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[AnVIL-mailing-list] New Funding Opportunity for Research on AnVIL
by Natalie Kucher 18 Dec '24

18 Dec '24

Dear AnVIL Community, We are excited to share a newly published NIH funding opportunity called “Enhancing Reuse of NHGRI Data Assets<https://grants.nih.gov/grants/guide/rfa-files/RFA-HG-25-005.html>”. These R03 awards will support researchers seeking to analyze NHGRI-hosted datasets in AnVIL for novel research questions, analyses across studies, or analyses combining these data with new datasets. Pre-application webinars describing the funding opportunity and open time for Q&A will be hosted in the coming weeks. Applications will open on January 14, 2025. Read more about the funding opportunity here: https://grants.nih.gov/grants/guide/rfa-files/RFA-HG-25-005.html. Any questions? Reach out to the Program Scientific Contact: Shurjo K. Sen, Ph.D. (sensh(a)mail.nih.gov<mailto:sensh@mail.nih.gov>). Best, Natalie -- Natalie Kucher / Project Manager Johns Hopkins University, Department of Biology Krieger School of Arts & Sciences e: nkucher3(a)jhu.edu<mailto:nkucher3@jhu.edu> / AnVIL<https://anvilproject.org/> / Galaxy<https://galaxyproject.org/> / GDSCN<https://www.gdscn.org/>

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[AnVIL-mailing-list] Decomissioning Gen3 GTEx V8 free downloads [AnVIL]
by Jonathan Lawson 17 Sep '24

17 Sep '24

Dear AnVIL Users, We want to make you aware that *starting October 1, 2024, the AnVIL Gen3 Commons and free downloadable version of GTEx v8 through Gen3 will be decommissioned*. Going forward, the AnVIL Data Explorer <https://explore.anvilproject.org/datasets>, which hosts over 250 AnVIL datasets will be the best path for accessing GTEx data through AnVIL. Details on the anticipated scope of impact are described below. Scope of impact 1. Users will no longer be able to download GTEx v8 for free, and downloads will be subject to Google Cloud Platform egress fees. However, GTEx v8 will still be available for analysis on AnVIL on Terra with access via either the AnVIL Data Explorer or AnVIL Dataset Catalog. 2. See the help articles linked here for more information on how to access data through the Explorer or Terra. 3. Data export as PFBs from https://gen3.theanvil.io/ to Cavatica and Terra will no longer be available. 4. Access to data via DRS from https://gen3.theanvil.io/ will stop. 5. Existing DRS URIs minted by AnVIL Gen3 will be resolvable and accessible in Terra and by external systems when AnVIL RAS is available. If you believe that this change will impact your work, please don’t hesitate to reach out to anvil-data(a)broadinstitute.org or the AnVIL Support Forum. We appreciate your patience and understanding. Thank you, The AnVIL Team

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[AnVIL-mailing-list] Join us at the AnVIL Community Conference this November - Registration Now Open!
by Stephen Mosher 28 Aug '24

28 Aug '24

Dear AnVIL Community, We are excited to announce that registration is now open for the inaugural AnVIL Community Conference (ACC24), scheduled for November 12-13, 2024, at Cold Spring Harbor, NY. This is a unique opportunity to connect in person with fellow professionals from the genomics community who share an interest in biomedical and genomic cloud computing. ACC24 precedes the Biological Data Science<https://meetings.cshl.edu/meetings.aspx?meet=DATA&year=24> meeting at Cold Spring Harbor (November 13-16) which requires separate registration. We believe this event will be highly relevant to AnVIL Community Conference attendees. The AnVIL Community Conference will feature: Scientific Talks: Hear from distinguished speakers including Anshul Kundaje, Michael Schatz, Tychele Turner, and Benedict Paten, as they showcase the latest advancements on the AnVIL platform. Workshop: Engage in a hands-on training session led by the AnVIL team, combining informative presentations with practical instruction. Collaboration Fest (CoFest): Collaborate and innovate with peers during our CoFest, and share your discoveries with the community at the conference's conclusion. We would love the chance to meet you in person and share in this enriching blend of instruction, collaboration, and cutting-edge scientific discourse. For more details and to register, please visit the conference webpage: AnVIL 2024 Community Conference<https://anvilproject.org/events/anvil2024-community-conference>. We look forward to seeing you in November! Best regards, Stephen Mosher ______________________________ Stephen Mosher | Project Manager Johns Hopkins University Department of Biology Krieger School of Arts & Sciences stephen.mosher(a)jhu.edu<mailto:stephen.mosher@jhu.edu> https://anvilproject.org/

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[AnVIL-mailing-list] Sign up for our next AnVIL Demo: Teaching on AnVIL on April 18
by Natalie Kucher 08 Apr '24

