Summer school: “Big data Analytics and Machine Learning Meets Omics”

In summer 2018 the faculties of Health and Life Sciences, and Science and Engineering, hosted a ten week summer school for students interested in data science, analytics and machine learning. The five successful students received supervision from leading experts in the field, as well as a stipend.

The projects focussed on the application of data science techniques in the area of biological and biomedical research, called “omics”. These areas include the study of genomes and related technologies that produce large amounts of complex data, suitable for data mining. Researchers at Liverpool are using these techniques for “personalised health” research (e.g. to understand how your genetics relate to your likelihood of getting a disease), for cancer research (e.g. for understanding how certain genes are switched on or off during cancer progression), and to understand how infectious diseases can spread or how we can better detect them.

“Insightful, collaborative, applied”

We asked the students to explain their research project and experience of the summer school:

Di LiuDi Liu (BSC Computer Science) worked on the project “Topological data analysis for bioinformatics”.

 Can you tell us a little bit about your current research project

The intention of the project is to visualize the gene-gene interactions by analysing correlation coefficient of gene pairs as the pair’s weight score.

To achieve this we are analysing glioma gene scores by MPI and visualizing the analysis’ results on Cytoscape.

 How have you found the project? What has been the highlight?

The project has been excellent! Working with Drs Kurlin and Krishna broadened my vision and enriched my experience of using the knowledge I have learned.

Also, the project group is awesome. Two supervisors and one teammate, they helped me to overcome any obstacles during my internship.

The highlight for me was successfully using the C++ knowledge to fix the problem we met in the project, and learning how to use MPI to complete parallel programming to save a lot computer running time.

Has anything surprised you about the project?

I was expecting a more reserved role and have solo solved the data part of tasks because of the trust shown in me by Drs Kurlin and Krishna.

Have you seen the University in a different light as a researcher, compared to being here as a student?

Yes, the research side of the University is awesome. On the one hand, it practised the knowledge I have learned at University. On the other hand, it gave me a chance to learn more skills that can’t be learned in lectures. I think this will assist me in the future studies.

Has the research project changed your expectations of the future?

This project is relational with my expectation of the future. So, it let me realize my future’s expectation more clearly. Besides, it also let me see more possibilities to connect my subject with other subjects.

If you were to describe the experience in 3 words, what words would you choose?

Enjoyable, teamwork, rewarding.

Weiyi Ren (BSC Mathematics) worked on the project “Building a statistical model to help quantify molecules important for cell signalling and cancer”

Can you tell us a little bit about your current research project?

The project aims to understand how genetics relate to the likelihood of getting a disease, and to understand how infectious diseases can spread or how we can better detect them. My task was to build a statistic model to predict the change of intensity or retention time between the modified or unmodified peptide.

How have you found the project? What has been the highlight?

The team lead by Professor Andy Jones was searching for undergraduate students to help them build a statistic model. We tried several new approaches: random forest and neural network. The results were very successful comparing with the linear regression model.

Has anything surprised you about the project?

The project was very smooth. We met each week to talk about the progress. The supervisors were very passionate to help us with our difficulties. We could get detailed explanations from them on time.

Have you seen the University in a different light as a researcher, compared to being here as a student?

Yes, the research side of the University is excellent. Participating in a research is very different from being a student. It involves much more communication between the supervisor and the students, which would be no doubt a valuable experience for one’s future academic life.

Has the research project changed your expectations of the future?

Yes, this experience provides me with more possibilities for my future career. Data science is definitely a very good choice for me.

If you were to describe the experience in 3 words, what words would you choose?

Enjoyable, productive, full.

Ash Myall photo.jpg BSC e-Finance student Ash Myall worked on the project “Distributed computing and analytics to annotate the human genome”.

Can you tell us a little bit about your current research project

The intention of the project has been to develop a web-based visualization suite for results of Peptide Search Engines within proteomics analysis, focused specifically on the crowdsourced search engine which operates on a distributed network.

To develop this, we have used R and shiny, which together can quickly produce interactive dynamic visualizations.

In lay terms….producing visual representations of large scale data sets, to identify trends in the behaviour of proteins in samples (e.g. the human body).

How have you found the project? What has been the highlight?

The project has been incredibly insightful, which subsequently lead me to pursue postgraduate research in the field. My favourite part has been consolidating my understanding and confidence in using R.

