Nextflow and Biology Computational Challenges

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Cédric Notredame is a molecular biologist and holds a PhD in Bioinformatics from EMBL-EBI. Since 2007, Notredame has been the senior group leader in the Bioinformatics and Genomics Programme at the CRG, where he and his team develop novel algorithms for the comparison of multiple biological sequences. He is also the former coordinator and lecturer at the Bachelor’s Degree in Bioinformatics.

Among his scientific acknowledgements, Notredame is the leading author of T-Coffee, a popular multiple-sequence alignment package able to combine structural information and sequences, and his team was also behind Nextflow, a very popular tool in the bioinformatics world.

Nextflow is a free open-source software that allows to write, deploy and share data-intensive, highly scalable workflows on any infrastructure. Through the example of Nextflow, he presented the cornerstone challenges computational biology faces nowadays and that they were trying to solve, which are: the reproducibility of the results, the stability of data, the scalability of sequence alignment accuracy, the deployability of computation, and the readability the results.

Regarding readability, he stressed the fact that full transparency “is the only protection science has against fake news”. The conceptual complexity of health in the years to come has nothing to do with what it was before. In this sense, the more readable the pipelines will be, the more transparent will be the medical process and, thus, the social engagement and trust in science.

Lastly, at the end of the talk, Notredame said that when he was a student, “if you were good, you would stay in Academia, and if you were a bit less good, you would move out from it. Those days are finished. The industry is now much more an option, especially in bioinformatics, than it has ever been”.

To encourage students, he presented shortly two of the companies incorporated around the Nextflow technology grown by people who stayed in his lab: Lifebit and Seqera Labs. The first one managed to raise 80M € and the second 22M €, which could be the first Catalan scientific start-up unicorn coming from Academia.