Tonight I started watching the KBase Educators Orientation meeting from December 2024. Ellen Dow facilitated the session and shared resources from the KBase Educators group and handbook. Dow explained the structure of KBase narratives and how to join the KBase Educators group. The Educators Org has several narratives that can be copied. There are a […]
Priya Ranjan from Oak Ridge National Laboratory was the next speaker I watched as part of the KBase Microbial Community Modeling Workshop recordings. The title of this session was “Pairwise analysis tools between strains” that would be very useful for us! Rnajan is collaborating with the Plant-Microbe Interfaces (PMI) project and is designing a series […]
Tonight I watched another KBase Science Session: Data integration to support (or refute) predictions. “Integrating data to predict functions for gaps in metabolic models” was the title of Bill Nelson’s session. Nelson is from the Pacific Northwest National Laboratory. The work was part of two PNNL SFA projects: a soil microbiome project and a persistence […]
Tonight I started watching day 2 of the ISME19 workshop “From Reads to Function.” Mikayla Borton from Colorado State University presented on “DRAM and genome-resolved inference.” Borton started with dereplication of bins/MAGs. After that step, MAGs are annotated with DRAM. The tool used to dereplicate metagenome assembled genomes (MAGs) is dRep. Borton explained that the […]
Philipp Rescheneder, the Senior Director of Applications for Bioinformatics at Oxford Nanopore Technologies, presented at the Nanopore Community Meeting in Boston. They presented an update based on an analysis of Rett syndrome, a rare genetic disorder that causes severe mental and physical disability. Rescheneder defined multi-omics for this study as the use of genomics, epigenomics, […]
Chad Pollard from Wasatch BioLabs spoke at the Biopharma Day at NCM Boston. The session’s title was “NESSI-Seq: novel cfDNA methylation assays for biomarker discovery and precision medicine.” Pollard described Wasatch BioLabs as a high-throughput nanopore sequencing lab. NESSI-Seq is a methylation analysis method. They developed a method to provide more methylation information than the […]
Tonight, I watched the second half of a new Knowledge Exchange session focusing on “Sequencing and analysis of nanopore-only microbial isolates with the NO-MISS workflow.” Different extraction methods produced varying yields. Bead-beating and enzymatic lysis extractions affect read length and throughput, while fungal samples produce lower yields. Some potential issues include incomplete lysis and contaminants. Additional clean-up […]
Tonight, I continued watching the ONT webinar I started last night, which focused on scalable human genomic characterization with nanopore sequencing. The second speaker was Anthony Doran, Associate Director of Bioinformatics Field Applications with Oxford Nanopore Technologies. Doran’s session was titled “Bioinformatics from beginner to production: EPI2ME, Oxford Nanopore’s data analysis platform.” ONT’s theme this […]
Tonight, I watched Rhys White from the Institute of Environmental Science and Research in New Zealand present “Real-time genomic surveillance with nanopore sequencing.” They have started a collaboration with the Wellington Regional Hospital. The goal was to make Nanopore sequencing accessible to the clinical lab. The team used a MinION device to sequence blood and […]
Tonight, I watched the London Calling EPI2ME product demo: “EPI2ME: democratising bioinformatics—from point-and-click analysis to custom integrations.” Natalia Garcia, a Bioinformatics Workflow Developer with Oxford Nanopore Technologies, explained how workflows use Nextflow and Docker containers. Seventeen workflows were available at the time of the recording during London Calling. Workflows can be run via the command […]