About a year ago, I bought an iPad 3, and during the first period I mainly used it as a leisure gadget; Internet browsing, e-mail, social media etc. But when I started my Ph.D. project in the Fall, I decided to extend the use to my professional workflow, in particular to completely eliminate paper in my working routines.

In this post, I will describe how this digital workflow has been implemented to function seamlessly. I have picked up ideas and routines from many different sites and blog posts, and I hope my post will inspire you to start your own or extend an existing digital workflow.

Let me start by the conclusion: I love my digital and paperless workflow, and I feel that it excels in almost all aspects; it is flexible and mobile, and only very rarely do I feel slightly limited as compared to a similar paper workflow.

My digital workflow has the following key components:

• iPad (tablet from Apple)
• Dropbox (cloud storage service)
• JabRef (reference manager for Windows/OS X/Linux)
• GoodReader (document reader app for iPad)
• PocketBib (reference manager app for iPad)
• Notability (note writing app for iPad)
• Simplenote (note typing app for iPad)

and in the following I describe what role each of these play.

iPad

As described initially in this post, I started developing my paperless workflow because I had acquired an iPad. It is, of course, possible to go paperless without an iPad (or another tablet for that sake), but for me it became a lot more interesting with an iPad due to its ability as portable document viewer and note taker.

As I will get back to in the following sections, the iPad contains all my documents, reference material, notes and all other work related files. So whenever I go for a meeting, a presentation, a lecture or a seminar, I bring the iPad and thus all material I could possibly need. It is as easy to bring as a notebook, and it contains as much material as a laptop which thus makes it ideal for a mobile and flexible workflow.

Before I had to charge the iPad at home every night, to make sure that it had enough battery for all the activities I use it for at work during the day. This would sometimes be a bit of a hassle, especially if I wanted to use it at home during the evening as well, and I therefore decided to buy an extra charger. Also, the cable of the charger provided with the iPad is ridiculously short, and I therefore bought an extra long cable for the new charger. So now I have a long charger at home (so I can bring the iPad anywhere while charging) and the original at the office which makes for a more flexible charging rhythm.

Dropbox

I used Dropbox long before I got my iPad, and I have therefore relied on this service for my studies and work before starting my digital workflow. Essentially, I put everything, including both personal and work related files, in my Dropbox which makes them available whenever I’m online. There are other similar services, for instance Google Drive and Box, but Dropbox is the de facto standard for cloud storage. This means that many other services and apps are designed to interface with Dropbox, which, as I will get back to in the following sections, is an important part of my digital workflow.

I have Dropbox installed on my private laptop, on my iPad and on my computers at work, and whenever I work on any computer I work on files directly in the Dropbox folder; the files are then immediately synchronized to the Dropbox server and thus also to the other devices running Dropbox. This synchronization is completely indispensable in a digital workflow since the files and documents are only present digitally – and these have to be up to date when moving from one device to another!

The digital workflow could not exist without Dropbox; it is connected to all other parts in the workflow, and it even ensures connection between several of the other components. I will elaborate on this in the following sections.

In my Dropbox, I havde a dedicated folder for everything related to my Ph.D. project. Inside this folder, there is a Literature folder with two folders, Original and Edited. Whenever I find new literature, I add a copy to both of these folders; the copy in Edited is the one I read and annotate, while the one in Original is the original document, e.g. for forwarding to colleagues, without any notes and annotations.

Previously I sorted literature after topics, but this was hard to maintain consistent; some papers, for instance, belonged in several folders, and it wasn’t always quick to find a specific document with this system. I therefore decided to start sorting the reference material according to the last name of the first author which is a unique identifier for each document. I also add the publication year, so as an example this article is called Ma2013 in my system. Initially, as you will see in the pictures below, I also added the title of the document, but I have found that the author name and year work well for me and therefore now stick to this. In the folders Original and Edited, I have folders for each letter in the alphabet, and the documents are then sorted into these according to the file names.

By the way, if you create a Dropbox account via any of the two links above, you and I will both get a little bit of extra space on our Dropbox accounts.

JabRef

When I was a student, I used bibliographies in my larger students projects and publications, and in most cases these were included in the LaTeX documents with BibTeX. But I never gathered all this reference material in one central database, as I didn’t feel the time frame for these projects were long enough that it would pay off to structure the references very systematically.

In my Ph.D. project, in turn, I will work extensively in nanophotonics for a couple of years (and possibly on after the end of the Ph.D.), and a structured literature database is a must-have for this kind of work. And needless to say, an efficient and flexible system is needed to make the most of this database.

I decided to stick with the BibTeX editor JabRef that I used for my bibliographies previously. JabRef is an open source reference manager that runs on both Windows, OS X and Linux, and in the following I explain how I use JabRef as a reference manager in my work. All details are based on the OS X version of JabRef.

