Blog posts

The Stratigrad Tradition!!!

I guess it’s my turn again. :). The last few weeks have been packed with a lot of exciting moments. First of all, I passed my ESA which means I am officially in year two. I would like to use this opportunity to thank anyone who had a part to play in this, Dr. Hector Keun, Prof. Bob Brown, Dr. Anisha Wijeyesekera and of course all the other stratigrads who had to listen to me talk about Otto Warburg like a million times 😉 . Thanks!!!

I also joined Prof. Brown’s group to go on a lab retreat to Cornwall over a weekend.

Student Representative!

We all can’t believe that it has been nearly a year since we started on the Stratigrad programme. Typically, time is going very quickly and it is already almost time to say hello to the next lot of students starting at Imperial College! This year, I have signed up to be the Postgraduate Student Representative for our section, Computational and Systems Medicine. This involves an induction for the new MRes students in our section, participating in post-graduate education committee (PGEC) meetings (which include free biscuits I’m told) and generally being available to listen to the students in our section.

The most important, however, is that I have the tough task of organising the section’s Christmas Party…Eek!

Open space

It is quite obvious from previous posts that our Early Stage Assessment (aka 9 month review) has been the center of our attention for the last couple of months.

My fellow STRATiGRADs summed it up well: writing the report made us look back at the rollercoaster of a year we all went through, from progresses, successes and more interestingly challenges we faced, and then we could more clearly plan the course of the next 2+ years. It was also helpful to get outside views on our projects and to have a good refresh on how to present our results.

Following my post on our hot beverage habits, I will digress this time about our work environment and another mandatory tricks we use to get on with our work…

We are all seated in the SAF building’s open area: 5 levels of metal, glass, wooden desks and labs.

Magnets!

Whoa, Torben really raised the bar for the scientific rigor and quality of this blog. A bar that I will happily swoop well under without it even grazing the top of my head.

The last couple of months have largely focused around preparing for our Early Stage Assessments, which entails a short report and a viva consolidating what we have been doing since we started and what our plans for the next two years are. Sounds fun right? It’s actually not. It is however a good opportunity to think about what has worked, what hasn’t and the direction our research is going in.

A network approach to integrate different –omics data

My everyday commute to uni is approximately 1 hour, so I try to use this time efficiently by reading relevant literature for my PhD project.  Inspired by a paper from Kuchel et al. in 2010 I developed a network approach to integrate different -omics data, such as gene expression data (transcriptomics) and NMR and/or MS data (metabolomics). My initial approach is outlined in this blog post.

Creating a differential gene co-expression network

Suppose you have gene expression data from a disease group and a healthy control group, and you create a gene co-expression network (where nodes represent genes and edges represent high absolute correlation values), such that high correlated gene profiles in the control group are represented by green edges, red edges represent high correlations in the disease phenotype and black edges are drawn of two gene profiles are correlated in both, control and disease phenotype.

It’s hard

On the occasional instant that I decide to return home, be it only for those couple days a year that I feel equipped enough to be haunted again by that small town I grew up in, I continuously get asked the question – ‘so what are you up to now’?

I start with the polite, ‘oh hello stranger, long time no see’ – stranger being the key word, you know for those former secondary school class comrades of yours that you only still vaguely recognize through a certain social networking website. ‘Still in London mate, but doing a PhD now’… Awkward silence now, as they decide where such a position ranks against a proper job.

The Three Mantras

Well, I guess its my turn again 🙂 . In the past few weeks we have been preparing for our early stage review. Initially it felt it was just one of those milestones one has to jump through but how wrong I was. It has allowed me to rethink the aims of my project and to think about the best means of executing them.

I have also been thinking about what makes a great scientist over the past few weeks and it has become evident to me that everyone has their own way of getting there. However, there are three things that no professional scientist can ever avoid.

Ducks and Snakes

ouch – I was really hoping this would work (and I assume that import PhD won’t work either…), but it seems I really have to write this post … I guess I’m definitely getting too accustomed to Python!

I’ve been programming a lot recently (as expected, given my project…), as my comrade Emperor Duck attests. I’m mostly using Python, a really neat, readable and powerful programming language designed by cool cats for cool cats. If the myriad of programmers expressing their happiness online and the barrage of compliments present on the first descriptive paragraph of its Wikipedia article are not sufficient to express how cool it is, I think this xkcd comic should suffice.

Biosamples and Babies

Warning: Not for the faint-hearted

In our group we are mainly working with different human and animal biosamples including blood and urine. What you might not know is that for the lucky(?!) few we have stool samples to work on too! Now I know what you are thinking, you’re a little disgusted…I was thinking the same at first but I’m actually really lucky as my project revolves around babies and baby stool just seems less gross…right?

I studied microbiology for my undergraduate degree and have been interested in gut microbiota ever since. I think it’s a fascinating subject which I used to try to talk to my non-scientific friends about but they always looked massively awkward…Thankfully I have many scientists to talk to at IC and medic student housemates who don’t even blink an eye!

Pushing on

“Don’t blink or you will miss it”

it became obvious when were told we needed to submit an Early Stage Assessment as we were 9 month into our PhD…

I can remember our Research Proposal, the Stratigrad meeting and even posters and conferences for some of us, but 9 months seems like a lot!

Happily things got faster in the last 3 months as we got more experienced with NMR and MassSpec sample acquisition, data preprocessing and other software needed for our respective projects: the data started flowing in.

More data meant also more and more time in front of the computer to make sense of it, and that’s when our secret weapon came handy…

Tea or Coffee 1 or 5 First thing in the morning before any verbal communication or Last trick to get a bit more out of the day

we all have our much needed styles and habits…

Recently a very good friend about to start his PhD told me how optimistic he is, but said it might change in a year and cited this PhDcomic which – in truth – is spot on.