Видео 21
Просмотров 4 446

Panel: Scaling Sustainably - Computational & environmental issues scaling bioinformatics workflows

1:00:39

Closing Remarks: Nextflow Symposium - Julia Wilson, Associate Director, Wellcome Sanger Institute

7:01

Automating Polygenic Score Calculation with pgsc_calc

9:24

Speeding up Variant Annotation with Nextflow

6:13

YASCP: Next-Gen Pipeline for Ultra-Large Scale scRNA Analysis

9:17

Resource Optimization in Sanger Tree of Life

20:54

Detecting Cancer Through cfDNA Methylation

Join Simon Pearce as he discusses the use of circulating cell-free DNA (cfDNA) methylation to detect and subtype cancer. Discover the Nextflow pipelines developed for demultiplexing, alignment, and classifier creation, achieving high sensitivity and accuracy in predicting cancer type from liquid biopsies.
Title: Using cfDNA methylation to detect and subtype cancer
Speaker: Simon Pearce, Cancer Biomarker Centre, Cancer Research UK
Abstract: Circulating cell-free DNA (cfDNA) is a biomarker for cancer, as tumour-released DNA is detectable in blood plasma. We have established an MBD-protein enrichment method (T7-MBD-Seq) to investigate genome-wide cfDNA methylation, and have developed 2 Nextflow...

Видео

Panel: Scaling Sustainably - Computational & environmental issues scaling bioinformatics workflows

1:00:39

Panel: Scaling Sustainably - Computational & environmental issues scaling bioinformatics workflows

Просмотров 159 месяцев назад

Join us for a captivating discussion on the current landscape and future trends in bioinformatics workflows. In this panel discussion, experts delve into the challenges and advancements shaping the world of computational biology. From hardware intricacies and software challenges to the impact of machine learning, data diversity, and the promise of emerging technologies, this conversation offers...

Closing Remarks: Nextflow Symposium - Julia Wilson, Associate Director, Wellcome Sanger Institute

7:01

Closing Remarks: Nextflow Symposium - Julia Wilson, Associate Director, Wellcome Sanger Institute

Просмотров 159 месяцев назад

Join us for the highlights of a remarkable event hosted at the Welcome Genome Campus. In this engaging session, our speaker expresses gratitude for the collaboration, innovation, and shared values that define the partnerships between Wellcome Sanger Institute, EBI, and the University of Cambridge. Explore the diverse range of genomics and bioinformatics research discussed, from cancer to infect...

Automating Polygenic Score Calculation with pgsc_calc

9:24

Automating Polygenic Score Calculation with pgsc_calc

Просмотров 2999 месяцев назад

Uncover the world of polygenic scores and learn about the PGS Catalog Calculator (pgsc_calc). Samuel Lambert introduces this Nextflow-developed tool that automates and reproducibly calculates polygenic scores, breaking barriers to their application by implementing genetic ancestry estimation and score normalisation. Title: pgsc_calc: A reproducible workflow to calculate polygenic scores Speaker...

Speeding up Variant Annotation with Nextflow

6:13

Speeding up Variant Annotation with Nextflow

Просмотров 539 месяцев назад

Dive into the world of Ensembl Variant Effect Predictor (VEP) with Likhitha Surapaneni. Explore how a Nextflow workflow enhances the speed and scalability of variant annotation, making VEP reusable by downstream pipelines. Title: Speeding up variant annotation in the Ensembl Variant Effect Predictor (VEP) using Nextflow Speaker: Likhitha Surapaneni, Ensembl, EMBL-EBI Abstract: Ensembl Variant E...

YASCP: Next-Gen Pipeline for Ultra-Large Scale scRNA Analysis

9:17

YASCP: Next-Gen Pipeline for Ultra-Large Scale scRNA Analysis

Просмотров 9179 месяцев назад

Matiss Ozols introduces the YASCP tool, designed for ultra-large scale single-cell RNA quality control and analysis. Learn how YASCP contributes to projects like the Cardinal project, setting new standards for studying millions of cells and opening doors for impactful research. Title: YASCP: A next-gen pipeline for ultra-large scale scRNA quality control & analysis Speaker: Matiss Ozols, Human ...

Resource Optimization in Sanger Tree of Life

20:54

Resource Optimization in Sanger Tree of Life

Просмотров 969 месяцев назад

Learn how the Tree of Life programme at the Wellcome Sanger Institute optimizes IT resources using Nextflow. Explore their approach to gathering resource usage data, estimating CO2 footprint, and defining improved resource-usage rules for efficient genome assembly and analyses at scale. Title: Resource optimisation and sustainability in Sanger Tree of Life Speakers: Matthieu Muffato & Damon-Lee...

