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AnVIL Project
Приєднався 25 чер 2020
Come to this channel for videos from the AnVIL Project!
The NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL) is a scalable and interoperable resource for the genomic scientific community, that leverages a cloud-based infrastructure for democratizing genomic data access, sharing and computing across large genomic, and genomic-related data sets.
AnVIL is a cloud based ecosystem that colocates high value data sets with commonly used bioinformatics tools in a secure environment. By providing access to data and tools in a secure environment that can scale to meet the computational needs of researchers, AnVIL eliminates logistical concerns and allows researchers to focus on biological problems. Providing access to such a platform with tens of thousands of human genome sequences will allow the genomics community to ask new questions that were not logistically feasible before.
More information at www.anvilproject.org.
The NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL) is a scalable and interoperable resource for the genomic scientific community, that leverages a cloud-based infrastructure for democratizing genomic data access, sharing and computing across large genomic, and genomic-related data sets.
AnVIL is a cloud based ecosystem that colocates high value data sets with commonly used bioinformatics tools in a secure environment. By providing access to data and tools in a secure environment that can scale to meet the computational needs of researchers, AnVIL eliminates logistical concerns and allows researchers to focus on biological problems. Providing access to such a platform with tens of thousands of human genome sequences will allow the genomics community to ask new questions that were not logistically feasible before.
More information at www.anvilproject.org.
ACC2024: Town Hall
The 2024 AnVIL Community Conference featured an opportunity for a full audience discussion with a Town Hall session. The topics discussed were:
00:00 Introduction of Town Hall
00:59 Long-term data management: storage, deletion candidates, and sustainability
13:49 Advancing computational tools for analyzing large data
15:44 Leveraging new formats for storing large data
17:40 Disseminating derivative data and preventing redundant analysis
21:01 Access and harmonization of diverse datasets: packaging datasets by type or processing for easier access, improving data discovery by allowing metadata search, data consent considerations
33:48 AnVIL onboarding and education: project ready for piloting, cloud credit availability, ready capability of AnVIL to support custom models, good support from teams, cloud cost limitations
00:00 Introduction of Town Hall
00:59 Long-term data management: storage, deletion candidates, and sustainability
13:49 Advancing computational tools for analyzing large data
15:44 Leveraging new formats for storing large data
17:40 Disseminating derivative data and preventing redundant analysis
21:01 Access and harmonization of diverse datasets: packaging datasets by type or processing for easier access, improving data discovery by allowing metadata search, data consent considerations
33:48 AnVIL onboarding and education: project ready for piloting, cloud credit availability, ready capability of AnVIL to support custom models, good support from teams, cloud cost limitations
Переглядів: 9
Відео
ACC2024: Breakout Sessions
Переглядів 1016 годин тому
The 2024 AnVIL Community Conference featured an opportunity for breakout sessions for the attendees to discuss topics of interest to the community. The two proposed topics were a discussion of data and a discussion of tools. 00:00 Introduction of Breakout Sessions 02:05 Data Breakout Session Recording 38:54 Recap Data Session 46:18 Recap Tools Session
ACC2024: CoFest - Deploying, training, and interpreting deep learning models for regulatory genomics
Переглядів 1216 годин тому
The 2024 AnVIL Community Conference featured a Collaboration Fest! or CoFest! where attendees participated in hands-on workshops for running analysis in the cloud on AnVIL on five topics: - Deploying, training, and interpreting deep learning models for regulatory genomics - How to run your tool in AnVIL with WDL - Polygenic Risk Score (PRS) Analysis in AnVIL - Brainstorming Feature Requests - A...
ACC2024: Using AnVIL: Long read sequencing for advancing rare disease diagnosis - Benedict Paten
Переглядів 3016 годин тому
The 2024 AnVIL Community Conference featured keynote speakers, including Benedict Paten from the University of California Santa Cruz. Dr. Paten discussed his lab's work in rare disease diagnosis using long read sequencing empowered by the cloud. Presentation: Benedict Paten, University of California Santa Cruz. 00:00 Keynote Introduction: Benedict Paten 01:44 Keynote Presentation 56:53 Question...
