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PhD journeys at Great Ormond Street Institute of Child Health

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Going rogue on the Bogue: my Bogue Fellowship at SickKids Hospital, Toronto

melanie.koelbel.157 November 2019

Written by Daniyal Jafree a MB/PhD student, supervised by Dr David Long and Professor Peter Scambler in the Developmental Biology and Cancer programme, studying how lymphatics in the kidney develop. Lymphatics are specialised tubes which clear debris, excess fluid and immune cells from organs. They have important roles in kidney disease, but how they appear and grow in the kidney in the first place has been a complete mystery.

The first year of my PhD was spent characterising how lymphatics normally grow in the kidney. Based on experiments I did, we had a strange idea about precisely where the cells that make lymphatics in the kidney might be coming from. However, we faced a major roadblock, as we didn’t have access to the right techniques to test our strange idea. Actually, no one in the UK did. With 2-3 years of my PhD left, a unique problem to solve and no way to solve it, what am I to do?

A few Skype calls, a short application form to UCL’s Bogue Fellowship scheme (https://www.ucl.ac.uk/prospective-students/scholarships/graduate/UK-EU_Res/bogue-fellowship) and a 7-hour flight featuring two screaming babies later, I found myself at the Peter Gilgan Centre for Research and Learning (PGCRL) at SickKids Hospital, Toronto. PGCRL is the equivalent of GOSICH in Canada, and SickKids is the largest centre dedicated to improving children’s health in the country. After acclimatising to Toronto’s skyscrapers (my apartment was on the 37thfloor), the team of Professor Norman Rosenblum (my supervisor in Canada) and I tried to tackle the mysteries of kidney lymphatic development using gene editing strategies to trace stem cells in mice.

Thanks to tremendous luck, an extremely supportive team and a mouth-wateringly fancy microscopy facility at PGCRL, it took us 9 weeks to test our strange idea of where lymphatic cells in the kidney are coming from. What we found was really surprising, and challenges what we thought we know about how lymphatics develop. The next trick will be to test whether we can exploit this to target lymphatics in kidney diseases; an ongoing aim in David’s laboratory.

I’m grateful to David for facilitating the trip, the GOSICH team and the MB/PhD programme for allowing me to go and Norm in Toronto for getting me involved in the amazing environment at SickKids. Whilst out there, I even got some time to travel, visit family and explore the Canadian wilderness.

Bottom line – if you’re a PhD student with an interesting idea and some time left till your thesis is due: go rogue. Go Bogue.

Writing retreats and groups

Kerry A Kite15 March 2019

Written by Caroline Fraser

I am a final year PhD student in the Child Health Informatics Group at the Great Ormond Street Institute of Child Health. In my project, I am using data linkage to evaluate rates of neonatal bloodstream infection in England. In my free time, I enjoy art, cooking and volunteering.

Twitter: @cfraserepi

What is a writing retreat?
A writing retreat is a great place to write without distractions and though the word retreat might sound very luxurious, unfortunately all the ones that I have attended were in UCL meeting rooms. Mostly they follow the format of a “shut up and write” group where you… shut up and write. They can vary in structure and length – some are a few hours, others a whole day and sometimes even spanning multiple days. At the more formal writing retreats (and usually the longer ones), you sometimes set a goal at the beginning of the day. You can then “check in” with your goals throughout the day to see how you are progressing. PhD students can use writing retreats to work on their upgrade reports, thesis chapters or papers. It is useful for writing from scratch, working through comments from your supervisor on a draft, or even reading papers and making notes.