Has anything surprised you about the project?

Yes, before I had little idea how essential data visualisations can be to understanding underlying trends, and how useful making interactive plots is; questions can be answered instantly about the data by a user.

Have you seen the University in a different light as a researcher, compared to being at here as a student?

Yes, I’ve found the independence to give greater flexibility in finding solutions to unseen problems.

Has the research project changed your expectations of the future?

Absolutely, I’m about to start an MRes in Advanced Biological Sciences with the bio informatics pathway following my interest in biological data analysis on the project.

If you were to describe the experience in 3 words, what words would you choose?

Insightful, collaborative, applied.

Is there anything else you would like add?

This has been a great opportunity, I’d recommend it to anyone who’s got an interest in biological sciences and comes from a computational background like myself. Not only has it provided an excellent application from my undergraduate skills, but it’s also set me in a great position for beginning a career or for going into a PhD.

Antoine Rohmer.jpgAntoine Rohmer (BSC Computer Science) worked on the project “Exploiting Graph Databases for bioinformatics” which included an internship at IBM.

Can you tell us a little bit about your current research project

The purpose of the project was to gain an understanding of the technologies underlying graph databases and parallel computing to create a large-scale visualization of gene-gene interactions from data provided by the University.

The technologies used in the project include Neo4j and the Cypher querying language on the graph database side. C++ and Python were used in tandem with supercomputers provided by IBM for data processing. Cytoscape was used for visualization. The open source pathway database reactome was used as the foundation of the database created for the project.

 How have you found the project? What has been the highlight?

The project was a great foray into the professional world. Working alongside experts in the field and absorbing their insight was a fantastic learning experience.

The highlight of the project for me was the moment the graph database and parallel computing sides of the project combined to form a coherent whole that until then seemed intangible.

 Has anything surprised you about the project?

Perhaps the biggest surprise was how largely independent I was in pursuing the project. Although a plan and structure existed, most of the meeting setups, deadlines, and choices in technologies were up to me. This in particular was a refreshing excursion from the otherwise rigid structure found in my studies.

 Have you seen the University in a different light as a researcher, compared to being here as a student?

Although at times the project felt like a continuation of my studies due to the large amount of research that had to be conducted, the knowledge that the end product will be used as a stepping stone to other research is a much greater motivator than grades.

 Has the research project changed your expectations of the future?

The project truly validated my interests in data analysis and got rid of any doubts previously had about which postgraduate program to pursue. More importantly it made me even more eager to enter the professional world.

If you were to describe the experience in 3 words, what words would you choose?

Insightful, refreshing, validating

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Telling tales of multiple Ps – Dr Lydia Cole

Several weeks ago, I had the opportunity* to talk, twice, about a topic related (slightly tenuously) to my research and very close to my heart.  On the evening of Wednesday 19th September I stood on the stage at Leaf, facing the Ignite Liverpool crowd, to present on “The Three Ps”; and on Saturday 22nd September I stood on a soapbox in Sheffield’s busy shopping district, to shout about “Peanut butter, palm oil and peat; getting un-stuck in the mud” to a bunch of slightly bemused passers-by.  They were quite different forums with which to share my knowledge and passion, but I learnt a good deal from preparing for and presenting at each.  Here’s a quick low-down of each event, which might hopefully inspire you to get involved in the future.

Ignite Liverpool is the brainchild of a community organisation that runs quarterly events, providing a platform on which anyone can talk for a whistle-stop five minutes about a subject they are passionate about.  The challenge is to convey a coherent story in five minutes, in synchrony with the visuals on your 20 slides which flash up for five seconds in a continuous reel.  I managed to mumble in time to the slides until the penultimate one, where my dialogue turned to dust!  It was a fun experience though, and useful in considering how to design succinct propaganda.  If you’d like to know more about the tale of The Three Ps, you can watch my performance here.  I would recommend giving Ignite a go if you live in Liverpool, or any of the other cities where it’s held (e.g. Sheffield); it’s a great opportunity to practice your public speaking and communication skills on any topic of your choice, in front of a very supportive, slightly tipsy crowd.  The most hilarious talk at the last event was entitled Any Colour you like, where all of the slides where shades of black!

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Reeling off about peat at Ignite Liverpool!

