Essential Software and Academic Tools for a successful PhD

Disclaimer: I am doing my PhD in marketing and I study consumer culture. But I think the tools suggested will be universal to all subjects but I didn’t specifically test it for STEM subjects.

It’s difficult to start as a PhD student. There are so many questions that come up when you begin your PhD journey. What do I read? How to begin writing? Where can I store my data? What if my current laptop is inadequate? I can’t imagine the days of typewriters and manual note-taking. I wouldn’t have survived those days, and with the chaotic work pattern that I have, I would have given up a PhD in a few months.

I am a techie. I am an IT engineer, but I study the impact of technology on human lives and don’t agree to techno-determinism (Long story, read it here). But I think the right dose of technology can help make any research better. Therefore, this post will have a detailed review of the tools that you can use to make your research life better. The devices and technology do not maketh your research, but they help you to fast track.

Most of the tools are universal, and I have carefully chosen based on compatibility. Some of them might be Apple Mac specific, but I will mention them clearly in the post.

The Device (The Resistance Base)

Most of you might have a laptop with you. But sometimes, you might want to start afresh and buy a new laptop while starting your PhD. The choice of your device should be based on the research project that you would do. There are two crucial things that you need to take into account while choosing the laptop.

1. Compatibility of the software that you might be using — for example, specific applications used by your department might not be compatible with Mac (mostly) or Windows. Get the information from your department before buying a new laptop.
2. The power needed for specific applications to run. Although most laptops have high RAM capacity, some of the apps might require even heavier RAM. For example, the current version of MacBook Air has an 8GB RAM, and the high-end MacBook Pro has a 16GB RAM. HP Pavilion 14 has an 8GB RAM — which is pretty good all-round student laptop in the Windows section.

If you check the laptops, the prices increase based on the capacity of RAM and the storage space. But I would suggest that you should be worried more about the RAM capacity and not storage space. The cloud services and external hard disks have expanded the ability to store. So, your laptop choice should be based on RAM.

Best Mac Laptop (if the majority of your work is with a word processor, reference management and statistical software): MacBook Air

Best Mac Laptop (if you have to work on some heavy applications): MacBook Pro with 16GB RAM

Best Windows Laptop (if the majority of your work is with a word processor, reference management and statistical software): HP Pavilion 14 with 8GB RAM

Best Windows laptop (if you have to work on some heavy applications): DELL XPS 15 with 16GB RAM

You can also install Linux on to your laptops for more stabllity. Most of the applications have support for Linux. I wouldn’t suggest chrome based laptops due to the lack of compatibility with majority of applications.

Word Processor (Light Saber)

I can hear the voices. MS Word should be an obvious choice, right? I differ. When you wrote your Masters’ thesis, if you had more than 50 pages, MS Word would have shown it’s real colour. MS Word has been designed for less bulky office documents. If you have been working on academic papers on MS Word, you would have encountered issues while typing formulae or while formatting a table or a simple footnote. Academic writing is an afterthought for MS Word, and they use Macros for citations, bibliography, cross-references etc. Macros functions make the Word documents bulkier and slow. There are word processors that have been designed with academicians in mind (or other bulky writers) that will help you with granularity, more comprehensive formatting options, categorisation and stability.

1. Scrivener

Scrinever 3 (Source: https://www.literatureandlatte.com)

Scrivener (comes from the Old French meaning ‘to scribe’) is a software created by Literature and Latte. The company call the software as something created by writers for writers. The software was designed for novel writers and screen-writers but widely used by academics because of the section categorisation, which allows you to work on chapters individually and compile it at the end. Recently, Scrivener came up with their latest update for the Mac (the windows version is expected soon), and they have done substantial visual and features rehaul.

