Nicole de Miranda Scherer
Dr. Nicole Scherer finished her undergraduate studies in biological sciences (Universidade Federal do Rio Grande do Sul – UFRGS – Porto Alegre, Brazil), and began a master’s degree in genetics in the same institution with a project in plant evolution to be performed totally in silico. Being the only student working with bioinformatics in the genetics institute at that time, she decided to deepen her knowledge in the field and applied to do a PhD in Germany. During her graduate studies in bioinformatics (Faculty of Mathematics and Natural Sciences - Heinrich Heine University, Düsseldorf), she learned programming in Perl and R, and acquired the necessary skills in GNU/Linux for the use of bioinformatics software. In 2011 she joined LBBC as a technologist in bioinformatics at the Brazilian National Cancer Institute (INCA – Rio de Janeiro). The research center of INCA was planning to start a bioinformatics multi-user platform to serve all research groups of the institute. Since the acquisition of the first cluster, in 2013, she has been the manager of the bioinformatics platform, offering technical and scientific support for over 50 users. She is currently engaged in education and bioinformatics outreach and is a member of the board of directors of the Brazilian Association of Bioinformatics and Computational Biology (AB3C), being on the organizing committee of the X-Meeting, the largest conference for bioinformatics in Brazil.
The Red Queen dynamics of a bioinformatics platform
The Red Queen hypothesis proposes that species must constantly adapt to “keep in the same place”. The same happens in a bioinformatics platform. As soon as we overcome the challenges to implement a new resource (technology, software, interface, database, policy), a new feature becomes urgent and we need to keep running in order to guarantee that the service stays up to date. The bioinformatics platform of the Brazilian National Cancer Institute (INCA) houses 75 research projects from 18 principal investigators and 50 current users. Over the 8 years since the starting of the platform, the HPCC evolved to a critical resource for the scientists, while bioinformatics analysis became an essential part of the experiments, requiring more storage and computational power. In 2020, due to the public health crisis, all users were sent home and remote access soon became the only available access. Another revolution accelerated by the quarantines was the wide availability of online training in bioinformatics. One good aspect was that the number of users increased, but most of them had no previous experience in Linux or HPC. They still have to be trained to work responsibly in a shared computational environment. At the same time, submitting batch scripts via command line did not suit the users’ needs for exploratory analysis of new types of big data, such as single-cell sequencing data. Users now require interactive IDEs and graphical interfaces. As managers, we need to search for solutions to incorporate these novelties in an instantly obsolete environment.