In the Literature folder in Dropbox (described in the previous section), I have a .bib-file, References, that I edit in JabRef. This file can also be used to generate references in LaTeX with BibTeX, but it mainly works as my literature database. Whenever I add a document to my Literature folders, I also add it as an entry in References. Most journals provide an option for exporting the reference in BibTeX format which is easily imported into JabRef (File → Import into current database). The Bibtexkey-field might be preset from the imported citation, but I set it to the file name, as motivated in the following.

When a document is saved in Dropbox, and the reference included in the database, I would like to have direct access to the document from JabRef. Which is possible as follows:

1. Go to Options → Preferences → External programs
2. At the top in Main file directory choose Browse and set the relevant path. For me it is …/Dropbox/PhD/Literature/Edited
3. Below check Autolink files with names starting with the BibTeX key. Click OK at the bottom

In the main window, double click the newly added reference and go to the General tab. In the File section, click Auto; JabRef locates the file, for instance Ma2013 in the M folder inside Edited, and it now shows a PDF symbol next to this reference in the main window of JabRef. By clicking this symbol, the PDF is opened, and I now have direct access to all my references from the JabRef interface.

Finally, I have added two custom fields for each entry in JabRef, Read and Tags. Read is either 0 (unread reference) or 1 (read reference) which allows me to quickly sort references into unread and read. In Tags, I include one or a few tags for each reference, e.g. fmm (Fourier Modal Method), blochmodes (Bloch modes) or phc (Photonic Crystal). I try to limit the number of tags so that I can always remember those that I use and therefore easily make a search for references within each tag. These fields are setup by going to Options → Set up general fields and adding read and tags in the General line.

Earlier when I read a paper, I would write a brief summary and add in the Review tab for the particular reference. But I found out that I never made use of these summaries, and therefore stopped doing it; the tags work more efficiently for me.

Before going on to describe how the iPad apps work in my workflow, it is worth noting that there are many options for reference managers – and that there is not a “one size fits all”. For OS X a JabRef alternative is BibDesk, and dedicated services like Mendeley, CiteULike, Zotero and Papers are also popular and widely used. Some of these services automatically retrieve the reference information for each PDF added, and this is simpler than in my system where I manually add the references based on the exports from the journal homepages. Personally, I don’t add references to my database faster than that I can do it manually, and in this way I also ensure the quality of the imported data (correct spelling of author names, correct spelling of journal name, complete information for required fields etc.). In any case, I urge everyone to look through the alternatives and test them for a period. JabRef works well for me, but something else might be the right solution for you.

As a final note, JabRef has a lot of neat features, e.g. export of databases to HTML format for use on homepages. It is even possible to define custom export filters to have a customized layout, and I use this for my literature database.

GoodReader

Before I decided which document reader I wanted for my iPad, I did a bit of research to find the best options. I was looking for an app that could annotate documents (PDFs mainly), but without too many advanced features, and additionally synchronizability with Dropbox was a requirement. While there are many interesting apps that can do this, the choice wasn’t very difficult: GoodReader was recommended by almost everybody and it had all the features I was looking for.

In GoodReader, you set up synchronization with your favorite cloud service by clicking Add in the Connect to Servers menu. Once the connection to the cloud service server is established, it occurs in the list under Connect to Server (tap to connect); if you click on the service, the folders and files in the cloud are displayed. By clicking a folder and choosing Sync at the bottom, synchronization of this folder is started. The chosen folder now appears in the list under Remote Sync, and by clicking the green button under the folder name, the contents of the folder is synchronized between GoodReader and the cloud service.

The synchronization is not the main feature of GoodReader, but because I only read documents synchronized from a folder in my Dropbox, I decided to include the synchronization part first. Once the synchronization has been carried out, or once documents have been added to GoodReader by other means, we are ready to start reading the documents in GoodReader.

When a document is open, a menu to the right and a menu at the bottom appear; the one to the right contains all the annotation features, the one at the bottom contains all other options (e.g. viewing mode, search, export options etc.). Most of the icons in these two menus should be self-explanatory, but have a look in the user manual for details on all the options. I more or less only use highlighting and popup notes for annotation and sometimes change the viewing mode, but you might find other features useful as well.

Once I’ve finished reading and annotating a document, I close it and tap the green synchronization buttom for the relevant folder in the main windows in GoodReader. The annotated document is then uploaded to my Dropbox folder, and the next time I open it via JabRef on a computer, the notes and annotations are included in the PDF.

PocketBib

At some point I realized that I needed the ability to access the BibTeX literature database on my iPad, in particular when I am away from a computer where I access the database in JabRef. I therefore started looking for apps that can display such a database and found a very limited number of apps. And only one, PocketBib, looked promising, so I bought this app.

