Zuckerberg will help scientists from St. Petersburg who “deciphered” COVID

Bioinformaticians from the Center for Algorithmic Biotechnology at St Petersburg University (CAB) received a grant from the Mark Zuckerberg Foundation for the development of their SPAdes and QUAST projects. According to the press service of the university, St. Petersburg specialists became the first Russian scientists to receive this grant. The money will be used to support open source programs needed for biomedical research.

Working with genomes

The SPAdes program (Saint Petersburg Assembler) restores the complete primary structure of genomic DNA, that is, it actually deciphers the genetic code. According to the press service of St Petersburg University, it is used by thousands of specialists in the field of genomics around the world. During the pandemic, the CAB team developed several new SPAdes modules. These are metaviralSPAdes for searching for virus genomes in complex natural communities (thanks to which 600 new viruses were recently found) and coronaSPAdes, which takes into account the unique features of the structure of coronavirus genomes and their sequencing data. Developments in 2020 allowed scientists to “work” with the COVID-19 genome faster and more conveniently, different from the genomes of other coronaviruses, and effectively monitor the mutations that arise in it. The progress of CAB genome assemblers contributes to a more thorough analysis of virus genomes and, thereby, to the creation of new and improvement of existing test systems and vaccines.

The second CAB program, QUAST (Quality Assessment Tool), determines the quality of genomic assemblies. As explained at St Petersburg University, the two programs SPAdes and QUAST are linked by the logic of the genomic project: data quality assessment - data collection - assembly quality assessment - scientific analysis.

Non-commercial use

In a conversation with RBC Petersburg, Alla Lapidus, Deputy Director of the Center for Algorithmic Biotechnology at the Institute of Translational Biomedicine, St. Petersburg State University, noted that all CAB programs are open source, which makes them available to everyone. At the same time, for the programs to work, they need to be technically supported, but it is unprofitable for companies to finance this support - it is impossible to make money on the use of open codes.

“Technical support for the project at this stage is based on the sheer enthusiasm of the CAB employees. The received grant will go to the technical support of the programs,” said Lapidus. According to her, the amount of the grant is about $150,000. The exact amount of the grant will be known after the signing of the agreement.