Tag: phd

MetID workshop

By Erika Dorado and Kiana West, STRATiGRAD PhD programme, Department of Surgery and Cancer

A workshop focused on the identification of metabolites was organised by the STRATiGRAD PhD programme in collaboration with the Centre for Metabolomics and Bioanalysis (CEMBIO). The MetID workshop took place between 12th and 15th June 2018, in Madrid.

MetID workshop participants

The MetID workshop started with oral presentations given by PhD students from both Imperial and CEMBIO. The PhD students had the opportunity to present their research projects in seven minutes to an audience composed of recognised researchers in this field. We had the opportunity to practice our presentation skills and share our research experience by providing concise information about our PhD projects. On the second day, the workshop started with an introduction by the director of CEMBIO, Dr. Coral Barbas. During the second and third days we attended lectures given by researchers from CEMBIO about fragmentation rules and mechanisms (Dr. Ana Gradillas), data curation (Dr. Javier Ruperez), as well as theory-practical lectures about annotation on MS and MS/MS level (Dr. Joanna Godzien). In addition, Dr. Joram Posma from Imperial presented two lectures about statistical experimental design, bias and confounding, as well as MetaboNetworks and graph theory.

Dr. Coral Barbas from CEMBIO giving an introduction to the workshop

On the third day, after finishing the lectures, we attended an exhibition on extended reality space offered by the Telefonica foundation from Madrid. We had the opportunity to experience different realities such as augmented, mixed and virtual reality. After this interesting activity, we enjoyed some sightseeing in the centre of Madrid on our way to have dinner together. During these activities the students from both universities had the opportunity to do some valuable networking.

On the final day, we visited the laboratories at CEMBIO. Dr. Antonia Garcia gave us a tour and showed us all the equipment in their laboratories, including liquid chromatography and mass spectrometers. The final day was concluded with a contest about metabolite identification to allow the students to apply all the knowledge acquired during this MetID workshop. Groups composed of students from Imperial and CEMBIO were organised randomly by Dr. Godzien, each group had the great opportunity to apply what we had learned about annotation on MS and MS/MS level by identifying 12 different metabolites. This contest allowed us to apply our communication and team work skills. The group that won the contest was composed of Vincen Wu and Erika Dorado from Imperial and Cecilia Barbas from CEMBIO.

Visiting the laboratories at CEMBIO
Dr. Isabel Garcia from Imperial, Dr. Coral Barbas from CEMBIO, and the winners of the contest: Cecilia Barbas, Erika Dorado and Vincen Wu

We want to thank the Graduate School for providing generous funding jointly with the STRATiGRAD PhD programme to carry out this workshop. We want to thank Dr. Isabel Garcia (coordinator of the STRATiGRAD PhD programme), all PhD students and researchers from Imperial and CEMBIO for all their effort organising and participating in this workshop. This workshop not only encouraged critical and independent scientific discussion on metabolite identification, but also showed us the importance of networking and scientific collaboration at an international level.

Inter-group Bowling Event 2018

by Adrian Brown, Clinical Medicine PhD student.

We originally decided to organise a social event to try and help our fellow colleagues beat the January blues! Once we had a spare moment, and to stop the students going on a New Year’s strike, we decided to organise an after-work bowling event. We invited students from Investigative Medicine and the Division of Brain Sciences to attend the inter-group networking event on Friday 12th January 2018. We were very fortunate and extremely grateful as this event was funded by the Graduate School. Attendees were randomly divided into teams across the three bowling alleys hired and participated in some friendly competition to find the top scoring team and player. We also shared some delicious pizza and drinks. After one game, the teams were reshuffled and play resumed. While the bowling skills among the group varied Jamie was the bowling champion among the group!

Aygul Dagbasi, a 1st year PhD student in Investigative Medicine particularly enjoyed the event commenting “I had a great time at my first PhD social event! It was a fantastic way to get to know people from the lab in a more informal setting”. Katerina Petropoulou, a final year PhD student also added “I haven’t bowled in years but the event was the most fun I’ve had at a social event during my PhD”.

Thank you again to the Graduate School for funding the event. As you can see from the photographs, everyone had a lot of fun and we look forward to the next event!

 

Three things I learnt at the Global Postgraduate Retreat

by Selina Cao

This January I signed up for the Global Postgraduate Retreat – Impact and influence at Cumberland Lodge, Great Windsor Park. It is such an elegant lodge with long royal history. This is my first retreat experience and I would like to share with you the three things I learnt from it.