Why should you consider attending a writing retreat?
There are some real benefits to a writing retreat compared to trying to write at your desk in the office or at home. First, there are no distractions – it is best to avoid opening email and to keep your phone on silent in your bag. There will be nobody asking you if you want a cup of tea or popping in to ask you a favour. Second, everyone else around you is also working in silence. There is definitely something to be said for the social pressure when you can see everyone else typing away. You don’t want to be the one person sat staring into space or scrolling on your phone.
All the retreats I have attended use a time schedule that helps ensure you take breaks and that you return to your work after a break. The schedules vary – some use a variation of The Pomodoro Technique – write for 25 minutes at a time with short breaks in between. Others have longer writing blocks, maybe 60-90 minutes with longer breaks in between. Either way, the structure helps if you know you will have a break in 20/40/60 minutes it is easier to just keep writing until that point. Also everyone breaks at the same time so you are not distracted by people chatting next to you while you are working. Another benefit, less academic but still appealing, is the promise of free lunch, snacks, or hot drinks. Depending on who is organising the event and the length of the event, but most at least have free hot drinks – and what student does not appreciate a freebie!
Even though I have not finished my analysis and I am not yet in full “writing mode”, I have found it useful to have some time set aside to write up what I have done so far so I won’t have to do it all completely from scratch at the end. Because my main focus is still my analysis it can be hard to find motivation to write while I’m sat at my usual desk. Having time set aside a few times a month has been incredibly valuable to me to get started and my thesis. As I am currently at the stage where I just need to get words on paper and I will worry about editing later. I have found that I can write at least 1000 words in a 2-3-hour session and I don’t believe that would be possible sat at my desk.

How can you find a writing retreat?
The ICH postgraduate society in collaboration with the PPP early career researchers group organise 2-hour writing sessions that include 3x 30-minute writing blocks. These are usually organised twice a month, subject to demand. Outside of ICH, the Doctoral Skills Development programme are running a “writing co-op” with 2x 1 hour 15 minute writing blocks – you can sign up as you would for any of the other PhD courses. There are also opportunities elsewhere, for example, I attended one organised by the Early Career Network that was advertised via email. You could also ask around if you have friends in other departments as they may know of groups that you might be able to attend.
Otherwise, organise your own! If there are a few of you in your team/programme/friendship group who need to write and you can’t find anything suitable then get together and organise your own. All you need to do is decide on a time, a quiet place with plugs and preferably some access to tea and coffee facilities, and set up a schedule.

How to prepare for a writing retreat?
One of the most important things to do before your writing retreat is to plan! If you are planning on writing your thesis or a paper, you can find great writing courses through the Doctoral School Skills website organised by a company called Think Write. One of the most useful takeaways for me from the thesis writing course was to plan your headings, sub-headings and paragraphs. It is a lot easier to write when you have this planned out. You don’t have to have planned the whole thesis beforehand but having an idea for the section you want to write is really useful.
Another key part of preparation is reading. I find it most productive to just write at the retreats and not waste ages looking up references. If you have a reference manager this should be fairly easy as long as you have already done the reading and saved the references. I also have a spreadsheet of papers I have read briefly summarised and separated into categories so if I want a reference and I can’t remember which papers are suitable, I can look it up in there and not do any extra searching.
It is also useful to have some goals to achieve in mind for the day. I find these are best if they are quantifiable, for example specify “add 1000 words to chapter 2” not “work on chapter 2”. If you are unsure of how many words you can estimate based on what you write in one session. For example, if the day is broken into four 1 hour sessions, note how many words you write in the first session then multiply it by 4 for your goal for the day. Inevitably, I find I write more in the earlier sessions than the later ones but I think a challenging but achievable goal is really useful. Personally, I find 500 words in one hour is a good ball-park figure – but more is definitely doable. Of course if you are editing a document it is much harder to have a goal. If you are working through comments from a supervisor or co-author you could aim to address all the comments.

Bonus: who to follow on twitter for writing tips and motivation

I have found two really useful accounts on twitter that give tips with regards to academic writing that I want to shout out
1) Dr Raul Pacheco-Vega (@raulpacheco)
2) Academics Write (@academicswrite)
They both post tips and tricks for academics, particularly PhD students, so I would definitely recommend checking them out.

Child Health Informatics Group website: https://www.ucl.ac.uk/child-health/research/population-policy-and-practice/child-health-informatics-group

Making science better: openness, reproducibility and teamwork

Emma J Butcher14 November 2018

Written by Sophie Adler-Wagstyl @sophieadler, MBPhD student and part-time post-doctoral researcher. Sophie did her PhD in the Developmental Neurosciences programme on neuroimaging of paediatric epilepsy. In her spare time she enjoys cycling and supporting Spurs.

