Directly inspired by Alexandra Lautarescu’s blog post (also see amazing blog on Repro2020).

I am continuously inspired by tech and amazing things. Forever impressed by stuff that makes life easier.

AIM: To keep track of all the cool things I use and the things I think look cool and might start to use at some point.

I hope that by having this page, you might also find something useful.

Contents


Computer setup

I currently have an Apple M1 Macbook Air 2020. The new Apple silicon chip makes this super quick! No problems running multiple programmes and lots of browser tabs. In fact, many apps are getting silicon-specific updates.  

Analysis

During my undergraduate and masters I conducted analyses through SPSS, but since starting my PhD I have learned to use R (and RStudio). The resources that I used to get started are:

I mostly use RMarkdown, which is great for compiling all your code and results into a PDF that you can then share with your collaborators. Bookdown Link

I haven’t yet gotten to it, but I’m planning to learn to use Binder, so I can share my code in an interactive, reproducible way for each of my studies.

For those who are still wary of writing code for analysis, JASP and Jamovi are great alternatives (with user interface similar to SPSS).

I share my code on Open Science Framework or Github.

Coding

I use MacDown (an open-source markdown editor for macOS) for writing and previewing markdown files. In fact, this blog post was written up in MacDown!

A useful tool for converting Microsoft Word-written pieces into markdown (including links and heading formatting etc) - Paste to Markdown

Brackets is an open-source HTML & CSS (plus other languages) text editor, very useful for catching simple errors or syntax errors such as missing brackets.

NOTE: On September 1, 2021, Adobe will end support for Brackets. :sob:

VS Code - Replacement to Brackets. It contains a lot of powerful tools and can even syncronise with Git. It takes a little bit of getting used to but is worth the investment.

If writing code for a script then this JSON Validator is super useful as I can never keep track of the [brackets].

Automating

One of my greatest desires, across both my personal and professional life, is to automate as much as possible. For a couple of reasons, first, it reduces error. Automating some of the boring data entry or manual administration removes nearly all* of the human error. Secondly, I’m lazy. I don’t want to do any of the boring administration/data entry/formatting/checking. The more of these tasks I can fully automate, the more time I will have to do other things!

* It is still fairly easy to make a mistake in the automation programming!

Integromat is a SUPER powerful online automation platform. I cannot recommend Integromat enough! I use it for so much across my professional and personal life. Integromat can connect to a large number of other services (and even if the service you use isn’t listed, they have a powerful API and web-hook service so that practically anything can be linked!). Linking together services you can create a process, thing A triggers process B which passes information to service C etc. The process that you create can be as long/short complex/simple as you require - take a look at just two examples below.

Integromat Example 1 Example 1 - Automating voucher sending and mailing list signup

Integromat Example 2 Example 2 - Inventory management

Parsehub is a free web scraping service. I tend to use this as part of an automation cycle to scrape new data from website to make comparisons to feed into a data dashboard. An example might be:

  1. Integromat uses a web-hook to trigger Parsehub
  2. Parsehub scrapes a participant sign-up page
  3. Parsehub scrapes the ID numbers of those who have completed the study
  4. A Shinyapp uses Parsehub API to pull the latest data, comparing both lists
  5. Shinyapp presents a dashboard indicating which participants completed the study and now require awarding credits

Otter.ai is a live transcription service. They offer 600 minutes per month on their free plan! You can live record a session with multiple speakers and Otter will use the AI technology to process the recording to work out who is speaking. You simply give it the names using the first few sentences and it will process the remainder of the interviews. It also has many other powerful features such as being able to highlight and add notes while still recording. It has some good playback features too, such as clicking on the script to jump to that position and playback that particular part.

Yet Another Mail Merge - See Communication

Sharing Code & ShinyApps

Sharing snippets of code:

There are a few choices and you ought to pick depending on your audience.

  • The visually pleasing way - e.g. for Twitter: Carbon
  • The user-friendly way - e.g. for helping solve an issue: GitHub Gists

Sharing full length code:

  • Create a repository on GitHub

Sharing Apps

Once you are familiar with R and RStudio, you might want to try creating your own app! I use ShinyApps to publish and share mine.

For each of my research studies, I aim to produce an app so that colleagues and the general public may interact with the data alongside the manuscript.

My own apps -

  • Pilot data explorer
  • COVID Vaccine
  • 632 VGS Weight Calculator
  • Open Research Calendar

Check out here

Writing

Microsoft Word combined with:

  • Simul - To share with collaborators and for version control.
  • Zotero - An open source citation and literature manager. Useful for generating formatted reference list.
  • Recite - Recite checks that your in text citations match the reference list at the end of your work.
  • Grammarly - Checking for spelling, grammar and excess words.
  • In-text comments - To have a chat to myself e.g. can’t think of the right word or the paragraph could be phrased better, but not right now.
  • AutoCorrect - Replacing text with formatted text to make it easier to find when finalising the document. E.g. Replacing (REF) with highlighted (REF).