Soapbox Science proved a less well-polished, more chilled-out and slightly chillier event!  The initiative was started eight years ago by two female Biologists, with the goal of creating a public outreach platform on which female scientists could promote their science, whilst simultaneously increasing the profile of women in the STEM sector.

I chose to talk about the same issues on the soapbox as I did on the stage: a narrative around the prolific commodity, palm oil, which links our consumption behaviour in the UK to the draining and deforestation of peat swamp forests in Southeast Asia.  Orang-utans, the people of the forest, were the protagonists, of course.  As part of my PhD research (a few years ago now!), I explored the long-term ecology and contemporary management of the coastal peat swamp forests of Sarawak, in Malaysian Borneo, and have since been monitoring their declining condition and the ever-expanding state of industrial oil palm plantations across the region.  Though my Soapbox performance was not as succinct as I’d hoped (more prep required next time to catch the attention of a transient audience), I managed to have an interesting discussion with several members of the general public on topics of environmental sustainability and the RSPO.  The conversation with one chap, as engaged as he was disillusioned, only concluded when we decided that capitalism needed to be scrapped.  Unfortunately, I didn’t feel qualified to propose an alternative solution.

Illustrating the link between peatlands, palm oil and peanut butter

I found both experiences hugely valuable, primarily because I gained some idea of the level of knowledge amongst the general public on some everyday consumer issues.  People were less aware than I’d realised.  To place your science into a ‘real world’ context, to understand how it might fit into the lives of your neighbours, and to learn how you can inspire people to care as you do, I would recommend standing up on as many platforms as you can.

*The opportunity was created by me through signing up to two events without realising they were in the same week!  I questioned my life choices many times when preparing for them into the wee hours of the morning …. though as per usual have no regrets, in retrospect.

Local schools take on Future Food Challenge

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An innovative schools outreach programme that encourages students to think about sustainable food production is set to return after a successful first run earlier this year.

Future Food Challenge, a 12 week programme delivered by social enterprise Farm Urban and the University’s Institute of Integrative Biology, challenges Year 9 students to think up new ideas for growing food in urban environments using aquaponics – a sustainable method of raising both fish and vegetables.

The programme, funded by Shaping Futures, the Merseyside partner for the National Collaborative Outreach Programme (NCOP), gives school teams the chance to immerse themselves in the science of aquaponics with their very own Farm Urban Produce Pod system, before forming their own start-up, developing a business idea and designing and building their own aquaponic food system.

The programme provides students with the opportunity to gain an insight into start-up businesses, social enterprise and how they link into Higher Education activity, whilst developing skills in project management, leadership, finance, teamwork, communication and scientific research.

This year’s finale event, held at Farm Urban’s agri-lab space at the Liverpool Life Sciences UTC in July, gave teams the opportunity to exhibit their work, display their systems and pitch their business idea to a panel of judges, comprised of local business leaders and university academics.

Business ideas ranged from systems for use in primary schools to hospitals and local cafes. The overall winners from Woodchurch High School in Wirral carried out research and spoke to local charities and churches to create a system that would provide fresh food for those accessing food banks. The winning team said: “We have loved our aquaponics journey from fish to free fresh food for everyone. It has made us more aware of food problems people face and how to help them using science.”

Dr Iain Young, University lead for the programme commented: “Teaming up with organisations outside the University can be a really powerful way of delivering public engagement, showcasing our science and involving the public in research. This project gave us the opportunity to partner with Farm Urban to reach hundreds of school children from less advantaged backgrounds. Farm Urban are an inspiration in themselves, promoting local, healthy food production, and they also deliver exceptional events and programmes. I have found the whole experience of working with them on this project very rewarding.”

Farm Urban is now encouraging the Future Food Challenge teams to act as Future Food Ambassadors, sharing what they’ve learnt and inspiring their fellow students to think about what they can do collectively to continue to tackle global food challenges in their own communities.

Registrations for the 2018/19 Future Food programme are now open for schools. Please visit http://www.farmurban.co.uk/future-food-challenge for more information.

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Woodchurch High School students were the overall winners for 2018.