 

 

 

 

 

 

 

PhDs can be challenging, involving tough tasks such as:

  • Learning new methods from scratch
  • Focusing only on one project and not being involved in small side projects
  • Not being part of a team and feeling lonely
  • Not knowing how to do something and being afraid to ask
  • Being asked to review a paper and not knowing how
  • Not being asked to review a paper but wanting to learn how

To address this, I helped to organise an open-science, reproducibility and teamwork session at Great Ormond Street Institute of Child Health (GOSICH) in October 2018. PhD students and post-docs spanning the breadth of research at GOSICH came along to listen and learn. Despite the diversity of methods and areas of research that people focus on at GOSICH, we discussed that there are a lot of skills required for research that are common to all of us. Many of us:

  • Have to learn stats and learn to code some of our analysis whether that be in R, Matlab, Python etc.
  • Have to think about ethics, IRAS applications, HRA approval, the GOS-ICH R&D department
  • Are doing longitudinal analyses
  • Are peer-reviewing work for the first time

And there are many more areas of mutual overlap…

In the October session, we discussed many of these topics. The outcomes of these discussions are outlined below, grouped into the areas of: collaboration and teamwork, reproducible research, open-science and peer review.

Collaboration & Teamwork

Collaboration and teamwork can help address some of the problems that PhD students face, such as learning new methods from scratch, not feeling part of a team and not being involved in side projects. However:

  • How can we create a collaborative and supportive environment where we can ask others for help?
  • How can we make our research more efficient by not repeating what others have already worked on?
  • How can we find potential collaborators?

To help with the challenges above, we have created a GOSICH SLACK workspace. This is an online space where members can post questions, events etc. and anyone from the community can respond. As well as a general channel, we have channels (groups) for early career researchers, a PREreview journal club, and social events. However, you can create a channel for anything, including for particular projects/topics, where you invite only your collaborators, a lab group, the post-doc society. If you are a current GOSICH PhD student or post-doc and would like to join the SLACK workspace, please email sophie.adler.13@ucl.ac.uk for more information.

Reproducible Research

We all want to do robust, reproducible, replicable and generalizable research. We want to know that our findings are real. We want the work to go beyond the lifespan of one PhD student or post-doc position and impact the wider scientific community.

So firstly, what is the difference between reproducible, robust, replicable and generalizable research?

@kirstie_j has a handy figure to explain it! Feel free to replace the word ‘code’ to ‘method’.

If you test a hypothesis using the same method and same data as some-one else (including your previous work), and you get the same result, your research is reproducible.

If you test the same hypothesis with a different method on the same data and get the same result, the finding is robust.

If you test the same hypothesis and use the same method on new data and get the same results, your findings are replicable.

Lastly, if you test the same hypothesis with a different method and different data, your results are generalizable.

Open-science

We can use open-science techniques to facilitate reproducible, robust, replicable and generalizable research.

 “Open Science is the practice of science in such a way that others can collaborate and contribute, where research data, lab notes and other research processes are freely available, under terms that enable reuse, redistribution and reproduction of the research and its underlying data and methods.” (fosteropenscience.eu)

Open-science practices include:

  • Publishing your work in open-access journals (so that anyone can read your work)
  • Sharing your methods (e.g. publishing them on protocols.io)
  • Sharing your data
  • Sharing your code (e.g. github.com)

 

We talked about how daunting it can be to release protocols or code but how beneficial it can be to both the wider scientific community and yourself.

PREreview

The last issue raised was about learning how to critically appraise work. One way to get practice at reviewing work in a safe and supported environment is by creating a PREreview journal club. This is a journal club that discusses and reviews preprints (manuscripts released by authors prior to peer-review).

PREreview (Post, Read, and Engage with preprint reviews) is a website hosting reviews of preprints created in journal clubs (https://www.authorea.com/inst/14743-prereview).

“Reviewing preprints benefits the authors, as they receive early feedback on their manuscript. Early-career researchers benefit from the opportunity to develop their critical thinking and peer-review skills. And the whole scientific community benefits from access to scientists’ discussions about the latest discoveries.” (https://elifesciences.org/labs/57d6b284/prereview-a-new-resource-for-the-collaborative-review-of-preprints )

We have started a PREreview channel on the GOS-ICH slack for those who are interested in improving their critical appraisal skills.

Hopefully through improving teamwork and being more open, we can help foster a supportive, collaborative environment at the Great Ormond Street Institute of Child Health. If you’re at GOSICH and want to join this endeavour – sign up to the SLACK workspace (find out how by emailing Sophie at sophie.adler.13@ucl.ac.uk) and get involved!