ACC2024: Deciphering regulatory syntax and genetic variation with deep learning - Anshul Kundaje
Переглядів 1716 годин тому
The 2024 AnVIL Community Conference featured keynote speakers, including Anshul Kundaje from Stanford University. Dr. Kundaje discussed his lab's work in regulatory genomics using deep learning models in AnVIL. Presentation: Anshul Kundaje, Stanford University. 00:00 Keynote Introduction: Anshul Kundaje 1:59 Keynote Presentation 1:01:16 Question and Answer
ACC2024: Unlocking the Power of Precision Genomics in the Cloud - Tychele Turner
Переглядів 2016 годин тому
The 2024 AnVIL Community Conference featured keynote speakers, including Tychele Turner from Washington University in Saint Louis. Dr. Turner discussed her lab's work in precision genomics leveraging the cloud. Presentation: Tychele Turner, Washington University in Saint Louis. 00:00 Keynote Introduction: Tychele Turner 02:05 Keynote Presentation 48:42 Question and Answer
ACC2024: Welcome and AnVIL Roadmap - Michael Schatz, Jonathan Lawson, Robert Carroll
Переглядів 2416 годин тому
The 2024 AnVIL Community Conference was hosted at Cold Spring Harbor Laboratory, and opened with a welcome and presentation about the AnVIL project plus a discussion of the near term roadmap for the project components. Presentation by Michael Schatz, Johns Hopkins University; Jonathan Lawson, Broad Institute of MIT and Harvard, and Robert Carroll, Vanderbilt University Medical Center. 00:00 ACC...
AnVIL Demos: Sharing Data in the AnVIL
Переглядів 63Місяць тому
In this demo, Robert Carroll (VUMC) discusses key considerations for setting up a data model when planning for AnVIL data submission. Learn more here: help.anvilproject.org/t/anvil-demo-setting-up-a-data-model-for-anvil-data-submission-on-october-24-2024/230
AnVIL Champions
Переглядів 62Місяць тому
This video will give you a quick introduction to the AnVIL Champions Initiative and how it can benefit your community as well as the broader AnVIL ecosystem. Check out the AnVIL Champions Guide: jhudatascience.org/AnVIL_Book_Champions/ See the list of current Champions: anvilproject.org/anvil-champions You can see the slides for this video here: docs.google.com/presentation/d/1FmFO5URoe_Eh1kL22...
Starting Galaxy on the AnVIL Platform
Переглядів 163 місяці тому
Learn how to: * Start compute for Galaxy on AnVIL * Run the FastQC tool to quality control sequencing reads * Stop compute to minimize expenses Give us feedback! : docs.google.com/forms/d/e/1FAIpQLScrDVb_utm55pmb_SHx-RgELTEbCCWdLea0T3IzS0Oj00GE4w/viewform?usp=pp_url&entry.1565230805=Using Galaxy on UA-cam Check out the slides here: docs.google.com/presentation/d/1yYCg4cPVBMMDghT17B4XzROieqyMH99...
AnVIL Demos: QC Analysis Pipeline from CCDG on AnVIL - 2024/06/20
Переглядів 445 місяців тому
In this demo, Jason Walker from Washington University in Saint Louis presented on the NHGRI consortium Centers for Common Disease Genomics Quality Control (QC) Analysis Pipeline for WGS data available to run in AnVIL. Learn more about upcoming AnVIL Demos: help.anvilproject.org/c/demos/5. Find the Github Repository for the qc-analysis-pipeline: github.com/genome/qc-analysis-pipeline.
