PhD Talk interview

I have done an interview for the great PhD Talk blog. If you don't know it, you should definitely check it out: Eva does a great job, there is sooooo much good advice over there. I really like all the guest posts too, it's nice to hear from a variety of people from different backgrounds and at different stages of their careers.

I am a sucker for workflows and optimisation, so the new series of posts describing how different academics work was going to be a must-read for me. Eva was looking for more academics to take part in the series and I thought why not?

If you would like to read the interview you can find it here: This is how I work!

Scrivener + Mendeley + LaTeX and references

There is a comment under my PhD Tools blog post asking about the workflow and using a reference manager with Scrivener. As I said in the comments, as far as I’m aware there isn’t a good and easy solution to that, although some workarounds have been suggested (I’ll try to find them and post links).

First, if you don’t know how LaTeX deals with references, it’s fairy simple. I store my references in Mendeley, assigning a unique cite-key to each paper. The library can be exported as .bib file, which will be automatically updated every time you add a new reference in Mendeley (it’s a one time setup, which is great). Imagine you have a paper written by Smith et al. in 2005. My cite-key for that reference would be Smith_etal2005. I tell LaTeX where it can find the .bib file (I give it the path to that file), so that it can access all the data.

When I write in LaTeX and want to cite this particular paper I use the cite-key Smith_etal2005 and a bit of code that tells LaTeX that this is a reference - it would look like \citep{Smith_etal2005}. LaTeX then goes to the .bib library, pulls out the full reference and sticks it in the “References” section at the end of the document. In the body of the text itself the reference is output as it should be i.e. "some text about the thing (Smith et al., 2005)”.

The beauty of this is that if I were to remove the reference from the body of the text LaTeX will automatically remove it from the reference list at the end. It saves me worrying about having references in text, but not in the reference list and vice versa. I really like it and plan on keeping using LaTeX and Mendeley combo to format and output my documents, likely including the thesis.

Now I am adding Scrivener to the mix. Scrivener will be used mainly for note-taking, early drafts, re-drafting, reverse outlining etc. Anything that doesn’t need to be formatted and look pretty will be done in Scrivener, saving me dealing with the majority of LaTeX syntax in everyday life and formatting once the text is ready to be seen by the outside world. Having said that I don’t want to wait with inputting all reference till the last minute, it’s just so much more efficient to deal with them as you go!

There are two options here.

(1) I can input references in the-LaTeX-way, as I go, just like I would have done if I were writing in LaTeX itself (i.e. use the \citep{Smith_etal2005} in Scrivener). Then, I can simply export (or even copy-and-paste) that document from Scrivener to LaTeX for outputting, compile it and voila! references are sorted.

(2) Alternatively, I could set up Scrivener with Multimarkdown (which is a syntax that allows you to write in plain text and then convert to a more complex format e.g. HTML), write using MMD to keep it simple and avoid having to put LaTeX-like bits of code in (the \citep{} in this case). It is then possible to export from Scrivener to LaTeX through MMD; all MMD specific syntax will be changed to LaTeX specific syntax.

I feel like after the initial set up the second option i.e. using MMD would be cleaner. But then again, I don’t really have issues with using LaTeX-style citation syntax, so that’s what I have stuck with for now, as I only needed to write fairly short pieces of text. For anything of a length greater than 5000-6000 words it might well be worth spending a couple of hours sorting MMD out and getting used to it*.

If you are interested in learning more about any of the above, check out the links below. If that’s not enough - google! There seems to be dozens of tutorials on those things out there already, hence my post is rather simple, no need to re-invent the wheel. 

BibDesk, Multimarkdow, Scrivener (those are way more detailed than this blog post too):
http://timbrandes.com/blog/2012/02/28/howto-write-your-thesis-in-latex-using-scrivener-2-multimarkdown-3-and-bibdesk/
http://timbrandes.com/blog/2014/04/08/optimize-bibdesk-multimarkdown-and-scrivener-for-a-nice-scientific-bibliography-and-citation-workflow/
More here: http://harrisonsweeney.com/posts/scrivener-multimarkdown-and-latex.html

Some good posts on having words too: https://onhavingwords.wordpress.com/2013/03/19/scrivener-multimarkdown-latex/
Using LaTeX code in Scrivener: https://onhavingwords.wordpress.com/2013/07/27/any-latex-scrivener/
Also replacements, if you are really into it all now! https://onhavingwords.wordpress.com/2013/10/06/replacements-latex-scrivener/

On Multimarkdown, from its creator: http://fletcher.github.io/peg-multimarkdown/mmd-manual.pdf

*but it’s not just because of the references, it’s because of the heading, subheading and other bits and pieces. 