Pros (for academicians)

1. Structure and built-in categorisation — you can break your thesis or paper into chapters, and each chapter can be worked individually
2. Scrivener has something called a corkboard view that allows you to see your document as a continuous text, and you can rearrange the sections efficiently. If you are a messy writer, this feature is a saviour.
3. Split-screen view to see two documents for comparison — if you want to copy from another document or to work on feedback from your supervisors, this is a timesaver.
4. Scrivener is available for iPad, iPhone and Mac, but I don’t know how many academics write on their iPhone (I do take notes and write a blog on my Notes app).
5. The other exciting features include word targets, scrapbook feature where you can write notes and multiple colours for drafts (so you know the number of changes), dark mode and a no-nonsense writing mode.

Cons

1. As the software was designed for novel and screen-writers, the reference management in Scrivener is an afterthought. Although Scrivener has a simple integration with major reference management systems like Endnote, Sense, Bookends and Zotero, there are a few issues. In this review of Scrivener 3, Katelyn Knox (an Academic) notes that Scrivener doesn’t format Endnote citations and with Bookends (my favourite reference manager), I had to copy-paste the citations.
2. The compile feature is little tricky, and sometimes it screws your formatting.

External reviews:

https://medium.com/@tpletcher/scrivener-3-review-9f35c710e413

https://katelynknox.com/academic-writing/scrivener-in-depth-review-academic-writing/

Pricing: Standard — £47 and Educational: £39.95. Note that Scrivener 3 is yet to be released for Windows. Expected anytime soon and you get a free upgrade if you buy Scivener 2

2. Ulysses

Ulysses (Source: https://ulysses.app)

If you like Markdown writing method, you will love Ulysses. It might seem like a simple writing app for your Mac or iPad, but this one packs a punch. The advantage of writing on Ulysses is the clean interface, and it has a goal-oriented approach to writing. Say, if you want to finish 1000 words a day, you can set them with Ulysses.

Pros

1. Focus on writing and forget the formatting when you write. One of the problems with existing word processors is that you have to spend a considerable amount of time in formatting the document.
2. Ulysses has smart folders called filters that can be used to filter your writing based on specific keywords (automatically) — this helps in finding stuff even if you have reams of documents.

Cons

1. Again, integration with reference managers. Ulysses tightly integrates with Papers but it loosely integrates with Endnote and Bookends. You have to create Markdown format, copy citations and formatting is a pain.
2. Ulysses doesn’t have instant categorisation, and you might not be able to do chapters ( you can work around with multiple documents).
3. If you are not well versed with markdown, this app is not for you, and most of us have enjoyed the rich text formatting mode of MS Word and might need something similar.

External review:
https://thesweetsetup.com/apps/best-writing-app-mac-iphone-ipad/

Pricing: £10.99/6 Months for Students.

3. Pages for Mac

Pages for Mac comes free with all MacBooks and continuously gets updated by Apple. If you think Apple is providing these applications for free and they might not be trustworthy, think twice. Pages is a robust word processor that might look simple on the face but pack a lot of customisation options that might be useful as an academic. Page layouts, customisable style templates and other usual word processor features are available on Pages. But what makes Pages better than other word processors, the way it handles graphics and images. It’s easy to produce, customise, format and rearrange charts/graphics in Pages. Pages is exceptionally stable for longer documents, autosaves on iCloud, and you can also have version controls.

Omnioutline of Mac for Pages

Cons

1. Pages has tight integration with EndNote but not with other reference management software. However, Bookends can scan and create bibliographies on Pages.
2. The templates available are more Americanised versions, and it’s not feasible for UK/European academic essays/documents.

Pricing: Free with Apple Devices.

4. Mellel

I kept the best for the last. Mellel is the word processor I use, and I found it after a lengthy investigation. Mellel was developed by academics for academics. This is the only word processor in our list that’s geared towards academic writing, and you might not find this by a simple google search.

