Friday, 2 May 2014

Getting Organised

The more time you spend developing your perfect organisation system, the better it has to be to help you catch up on all the time you spend developing it. This problem is reminiscent of the issue of improving routine tasks via xkcd:

Diminishing returns aside, as I find myself in the early stages of my PhD, the tension between working, worrying about how much I am working and deciding to reinvent my  entire organisational system is.... rising.

It's easy to blame your organisational system when you are feeling stressed and unproductive - and I choose to do that. Acknowledging that you are taking the easy option is half the battle. First some

Being a dry lab scientist (in training), how to effectively have a bioinformatics equivalent of the lab notebook has been something I've spent some time thinking about. A place to record experiments, ideas, outcomes and future directions, in a way that works with a general system for keeping track of day to day tasks and activities has been my goal.

For the last few months I've been using Evernote.  I've gone to and from Evernote a few times, but have again returned to it due to 3 simple uses that work for me:
- Combine paper based and computer notetaking
- Clients available for almost any platform I find myself
- Syncing is Somebody Else's Problem.

I'd tried TiddlyWiki previously, but the number of clients I could use it on, and keeping the syncing up to date proved difficult in practice. If I was on a remote server I'd open text files and add notes to them. If I was away from a computer I'd find the various apps a little fiddly to use and  kept resorting to paper, and then promising myself I'd transcribe that paper later. All this really mean was that I had another task to do before I could even get to doing my actual tasks.

Frustration with this setup coincided with two separate features I came across for Evernote: Geeknote, an open source command line tool and Evernote moleskin notebooks.

I'll write more about how Geeknote and using it from the command line in another post. Briefly though, the ability to type 'todo "Upgrade server to latest Ubuntu"' in the middle of a remote command line session on a server and be confident that it will be captured along with all your other tasks and notes has been a real benefit.

The Evernote notebook has also solved a problem I've had whenever I've been tempted to get a moleskin notebook before - they are too nice to write on! Rather than being a place for notes, they'd be book I'd carry around but hesitate to write in them for fear of marking the expensive book with something less than profound.

Evernote moleskin works around this by bundling in 3 months premium subscription to Evernote. A key feature of this is offline access to notebooks, which can be handily on things such as planes or when wireless is unreliable. I treat the moleskin Evernote notebook as paper I need to get through, rather than try to avoid spoiling. It’s been great, though I still need to get a handle on scanning in the pages on a regular basis.

However this system  hasn't been completely useful. It’s approaching a 'capture everything’ system ala GTD, but as way to plan tasks ahead, with a distinct todo list etc, it remains sub prime.

The addition of reminders to Evernote had made me think about how to use Evernote as a real GTD single collection point, but keeping track of the reminders isn't working with so many notebooks in my account, and the mix of scanned paper and computer tasks together meant that I never really had a to-do list.

That's about were I was up to from last week. Geeknote didn't support reminders, and I had one of those 'how hard can it be' moments. Fortunately, a day or two of using my limited python skills resulted in my first pull request to an open source project.

It is working. Sort of. My Geeknote extensions seemed stable, and the habit of adding notes into Evernote is almost a natural instinct. But I still don't review it; notes go to my @Inbox ( a GTD holdover) to be neglected.

But I feel that, like with so many things, you have to use what works for you. This setup is working for me better than anything else, and we can't let the perfect be the enemy of the good. So today, in an attempt to get something done, I'm making the setup a little bit neater.

After putting together all of my rough sketches of how I think I should get organised, I managed to merge all the notes and notebooks into some rough categories  as notebooks and notebook stacks for getting me through the PhD:

These generally reflect how I view most activities, and how I'm spending my day:

  • @Inbox - the capture everything notebook. Moving things out of this notebook (current size 370 notes) is one of my biggest weaknesses. 
  • @Someday - A catch-all for ideas that are, perhaps, before their time. 'Develop my own aligner' goes here. 
  • Infrastructure - Servers, scripts, tools and environments for getting bioinformatics done. There can be some overlap with research (for example, reviewing available bioinformatics workflows for a paper) but the essential criteria for infrastructure activities is that they are designed to help the research get done.
  • Networks - This is devoted to any activities that are about networks. These are professional organisation, informal journal clubs, student groups (local and international) and any other way that I'm trying to interact with the scientific community outside of (published) research. 
  • PhD - see below. 
  • Planning - This goes towards having an organising notebook - somewhere to plan how I plan, and ensure that I review where I'm going and why I'm doing it. Another problem at the moment is planning my week ahead. I hope to use this area to help get into the routine of stepping back, and being mindful of upcoming tasks, rather than only go to the squeaky wheel. 
  • Research - Finally, but equally important is the actual research that my PhD (and beyond) is based on. 
The PhD notebook stack is really concentrated on 'Getting the Dr on the door', a phrase a mentor uses and in the spirit of  the advice in 'How to Write a Better Thesis' that the thesis is an a examination; This folder is all about the experiences and deliverables required to get that PhD. The Research folder is where the content is created/modified/discarded/revisited. Keeping track of hurdles, requirements and personal goals - as well as writing (e.v.e.r.y d.a.y) -  is a distinct responsibility from doing the actual PhD research and I think it deserves it's own mindset.

There is still a lot to be done with my organisational setup. Having defined the broad areas of how I work, I still need to go through the 370 notes in my inbox, and then actually complete some of the tasks they include. I also need to make sure that I review things regularly.

I haven't done all that much today on the system - renamed a few notebooks and moved some notes around. But I feel better about it already. Acknowledging the shortcomings has helped me see it as a work in progress, and a way to move it one stop closer to the goal of a perfect good enough system to get me through my PhD (and beyond).

Saturday, 29 March 2014

From Research Assistant to PhD student

This post has been a couple of months coming (cue freak out that PhD is already two months in...) but was inevitably delayed. I had planned a very big post about my decision to start a PhD, what I enjoyed about working as a research assistant and what I was looking forward to with my reactivated student status.

But, the post was going to have to be perfect, and I'd have to capture everything about the transition so that I could revisit it later on. It was going to be the post that signalled I had started my PhD, but the delay meant that I kept running into friends who were surprised I'd not told anyone! As a temporary solution I posted to the local uni bioinformatics group the news and a question:
So, friends/colleagues/peers/etc, it has come to my attention that perhaps I haven't brought to everyone else's attention that I've started my PhD. So consider this post me telling you. Any advice from the collective intelligence of the Bioinformatics Graduate Student Association?
If you  read enough blogs and books about starting and finishing a PhD, 'write every day' is a recurring piece of advice, and it was one of the more frequent responses to my question from my friends. I suppose it's time to take the hint. 

The most obvious difference between being a Research Assistant (left)
and PhD student (right) so far is the size of coffee I can afford. 
This post therefore counts as writing, even though it isn't a large amount, and even though it isn't exactly profound, it's done. It's not the perfect welcome to PhD post I'd imagined, but I managed to  include the amusing picture about KeepCups that I wanted to and, as I'm about to hit publish, it's off my todo list and I'm thinking about the next thing I'm going to write. Which I guess is the point.