Evernote: Tags

I wasn't convinced by tags at the beginning, but using a notebook-only approach wouldn't work due to Evernote's rather simple nesting capabilities (notebooks can only go one level deep). I actually see some advantages of tags now too - for example I can have a bunch of notes on a program (e.g. Evernote!) in lots of different notebooks (Blogs, PhD Advice, Programming). I can easily have a look at them all (across notebooks) using the tag, but I can also look at those notes linked to programming (both Evernote and non-Evernote related) by just checking the relevant notebook.

Organisation

I organised my tags by using parent-tags (normal tags can be nested within other tags by simply dragging and dropping). I don't actually use those parent tags for tagging notes, they are just there to help me group other tags, so that I can find them easily. When on a computer I often tag notes by dragging them onto the tags, so being able to locate each tag quickly helps.

For example, I have a parent-tag "Activities" within which I have (not surprisingly) all my activities, such as writing, climbing or programming.

The only exception to the rule is my "tools" tag - it's nested within a parent tag and there are tags nested within it, but I do use it to tag notes that talk about a whole bunch of programs I might want to check out (but don't want to have a tag for each of them). 

You can see that each of my parent-tags has ... in front of it. This is so that I know which tags are the parent-tags and don't tag any notes with them when tagging by starting to type the tag name (which I do when I'm away from my computer, tagging on a mobile devices).

Robustness

I decided to create a whole bunch of tags at the beginning and then try and stick to them, i.e. avoid creating new tags on a whim, so that I don't end up with each tag only being used once (which would render tags useless).

I also keep my naming consistent. Anything that is an activity, that can be written with an ing ending gets written like that, i.e. travelling instead of travel, meal planning instead of meal plan. Similarly, I keep the names in plural, for example definitions, books, conferences. Those rules arbitrary, but easy to remember, and they help to ensure that I don't accidentally create multiple tags for the same thing (i.e. so I don't have "book" and "books", which again, would make searching via tags less useful).

Sometimes I wonder how necessary the tags actually are - the search function in Evernote is excellent and most of my notes can be probably found relatively easily without tags. For instance, most of my Scrivener notes have the word Scrivener in them, so using the tag "Scrivener" doesn't really add much. However, there are also instances where tags add some extra information, for example if the note is based on something I found on Twitter it gets tagged with "Twitter" (and it happens automatically when done through IFTTT). The note doesn't actually have anything to do with the Twitter as a platform, so won't have the word "Twitter" in it and couldn't be found this way - but thanks to the tag I only need to remember that this thing I'm trying to find was initially spotted on Twitter. So I will use tags for now, even if only to figure out in what scenarios they are actually helpful!

Side Note: I do wish there was a way to automatically tag notes with a parent tag, e.g. if I tag something with "Twitter" it should also get tagged with "tools" automatically. As far as I know there is no way to achieve that easily though.

Evernote: update on the way I'm using it

I am taking some taught courses and have decided to create a separate notebook called Courses. I initially put notes on the courses in the Meetings notebook, but for some reason it didn't sit well with me, it felt like those notes didn't belong in Meetings.

I might also get rid off PhD Concepts & Definitions, Ideas & Notes notebook - I have created a document in Scrivener that keeps the definitions important for my PhD, so most of the basic things went there. This notebooks currently contains notes about my ideas linked to organisation of certain project, but I wonder whether those couldn't live in another notebook (e.g. PhD Advice & Resources or Lab Journal). I will see what happens, if it doesn't get much use it will need to go.

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.

See: Scrivener + Mendeley + LaTeX and references

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.

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).

Evernote

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.

