers was already in year order, which it should be if you followed the steps above) – and this allows me to really easily scan through and get an intuitive feel for the area very quickly – sometimes if possible I just put the main graph from each paper and one sentence like ‘No effect’ ‘Mild Effect’ etc …. This is often the first stage in preparing to write a literature review (or part of one) for me. At the top of this note it might be nice to write a brief summary of the area as a whole also e.g. ‘Mixed findings, some found a difference between the groups, some didn’t’. Now this is as high as I have ever gone in terms of ‘Summaries of summaries’ but in theory, depending on your area it might be helpful to keep going, so I might have another even-higher-level summary note with links to the ‘Visual’ and ‘Non-Visual’ areas of my field, to compare them perhaps, or compare the ‘Frequentist’ and ‘Bayesian’ areas…. In theory you could have one master summary note just called ‘Statistics’ which would define your entire field and then have links to these four areas, which would have links to …. You get the idea.

Ok I hope all of this has been helpful to you. If you’re thinking ‘But what about the actual write up?’ check out my companion post here

If you still aren’t satisfied, read on for some extra tips and tricks.

Some Final Tips

When you don’t have time…

Firstly, if I ever come across a paper but I am in way too much of a rush to go through the whole process above, I just make a tag / notebook for the paper, make a blank summary note immediately (you can copy the note links in later – you don’t have to do it by making a table of contents note), tag it as ‘PaperSummary’ and ‘ToRead’ and then just screenshot the Title and Abstract over. Done. Once you are quick this takes maybe 30 seconds and if you stick religiously to the rule that you will always do at least this for any relevant paper you come across, it ensures no papers get lost or forgotten about. I guess if you are out and about with just your phone you could even just make the summary note with the year, author, PaperSummary and ToRead tags, and that would suffice to remind you in the future to look into the paper – but I don’t really come across many papers when I am out and about to be honest …

Reference Notes

Another thing which can be handy is to create a note for every paper and copy over the text from the reference section from that paper. Tag all of these notes ‘References’ or whatever. Then you can search within just these notes for a given paper to easily see who has cited them.

Finally, if you go the full-tag route … [serious nerdiness alert]

So I am one of those nutty Evernote users who only has three notebooks. One for Inbox i.e. if I don’t have time to sort a note right now, it just goes in inbox and I sort it later. I also have one main notebook (Cabinet) where almost everything eventually goes. The entirety of my organization beyond this point is achieved through tags.

Tags are in theory better than notebooks because notes can belong to multiple tags but only one notebook, and everyone knows the anxiety created by grey areas between two hard-categories (e.g. is this bioengineering note really about Biology or Technology? – well both dangit!). Tags are soft categories – no anxiety needed, just tag them as both! Also you can only have 250 notebooks max, which didn’t take me that long to hit when making a new one for every paper I read.

Anyway, if you do want to go the full tag route, I recommend a system broadly like these:

http://lifehacker.com/organize-evernote-with-this-powerful-tagging-system-1680945078

http://michaelhyatt.com/evernote-tags.html

You don’t have to do it exactly the same but the key point to take away is to use punctuation marks to create different ‘types’ of tags. I use the ! sign for tags relating to areas of my life (e.g. !Personal, !PhD, etc.), the @ sign to refer to tags relating to areas of knowledge (e.g. @Psychology, @Biology) and the . (full stop sign) to refer to tags relating to the type of note it is (e.g. .Article, .Paper, .Idea). I also use the $ sign for tags regarding important people (e.g. $JosephThomas). This system is helpful when you are both tagging your notes and also when searching your massive ‘Cabinet’. For instance if you click on Cabinet then click on tags, and type in ! it will bring up a drop down list of all your ‘Areas of Life’ because they are the only tags that begin with ‘!’. Then once you have chosen an area of life, e.g. ‘!PhD’, you could type in the @ sign, and it will bring another drop down list of all the areas of knowledge within PhD (it will only show tags with at least 1 note within your current search area), and so on … So this system stops you feeling like you are just lost in a sea of a hundred tags and allows you to feel like you understand the ‘structure’ of your note system a little better.

A system like this is also far more minimalistic / clean than a full-notebook system as you can have ‘.Idea’ notes about ‘@Biology’ or .Idea notes about your ‘!Writing’ or even about ‘$JosephThomas’. With a notebook system you would have to have a sub-notebook within the Biology notebook for ideas on that, another one within Writing for ideas on that, another one within JosephThomas … once you give in to the full-tag system, this kind of messy organization will send a shiver down your spine.

 

[06/05/16 Note: I believe the below has now been incorporated natively into Evernote version 6.0 so you shouldn’t have to go through the hassle of changing regedit files yourself – I’ll leave it in place a while just in case it’s helpful for someone]

However ..

However, if you do go the full tag route, there is one more really important thing you will have to do. What drove me nuts when I first did this, was that if I clicked on a tag, then made a new note, the new note would not be tagged with the tag that I was ‘in’. This is different to notebooks. If you are currently ‘in’ a notebook and make a new note, it will be stored in that notebook. This lack of function with tags led to waay too many of my notes being lost in the ether due to me forgetting to tag them with the current tag. However, there is a fix. It requires a little fiddling around in the windows systems – but don’t worry it isn’t too hard.

Firstly close Evernote. Now to go to the ‘Run’ application (you should be able to just search for it from the start menu) then type in ‘regedit’ and click ok. When the window pops up go to HKey_CURRENT_USER/Software/Evernote/ Now click on the Evernote folder and scroll down the list of … whatever they are … until you get to the one called ‘SetNewNoteTags’. Double click on this and change the ‘0’ value to ‘1’. Don’t worry, you won’t break Evernote!

NOW, click on a tag, any tag. Make a new note. Fill in the title of the note and press enter. Magically, the current tag will be assigned to the note. AHHHH. No more stressful losses of notes. So when we make a tag for a paper, and click on that tag and start making notes on the paper, they will all automatically be assigned to that tag – goodbye notebooks!

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