Monday, 25 August 2014

PhD Tools

This is the set up I've used during my undergrad/Masters and that I'm going to carry through onto the PhD.

I'm using a whole bunch of different tools to streamline my work and offload my brain - I have a goldfish memory (the castle around the corner is a surprise every time!*) and tend to worry about everything. All the time. I can't be very efficient without knowing that I can "forget" certain things because they have been recorded somewhere (and that I will get a reminder when the time comes).

The ease of recording things, as well as the ability to access the information is paramount, as I work from several locations and need to be able to get my hands on all that data anytime, anywhere. I need a set up that will not only work between office and home, but also between 4 different countries on 2 different continents. Something that will work cross-platform, as I use both a tower PC and a MacBook, as well as an iPad and an Android phone.

I am currently using:

The Trio of Skim, Scrivener and LaTeX - Skim for reading and marking scientific papers, Scrivener for the bulk of my writing, including notes taken on the papers all the way to, hopefully, the Thesis. LaTeX is my secret weapon of choice when it comes to formatting, it's really second to none in this category.
Mendeley - for keeping track of my references. It produces a bibtex file that can be used with LaTeX to automatically input and format references, both in text and at the end of the document as a bibliography.

For keeping track of most of my life I'm using Calendars (used to do Google, but swapped to iCloud now for no real reason), Evernote and Wunderlist. Each of those plays a slightly different role, Calendars organise my day/week/month, Evernote collects things that might be of use one day (meeting and lecture notes, recipes, manuals, travel arrangements, blog ideas…), while Wunderlist is there, well, to keep track of my multiple to-do lists and my daily agenda.

Mailbox - I have also recently started using Mailbox on my iPad and Android in order to achieve "inbox zero". I wasn't sure I will likely, but I'm totally digging it.

I'm also using Bloglovin' and Pocket to read things that are not scientific papers. Bloglovin' keeps track of all blogs (I read mainly academia/science-related blogs). Pocket is the "I'll read it sometime later" bucket, where I throw stuff that might be interesting, but that I'm not sure I want to keep - if I do want to keep it, it will probably end up in Evernote.

I am still working on my cross-platform links, as an iPad is a fairly new addition to the family - I was lucky enough to win one in a contest and so haven't been building those systems with an iPad in mind. I am also attempting to use IFTTT to automate some processes, but I think I have a long way to go here.

I am going to write a separate blog post on how I'm using each of the above, in case anyone out there is curious, but also so that I can see how my habits evolve over time. Once the posts are written I will link to them in this post (probably make the names of the programs clickable too).

*I'm pretty sure I have heard this somewhere, but for the life of me can't remember where.

Thursday, 7 August 2014

Evernote: Notebooks

If you google Evernote you will be flooded with articles and blog posts about it. This is by now means the way to use Evernote, it is just my way of using it. And it will most likely change.

I started from creating a bunch of notebooks. Since I wanted to keep everything in Evernote I have quite a spread of different topics here.

Some of my Evernote notebooks. The arrow points to a notebook stack including two notebooks.

My current notebooks are:

0. Default Inbox - this is the default notebook where things go before being sorted. If I don't have the time, or if I'm just sending something to Evernote (e.g. through email - yes, you can send emails to your Evernote!) it will go here. I will move it from here later and put it in an appropriate notebook.

1. Lab Journal - this is a place where I will keep track of my everyday work. I'm going to attempt being fairly paperless and not having a physical notebook - I will instead use my iPad to make notes.

2. Meetings - notes from meetings, as well as agendas for future meetings go in here. This includes meetings with my supervisors, but also meetings with any other group of people, e.g. a journal club or admin meetings.

3. PhD Advice & Resources - this is where I put links and notes on anything that might make my PhD journey easier. It might be articles on academic workflows, courses worth doing, productivity tips, software worth checking out, thesis writing advice etc.

3. PhD Concepts & Definitions, Ideas & Notes - this title is pretty self explanatory I think!

3. Programming (stack):

  • Code Bits - I would like to put useful pieces of code in here. I found that while using R and LaTeX I would sometimes encounter a problem, then do a fair bit of research and find a neat way of solving the issue. Then 8 months later I'd have no clue how I sorted it out… I had no place to put such bits of information and would end up having to dig through my old pieces of work in order to find out how I did something.
  • Web Archives & Resources - pretty self explanatory, things related to programming that are not bits of code!

