Title of the article

Title of the article

EXPERIENCE: Stimulating / Enriching / Playful / New / Interactive / Accessible / Interesting / Friendly / Motivating

Whether genomics, imaging data vitro ou in vivo, animal or plant models, data in life sciences are now mostly processed “in silos”. The MoDaL unifying project (Multi-Scale Data Links), carried by the network Biogenouest, intended to decompartmentalize resources and promote moments of exchange and collaborative work around the integration of multi-scale biological data. The purpose of these meetings is to discover the diversity of profiles of research in biology and health in the West.

The MoDaL hackathon was born with the idea of ​​federating the scientific community and decompartmentalizing resources. This event, which took place online on January 25 and February 1, was intended to be a moment of exchange and collaborative work. During the hackathon the keyword was collaboration : from projects to presentations, the program was built with the contribution of the participants who remain, throughout the duration of the event, protagonists and animators.

During these two days, a variety of profiles from different backgrounds met and worked together around data integration and interoperability. Here is a cross interview with three participants: Thomas Darde, Isabelle Hue and Nathan Chate.

Presentation and scientific background: 

Thomas Darde:

Thomas Darde

Bioinformatician, Thomas Darde supported his doctorate in toxicogenomics in 2017 within IRSET. His research aimed to study the mechanisms of action of compounds, to identify markers of exposure, but also to generate molecular signatures with predictive potential. 

During his post-doctorate, Thomas continues to work on heterogeneous data integration issues as well as on the development of web tools for visualizing genomic data, such as RGV et TOXslgN

In March 2020, he joined the R&D section of the young Rennes start-up Nahibu, with the objective of develop analytical pipelines and tools user-friendly to allow customers to easily visualize the results obtained. It is in December 2020 that Thomas creates SciLicium, a service company specializing in the analysis of omics data and the development of bioinformatics tools. 

Isabelle Hue:

Isabelle Hue

Agronomist by training, Isabelle Hue obtains a thesis in immunology and a post-doctorate in plant biology before joining an INRA team in 1992 to work on the maturation of goat oocytes. She continued her research in animal biology by joining a team in 1997 that works on the anomalies of bovine embryos developed following fertilization. vitro or cloning, and she studies the uterus / embryo interactions and the impact of maternal physiological status on the development of the embryo.

In 2019, she joined the LPGP team of INRAE ​​to tackle a new facet of biology, with questions of molecular and cellular interactions between different tissues (adipose, connective, muscle), to study the expression of differently expressed genes. , functional pathways and statistical processing of these data. 

The integration of data and their interaction constitute a major point of interest in his scientific research. 

Nathan Chate:

Nathan Chate

After a bachelor's degree and an M1 in biology and health, Nathan Chate began an M2 in genetics, genomics and systems biology in order to open up and learn about bioinformatics analysis. Currently on an internship at the Thorax Institute in Nantes (Université de Nantes, Inserm, CNRS), Nathan is participating in a study on cardiac arrhythmias by analyzing ATAC-seq, Cut & Run and ChIP-seq sequencing data, to study key transcription factors in open regions of chromatin.

Feedback on the hackathon: 

1. Have you taken part in a hackathon before? 

Thomas :

Yes, the hackathon is a well-known format in (bio) -informatics. I participated in GCC (Galaxy Community Conferences) in 2015 and at the MétroMix, a hackathon organized in 2017 by Rennes Métropole. 

Isabelle: 

No, it was a first experience. I had heard of this kind of event before but hadn't taken the plunge yet for fear that too much coding would be required.

Nathan:

No, I had vaguely heard of it, but I had not yet had the opportunity to participate in this type of event. 

2. What motivated your participation? 

Thomas :

First of all the subject: the integration of heterogeneous data and the reuse of data over time are hot topics in the scientific world and represent two major issues that I have encountered throughout my career, from the thesis until today. 

Then, the desire to meet people sharing similar issues. What I find interesting in this type of event is the possibility of discussing with people who, through their training and experience, will approach the project on another level and will enrich the discussion with a crossed perspective. 

Isabelle: 

The theme and the desire to meet people who also seek to integrate data. In addition, it was an opportunity to meet colleagues who work on other sites or on different disciplines, and whom I would not have been able to meet otherwise. 

Nathan:

The desire to broaden my general knowledge by discovering other activities / fields of research and also the desire to get closer to the world of bioinformatics. 

3. Three adjectives to describe this experience: 

Thomas :

Stimulating, because it was an opportunity to meet new people and discuss issues shared within other projects.

Enriching, by its multi-domain side. By working together, each has made a contribution to the building. 

Cheerful, the hackathon took place in a good mood and in a happy and productive spirit!

Isabelle: 

New.

