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Organising Your Research: Advanced Zotero
Now where did I read that quote? What did that book say again? Was the argument in this chapter coherent?

For anyone working in a research field I’m willing to bet that you have asked yourselves such questions, and it only gets worse the more you read. So after the post on Reading last Friday comes this timely post on how to organise what you have read. As with most items in our toolkit there are several different options for working at this stage of the process, however I’m only going to consider one today: Zotero. This is mainly because Zotero works at engaging with multiple different tasks in the research process. At one level it is a full fledged reference and citation manager, while at another it is a synopsis and summary database, and at yet another it is a library and database organisation tool. I feel that Zotero combines the best aspects of several other tools, and does it without a lot of the bugs or cost of some of the bigger names (cough Endnote comes to mind). Personally I use Zotero as a bit of a hub within my research process, articles and information get funnelled in and then spokes radiate out towards different tasks and then information is returned for further collation and use. This post is how I use Zotero.

The Basics

Simply speaking the basics of Zotero work as follows:
- Import or add reference into Zotero from the various plugins and data sources (Amazon, Ebsco, PubMed, Libraries etc) or input by hand.
- Cite reference in your text
- Sit back and marvel at not having to manually format references.
My Zotero Library

At the first level, that of making your work of referencing easier, Zotero does an admirable job. It is quick, easy to get data into, doesn’t crash regularly (Endnote should take notes), syncs over the web, and outputs in a wide variety of formats with little fuss. Even if this is all you use it for, it is a great time saver and helps with taming your citations from brusque unruliness to a general surly attitude. However, Zotero is capable of so much more than this, and to leave the process here would be to hamstring the use of the tool. But first a brief caveat.

Caveat: Zotero is exactly like every single other computer application, in that it is a bunch of mechanically executed code. [ref] ok some genetic algorithms excluded[/ref] It cannot think for itself, and while it has a whole bunch of smarts built in, it can only deal with the data that you feed it. So in true computer terminology it is susceptible to the failings of Garbage In, Garbage Out. Simply put if you feed Zotero, or any other program, garbage data, then expect garbage in return; it can only work with what you feed it. So if your citations have the wrong publisher, or incorrectly entered titles (yes capitalisation here counts), then you will get that out in return. This is the most common mistake I see with Zotero usage. I cant emphasise it enough, police and parse your data on the way in so you get well formatted, rather than unruly, data on the output. It is also worth noting that most library systems, including Library of Congress, and publisher data won’t conform exactly to your requirements. So things like the publisher ‘WB Eerdmans Inc.’ will need to be manually stripped back to ‘Eerdmans.’ This is extra effort, and is actually why I recommend that students only writing shorter essays (commonly ~2000 words) simply write and format their citations manually.

Research & Organisation

That caveat aside, and arguably because of that caveat, we will continue on to the bigger and greater things that Zotero is capable of. If you are anything like me, you will probably dislike having a desk full of pieces of paper and various journal articles that have been read, or still yet to be read, or have been read but not summarised etc. For about 10 years of my prior research life this was my overwhelming bugbear. I would regularly lug a ream of paper around with various journals articles printed out, and swathes of postit tabs throughout them. These days I deal primarily in PDF, and digital highlighting and annotation make this process much easier. But how do you organise this information? All those a3532582920.pdf and pubmed_83928932.pdf, not to mention the assorted .epub files of Open Access books, and much more. Well this is the second phase of how to use Zotero, and where it comes into its own.

The first feature is somewhat mundane: renaming. Once you have a reference in Zotero you can attach or link a PDF to the reference and simply rename the file from the metadata in Zotero. It’s a simple feature, but saves a bunch of time and effort.

