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 […]
Continuing with the KBase Science Session: Data integration to support (or refute) predictions, tonight I watched Chris Henry from Argonne National Laboratory present on “Predicting Protein function using structure nd sequence similarity in KBase.” Henry and team built a pipeline in KBase to analyze structure and sequence similarity data. Henry noted that KBase has a […]
Matt Parker, the Director of Clinical Bioinformatics Software at Oxford Nanopore Technologies, facilitated the Nanopore Community Meeting Boston 2024 session on variant analysis with EPI2ME. The title of the presentation was “Ultra-rich human data – variant analysis with EPI2ME.” They shared the EPI2ME user interface updates that were recently released. There is a new element […]
Basecaller updates are more frequent now, with new models and speed improvements. Tonight, I watched the London Calling 2024 session on basecaller advancements. Sam Davis, Principal Scientist, Machine Learning with Oxford Nanopore Technologies (ONT), spoke about the recently released models and chemistries. The V5 models offer 1.5Q accuracy improvement when compared to previous versions. Davis […]
Mark Bricknell, a Realtime Analysis Fellow with Oxford Nanopore Technologies, spoke at London Calling 2023. The title of the session is “Dorado – the future of basecalling.” I have been thinking about basecalling and duplex reads today. Bricknell explained that basecalling uses recurrent neural networks that are computationally intensive to interpret raw signals into sequences. […]
Feng Luo from Clemson University presented at the Nanopore Community Meeting 2021 about “Genome-wide detection of cytosine methylations in plants from nanopore data using deep learning.” They are faculty in computer science at Clemson. They spoke about detecting methylation from nanopore signals. They developed the DeepSignal tool. Nanopore has developed Megalodon, and there is also […]
Anne Kristine Schack from the University of Copenhagen and gMendel, Denmark spoke at London Calling 2022 about “A novel assay based on Oxford Nanopore technology for potential mass screening of Klinefelter syndrome.” They explained that Klinefelter Syndrome is a genetic disorder in which there is an additional X chromosome and it affects one in 500 […]
Mike Vella spoke at London Calling 2022 about “Dorado – a modern, C++, Torch-basecaller.” Vella is the Director of Machine Learning Operations with Oxford Nanopore. At the time of the recording, they had released a preview. Vella defined a basecaller as something that takes data from sensors and translates that into nucleotides… but Vella noted […]