AnVIL Demos: Single Cell with Bioconductor - 2024/05/23
Переглядів 115 місяців тому
In this demo, Elizabeth Humphries from the Fred Hutchinson Cancer Research Center showed the Single Cell with Bioconductor activity as part of the AnVIL Demos Book: hutchdatascience.org/AnVIL_Demos/single-cell-with-bioconductor-overview.html. Learn about upcoming AnVIL Demos: help.anvilproject.org/c/demos/5.
AnVIL Demos: Collecting and subsetting SRA data - 2023/12/14
Переглядів 105 місяців тому
In this demo, Ava Hoffman from the Fred Hutchinson Cancer Research Center will describe how to pull data from SRA into AnVIL and use a public workflow to subset data into smaller files for analysis testing and training. Learn about upcoming AnVIL Demos: help.anvilproject.org/c/demos/5. Find the AnVIL Book with the demo instructions to bring SRA data into AnVIL: hutchdatascience.org/AnVIL_SRA_Da...
Epigenetics on AnVIL: Unraveling the Epigenome using ChIP-seq
Переглядів 517 місяців тому
This video gives a quick introduction to ChIP and ChIP-seq methods. It's mean to accompany the AnVIL activity here: hutchdatascience.org/AnVIL_Book_Epigenetics_Intro/ . Feel free to use this content if you are an instructor teaching these concepts! ⭐️ Give us feedback: docs.google.com/forms/d/e/1FAIpQLScrDVb_utm55pmb_SHx-RgELTEbCCWdLea0T3IzS0Oj00GE4w/viewform?usp=pp_url&entry.1565230805=ChIPseq...
Epigenetics on AnVIL: Nature vs Nurture
Переглядів 77 місяців тому
This video gives a quick introduction to Epigenetics. It's mean to accompany the AnVIL activity here: hutchdatascience.org/AnVIL_Book_Epigenetics_Intro/ . Feel free to use this content if you are an instructor teaching these concepts! ⭐️ Give us feedback: docs.google.com/forms/d/e/1FAIpQLScrDVb_utm55pmb_SHx-RgELTEbCCWdLea0T3IzS0Oj00GE4w/viewform?usp=pp_url&entry.1565230805=Nature v Nurture on U...
AnVIL Demos: DUOS - a tour of AnVIL's innovative data sharing platform - 2023/10/26
Переглядів 77Рік тому
AnVIL Demos: DUOS - a tour of AnVIL's innovative data sharing platform - 2023/10/26
NIH Data Management and Sharing on AnVIL
Переглядів 56Рік тому
NIH Data Management and Sharing on AnVIL
AnVIL Demos: Epigenetics in AnVIL - 2023/09/21
Переглядів 39Рік тому
AnVIL Demos: Epigenetics in AnVIL - 2023/09/21
AnVIL Demos: Running Galaxy in AnVIL - 08/31/2023
Переглядів 36Рік тому
AnVIL Demos: Running Galaxy in AnVIL - 08/31/2023
AnVIL Demos: Interactive Genomic Data Science with Bioconductor - 07/20/2023
Переглядів 41Рік тому
AnVIL Demos: Interactive Genomic Data Science with Bioconductor - 07/20/2023
AnVIL Demos: How to combine data across workspaces - 06/22/2023
Переглядів 63Рік тому
AnVIL Demos: How to combine data across workspaces - 06/22/2023
AnVIL Demos: WARP Pipelines in AnVIL/Terra - 2023/05/18
Переглядів 63Рік тому
AnVIL Demos: WARP Pipelines in AnVIL/Terra - 2023/05/18
AnVIL Demos: Using the Human Pangenome on AnVIL - 2023/04/27
Переглядів 132Рік тому
AnVIL Demos: Using the Human Pangenome on AnVIL - 2023/04/27
AnVIL Demos: Introduction to AnVIL - 2023/03/23
Переглядів 152Рік тому
AnVIL Demos: Introduction to AnVIL - 2023/03/23
Sequence Read Archive (SRA) data on AnVIL
Переглядів 103Рік тому
Sequence Read Archive (SRA) data on AnVIL