Secondly, and more critically, as a digital reference manager you can add all your references to Zotero, and then sort and organise them by two different methods. Firstly, you can sort them into categories. I predominantly use collections for thematic organisation, as you can see in my screenshot: ‘Christology’, ‘Luke.’ Furthermore these collections can be nested, as in my ‘Psych’ collection with various sub-collections underneath. The second way to organise your library is through the use of tags. I tend to use tags in three different fashions: topical, procedural, and project oriented. Topical tags simply delineate the various topics that are addressed by an article or book. Procedural tags generally mark whether something is yet to be read (toRead), or yet to be marked up (toMarkup). Project tags simply note that I used a certain article in a project I have worked on. The entire Zotero database is searchable by these tags so you can easily and quickly have an idea of what is yet to be read or marked up, or what you cited for a certain paper, or what deals with certain topics. Super simple stuff, but invaluable in being able to find material quickly when your library grows large.

Documentation & Gathering

The penultimate phase of the Zotero experience comes in being able to collate and find your documentation and notes on all the books and articles. Within Zotero you can add ‘Notes’ for each reference. I use these notes in two ways. Firstly if I’m working with a digital resource tend to have a single note dedicated to all the highlights from that resource. You can extract these simply, and I’ll cover that in coming weeks. If it is a physical resource then I tend to transcribe either the full quote of interest, or briefly summarise the idea at hand, and note page number. That way the key pieces of information are easily at hand. This is the markup phase of my ’toMarkup’ tags above. Secondly, I also write a brief 50-100 word synopsis of each chapter or major logical section of the reference, in my own words. This allows for better memory retention of the material, but also provides a good reference synopsis of the work and therefore makes it easier to engage with at a later date. These Notes are stored alongside the reference and are synced across devices, and so are easily accessible anywhere. Furthermore, they are eminently searchable and while my office used to look like it was overflowing with a small dead forest, and previously I would be scrambling around in various manila folders and a whirlwind of post-it notes to try and find the source of a quote, I can now search for it in Zotero, and in pretty short order I have found the document I am after. This is one of the features of Zotero that I find invaluable these days.

Output

The final phase of my Zotero workflow is to actually output the references as citations in my documents. While Zotero does come with Word, LibreOffice and OpenOffice plugins, I find all of those word processors annoying and ultimately unsatisfying. I prefer to use Scrivener, which I will talk about in due course. But unfortunately Zotero doesn’t come with a default Scrivener plugin, although I’m hoping for one eventually. Rather you can use the RTF Scan feature of Zotero, which makes it useable with anything that can output in RTF format. In order to reference material you simply use the short code, consisting of {Author, Date, Page} or any one of the other short codes depending on your usage. You then run your output through Zotero and choose your stylesheet and bam, all your citations are done. It doesn’t get much simpler than that.

The final note goes to the stylesheet functionality. There are many referencing formats out there, and Zotero is invaluable when you need to reformat an article or paper for a different referencing system. All you have to do is download the new stylesheet and apply it to the document. There is a whole database of Zotero stylesheet (CSL) files out there for various formatting systems, and the majority you can find here: https://www.zotero.org/styles

If you are an SBL 2.0 user, you will find that the style on the repository is one that uses Ibid. notation. Given that the no-Ibid option seems to keep disappearing, here it is for posterity. society-of-biblical-literature-2nd-edition-full-notes-no-ibid

That just about wraps up this post on Zotero, as I said I find it the central hub of my research methodology. Although I’m sure that there are other tools out there. Perhaps Endnote has become the phoenix from the ashes and resurrected itself without crashing every 15 minutes, or perhaps you prefer a different tool. As usual I would love to hear your comments and what you use in the section below.
February 16, 2015
How to be Productive? – Time Management and Organisational Skills

When it comes to time management, organisational skills and plain old doing stuff there are a ton of pithy sayings out there: ‘to finish first you first have to finish’, ‘to do what you need to do, you need to know what not to do’ etcetera etcetera. Indeed it seems sometimes that there are almost as many methodologies for doing things, as there are pithy sayings, and things to be done. Welcome to the Friday ‘theory’ portion of the skills posts.