4. Conferences
4. Travel - I wasn't sure whether to split those two or just keep them as one folder, but then I thought that I might want to keep other information on conferences, not necessarily strictly related to travel. So there are two folders for now.

7. Blogs (stack):

  • About Blogging - where I keep generic information related to the activity.
  • Blog Ideas & Drafts - some bloggers write their blog posts in Evernote. I'm not sure I will do that, but I think it might be useful for storing ideas and resources. For instance, if I read an article and it gives me an idea for a post, I can not only jot the idea down, but can send the article to Evernote too, so that it's kept there for reference.

Food & Drink (stack):

  • Baking, Cooking, Wine, Basics & Resources - those 4 notebooks should be pretty self explanatory. I keep my favourite recipes there. It's pretty handy - I just took some photos of my mum's cookbook when I went home, which saved me having to copy out things by hand. I can also copy things sent by friends or found on the web into there. And when I go shopping and want to check what I need for lasagne I can get access to the ingredients on my phone.

House - I live in a shared house, so anything relating to the house, like bills or inventory, goes here. I can easily email the information to my housemates from Evernote too, or I could share the notes or even the whole folder with them.

Manuals & Documentation - I want to try to be fairly paperless, so any manuals, timetables, schedules etc. go here.

Other Interests & Cabinet - I have quite a range of interests and I didn't want to create a whole bunch of folders, so everything else that doesn't fit into the folders above goes in here. This can be things like good articles on organising your wardrobe, blog posts on sexism, article on diseases in pet parrots or a business card of this awesome rock climber I met on my last trip.

Wish List & Gift Ideas - what it says on the tin!

Note: numbers in front of some of the notebooks above are there to force the notebooks to appear in certain order (the most wanted ones on top).

Monday, 4 August 2014


I used to jot down the most random things in order to get them out of my brain - a song that I heard and liked, a book someone recommended, a gig in town 3 months from now, a bit of code, idea for a blog post, what I need to tell my mum the next time call her… This resulted in dozens and dozens of random pieces of papers lurking around my desk. Getting lost. Making mess. Not being there where I needed them for reference.

Notebooks sorted this problem to an extend, but still left a lot to be desired - every single time I left the notebook at work I needed to check something while I was at home. Every time I visited someone the notebook wasn't there. When I went to visit my parents (which requires a plane trip) I had to pick and choose what I can take with me.

You get the idea.

I have had an Evernote account for a while, but I never really got into it. People would rave about it and I just couldn't make it work.

I like to keep organised and I was getting annoyed at not having an efficient way of dealing with bit and piece of information. Since PhD would involve more information that I have ever had to deal with (or at least so I suspect!) I thought it's time for a change.

I decided to go all in and really give it a shot. I think that one way to make it work might be to put everything into it. All the information, so that it becomes the default place to go for inputting new information, but also for looking for things.

I like to keep information categorised and so I quickly set up some folders. I then equally quickly found out that folders can be nested within stacks, but that's it. Organisation with folders is only one level deep in Evernote and that's not enough for me. Or at least, it's not enough to work the way I worked before.

I never got the idea of tags in general and I tried to avoid them in Evernote, till I realised that I could use them the way I wanted to use folders. Now I have a mix of folders and tags. I have a rule though - I created both notebooks and tags at the beginning and I will not create any more ad hoc ones. This is to avoid having a folder with just one thing in it or a tag that only refers to one note (rendering them pointless).

Every time I feel like reaching for a piece of paper to note something down I make a note in the Evernote. I use it to store notes on various events, to keep links and blog posts that I want to have access to. I sent itineraries there. I can get access to it on any of my devices, so I can use it on the go, but I can also make sure I keep my desks clutter free (or at least random-pieces-of-paper free!).

If you'd like to know how I organised my Evernote for (mainly) academic use you can read about it in separate blog posts about my Notebooks and Tags.