Bold and systematic answer for why

This retreat helps me start to think early in my academic career why I am doing what I am doing now – the potential outcomes and impact of my research. While you might think that we have this figured out already when we applied for Ph.D. programs or when we started our research, however, this retreat enables me to think more boldly and systematically how my research can make a difference not only in my chosen field but also, more importantly, for the whole society and human beings. Specifically, I found the four-audience framework (academic, business, government, and public) very helpful in guiding me to develop my impact statement and strategies for different audience. The group-based and interactive activities further deepened our understanding of our own research. For example, we were asked to draw our own impact statement and then present to team members in a straightforward and plain manner. Since the students came from a variety of disciplines, we are also developing our communication skills through describing our research and impact in a way that anyone without a related background can understand. This mirrors the real time scenario since most audiences in real life possess less knowledge in your field. For example, how can we convince government officials with less scientific background to provide funding by framing our research impact in an easy-to-understand manner and in line with their political objectives? What’s more, interactions and peer-learning enabled us to further refine our initial plan and expand our impact. In the end, answering this why question boldly and systematically built up my confidence and motivated me to make a contribution.

Real-life exercises for how

One of the most precious parts of this retreat is that the learning is very interactive and situated. Instead of walking through slides after slides of normative guidance, we are learning through real life cases and working in different teams to solve problems originated from our own research. For example, during the first day, each group was asked to provide detailed plan to engage one of the four audiences for a real life project called “Tiger Toilets”, a no-frills latrine which uses composting worms to convert human waste into useful fertiliser. The principle investigator of this “Tiger Toilets” project gave us feedbacks on our results after our presentations. For the second day, each group was asked to pick one research topic from their own team members’ fields and try to present to four audiences for funding. The one-hour preparation time put us under huge pressure. This activity is organized in a competition format and all judges are acting in a very professional and real-life setting. During the interactive exercise, we developed our negotiation and communication skills. I still clearly remember all the tough questions we obtained during the competition. Being the only Ph.D. student from business school with research interests in Entrepreneurship, I think the experiences I can gain from this competition are no fewer than the Dragon’s Den or Shark Tank pitching. Key takeaway is the importance of understanding audience’s need: different strategies for different audiences! Knowing your research is important but knowing how to sell your idea is equally important. The winner is the one who secures the most funding and luckily our group won the competition with a box of chocolate!

Opportunities arising from diversity and interactions

Lastly, this retreat impressed me with the backgrounds of the participants in terms of their nationalities and chosen disciplines. Diversity entails great opportunities to expand knowledge base, build network, and innovate through interdisciplinary collaboration. Personally, being the only one from business school, this is my first time getting exposed to so many interesting scientific research outside my field at the same time. Through discussion, their studies inspired me to think differently about the taken-for-granted principles in my field that no one ever asked me before. We were very often amazed by so many interesting facts about cultural differences. We were also enjoying each other’s company through playing Ping Pong, table tennis and other recreational games. Quite many students had a walk to the beautiful park and enjoyed a moment of quietness outside busy city life. These close interactions and knowledge sharing in such a relaxing environment indeed provided us great potentials for future collaborations. For the final part, we were asked to present in any format a summary of the learning from this retreat and our group provided this poem. Hope you enjoyed it.

We went to Cumberland house the 22nd and 23rd,

To do a bunch of stuff of which we never heard.

Making our plans bigger and bolder,

Thinking about all our stakeholders.

We heard about cancers, faeces and germs,

All gobbled up by hungry tiger worms.

We all stand in lines, us girls and us boys,

Trying to speed network despite the noise.

We worked hard and fast, ok with mistakes,

Worried we might miss out on the next round of cakes.

We all tried our best but when ready to can it,

We got another nudge from Bethan, Amy, Valentina, Elena or Janet.

Half of us met on the way from the station,

Proving invaluable for ensuring negotiation.

Connecting made here are no coincidence,

As we go out into the world to have impact and influence.

All in all, I had a fantastic time in this impact retreat and met many new friends there. I really appreciate ICL for providing me such a great training program. And I am very grateful for all the knowledge and encouragement from my teammates. Now I know who I can reach out to for a coffee break at campus through our “Martians of Cumberlodge” WhatsApp group chat!

Next Global Postgraduate Retreat – Impact and influence is from 19 July 2018 – 20 July 2018. So hurry up before it is fully booked!

Meet the Scientist – Open Days at the Division of Brain Science

By Luigi Montibeller

The laboratories of Brain Division of Imperial College London (ICL) opened its doors on the 23rd and 25th of October to display it’s state-of-the-art technology, experiments and research through interactive talks and guided tours run by its researchers, specializing in the field of neurodegenerative diseases.