Live Bibliography and character level formatting of Mellel

Pros

1. Live Bibliography: Mellel tightly integrates with Bookends (actually integration is an understatement. They are literally one application in two different windows). Live bibliography is an excellent feature that sits on a palette. You don’t need to go to bookends to repeat the citations. Cross-references are easier in comparison to Word because you just need to add the relevant
2. Granularity: Mellel has granular formatting options. You can have different and multiple formatting styles for section, page and paragraph, line and character levels. In any commercial word processor, the character level styles have to be made manually.
3. Auto-tiles: Auto-tiles is a unique feature. It’s the heading and subheading hierarchy that you see in different word processors. But in Mellel, you can format how these need to look at different levels. This makes the outline and indexing easy. This is arguably the most crucial feature of Mellel.
4. Sections and sub-sections: If you have clear boundaries of section and sub-sections, Mellel’s outline work likes a charm when you want to move sections around.
5. Find and Replace: This is an exciting feature where you can store your find and replace expressions. I recently used it to change “Quantified Self” to “quantified self” as I was exchanging drafts with my supervisors back and forth.
6. And it has a fully functional iPad app!

Cons

1. It’s a Mac-only application. The application targets academics who are fed up with MS Word on Mac.
2. It doesn’t appeal to the normative aesthetic expectations of a word processor. The band designs, icons and palette designs look retro, and if you are used to the colourful designs of Word, Mellel is not your application.
3. With Mellel, the learning curve is quite high. It will take time for you to master the word processor, but when you master it, you will love the flexibility, stability and sheer pleasure of writing with Mellel.

Mellel: Education License — £32.10. iPad App — £19.99. Look at the reference management system — Bookends part for a combo offer with Mellel.

Other Word Processors to consider:

1. LaTEx ( it’s more of a document preparation system and has a steep learning curve)
2. Libre Office
3. Open Office
4. Nisus Writer
5. Manuscripts (originally a Mac based word processor now a web based authoring system — quite interesting because it boasts 1300 Journal styles)

Reference Management System (Millennium Falcon)

I have just completed my first year of PhD, and I have 665 references on my Bookends database. The length and breadth of your PhD research are enormous, and I still can’t imagine how our predecessors of the yore survived without a research management system. A research management system is vital for the following reasons.

1. Smooth organising, managing and retrieving your references
2. Store (or at least link) to full-text PhDs
3. Take notes and annotate relevant material while reading the paper
4. Easy citations and bibliography

All the applications in the market (free or not) definitely do the essential functions that are expected from a reference management system. The vital features include importing the references, organising PDFs, generating citations and bibliographies, annotations etc. But each of them approaches this differently and also the depth of integration with the word processor differs. I am going to point out the select pros and niggling cons.

Endnote and Endnote Online

Endnote is an obvious choice used by many academics, but it’s the most expensive product out there. Endnote was owned by Thomson Reuters, but they spun off all the analytical and academic brands into a separate company called Clarivate Analytics. For example, Clarivate owns Web of Science Group.

Pros

1. Endnote is robust and was one of the earliest products in the space. They have more than 6000 different bibliographic formatting options and every university (including mine) have a downloadable .ens file.
2. Endnote worked out through the university network, and most of the universities have licenses for Endnote. Endnote Online is widely publicised by universities.
3. You can customise bibliographic styles, create multiple libraries and complete search of PDFs.
4. Tight integration with MS Word, Pages for Mac and Open Office.

Cons

1. Endnote is expensive — it will cost you $250 and not a worthy investment with other good options available for free or fraction of the price.
2. One option is to use Endnote Online but according to me to it’s suitable for masters/undergraduate courses but not for PhD. With Endnote Online, you will not be able to search the content inside PDFs, can’t import or edit the bibliography style, customise views and displays, cite tables or figures or images etc. Also, you have to be online to work on Endnote Online/Basic.
3. The learning curve is quite steep for Endnote. In short, there are courses to learn Endnote.