Interactive, I really appreciated the spontaneous and open nature of the discussions. 

Accessible, the language was understandable even to those who were not command line and bioinformatics experts. 

Nathan:

Interesting, the proposed projects were very varied and I was able to try to understand the problems encountered by other people, linked to different subjects. 

Friendly, tool gather.town allowed to live an experience in distance very close to what one could have lived in face-to-face. 

Motivating, we were driven by the desire to move forward with the project! In addition, time was marked by collective moments of feedback on projects, thus adding a stake and a timing to be respected. 

4. Any advice for participants in future editions? 

Thomas :

You have to register ! It's a great experience that allows networking and promoting inter-laboratory exchanges. 

And don't hesitate to come up with a project and talk without being afraid of being judged. Hackathons are moments of discussion to try to find avenues for improvement to a common problem, they are based on benevolence and you should not hesitate to reach out to people. 

Isabelle: 

As the promoter of a project, I advise future promoters to clearly identify the questions and to have a short, powerful title, and a long title, more explicit on the content of the project.

Also, before participating, it may be interesting to read the profiles of the other participants, to be able to target your questions and better understand the presentation of the project as well as the expected objectives. 

Nathan:

In this case, the hackathon took place over two days, one week apart. Keeping in touch with the other participants during the week helped me stay on track and move forward on the project. I think it's a good strategy not to disconnect between the two days and gain efficiency!

5. What did you discover during this hackathon? 

Thomas :

I was able to compare different working methods. For example, I tend to use snakemake for my workflows analysis, while other participants use other tools, such as nextfkow ou COOL. We were able to compare them and discuss these tools. 

In addition, I was able to discuss around warehouses of workflows and data repository as well as versioning in other fields (eg, neuroimaging). 

Isabelle: 

I discovered the MoDaL team: the project that was the driving force behind this event! I was also able to identify colleagues who work on ontology and metadata issues that are likely to interest me.

Nathan:

I was very interested in the Sport Horse Welfare Project, both because the topic was new to me and also because it led to a very rich and interesting discussion during the presentation of this project on day one.  

6. What can represent an obstacle in your daily life in the analysis of your data?

Thomas :

First of all, the size of the data. Indeed, the data sets are increasingly large, something that requires dividing the analysis into several steps and then grouping them together, which is not always easy. 

Then, the not very explicit annotations often used to describe the data. 

Isabelle: 

There are a multitude of tools, it is not easy to find the most suitable and learn how to use it. 

Nathan:

During my internship I heard a lot about analysis bias. I think it's very important to keep in mind that every time we process the data we are going to generate errors. Knowing how to identify them is essential to properly interpret the results obtained.

7. What are the “more” than an approach integrated could have on your daily work? 

Thomas :

The integrated approach makes it possible to better structure the analysis, to make it reproducible and thus to gain in quality and time! 

Isabelle: 

Data integration makes it possible to have a global look at the data, to broaden its understanding, but always with a careful eye: the integrated data can disturb the information if it is not adapted or correctly interpreted!

When working in life sciences, the integration of data is a plus because we do not formulate the same assumptions if we only look at a small part of the information. A more global view can broaden / enrich the research questions.

Nathan:

Highlighting the existence of a correlation between genetic and phenotypic characters makes it possible to broaden the research panorama and also to have more confidence in what one finds.

Virtual space dedicated to the hackathon in Gather Town. In this fully customizable space, an avatar is assigned to each participant and participant videos are displayed when two or more participants are close to each other. 

Screenshot with the project leaders and part of the MoDaL team (from left to right): Gabriel Markov (LBI2M UMR 8227 CNRS / Sorbonne University), Audrey Bihouée (Université de Nantes, CHU Nantes, Inserm, CNRS, SFR Santé, Inserm UMS 016, CNRS UMS 3556, Nantes), Sofia Strubbia (UMR 1087, Inserm, Nantes), Adrien Foucal (Université de Nantes, CNRS, INSERM, the thorax institute, Nantes), Isabelle Hue (LPGP UR 1037, INRAE, Rennes), Alban Gaignard (Université de Nantes, CNRS, Inserm, the thorax institute, Nantes), Thomas Darde (SciLicium, Rennes), Aline Foury (UMR 1286 INRAE ​​/ University of Bordeaux), Alban Besnard (Laboratory Health Environment Microbiology, Ifremer, Nantes) , Philippe Bordron (Université de Nantes, Inserm, TENS, The Enteric Nervous System in Gut and Brain Diseases, IMAD, Nantes) and, bottom right, Camille Maumet (Inria, Université Rennes, CNRS, Inserm - IRISA, Empenn, Rennes).

Find project titles and descriptions on the Hackathon GitHub !