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EPI2ME Labs as a Learning Platform

Tonight I started an EPI2ME Metagenomics workflow to analyze our two 16S runs for the metagenomics class. I also watched the Nanopore Learning Human Genome Sequencing and Analysis course video on “Data Analysis: EPI2ME Labs Introduction.” Anthony Doran, a member of the Technical Services Team with Oxford Nanopore Technologies, described EPI2ME Labs as a “point-and-click” […]
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The MinKNOW Graphical User Interface (GUI)

Tonight I watched the MinKNOW GUI video from the Nanopore Learning course on Human Genome Sequencing and Analysis. Before watching these videos, I reviewed the Kit 14 videos. The MinKNOW graphical user interface (GUI) session was presented by Marta Verdugo from the Technical Services Team at Oxford Nanopore Technologies (ONT). The MinKNOW software is used […]
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An Overview of ONT Devices

Hazel Johnson, member of the Technical Services Team at Oxford Nanopore Technologies, presented the second video in the Nanopore Learning Human Genome Sequencing and Analysis course. They shared the range of products for sample preparation, instruments, and software offered by ONT. Johnson shared a graphic with the nanopore sequencing platforms. The Flongle is low cost […]
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Accelerating Nanopore Basecalling with GPUs

Georg Kolling, a Principal Algorithms Scientist with Oxford Nanopore Technologies, presented at London Calling a session entitled “How we get the most out of GPUs (for sequencing).”They began with an overview of basecalling: interpreting the read sequence with machine learning as bases. For this, a deep neural network (deep learning) is used to approximate with […]
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Ultra-rapid Nanopore Sequencing for Diagnosis

Tonight I watched John E. Gorzynski and Sneha D. Goenka from Stanford University present at London Calling 2022. Their fifteen-minute presentation entitled “Accelerated identification of disease-causing variants with ultra-rapid nanopore genome sequencing” was packed with information even though it was an informal session. This was an in-person session last year. Gorzynski is a postdoctoral scholar […]
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Real-time RNA Analysis with RISER

Adaptive sampling and real-time in silico enrichment have come up frequently in the last couple of months. I still haven’t used this feature and want to learn more. Tonight I watched the London Calling 2022 session by Alex Sneddon from the Australian National University entitled “RISER: real-time in silico enrichment of RNA species from nanopore […]
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Stereo Duplex Nanopore Sequencing

Katherine Lawrence, a Machine Learning Bioinformatician with Oxford Nanopore, spoke at the Nanopore Community Meeting 222 about “Advances in duplex basecalling.” They defined duplex sequencing as both ends of the DNA with adaptor motor proteins and two reads from the same molecule. Duplex basecalling incorporates information from both reads’ signals and improves accuracy with the […]
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Writing and Reading with Digital Help

Tonight’s CAST UDL Symposium session was “Cheating, Or Empowering Learner Voice with Reading and Writing Tools In The Digital Age?” by Luis Perez, Tracy Hall, and Joni Degner. They shared a handout at: bit.ly/SymposiumJTL Perez explained that the document shared had links to the slides, back channel, and resources. Luis Perez described the Accessibility Commitments, […]
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Grasple and Two Universities

We finished the first week of classes! Tonight we watched the Open Ed 2021 session entitled “Entering Mainstream Adoption: How TUDelft and UTwente Collaboratively Embrace OER Through Grasple” presented by Pim Bellinga, co-founder of Gasple, and Pim Stuurman, mathematics content expert at Grasple. They spoke about how TU Delft and University of Twente moved from […]
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The Penguin Corps and Learning about Open Source Software

Open-source software can be so helpful but often challenging to learn. Tonight’s Open Ed 2021 session was about open source software and… The Penguin Corps. The title was “Open Source Belongs in School. Let’s Put It There!” with Stu Keroff from the Aspen Academy and several students from Penguin Corps. Keroff talked about using open […]
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