Overall the huge breadth of books and material on the topic can easily lead to analysis paralysis. I have a friend who I think has probably read every book that there is going on productivity and management and all the cookie cutter approaches, but still is absolutely hopeless at actually settling down and doing things. So what is there to do about productivity, do we simply adopt one methodology and hope it works, or swap and change between them at will? Well in many ways either of those options would be better than nothing, as usually going about our lives in a haphazard manner only leads to getting snippets of jobs done and overall lower productivity. But there are some systems that are better than others.

I must admit here, I don’t follow any one system, but rather adopt little pieces of each of them. I like the list making approach from GTD, but hate that it commonly ends up in swathes of lists without any action. I like some of the Seven Habits, from Stephen Covey, but find that a lot of the time they don’t really lead anywhere and you can end up like a guinea pig on a treadmill. So on and so forth. However, last year I read a book that sought to synthesise many of the different methods and come up with another system, the book is What’s Best Next by Matt Perman. It approaches things from a Christian perspective, anchoring theory in the Gospel, but I think it is equally as relevant to a secular endeavour and secular people. Again, I don’t adopt his entire structure point by point, but I think his overall architecture works quite well.

He has organised his method around four aspects: Define, Architect, Reduce, Execute; and yes they make a cheesy acronym: DARE. Now each of those is split up into a whole bunch of sub categories and methods, which I won’t reproduce here in whole because they would essentially be plagiarism. However, I think the four work fairly well as an overall architecture, and this is how I use them.

Define: I have a series of goals, both shorter and longer term. For example a long term goal is to do with working in Theological Academia, while a short term goal is to finish the papers I want to submit for a conference. These are written down, because if they are merely floating about in the ether then they become overly fluid and changeable. I generally revisit my longer term goals (more than a year) every year between Christmas and New Years. While I maintain my shorter term goals and tick them off as I go, and refresh these goals regularly. Longer term goals tend to be noted in a journal or note taking app. While shorter term goals are put into a task manager; more on those in the tools post on Monday. Having goals helps with knowing where the finish line is, rather than wandering aimlessly around. Plus it assists in reward based motivation and management.

Architect: Having a child has taught me that routine is relatively important. When I was at uni for my undergrad I generally just worked when I felt like it, and commonly pushed myself so hard for several months at a time that I would just collapse during holidays. Now while I still am capable of pushing that hard, it is actually far more effective to architect a routine for myself so that things get done at a good rate throughout the week, month and year rather than being in spurts and starts. To do that I have roughly mudmapped out my week. From the simple things such as the days I am at home with the little man, my research slots, through to roughly where the admin for work, college and church fits in. It is best to start with the big items first, that way you know there will be time for doing them. I tend to have things at a relatively high level, in blocks rather than to specific times, as this works well for me with changeable patterns with the little man. Others I know have a lot more set times, down to the hour or half hour. You will need to figure out what works for you. As well as planning the week, it is good to plan ahead for a 3 or 6 month block, so that things like holidays and other deadlines don’t creep up unawares. Tools for doing this include calendaring apps and task managers, which in apt timing will be covered on Monday.

Reduce: The third aspect of Perman’s approach is simply reduce. Cut out the things that are not productive in any fashion. It may be that for you sitting down and watching some TV is cathartic and helps you relax, I know it does for Gill. But if watching 5 episodes of your favourite TV show each night is causing time issues because things aren’t getting done, then perhaps its time to reduce a bit. Ultimately its up to you how much you reduce and lean out your week. But one thing to consider is how you can multitask with your time. If you take public transport to wherever you do your work then consider reading or doing some other work on that trip. Or if you walk then perhaps a relevant podcast you have wanted to listen to. This is a good way of helping you reduce without having to completely remove the things you are working on. Just make sure when you are reducing you aren’t eliminating the big things you need to get done.

Execute: This is probably the easiest stage. You have some time set aside, now do the things you have tasked to do… and don’t procrastinate about it. While there are a bunch of different methods for doing tasks, such as reading or writing, and I’ll cover some technique to make these easier later in the series, ultimately its down to just doing the tasks. There are some tools that can make this easier, such as good task managers, the Pomodoro technique, and apps to assist with self control and defeat procrastination, and I’ll cover those on Monday as well.