Searching for related articles:

Connected Papers this website can produces a visual graph for all articles that are related to one article paper.

Communication

Collaborative group workspaces - Slack 

Social messenger (Encrypted) - Signal

Social Platforms:

  • Gathertown is great for hosting a virtual space with a controllable avatar. As you walk towards a person/people, they become visible and audible.

  • Backyard is a fairly new platform that allows you and your friends to play online collab games whilst also being able to see each player in circles around the game. Features a few versions of well-known games.

Setting expectations RE: emails, use The Email Charter in your email signature. This webpages sets out 10 tips to avoid email overload.

When designing emails for research studies I will often use HTML and CSS to make sure it looks nice. HTML Email.io is a great website to check that you have done this properly and that the CSS is embedded inline with your code. Some email clients will strip styling that is not inline so this is a great way to make sure your email looks great no matter which email client opens it.

Yet Another Mail Merge - (Integrated with Google) Used for sending batch emails. This is also useful for sending personalised emails with individual attachments. I use this as part of my research automation to help with sending out vouchers or study updates.

Organisation

Trying to keep track of all the amazing Open Research events taking place all the time? Try Open Research Calendar to keep track!

Trello is a visual task-manager where you can have task boards and move your tasks around (from “to do” to “doing” to ‘done”, sort of like post-it notes). It’s great for individual work, but also for collaboration, as you can share your boards with colleagues and assign tasks to each other.

Google Drive - Quite a few of my automation processes use a Google Sheet to store information for me. I find this useful as you can view the spreadsheet to view a history of your data that has been processed. I use folders in Drive to keep the spreadsheets sorted into categories (usually by study, e.g. Study 1, Study 2).

To organise meetings (both in-person and virtual) I use X.ai a smart meeting scheduler that uses AI to process requests. You get your usual calendar pages which you can link to, but the great thing about X.ai is that you can CC the AI in your email to the person you are meeting with and give them ‘plain-English’ instructions e.g. “Scheduler, please find a 2-hour slot for a Zoom meeting at the end of next week with John, Mary and Anna. Call the meeting “Session 1” and make Anna optional.”

Are We Meeting Yet? - To organise meetings across different timezones

Statistics

Lots of great visualisations from R Psychologist (Kristoffer Magnusson).

Statcheck - A website that can help you detect errors in statistical reporting. They are also working on a MS Word Plug-in.

Draw Data xyz - See Teaching

Survey software

FormR - Chain simple surveys into long runs, use the power of R to generate pretty feedback and complex designs

Tripetto is a conversational form builder that is similar to Typeform but allows for much more customisation and various data validation/calculation processes. Plus, it looks super pretty!

Qualtrics is my favourite survey software for research. Do note that it is not free and requires a licence!

General tech-y things

Google Remote Desktop - Connect to other computers easily. Super useful if working from home and needing to connect to work computer. Does need to be set up beforehand!

Caffeine - Use this to keep your Mac screen awake and prevent the screensaver.

OpenVPN - I use this to make a secure connection to my campus network to safely transfer files etc.

Pym - A super light-weight image compressor and format converter (Mac only).

Password Generator - Secure password generator.

Chrome Multi-tab opener - Chrome add-on to open multiple URLs (handy for marking and opening multiple Turnitin pages simultaneously).

Teaching

Poll Everywhere - A super easy way to embed live interactive polls into presentations. They also have a really great ‘Live Slide’ add-in which allows you to insert a live webpage into your presentation. This is super useful if you want to demonstrate an app etc. without needing to close and restart the slides.

Answer Garden - Simple interactive word-cloud software.

Draw Data xyz - Draw your own data and download it! Useful for teaching purposes.

Online Presenting / Video Conferencing

Teleprompter - Great auto scrolling teleprompter software. Useful for presenting when there is a written script to follow. Can switch between auto scroll and voice-activated scrolling! Note - I have had mixed results with the voice activated scrolling, but here is hoping it just gets better with age.

OBS - Live streaming video control. This is super powerful if used alongside video software such as MS Teams or Zoom. Combined with a green screen, the possibilities are endless.

StreamDeck - Originally designed for gaming streamers, this is a super useful customisable control pad that includes a number of LCD keys. I think this is great for teachers too. Controlling scenes in OBS or making convenient keyboard shortcuts in other programs. I have used mine to quick mute/unmute in Teams, insert predefined paragraphs of text in marking comments and even control lights in my room! The software allows for endless customisation.

Storage

Dropbox - The plus plan for 2Tb storage is amazing. Combined with the ability to make and monitor file requests securely is priceless. Dropbox has a feature to SmartSync the files on my Mac which means that it is never using up excess space on files that I don’t regularly access. However, those files are there and available should I wish to use them (it just takes a second to redownload it to the local machine).

I use GitHub with Github Desktop to keep local copies of repositorys updated. I make changes using the software I listed in the Coding section and then make commits and pushes using the desktop app.


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