Summer camp in Angers 2015

Kamila Machová: I would like to tell you about my experiences with Summer School of Bioinformatics. I would like thank both my universities (South Bohemian University and Johannes Kepler University) for financial support of this school.

The summer school took place at the University of Angers in France from 29. 6. to 10. 7. 2015. This university have been organising summer schools since 2010 but the topics of bioinformatics was provided for the first time now. 28 students from whole Europe and India, Mexico, Tunis and the USA participated on this summer school. Majors of the students varied from bioinformatics to biology, informatics, medicine and mathematics. Students were differently experienced  in the field of bioinformatics and their expectations on the summer school programme also varied. Personally, I study bioinformatics and wanted to broaden my horizons in this field. We obtained 6 ECTS credits for participation on this summer school.

Our coordinators, biomedical students Marie and Esther, were looking after us for whole summer school. Our program usually started at nine clock a.m. and finished at half past five p.m. We were given our lunch in the university cafeteria, where we could choose pizzas, pastas, salads or sandwiches. We lived at students dormitories in another part of the city and we could go by bike or but to the campus. The weather was very hot the majority of time.

On the first day, we heart an interesting talk about the implementation of a vaccine against the polio virus. Unfortunately we spent the rest of day by introducing ourselves and listening to very long introductory talks. The second day we obtained basic knowledge of programming languages R and python which we used in some of the next workshops. I already know R from my university lectures but python was completely new for me. In following days we were taking classes focused on various bioinformatics topics. In addition to theoretical lectures we could try some of methods by ourselves in practical workshops. The majority of speakers came from Angers and Nantes universities. Now I’ll introduce you the topics of our sessions shortly.

Firstly we tried classification of (genomic) samples. We passed the (micro-array) data of healthy controls and patients with distinct disease to a function which was able to learn how to differ between these two groups. Afterwards the function was able to predict if an unknown sample came from healthy or ill person (glmnet). During the same session we also learnt how to find subgroups in our data (e.g.: subtypes of cancer) without previous knowledge of these groups (mixture models).

Two of our sessions were focused on modelling biochemical processes in a cell using linear equations. Firstly, we tried to solve a simple problem with the solution in 2D space using a pen and paper and then we solved more complicated one with the solution in many-dimensional space using computers.

During another session we learnt how to efficiently find a good solution of a problem with many possible solutions without trying and comparing all possible solutions. One way to do that works similar as the evolution of organisms (genetic algorithm). In the beginning we create a population of random solutions. These solutions can “mate” and produce new solutions. The newly produced solutions can mutate (change themselves). Some of the best solutions are selected to create the new generation of solutions. We focused on biology tasks.

Other lectures were focused on assigning a distinct disease to its corresponding mutation (change in DNA) in genome (all DNA information in an organism). Dealing with that can be pretty complicated. The mutation can occur just in minority of our samples, not all of the samples with the mutation has the disease, moreover we are not sure if we have the part of DNA with the mutation and wee need lots of samples to be able to draw some conclusions.

At one day we attended an excursion to Nantes. We visited Genomic and Bioinformatics core facility there and listened to the talk about reading efficient reading of large amounts of DNA information (next generation sequencing). Finally we saw how to find new mutations in genome of an individual using genomes of its parents in praxis.

Even though we mainly focused on general and human problems, we get known something about microorganisms too. We learnt how to characterize a sample of ocean water which is composed of a huge number of microorganisms species (metagenomics). Majority of these species can’t be cultivated in lab and we can’t differ them under a microscope.

Other session was related to medicine. We found out how clinicobiolcal databases work and after that the speaker showed us how is a database containing mutations of one gene (locus-specific database) created and we could try to upload the data extracted from scientific articles into it.

In addition of university scientists, scientist from business companies held several talks. They told us which types of research these companies do and how to calculate cost versus effectiveness ratio and of a new medicament and infer if we can start selling it even though the accuracy of our parameters isn’t high (Monte Carlo algorithms). The second speaker told us how to improve visualization of tumours. During optional evening session we discussed how do these companies work from employees point of view in these including our possible future carrier in these companies.

Also after our sessions we had still something to do. The summer school provided diverse free time program including city tour in Anger by “train” for tourists, competition in several sports, kayaking at the lake, city tour in Nantes with a guide, barbecue, last evening in museum of tapestries and a lot of parties. If I had time or didn’t want to take part in the program I was cycling around in Angers and the interesting landscape in its neighbourhood. I saw the city centre and many beautiful parks including ones important for many rare species, sand beaches surrounding the Loire river and amazing old slate quarries.

On Saturday I made a longer trip along Loire and visited castles, towns, old mills and smaller rivers nearby. On Sunday I visited two towns on Atlantic sea-cost together with other students and organizers.

To sum up, I gained a lot of new knowledge about diverse bioinformatics methods and research tasks. In addition to this I met many interesting people from diverse countries and I enjoyed these two weeks much.