So how do we be productive? Well its not entirely by following a series of steps and rules. I have outlined a high level method above, which comes from Matt Perman’s book, that I highly recommend you get a copy of and read. But ultimately you need to adapt it to your own life. Perhaps a good piece of homework is to sit down and do the D-A-R-E methodology and see where you end up.

I would love to hear in the comments your own techniques for the overarching methodology you use.

February 6, 2015
Work, Research and Organisational Tools Overview
When working, or studying, or for that matter going about daily life there are a multitude of skills and disciplines that will help us be better at whatever we are doing. Some of those skills and disciplines I will look at in the Wednesday and Friday sessions. But in addition to these skills and disciplines there are a whole host of software tools that can make the tasks at hand easier, more productive, less painful, and assist us overall. However, there are two caveats with any toolset.

Firstly, they are only tools, they do not replace the tasks that are at hand, or the skills and discipline needed to complete the task at hand. One common trap I have seen many students and colleagues fall into is assuming that because they are using the right tools that the task will become self-completing, or that they can use less effort for the same results. Using the right tools will make your life easier, but they wont do your work for you. Just because you have a Phillips screwdriver rather than a hammer to undo the screw, doesn’t mean that the screw will automatically undo.

Secondly, there are a lot of tools out there. In putting together this series I have experimented with some tools outside of my normal toolkit, or tried to find free, cheaper or better alternatives. But commonly this can lead to tool paralysis, where we wonder whether Tool A is right for the job, or whether we would be better served with Tool X, Y, Z and the rest of the alphabet. The truth be told there is no one perfect tool for any job, each has their own quirks and idiosyncrasies, and it is up to the user to decide whether the tool at hand fulfils their requirements accurately. On the flip side there is something to be said for maintaining a relatively stable toolkit, as chopping and changing regularly tends to waste time with the learning curve of the new tool. The toolkit I work with, that I will showcase in this series, has has several tweaks and minor changes, but hasn’t had any major upheavals for several years now. It is stable, and the oddities I have either embraced or learned to work around.

This Monday series will document my toolkit that I use for my research, synthesis and output in my academic life. In various incarnations this toolkit has served me well through the last ten years of academic research after I finished my undergrads. Some of the software has changed, and certainly the proportion of digital work has increased with new technology, but the overall process has remained relatively stable. While ten years ago I worked mostly in paper, I have transitioned to being predominantly digital in workflow over the last five years. This certainly helps with being able to search and access data easily, and assists in the synthesis and output process.

Overall my workflow looks something like this:

(Click for a bigger view)

Roughly speaking I take input either already digital or physical, digitise the physical media, manipulate it so that it is consistent with Briss and OCR (Acrobat) tools, and then add it to my library (Zotero and Devonthink). From there I maintain my library and process the material through reading, note taking and writing synthesised summaries. On the output side I use a mindmapping tool (Scapple) and a word processor (Scrivener) to synthesise my ideas into their final forms.

Alongside this process sits a bunch of task management tools, note taking apps, and productivity tools that assist me in getting my work done. I will come to each of those in turn.

The next six blog posts will cover this entire process in more detail, and will roughly follow the workflow. The six posts will be on:
- Task Managers & Focusing (Tools for Getting Things Done)
- Briss & Acrobat (Wrangling Digital Files)
- Zotero (Citation and Library Management)
- Dropbox and Devonthink (Storing and Accessing Digital Media)
- Note Taking Tools
- Synthesis Tools (Scrivener and Scapple)
I’m looking forward to this series, partly because I’m keen to help others be able to organise their research and writing better, but also because it helps me review my own toolkit and see whether anything needs further tweaking. I would love to hear your thoughts on the process I have outlined, and what tools you use. Comment here or on Facebook.
February 2, 2015