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Well that is a wrap! The final day took off and ended with a bang. Today saw a full day of technology with the long awaited Technology Track, the final 7 COSI sessions, and the last Special Session on Single Cell and Spatial Data Analysis.
Highlights
ISCB Accomplishments by a Senior Scientist Award Keynote, Peer Bork gave a the final talk of the conference on Analyzing microbes in us and on our planet. Environmental sequencing, that is metagenomics, has become a major driver for uncovering microbial biodiversity and increasingly also for cataloging molecular functions on our planet. The exponentially increasing metagenomes need computational tools and resources to allow researchers to access and digest these valuable data. Based on methods and resources, developed in their group, but also utilizing public bioinformatics resources, here he introduced into their work on the gut microbiome, aimed at basic understanding, but also at medical applications, showing a few examples from tracing the structure and function of microbiomes in different habitats on earth (ocean and soil) and briefly outlining the concept of interacting computational resources, developed and maintained by a network of researchers across Europe.
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COSI Recaps
Bioinfo-Core
The Bioinfo-Core COSI session brought together managers and staff working in bioinformatics core facilities around the world. The excellent work done in the following core facilities was presented:
- Nicole Scherer from the Brazilian National Cancer Institute talked about the hard work and challenges of establishing a core facility from the ground up in a hospital.
- Gregg TeHennepe from The Jackson Laboratories talked about applying the methods of tools of Agile project management to bioinformatics research support, and presented a case study of a real-life case.
- Fatima Mitterboeck from Agriculture and Agri-Food Canada presented on the Bioinformatics Research Support Network, community of practice sharing best practices and working towards supporting users at a national scale.
- Fleur Gahwens presented about building up a bioinformatics community at the Dutch Institute of Ecology, and shared the lessons learned during the development of the epiGBS2 Snakemake-based workflow in that community.
- Krishna Karuturi from The Jackson Laboratories discussed the comprehensive approach for embracing machine learning and imaging advances in that organization, and the linkages and collaborations required to make that a reality.
- Ning Zhang from the Stowers Institute presented RiboSeeker, an end-to-end package that integrates a Snakemake workflow and an R package for ribosome profiling.
Our keynote speaker Johannes Köster presented on Snakemake, one of the most widely used and cited workflow management systems. Snakemake's new approaches for modularization and deployment and other new approaches and features were introduced to an audience of nearly 80 attendees.
After the keynote, we had our breakout room discussions where the following topics were discussed:
- Workflow managers / pipeline tools
- Training
- Spatial transcriptomics
- Project management
- Core facilities during the pandemic and knowledge sharing
- Protected data
BOSC
The second and last day of BOSC 2021 started off with a keynote talk by Thomas Hervé Mboa Nkoudou on “Contribution of the maker movement to biotechnology in Africa: An open science perspective”. This is the first BOSC keynote talk that was not given in English: Thomas spoke in his native French, with English subtitles. Thomas emphasized that open source / open data are key to wide dissemination of knowledge in the biosciences and beyond. An example of this openness in practice is the way the Maker movement, which embraces openness, has contributed to the democratization of biotechnology in Africa. Thomas observed that universities have not yet embraced openness and the maker-movement philosophy in African countries; an attendee noted that this is also the case in Europe. Thomas responded that to address this, we need to teach principles, philosophy and give practical experience as early as possible so that new generations consider maker/DIYbio solutions when they are faced with problems themselves.
In the ‘Analysis tools’ session, we heard from David Twesigomwe about a pipeline that incorporates graph based variant calling for Cytochrome genes. Patrick Kunzmann talked about updates to the Python library Biotite that performs sequence and structural analyses. Charlotte Herzeel talked about elPrep, a set of tools that has improved computing performance of popular NGS pipelines. This session also had two talks from the Broad, the first one by Bhanu Gandham on how the GATK pipeline has been adapted to microbes; the final talk was from Michael Gatzen about assessing batch effects for variants generated by two different pipelines.
Workflow Management Systems are always a popular topic at BOSC, and this year was no exception. This session included updates on widely used workflow systems such as Nextflow, Dockstore and Sapporo, and introductions to newer resources such as WARP and WFPM.
A short session on visualization tools and platforms focused on the venerable genome browser, JBrowse, now deployable through Docker and with a major update. It also introduced GO-Figure!, a new viz tool for Gene Ontology terms. The final session of BOSC, Translational Bioinformatics, included hot topics such as knowledge graphs and drug discovery, all in an open source context.
BOSC Chair Nomi Harris ended the day by thanking the many people who helped to make BOSC 2021 possible, including the organizers, reviewers, sponsors, and presenters. We look forward to seeing everyone (hopefully in person) at BOSC 2022!
VarI
VarI COSI’s second day at ISMB ECCB 2021 started with a keynote presentation titled “Mutate everything” by Ben Lehner from the (Centre for Genomic Regulation, Barcelona). Ben presented recent work on mutational scanning of protein coding genes allowing to quantify mutations’ effects on protein folding, binding and aggregation as well as to characterize protein free energy changes for the identification of allosteric sites. Mutational scanning was also a main topic of the round table discussion moderated by Yana Bromberg (Rutger University) with Douglas Fowler (University of Washington), Daniel Gilchrist (NHGRI) and Predrag Radivojac (Northeastern University), where current challenges on variant annotation and interpretation were addressed. Adding to the round table, a total of 7 selected talks were presented with a major focus on clinical interpretation of human variants from sequencing studies, covering a broad range of aspects such as the structural and mutational features of pathogenic variants, the interpretation of Copy Number Variants, and the characterization of gain-of-function variants. The session included a presentation from Variantyx, VarI COSI’s main sponsor, where Alexander Kaplun presented recent computational developments for variant calling in non-uniquely mappable regions from short-read WGS data.
iRNA
The third and last day of the 2021 iRNA COSI had an emphasis on RNA structure/RNA interactions/RNA quantification using long reads and featured two fascinating keynotes. Yue Wan discussed mapping of RNA-RNA interactions with applications illustrated in the analysis of SARS-CoV-2 while Liang Huang talked about the prediction of RNA secondary structure, with interesting historical considerations and comparisons across fields, finishing with the important application of their linear tool to SARS-CoV-2. Contributed talks discussed the transcriptomics analysis of a lncRNA, a snoRNA and a miRNA network as well as important considerations in the analysis of long read and direct RNA sequencing. In addition, the community heard about two challenges started within the context of the RNA society meeting with calls for participation. Overall, the 2021 iRNA COSI was very successful with varied aspects of computational RNA research explored, a timely live panel discussion, fascinating keynotes and enthusiastic poster presentations.
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