Dementia Public Engagement Day

On Wednesday 23rd May, scientists from Team Madine and Team Turnbull went on a mission to educate the public about dementia research as part of dementia awareness week, at the Alzheimer’s Research UK North West public engagement event hosted at the Institute for Dementia (University of Salford). The event was a hive of activity and a cornucopia of fun! Through the media of Lego®, giant KerPlunk!, cells and real brains members of the public were introduced to all things dementia, including how diet can affect your dementia risk, the development of novel inhibitors of dementia-associated proteins and the links between dementia and other diseases.

Kiani Jeacock, James Torpey (Madine group) and Scott Guimond (Turnbull group) showcased the fantastic research happening at the University of Liverpool through informative posters and a ‘Draw for Dementia’ activity. People were invited to draw the first thing that came to mind when they heard the word “dementia”, which resulted in some really interesting and thought-provoking work!

On the day, they also met people who had dementia themselves or who had friends or family with dementia. This was an educational experience for the scientists too, as it highlighted the translational aspect of their work and emphasised the importance of research into these poorly-understood conditions.

Overall it was a well-organised and enlightening day, and events like these are fantastic for both researchers and the general public alike.

Thanks to ARUK and the Institute for Dementia for hosting!

 

Warrington Collegiate Student Work Placement

Louis O’Brien, a student from Warrington Collegiate, sitting their BTEC Level 3 National Diploma in Applied Science, applied to do a work placement in the lab of Natasha Savage.

Louis worked with Natasha for a full week during February 2018. They did a variety of experiments and simulations together:

  • Plasmid Preparation. Bulking up plasmids using bacteria, performing a midi plasmid prep.
  • Cell culture. Growing up 3T3 cells from frozen, ready for plasmid transfection.
  • Time Course Imaging. Bacterial colonies, grown from swabs of Louis’s phone, were put in suspension and filmed under a light microscope to observe their proliferation.Polarity Simulations. Louis ran simulations of cells breaking symmetry. By changing reaction strengths Louis worked out the key molecular components.

    Louis doing bacterial work for time course imaging. Growing 3T3 cells from frozen stocks. DNA extracted using midi plasmid prep.

Farm Urban’s Future Food Challenge – launch Event – Speed Date a Scientist

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150 year 9 pupils from local schools visited the University of Liverpool for one day in
February to take part in the Farm Urban Future Food Challenge Launch Event. During
the launch event students engaged in a number of activities, including speed dating
scientists.
The speed date scientist event was great fun. The scientist sat at a dating table and awaited the students. Students arrived in groups of around 6. During a 5 minute period the scientist introduced themselves and their work, after which the students were free to ask any questions they wished. Questions ranged from, ‘Is being a scientist hard?’ to ‘Do you think there is a god?’ Once a conversation started it could go anywhere from eprogramming humans to the origin of names. The event was great fun for all.

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Pint of Science

The Pint of Science events around Liverpool ran for three nights (14-16 May 2018), all evenings were sold out!

The Centre for Cell Imaging’s technician, Jen Adcott, took to the stage at LEAF on Bold Street on the first evening of #Pint18 to present a two minute shot talk about ‘The science of imaging, a technician’s perspective’.

Jen took on the challenge, initially not realising that PowerPoint slides were not permitted for the shot talks, only small props that could be carried on stage… adding to the challenge of giving her first public talk, by discussing microscopy without being able to show any images!

The training provided by Steve Cross, organised by the University of Liverpool, was a huge help, and it was great to see how everyone’s talks progressed following the training.

Jen talked about how technicians support scientists in imaging. She demonstrated the use of different microscopes using a laser pointer to show the principle of the laser scanning confocal microscope, with the addition of a cylindrical lens (glass stirrer borrowed from lab B!) to turn the laser beam into a Lightsheet, as used in Lightsheet imaging.

 

Unfortunately due to broadcasting issues Jen’s talk was just missed off the live Facebook feed. The recording from the night started from the third talk in, and can be viewed here. Feedback from the event was very positive, with many people stating that ‘the shot talks were the highlight of the night!’

Jens advice for anyone thinking about taking part in the Pint of Science events is

“Do it! It’s great fun, although slightly nerve racking. It’s great to be a part of an event like Pint of Science, meeting new people, learning new things, and talking science. The support and training was fantastic! I was nervous that a technician giving a talk may not go down well with a room full of people wanting to hear science, but later at the bar I had people coming up to me wanting to learn more about the microscopes – it was great! And made me realise that anyone working in science, no matter at what level can take part in events like this.”