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.

I did it!

The choice has been made, the funding sorted, the paperwork signed. I will be starting my PhD project in mid-September, with fieldwork in the Land Down Under before the end of the year. I'm excited and apprehensive and very aware that the real stress and seriousness of this choice will probably hit me closer to the time.

The topic is very interesting, the department, group and supervisors are meant to be great (and really did seem so from the little interaction I had with them - good sign!), the fieldwork in Oz is an amazing bonus. The city itself is also a great place to live, although  I will probably complain about the darkness and rain (the cost of living up north). I was trying to be careful when applying, trying to only apply for places I really thought I could fit in. But until you get a chance to talk to those people and to have a look around you can't really get a real feel for it. Of course a couple of conversations and a visit are not the same as a few years of actual work that the project requires, but one can only try their best while collecting the intel. Pull some strings, keep your eyes and ears open, ask questions. Be prepared.

I will have a lot of independence with a supervisor who is very hands-off (or so I'm told), but that also means a lot of responsibility. I don't like people looking over my shoulder and I don't need spoon-feeding, so fingers crossed that I can manage to truly be in charge of my own learning and development, of my own research. At the end of the day, I think this is what it is about. It's time to fledge.

Some wing stretching and exercise might be necessary first though.

PhD interviews

There is a myriad pages and blogs out there with interview advice, so I won't bother to give tips here. What I will say though is that I was invited to several PhD interviews (both PI interviews and funding interviews) and that pretty much all of them seemed to follow the "stress interview" path.

Of course it might just be my personal impression, but all official interviews were panels interviews, with people asking unrelated questions in quick succession, frequently forcing me to forget about my current train of thought and jump onto a completely new, seemingly random (as in: not following from the previous question/answer) idea. Some questions were relatively easy and predictable - about me, my current research project, ideas, experience. But there were also questions about aspects of methodology and analysis for the PhD project (which I would be starting in 7-8 months time) and let's face it, it's pretty much impossible to know details of those this far in advance, while applying for several projects. There were questions of the predicted impact of the PhD project, how it would change the field, what post-doc projects would I like to create based on the PhD outcomes... Again, that's about 4 years from now. Those big picture questions, asking for a lot of detail were probably the hardest, although I was also asked a bunch of modelling questions despite the fact that I clearly stated in my application I have no modelling experience.

During one of my interviews I gave a 3 minute presentation on my Masters project - and afterwards I was left there hanging, the questions started without any indication I should sit down with the panel (I figured what the heck and crossed the room and pulled a chair for myself). After some of the answers I gave I was told "this is not what I wanted you to say".

I also had at least one "mean" interviewer on each panel, one person clearly disinterested in me and my answers, interrupting or looking out of the window. I was incredibly grateful that someone warned me about this type of behaviour before my interviews. Once I spotted it and knew I can safely assume it's just an interview method, paradoxically it calmed me down instead of adding stress - I expected it to happen, it happened, therefore things were going how they were "supposed to" go. I knew it wasn't personal and it helped.

The hardest part of the process ironically turned out to be linked to the fact that I was made more than one offer and had to make a choice. And I wanted it all.

Masters and PhD hunt

The first semester of my masters year is nearly over. It's been great so far, busy, but great. It is the first time when I could really really get into a topic - from both the theory side (dissertation) and empirical side (practical research project). It's a research-based year and so it's different from the first 3 years of my degree. I get a chance to explore, play and think for myself, instead of focusing a lot of my energy on deadlines and marking criteria for different little pieces of work. I can plan my own experiments and I'm also responsible for my work and learning to a new degree. My time is unstructured unless I structure it.

I loved most of my degree and I'm glad I had a chance to try and learn lots of different things, as I think it helped me to not only develop a range of skills, but also allowed me to realise what my interests are and what type of research I'd like to be involved in in the future. This year confirms what I thought before: research is it for me. This is what I should do. This is what I will do.

Having this confirmation is helping me through the PhD application process, which is tough and stressful. There is however something incredibly exciting about learning, researching and possibly teaching, sharing the passion and knowledge, as a career, and this also helps to push through. The competition is high and the funding situation is not great, but hopefully, with a bit of luck, there is a PhD out there for me.

A real scientist?

When can one call themselves a real scientist? I guess in case of other jobs one has to be paid for what they do to call themselves a professional. In case of being a scientist I also think one should be active in their field, doing research and preferably publishing papers.*

Recently though I felt like a scientist. And let me tell you, it's an amazing feeling.

As I mentioned before I have been awarded a grant from the Genetics Society (@GenSocUK) to do a summer project this year. It has been a great experience, the people in the lab, staff and visitors, have all been very friendly and supportive. I've learnt new techniques, got to play with some cool machines and got to actually do a bit of proper science. It was more than that though: I also tried to help out visitors in the lab and I discovered just how complicated a "simple" analysis can be. Learning how to use R alongside attempting to use several programs I have never even seen before to deal with my data has been challenging. I never knew people still used DOS for anything. I think the last time I saw DOS before this summer was when my home PC was running Windows 98. I'm still waiting for algorithm-paper-nightmares to come. I don't have anything against maths in general, but when I open a paper and it has more equations than words I know it's going to be a very long night. Then again, I think this is what it's about. About learning, discovering, trying, sorting problems out and overcoming all those little, but-oh-so-very-annoying difficulties.

It was however after the project itself that things somehow shifted for me. It wasn't just one thing, but a whole series of smaller and bigger events. The Genetics Society organised a series of workshops at the UEA where all their grantees could present their work as well as work together during several activities. It was good to see what others did and the range of project topics was definitely worth noting too, I think we all learnt something new and were pleased to meet so many great people. The whole thing was fun, but also educating - I think this is what 'school' was supposed to be like! Presenting my project at the workshops definitely gave me a little bit more confidence too. I got asked to present my work to three labs in our department next February and I agreed to do it, hopefully it will go alright. This is the first time I got asked to do any scientific presentations outside of my degree. Nerve-wracking, but also exciting! Similarly, I got several emails from various people asking me for advice and help with programs, data sets, primer design etc. and to my surprise all those people are higher up the scientific ladder. It's flattering and I'm very pleased that I'm finally getting to a point where I can be of use to the community.** Even if it is in such a tiny way!

I was also lucky enough to be able to go to the Biology of Spermatozoa conference. It was brilliant, with crazy-smart, but really nice people. I loved the atmosphere and sharing of the unpublished work in progress. It was great to be able to talk to people about science and sperm without getting some silly looks too. I just tried to explain what my Masters is going to be about to some colleagues at a training session for work the other day and they looked at me like I was slightly mad. Just a bit, but still, "better nod along and don't make eye contact" sort of reaction. Strange reactions never stopped me from telling people just how awesome science/sperm is, but it tends to be a one way conversation, where they ask what I do and then try to change the subject before I go into too much detail - all excited and waving my hands around. But at BoS we could all get excited about sperm rather openly! The conference was also followed by two days of CASA workshops where once again all things science were cool - including a nearly jump-up-and-down excitement while watching fly sperm twitching under a microscope.

I feel very blessed that I could be a part of it, all the talks and the less official dinner chat were very inspiring. It was strange, meeting the people you know and admire because of their work, because of what you think you know about them and finding out that they are even cooler in real life than you imagined. I hope that I can become a real scientist and always be a part of this amazing community.



*When I look at it like that I'm not a scientist yet. I don't really get paid and I haven't published a single paper. But I got some small grants to do projects and I'm trying to get bits and pieces of research in (it should get better seeing as I'm about to start my Masters!).
** People with proper scientific jobs are probably laughing at me here...