Notes, notes, notes...

I have been rather busy over the past month, working on a project involving genetic basis of behaviours. I haven't done much molecular work before and so I had a lot to learn. I have been also building my first PC and writing up some project reports and protocols created over the  last year.

It is incredible how much difference can be made by well kept lab book and by detailed notes.

To start with, the protocols. I wrote and tested some of them last summer. A few are rather lengthy and complicated - several pages A4 long, take a week of work to complete. When you are running a time limited project losing a week of work can be catastrophic and so it's really important to get it right. It's of course easier to follow it when you are in the lab and you carry out the same protocol time after time. However, after a year of not using the protocol it could be really tricky to avoid mistakes. It's also important that the protocols are written clearly enough for other people to follow without additional instructions. I wanted to type up some of those old protocols from my lab books, as I needed to include them in one of my reports. My obsessive note taking turned out to be really useful: I have lots of notes, clear, numbered, organised, with important parts marked, with safety notes included. Writing the reports up was just a matter of typing them up and in some cases making them a little bit more formal. It wasn't difficult though, just time consuming. If my notes weren't clear it would have been much more complicated - I would have to consult several sources and manuals to ensure that I include all the necessary steps and caution notes for all procedures.

Things look similar with the project I'm working on now. Everyone in the lab is incredibly helpful, but also rather busy - people usually only have the time to explain something once, twice tops. It's necessary to ensure that after being shown how to use a machine or how to carry out a procedure you can actually do it. What's more, since I'm working in a training lab I should be able to not only carry out the procedures myself, but also to walk new students through any procedures I know and can teach. Again, it's crucial to have good notes and communicate things clearly.

During work in the lab it's also very important to ensure that all the samples and solutions are labelled correctly and kept track of - during molecular work there is no other way of recognising and telling apart the samples/solutions once you taken them out of their respective containers. They all look alike, have no distinctive characteristics or even worse: they can't be seen with a naked eye or are toxic and dangerous, while looking like something harmless, e.g. like water. Label things and once again: notes, notes, notes! It's a good idea to keep a lab book in addition to any digital notes you take and it's necessary to back up your digital data too.

Now off to write some more reports and do more data analysis. While writing protocols and reports up is relatively straight forward (although can be lengthy and a bit tiring) data analysis and stats are proving to be a lot more complicated and tricky. Each step I attempt to make seems to require learning a new program!

Working smart

I've been thinking about my progress through the years over the past semester, mainly because my style of working has changed drastically since I came to uni. I learned how to make the work easier and how to be more efficient. I thought I might post some pointers here - who knows, maybe a fresher out there reads this and learns from it.

I rarely delete anything from my computer and rarely throw things out - which means that I have copies of most papers I've ever read and a lot of notes. I decided to try and organise it all (in progress, it takes a while to organise over 6 years of stuff spread across several computers and two countries!).

I decided that instead of having dozens of random folders with papers I should create one huge library and keep adding papers to that in the future. I've been slowly adding all those papers and references from notes into a referencing program. I used Bibdesk/Mendeley combo for a while and had a little set back a couple of months ago due to my library file getting overwritten... I had to start from scratch and now I'm using only Mendeley, since the library can be also stored online, which makes it a bit safer. So a note of caution here - it's probably better to pick one referencing program, not mix them together!

Having my references and papers in one place makes things easier. First of all, I don't have to search my entire computer, but can go straight into my library, make a key word search and see all relevant papers - papers that I have already read, many of which are highlighted/with notes. No more "I read it somewhere, but can't remember where".

I found that having a library like that helps me to make links between modules and to integrate the reading I've done for pleasure/during holidays into my university work. Which is a great thing when you are short on time, but want to support a point you are making with a scientific reference - for instance if I needed a general reference about habitat fragmentation I just search my library and quickly recap a couple of papers I'm already familiar with, rather than go and pick a random paper and attempt to read it back to back. It really does help hugely when you are working close to a deadline and need to ensure that all facts in your essay are appropriately referenced. Why not use the directed reading you did in your first year? Why not use those books and papers read in College? Why not use papers found on Twitter and read over breakfast? It speeds the process and makes it easier to get coursework done, but I also love seeing how different bits and pieces come together - I think this is what making progress at university is all about: it is learning to see the connections, to see the bigger picture. It's getting away from doing the bare minimum of work, of having a couple of papers per module - it's bringing it all together and applying knowledge, thinking like a scientist. Soak up all the knowledge you can get.