Importantly, PocketBib synchronizes with Dropbox; In the Libraries pane, click the Dropbox symbol to setup the connection to Dropbox. Once this is done, I locate References.bib, my literature database, and PocketBib then synchronizes this file with my Dropbox. So when I add a reference in the database in JabRef, it is automatically included when I open PocketBib on the iPad.

In the Library pane, the entries in the database may be sorted according to different criteria by tapping on Sort, and the entries may also be searched by tapping in the Search Field. By clicking on the title of a reference, the associated PDF is opened; this relies on the association of the relevant PDF file with each reference, as described in the JabRef section above. Possibly PocketBib cannot locate the file on the first try, but if you then locate it manually, the app remembers this location and is able to locate the PDFs automatically onward. This again demonstrates the central role of Dropbox in my digital workflow.

By tapping the blue arrow next to an entry, the key information is displayed, and at the bottom Raw BibTeX allows one to see the raw code. At the top, the Edit buttons gives access to editing any field for the reference, and new fields may also be added by tapping the + at the bottom.

When I first bought the app, the editing feature wasn’t available which I found a little bit limiting; when I read an article, I would like the ability to edit, for instance, the newly defined read and tags fields for this reference without having to return to a computer to do this. I therefore contacted the developer, Graham Dennis, to request the editing feature, and soon after he implemented it. Probably others requested it as well, but I believe our communication helped him decide to include this feature. By the way, I have had several communications with Graham Dennis, and everytime he was very helpful and eager to improve and develop the app – which is yet another reason it is worth buying.

Notability

During my studies, I have written enormously many notes, reports and assignments, and they now fill up several moving boxes in my apartment. Occasionally, I need some of these notes to brush up something I learned in a course, so I don’t want to throw them out, but I really would prefer to store them more compactly. Therefore, at the beginning of my Ph.D. project and equipped with my iPad I decided not to fill more binders with all the notes and derivations I’ll write during my project; instead, I’ll fill folders in my Dropbox with these notes and only have them electronically.

There are a lot of note taking apps for the iPad, and I spent a couple of days doing research on these before deciding to purchase Notability. This app (need I say it?) synchronizes with Dropbox, and other popular services, and the notes can be exported in PDF, RTF or Note format. I only use the PDF format since most of my notes are handwritten where RTF does not apply and since PDF is convenient for reading the notes on the computer.

To start writing a note, tap the the writing symbol in the top right corner. This opens a blank note with the default file name Note which can be edited to any desired file name. In the central part of the top bar, the input format can be chosen: (from left) typing (t), writing (two pencils), erasing (the rubber) and copy-paste (the scissors). I mainly use the typing (for editing file names and for making headers and titles inside the notes), writing with the thin pencil and the eraser.

The most prominent feature is the functionality for writing: by choosing one of the pencils and tapping on the magnifying glass at the bottom, a new section appears at the bottom of the screen, and a box appears somewhere on the note. Tapping somewhere on the note moves the box to this place, and the actual writing now takes place in the section at the bottom of the screen. This means that it is possible to write in relatively large size in this section and still have the text appear in relatively small size in the box on the screen. When you continue to write into the green part in the section at the bottom, the box automatically moves to the right, and this makes it ideal for writing handwritten notes on the iPad.

It is also possible to draw sketches (tap the + and choose Figure) and include photos (tap the + and choose Photo), and even to include audio, e.g. recorded at a lecture.

I write all my notes and derivations in Notability, and this works really well for me. Sometimes I use a piece of scrap paper for some initial thoughts and calculations, but the final version is always written in Notability.

Simplenote

Simplenote is a note app for the iPad that I use for typing all sorts of notes. The app is really basic and does not allow any text formatting which at first might seem limiting. However, I use it for writing notes at meetings, for writing down ideas and thoughts that I need to remember, for to-do lists and similar things that are “in progress”, and none of these need any fancy formatting; therefore, Simplenote is perfect for this purpose for me. The lack of folders may seem like an unorganized way of handling a large number of notes, but the built-in search function makes it easy to find any note.

The notes are synced to a central server, and they can be accessed via Simplenote’s homepage. So I also use Simplenote on my computers, and this flexibility makes Simplenote perfect for quick notes, both in my work and privately.

Many people use Evernote for these types of notes, and Evernote can do a lot more than Simplenote. I also use Evernote for saving different things, but for the basic notes that don’t require all sorts of folders, text formatting and other bells and whistles Simplenote is still my preferred tool; it is simple and allows me to focus on quickly typing the notes, without spending time and energy on the typesetting.

Wrap-Up

The above outlines my digital workflow, including the apps and tools that I use the most. On top of those mentioned I also use Feedly for my RSS-feeds (including subscriptions to a number of journals that I follow), the Matlab iOS app, vSSH (a terminal app for iPad), Twitter and many more. And to recap and repeat myself: I love the digital way of working.

Therefore, I encourage everybody to start working on their own digital workflow. And to share experiences, ideas, comments and questions below.