More than 100 people including patients, relatives and members of the public attended the event. The tour and presentations gave attendees the opportunity to talk to leading researchers and medical professionals, exploring the latest research, tackling conditions like Parkinson’s disease, Alzheimer’s disease and brain injury.

A presentation about each specific neurological disorder was given followed by a visit through the labs and the Brain bank. For example, visitors witnessed the dissection of a human brain by Dr. Steve Gentleman, highlighting brain function and it’s impairment in such diseases.

With additional ‘hands-on’ demonstrations, the participants had the unique opportunity to participate in experiments that researchers conducted inside the labs. These included learning about cell culture, immunohistochemistry and microscopy.

The event received great feedback from attendees. With comments like “Very well organized. Complicated research presented in plain English. Very enthusiastic stuff. Thank you all”, “Super day: excellent, translated well for lay man’s language”.

Cross-CDT Fair – Pain Relief for Scientific Computing

Did you ever wonder what most of PhD students at the College have in common? They need to compute to finish their degree. The task can be as simple as a quick data analysis or as complex as creating a new software package. Did you also know that most of the students arrive with a minimal background in computing? A lot of them find themselves in a “sink or swim” situation. After experiencing this ourselves, we decided that we don’t want others to suffer the same fate and make the same mistakes. To bring the issue into the spotlight, we decided to organise a Fair that featured exhibits dedicated to essential computing skills that every student should know before they attempt to “swim”.  

The Fair happened on October 11th, 2017 and it was a success. We had at least 60 visitors – after that we lost count. We invited CDT cohorts as well as PhD students across the College to come, network and pick up useful tips. The event started on a high note, almost everyone showed up right when the door opened. The visitors dispersed around the exhibits and listened to what we had to say. The ones that needed a bit of help with getting enthusiastic got cookies coffee or tea. We had an incredibly busy three hours at the exhibits as well as giving short talks.

After picking up useful computing tips and hints, the audience had a chance to visit a poster session at the Fair. We invited open source software projects from the College to present to the students. Many of these packages can be applied to various types of projects. Who knows, maybe we encouraged future collaborations.

The pizza and beer arrived just in time, one could not keep this pace much longer. The networking part that followed went very smoothly.

With the Fair out of the way, we intend to continue our effort to educate the cohorts via the Scientific Computing Support Network. There is a good chance that we’ll organise the Fair again. Note to self – keep it simple and order more pizza.

Many thanks to the Graduate School, Platform for Research in Simulation Methods and the Research Computing Service for funding and many thanks to everyone who contributed to the poster session.

Thomas Bendall, MPE
Eduardo Ramos Fernandez, TSM Matthew Garrod, MPE
Thomas Gibson, MPE Michael Haigh, MPE
Hemant Khatri, Math Department Smitha Maretvadakethope, Fluids Josephine Park, MPE
Sergio Perez, Fluids Matthew Taylor, HiPEDS
The Computational Methods Hub

A diary of the LERU Doctoral Summer School

by Holly Jenkins

A diary of the LERU Doctoral Summer School 

My name is Holly, I’m a second-year PhD student in the Section of Neonatal Medicine. This July I was fortunate enough to represent Imperial College at the League of European Research Universities (LERU) Doctoral Summer School, held at University of Zurich. LERU is “an association of 21 leading research-intensive universities that share the values of high-quality teaching within an environment of internationally competitive research.” The topic this year was: Citizen Science – nexus between research and public engagement. If you are scratching your heads wondering what citizen science is it can be broadly described as the involvement of non-professional scientists in research. This can range from small-scale projects like bird watching to large-scale international projects like Zooniverse (https://www.zooniverse.org) and due to the rapid boom in technologies, citizen science is becoming available to a much wider audience.

The aims of the LERU Summer School were twofold: to explore the importance of engaging citizens in research and to highlight the ethical, technical and legal issues associated with doing so. Over the week, we examined various definitions of citizen science, designed our own projects and ate a lot of cheese!

Day 1:

I had high hopes of exploring Zurich city centre before going to the LERU Welcome Event …but after my crazy experience on the Piccadilly Line at 2.30am to Heathrow, I successfully managed to sleep away my free hours in the hotel.

After a short, yet incredibly wet walk to the welcome event we were greeted by the organisers. As the evening progressed and the ‘organised fun’ became more elaborate we learnt more and more about each other including several embarrassing PhD stories!