Endnote : Price — $250. No restrictions on storage.
Endnote Online/Basic: Price — Free. 50,000 references.
Compatible with Mac and Windows
Integration with MS Word, Apple Pages and Open Office

Mendeley

Mendeley was started by three German students in 2007 as an alternative to Endnote with investors from various companies like Last.fm and Skype, along with academics from Cambridge and John Hopkins. They named the application after Gregor Mendel and Dmitry Mendeleyev. It was considered to be a rebel system to Endnote but lost a bit of that sheen when it was acquired by Elsevier in 2013. But Elsevier acquisition has helped Mendeley to proliferate into different segments of reference management.

Mendeley collaboration and PDF viewer

Pros

1. Mendeley is the easiest to use of all the reference management systems with the minimal learning curve. The web and desktop versions don’t have much of a difference. iPhone and iPad apps compatibility.
2. Mendeley uses plugins to import journals (all the reference management solutions capture the metadata from pdfs/webpages) and for citations — compatible with Safari, Internet Explorer, Firefox and Chrome.
3. Mendeley has an inbuilt PDF viewer. Although most of the systems have that, I found Mendeley’s the best and most stable. It also has collaborative reading and note-taking if you are working on a project with your peers.
4. Mendeley has a papers catalogue that suggests related articles based on your papers and keywords. I still get suggestions although I don’t use Mendeley anymore.
5. Mendeley has an inbuilt social media that can be used to connect with fellow researchers

Cons

1. Mendeley has a freemium model and the free version can hold only 2 GB of data on the web. This could be a problem for some, but my friends say that they haven’t crossed the limits until now.
2. The sync between online and offline is not automatic.
3. Mendeley takes the citation styles from citationstyles.org, open-source repository of over 7000 styles. If you need to make a customised version of the citation style (like my business school’s), you have to use the CSL editor, and I wouldn’t suggest it (believe me!). You can’t export .ens or any other third party file into Mendeley.

Since June 2018, Mendeley started encrypting and locking the PDFs if people tried to export the database.

https://getpolarized.io/2019/01/23/mendeleys-encrypted-repository-is-fundamentally-anti-science.html

This is a predatory move from Elsevier and not a good for the brand as it stood for openness at one point of time. Zotero is a better choice if you are looking for something free.

Mendeley: Freemium. Desktop Version: No restrictions on storage. Cloud: Free until 2GB and after that subscription starts from $4.99/Month
Compatible with Mac, Windows and Linux
Integration with MS Word, Apple Pages and LaTEx

Zotero

Zotero is an open-source project from Centre for History and New Media at the George Mason University supported various foundations like Andrew W. Mellon Foundation, the Alfred P. Sloan Foundation, and the Institute of Museum and Library Services.

Zotero and Mendeley have similar features, and there are only a few things that are different

1. Zotero supports Google Docs, and it’s the only software on the list that supports Google Docs. If you are really thinking about writing your thesis with Google Docs, Zotero is the reference management system.
2. Zotero creates snapshots of the webpages that you add to the reference list, which is not available on Mendeley.
3. Cloud storage on Zotero is optional, unlike Mendeley. This means with Zotero, you don’t need to be online to access your data. But if you start using the cloud, Zotero limits you at 300MB, which is quite less for a PhD thesis.
4. Zotero also has a Firefox App

Zotero: Free. Desktop Version: No restrictions on storage. Cloud: Free until 350 MB and after that subscription starts from $20/year
Compatible with Mac, Windows and Linux
Integration with MS Word, Apple Pages and Google Docs

Readcube Papers 3

Papers was an independent multi-platform reference manager system developed by two PhD students from the Netherlands Cancer Institute. They wanted to create an iTunes style approach to reference management. It was owned by Springer Nature, an academic group and couple of years back Readcube acquired Papers. Readcube had its own reference management system, but they merged everything, and the brand is now called Readcube Papers.

Papers, when it was independent, was used by many academicians due to the robustness and the sheer volume of citation styles. Post the acquisition, some of them moved (especially Mac users moved to Bookends), but the new app is as stable and comprehensive as the old one.