Reproducible workflows with Nextflow and nf-core - Harshil Patel, Seqera Labs

39:04

Reproducible workflows with Nextflow and nf-core - Harshil Patel, Seqera Labs

Просмотров 1,7 тыс.9 месяцев назад

Join us for an insightful talk on the transformative impact of Nextflow and nf-core in the field of genomics and bioinformatics. Learn how these tools simplify complex genomic pipelines, enhance reproducibility, and facilitate collaboration in the scientific community. Discover the exponential growth of nf-core, with over 16,000 users and 900 contributors, making genomics research more accessib...

4:06

Ensembl Metazoa's Shift to Nextflow

Просмотров 1999 месяцев назад

Embark on the Ensembl Metazoa journey as Disha Lodha shares their strategic shift towards flexibility and portability through the migration to Nextflow. Discover the challenges faced, lessons learned, and the benefits of using Nextflow to develop production-ready pipelines for scientific research. Title: Migrating Ensembl pipelines to Nextflow for enhanced production-ready workflow Speaker: Dis...

Modernizing MGnify with Nextflow and nf-core

10:26

Modernizing MGnify with Nextflow and nf-core

Просмотров 239 месяцев назад

Join Martin Beracochea as he shares insights into the ongoing migration of MGnify production pipelines to Nextflow and nf-core tools. Discover how embracing modern development practices enhances the robustness and versatility of MGnify pipelines, contributing to more effective microbiome research. Title: Modernizing MGnify: Nextflow and nf-core for microbiome research Speaker: Martin Beracochea...

Digital Transformation at Wellcome Sanger Institute

23:55

Digital Transformation at Wellcome Sanger Institute

Просмотров 139 месяцев назад

Explore the digital transformation journey at the Wellcome Sanger Institute. Nathan Cunningham discusses the challenges faced by pipeline teams and how adopting Nextflow plays a pivotal role in overcoming these challenges, leading to enhanced efficiency, standardisation, and flexibility. Title: How Nextflow is a key to the digital transformation of WSI's pipeline solutions Speaker: Nathan Cunni...

Predicting Protein Function Impact of Substitution in the Human PanGenome

10:16

Predicting Protein Function Impact of Substitution in the Human PanGenome

Просмотров 319 месяцев назад

Delve into Ensembl's open-source Nextflow pipeline to analyse the human pangenomes dataset. Learn how they predict the functional impact of every single amino acid substitution (SAAS) using SIFT and PolyPhen-2, and how Docker containerisation enhances portability and data sharing across pangenome assemblies. Title: Predicting the protein function impact of every single amino acid substitution i...

Keynote: Evolution of the Nextflow Ecosystem - Paolo Di Tommaso, CTO and Co-founder, Seqera Labs

54:18

Keynote: Evolution of the Nextflow Ecosystem - Paolo Di Tommaso, CTO and Co-founder, Seqera Labs

Просмотров 469 месяцев назад

Dive into the future of scientific pipelines with this comprehensive overview of Nextflow, WAVE, and Fusion. In this detailed presentation, Paolo Di Tommaso, the creator of Nextflow, takes you through the groundbreaking technologies shaping the landscape of containerisation and workflow orchestration. - Explore the evolution of Nextflow, the robust workflow manager, and its crucial role in simp...

Opening Remarks: Nextflow Symposium 2023 - Andy Yates, EMBL-EBI

9:16

Opening Remarks: Nextflow Symposium 2023 - Andy Yates, EMBL-EBI

Просмотров 429 месяцев назад

Join us for an insightful journey into the world of bioinformatics workflows, as our speaker shares experiences, challenges, and tips. Explore the stunning architecture of the venue, learn about the supporting organisations like the Wellcome Sanger Institute and EMBL-EBI, and get a glimpse of the global participation in this diverse community. Discover the role of Nextflow workflow managers in ...

Adopting Nextflow in Sanger Tree of Life

24:01

Adopting Nextflow in Sanger Tree of Life

Просмотров 6910 месяцев назад

Speaker: Matthieu Muffato, Tree of Life, Wellcome Sanger Institute Description: Tree of Life is the latest scientific programme of the Wellcome Sanger Institute, aiming at producing reference genome assemblies for tens of thousands of species. We decided early on that Nextflow would be the workflow manager of choice - what an adventure it has been ! In this presentation, I will tell you about o...