Day 2:

Monday morning kicked off with presenting our PhD projects in the style of the ‘Three Minute Thesis’ competition. In the afternoon, we listened to two keynote speakers. Professor Bruno Strasser’s talk “The Rise of the Citizen Sciences: Rethinking Public Participation in Science” focused on whether citizen science projects will change the way we ‘do’ science (answer = yes!) Professor Effy Vayena’s talk “Citizen Science: Ethical Challenges and Opportunities” then highlighted the issues of quality, accountability, trust and autonomy.

Left: Identifying our unique selling points which ranged from being confident to thinking outside of the box. Right: One of the keynote speakers, Professor Bruno Strasser.

 

In the evening, we travelled to another campus – Irchel, where a Citizen Science Exhibition was running. A number of university projects were showcased (http://www.grc.uzh.ch/en/focus/exhibition/CitizenScience.html), a personal favourite of mine was a project involving citizens in mapping plant diversity around the city. The aim of this project is to show the public that the city air is filled with plant seeds that repopulate very quickly. Plant trays filled with sterilized soil are distributed to citizens and are placed somewhere in the city – the garden, in a school, on a balcony or on a roof terrace. It is then simply a waiting game! Photos of plants growing spontaneously in their trays can be uploaded to an online platform where it is possible to compare them to their neighbours or other people in the city.

After the Exhibition, we had a BBQ which stayed outside for several hours before a freak thunderstorm caused us to seek refuge inside or brave the weather with broken umbrellas and sodden shoes.

Top: Citizen Science Exhibition at Irchel Campus. Note the commissioned art on the sides of each poster – such a fab idea! Bottom Left: Agnieszka, Judi and Ray taking shelter during the monstrous thunderstorm.

Day 3:

On Tuesday, we attended one of three workshops: Improv, Storytelling or Crowdfunding. I chose Storytelling run by Dr Mirko Bischofberger, a respected filmmaker who works in science communication and science policy. The workshop was designed to improve and apply basic storytelling concepts to our scientific writing. In the evening, we went to the Uetilberg mountain for a traditional fondue dinner. Post cheese and veal, we decided to attempt the 30 min ‘walk’ (if you can call it that) down the mountain…It’s safe to say we all hurt the next day!

Left: The beginning of a very cheesy night. Right: The panoramic view from the top of Uetilberg mountain.

Day 4:

HACK DAY! Today was dedicated to working on our Citizen Science Projects. We laughed when one of the organisers said we could stay at the Graduate Campus until 11.30pm….until it got to 10.30pm and my group was still there suffering with acute cabin fever! Thankfully we managed to turn our alarm clock idea into a demo app (LetsWakeApp) in under 24 hours!

We chose to focus on an alarm app because over the last few years there has been an explosion of sleep related apps. There is however, a lack of research on the types of sounds that wake you up and how they make you feel once you’re awake. The LetsWakeApp project aims to bridge this gap in knowledge by allowing citizens to rate random alarm sounds each morning e.g. did this sound make you happy or sad? Without giving too much away, through citizen participation, machine-based learning, and some snazzy statistical methods, the app will provide the user with a personalised alarm that wakes them up in a positive mood.

The LetsWakeApp team in action.

Day 5:

After some last-minute pep talks we presented the LetsWakeApp project to a panel of judges that included the likes of Professor Deketelaere (Secretary General of LERU), Professor Kevin Schawinski (co-founder of Galaxy Zoo) and Professor Daniel Wyler (former Vice President for Medicine and Science) Despite some tough competition, our project was picked by the jury and we won 2500 CHF (£1,900), to develop our project!! In the evening, the winning teams (LetsWakeApp and AstbeSTOP – the student choice) presented at the Graduate School’s Annual Ceremony.

Left: The LetsWakeApp Team. Middle: Ray showcasing a demo of our app. Right: Shauna (L) and I (R) celebrating the LetsWakeApp win.

Day 6:

A morning city tour was met with great enthusiasm by the LERU group on our last day. Finally, after an intensive week, we could actually explore the city. Our tour guide Julian, who was as witty as he was knowledgeable, took us on a whirlwind tour. Did you know Lenin lived in Zurich for a few months after he was exiled from Russia? Apparently, he still has a Swiss bank account with 50 CHF in…

Alas like all good things, the LERU Summer School drew to a close. On reflection, I had an incredible time that I know will lead to some very exciting opportunities (keep your eyes peeled for the LetsWakeApp).

Left: The city of Zurich. Right: My first experience of a double decker tram.