Papers does all the typical things that a reference manager should do, but it has few things that trump other systems like

1. The enormous amount of citation styles
2. Floating citation plugin (only for MS Word)
3. Collaborative reading, sharing and social network

I tested Papers before choosing Bookends. I am not that fond of MS Word for my writing, and I had chosen Mellel as my word processor for which Bookends was a perfect fit. But Papers is the best alternative to Endnote if you don’t want to spend a large amount of money.

Readcube Papers: Subscription-based service. $3/Month. No limits on online storage space. Student discount on request with a valid student ID.
Compatible with Mac and Windows. IOS apps are available. The cloud version works on any browser, but Chrome-based browsers are better.

Bookends

Bookends is my favourite reference management software and the one I currently use. I was using Mendeley for my references and moved to Bookends after a careful investigation. Bookends is such a secret that even a google search for the name wouldn’t suffice to find it (search for Bookends reference manager instead). Bookends is a Mac-only reference management system that’s developed by Sonny Software based in Maryland, USA.

I found it after I discovered Mellel and Mellel had a combo offer with Bookends during the Black Friday sale of 2018. But I didn’t buy Bookends because it had an offer. This piece of software has saved me a lot of time this year.

Pros

1. The citations and bibliography are customisable. Bookends uses .fmt format to address this issue, and it has all the standard styles. I modified the Harvard format to suit my Business school style, and it worked like a charm.
2. Bookends uses temporary citation format (usually parenthesis). When you insert a citation into a document, and when you are ready to finish the material, you can scan the document to generate the citations/bibliography in the required format. This will help if you have to submit of the same material (or versions of the same document) in different styles. This also helps because the software can be used with any word processor of your choice, although Bookends tightly integrates with Mellel and MS Word.
3. Floating citations (also available on Endnote but not the best) is a small citation box that pops up when you click any of the hotkeys in Mac, and you can search, add the citation in a jiffy.
4. Smart folders automatically categorise your papers based on keywords, and the Bookends is one of the better applications for document searches on the list.
5. Autocomplete and database (Pubmed, Google Scholar, JSTOR, Amazon, Google Books, etc.) search is a nifty tool. My typical bookends process goes like this — I find a paper online, I open it on Bookends using the “Open in Bookends” bookmarklet, copy the title of the article, autocomplete it using Google scholar search on the Bookends.
6. You can set up all your preferences in the settings pane, customise the look of your software, citations, bibliographies etc., In short, everything is customisable.

Cons

1. Bookends doesn’t have a cloud version. It saves your libraries on iCloud. The IOS app is the only other way of accessing your library. But I don’t feel the pinch because I don’t like to use my library on the cloud.
2. Users have reported specific issues regarding the migration of databases from other systems like Papers, Sente and Mendeley. But I didn’t find any problems when I imported my Mendeley database. But mine was not a huge one.

One of the things I like about Bookends is that they listen to their users and solve issues in subsequent releases. Last year, the application was crashing while importing web pages with heavy JavaScripts (mostly because of GDPR popups) and the bookmarklet was not importing PDFs on Chrome-based browsers (I use Brave). They solved both and many issues reported by users within a few months.

Bookends: Demo version is free with 50 references limit. $59.99 for one-time purchase and two-years of updates. They come up with offers for further upgrades.

Verdict

Best Windows and Mac (Free): MS Word (provided your university provides a free license for Office 365) + Zotero (leaving Mendeley because of their move to stop data export)

Best Windows (Paid): Scrienever (£36.55 — One-time academic license)+ Papers 3 ($3/Month)

Best Mac (Paid): Mellel+Bookends Combo (£73.20) but Mellel offers a discount during Black Friday Sale (during Thanksgiving). I bought the combo at £51.80 and the best investment I made for my PhD.

Other reference management systems to consider:

1. Refworks
2. Paperpile

Storage (The Raddus)

One of my colleagues in PhD left her laptop near the window on a rainy day, and I don’t think I need to explain what happened to the computer. Although she didn’t have much to lose because her research was in the early stages. But the mistake is she didn’t have a cloud backup of her study.