The above is more about keeping tract of things and organisation, but what about writing itself?

I cannot stress enough - if you make notes on papers make sure that you write down where are those notes coming from for further reference (section or page numbers help too) and write the notes in your own words. It's really important. I find it easier to write notes as I go, on each paper that I read. Then later on I can just pick and choose from my notes, copy the relevant bits out to a new file and edit that. I don't have to re-read the papers, but if something is unclear I can quickly find the sections I should have a look at to clear any confusion. Writing the notes in your own words ensures that you don't commit plagiarism. It's easy to forget what's re-written and what was copied out of the paper, so if you ever copy and paste make sure you have a way of explicitly marking those passages and re-writing them later.

I was also persuaded to give LaTeX a try. I did and I really like it - it's a typesetting system, check it out. It produces beautifully and professionally looking documents, takes care of all the formatting details for you, can be even used to make figures and tables - and I especially like the tables, you can get really nice scientific tables. Some of the scientific journals out there even give you templates, you can download them and then just drop your text in and voila, you have a paper that looks exactly the way it should for that particular journal, references included. LaTeX can also handle references from Mendeley, so I just link the two. I know some people who still do their references for coursework by hand at the end of each essay... This is a silly waste of time to say the least. There is more to LaTeX that the "technical" side too: I find that since I don't have to worry about the formatting at all I can focus on the content and content alone. No more playing with subtitle font for half hour.

I think it's also good to get into the habit of doing all of the above as early in your scientific career as you can - I cannot imagine writing my Masters/PhD thesis in Word! LaTeX deals very well with big documents and a paper library and a good referencing system will be crucial then too I imagine. It's good to stretch and to try out different programs and style of work. Above works for me, maybe it will for you too, but even if it doesn't you should be able to pin point why it doesn't. Once you know that you can move on and try out something more appropriate. Get in the habit of paying attention to detail, but thinking big, of doing more, of reading broadly, even if the papers seem unconnected. It will make you better at what you do, more efficient. It will teach you how to read quickly, but also how to get the most out of each paper, what to look for. With time you will work out your own system of highlighting and note taking, build a reference library and find an efficient way to compile your work. It will make things easier and more enjoyable. Being able to enjoy your work is a truly great thing.

Behind the schedule

Last semester was pretty busy. It sounded like this semester is going to be easier - no group work, so studying should be easier to fit around work, a lot of coursework, but if one gets organised it all should be fine. If one gets really organised, one might even have some free time! All the reading I will be able to do...

I planned and scheduled.

Then I needed to prepare a project proposal for my masters year and started applying for funding to carry out a piece of research over the summer and got so stuck in in personal statements, CVs, drafts of proposals and applications that somehow I've 'lost' a month*.

I was a month behind the schedule I prepared. So I prepared a new schedule. Currently I'm about two weeks behind that new schedule.

Am I just unlucky with lots of things popping up here and there and eating up my time, schedule badly with not enough time or am I simply not organised enough to stick to the schedule? I guess it's probably a mix of the three - I didn't realise that project applications will take so much time, but then I could have probably squeezed a bit more work in-between lectures. I find it hard to do 10 different things one day though, I much prefer to have a big chunk of time to work on something and get it done, as it takes me a long time to warm up. Maybe that's the problem, maybe I need a different way of working. How does one go about re-wiring their brain though?

All will get done in the end, no matter what. It always gets done and I work better under pressure.

Maybe there is no point in planning and scheduling. Go back to general to-do-list instead of a schedule? Or maybe there is some secret way to schedule so that it's actually achievable to do everything according to the schedule?

So to sum up, I'm attempting to find out what's the secret of perfect scheduling and how to re-wire my brain. There must be a way... I'm only going to get busier over the next few years and have to deal with it somehow!


*Will be really worth it if I get the funding and can do the project!