Most universities provide Office 365 subscriptions for students, and with Office 365, One Drive is offered free with unlimited space. I can’t emphasise enough to avail something that is provided for free. But other cloud services that can be used are

1. iDrive — $13.90/Year for 2 TB
2. Degoo — 200 GB Free
3. iCloud — 5GB free. $0.99/month for 50GB
4. Google Drive — 15GB Free. $1.99/Month for 100GB

Please note that the primary data collected from your research participants (like survey, interviews, photos, videos, etc.) should be stored in University servers due to ethical reasons.

Note Taking Tools (X-Wing Star Fighters)

1. Evernote: Evernote is the best note-taking available on the market. The integration, sync between different devices/OS, the collaboration between users, PDF reading, screenshots, etc., If you are using different operating systems and devices, Evernote is the best option.
2. Apple Notes: If all your devices are Apple, Notes is the best option for taking notes. It has an inbuilt scanner (so that you can scan images, notes, etc.), has collaboration available between users and synch between devices makes this the best option for Apple users.
3. Microsoft One Note: I am not fond of this app because of the bloated nature of the app, but this is freely available for Office 365 users. You can use any type of note-taking including stylus, clip web pages, screenshots and can have colour code sections, custom labels and tags. It speaks well with Microsoft apps like MS Powerpoint and MS Word.
4. Google Keep: It uses the post-it note type of arrangement, which is quite fun. The app has all the usual note-taking app features and has stronger integration with Google Docs.

Mind Mapping Tools (StarFortress bomber)

There are no much differences concerning mind mapping tools, and mostly the issues are with free/paid versions. Some of them have limited mind maps in the free version or restrict exporting capabilities. These are some of the best mind mapping tools that are available in the market.

Note: Please check your university network as they might have licenses for some of the mind mapping tool. My university Reading) has MindManager on the AppsAnywhere.

1. Mindmanager by Mindjet (Mac version is limited)
2. XMind (can’t export in Free)
3. MindNode (only Mac)

Free

Free Mind (not intuitive and user-friendly)

Bonus 1: Scanmarker

Scanmarker

I had to read a lot of books (not e-books) for my literature, and I had a massive issue of taking notes from users. I discovered this while researching for a portable scanner.

Scanmarker is a digital highlighter and scanner that can be used to scan line-by-line to convert into digital text on Microsoft Word or their own app or any text editor. The scanner is not perfect, and when I used it, there were some issues — it missed letters in the corners, and it takes time to practice the speed of scanning. Having said that, it has saved me a lot of time last year. It’s one of those devices that you don’t know that you need it until you use it. It can scan 43 different languages.

There are two versions of the device — wireless version (retails at £95 on Amazon) and USB version (retails at £69). Another good investment for my PhD.

Note: It doesn’t scan your handwritten notes. It might work if you have crisp handwriting like printed books. I have terrible writing skills.

Bonus 2: Setapp (only Mac Users)

Setapp is touted as the Netflix of apps for Mac that contains 100s of apps that you can use on-demand for a subscription. The regular subscription is at $9.99/month while the student discount is $4.99/month. Apart from popular apps like CleanMyMac, MacPilot, Photolemur, AnyTrans, there are apps for students and researchers. We also discussed some of them.

1. Ulysses (Word Processor)
2. Studies — clipboard for lecture notes, images, web screenshots
3. Findings — if you want to track field and science experiments, this is one of the best apps out there.
4. XMind
5. MindNode
6. Noizio (if you like Ambient sounds to focus on your writing)
7. 2Do (Task manager app)
8. DiskDrill (if you lose your data accidentally, this is the app to use recover data)

I know it’s a long read, but I wanted to make a comprehensive post that will provide as many options as possible for a new student/researcher. As I said at the start, the tools don’t maketh research, but they help you make the process easier. The best tool that humans have is their brain. Let’s use it :)