08 Apr '24

[A blue and white logo Description automatically generated] Sign up for our next AnVIL Demo! Teaching on AnVIL April 18, 2024 at 11:00 AM EDT (your time zone<https://www.timeanddate.com/worldclock/fixedtime.html?msg=AnVIL+Demos&iso=2…>) on Zoom 11:00 AM - 11:30 AM EDT– Demo on AnVIL In this demo, Natalie Kucher from Johns Hopkins University will describe how AnVIL can be used in the classroom as a platform for teaching and analysis, the advantages of using AnVIL with students, and the AnVIL Outreach team’s best practices available in the AnVIL Instructor Guide (https://jhudatascience.org/AnVIL_Book_Instructor_Guide/) 11:30 AM - 12:00 PM EDT – Q&A We’ll open up the floor to answer questions about the demo or any general questions about AnVIL you might have! ✏️ Sign up: https://forms.gle/7CcaLE9AM7FrYqpP7 What are AnVIL Demos? AnVIL Demos are a monthly, virtual meeting where we highlight what you can do on the NHGRI<https://www.genome.gov/> Analysis, Visualization, and Informatics Lab-space (AnVIL<https://anvilproject.org/>), a cloud-based computing platform for genomic data science! AnVIL Demos will start out with a 30-minute demonstration on the platform followed by open time for Q&A and user support. The demos will highlight a range of topics, from a capability of the platform to a scientific analysis powered by AnVIL. If you’re interested in showcasing how you use AnVIL at a future AnVIL Demos session, reach out to Natalie Kucher (nkucher3(a)jhu.edu<mailto:nkucher3@jhu.edu>). After the demo, we’ll open up the floor to answer questions about the demo and to answer any general questions you might have about AnVIL. Watch our past Demos from our YouTube playlist<https://www.youtube.com/playlist?list=PL6aYJ_0zJ4uC978C57P3TgAAfB38uy58E>! ✏️ Sign up for more demos: https://forms.gle/7CcaLE9AM7FrYqpP7 Resources * AnVIL Getting Started Guide. An opinionated guide on how to get set up and start your work on AnVIL. Get started here<https://jhudatascience.org/AnVIL_Book_Getting_Started/>. * AnVIL YouTube Channel. Learn about AnVIL capabilities and features with our “AnVIL in 2 minutes” videos. Watch AnVIL in 2 minutes here<https://www.youtube.com/playlist?list=PL6aYJ_0zJ4uCABkMngSYjPo_3c-nUUmio> or watch past AnVIL Demos here<https://www.youtube.com/playlist?list=PL6aYJ_0zJ4uC978C57P3TgAAfB38uy58E>. * AnVIL Support Forum. Join the conversation at help.anvilproject.org<http://help.anvilproject.org/>. Upcoming Events Sign up to hear about future AnVIL Demos and announcements at bit.ly/anvil-mailing-list<http://bit.ly/anvil-mailing-list> and learn about upcoming events at https://anvilproject.org/events!

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[AnVIL-mailing-list] Days left to share your ideas! 📢 State of the AnVIL 2024 Community Poll
by Natalie Kucher 13 Mar '24

13 Mar '24

Dear AnVIL Community, Your contribution is essential in shaping the future of the AnVIL platform, and we are excited to invite you to participate in our State of the AnVIL Community Poll! The poll is open for a few more days, so take a few minutes now to share your thoughts! Your insights and preferences are invaluable as we strive to enhance the AnVIL experience for all users. By taking a few minutes to complete this poll, you'll be playing a crucial role in influencing the direction of our platform and ensuring it meets the diverse needs of our community. Take the poll here: https://bit.ly/sota2024 Why participate? 1. Voice Your Opinion: This is your chance to share your experience with biomedical data science, how you use AnVIL, and let us know what matters most to you. 2. Community Collaboration: Your feedback will contribute to a collaborative effort in making AnVIL a more powerful and user-friendly platform for everyone. 3. Future Development: Help us prioritize future developments and enhancements based on the needs and preferences of our diverse user community. How to Participate: 1. Click the following link: https://bit.ly/sota2024 2. Complete the brief poll. We estimate it will take 10-15 minutes in total. 3. Submit your responses and become an integral part of shaping the AnVIL Platform's future. Optionally enter a drawing for training with our team and more! We appreciate your time and commitment to making AnVIL the best it can be. Your feedback is crucial, and we look forward to hearing your thoughts. Thank you for being a valued member of the AnVIL community! Best regards, The AnVIL Team

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[AnVIL-mailing-list] 📢 Shape the Future of AnVIL: Participate in Our Community Poll!
by Natalie Kucher 15 Feb '24

15 Feb '24

Dear AnVIL Community, Your contribution is essential in shaping the future of the AnVIL platform, and we are excited to invite you to participate in our State of the AnVIL Community Poll<https://bit.ly/sota2024>! Your insights and preferences are invaluable as we strive to enhance the AnVIL experience for all users. By taking a few minutes to complete this poll, you'll be playing a crucial role in influencing the direction of our platform and ensuring it meets the diverse needs of our community. Take the poll here: https://bit.ly/sota2024. Why participate? 1. Voice Your Opinion: This is your chance to share your experience with biomedical data science, how you use AnVIL, and let us know what matters most to you. 2. Community Collaboration: Your feedback will contribute to a collaborative effort in making AnVIL a more powerful and user-friendly platform for everyone. 3. Future Development: Help us prioritize future developments and enhancements based on the needs and preferences of our diverse user community. How to Participate: 1. Click the following link: https://bit.ly/sota2024 2. Complete the brief poll. We estimate it will take 10-15 minutes in total. 3. Submit your responses and become an integral part of shaping the AnVIL Platform's future. Optionally enter a drawing for training with our team and more! We appreciate your time and commitment to making AnVIL the best it can be. Your feedback is crucial, and we look forward to hearing your thoughts. Thank you for being a valued member of the AnVIL community! Best regards, The AnVIL Team

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[AnVIL-mailing-list] Scheduled Downtime for AnVIL Data Storage Workspaces for Data Migration on February 15-19, 2024
by Natalie Kucher 02 Feb '24

02 Feb '24

Dear AnVIL Users, We want to make you aware that from Thursday, February 15 thru Monday, February 19 there will be scheduled downtime for all AnVIL data storage workspaces which includes all released workspaces to researchers, consortium access workspaces, and submission workspaces; please note that only workspaces housing AnVIL data will be impacted during this downtime. The Broad Institute’s Data Sciences Platform migration team will be using this time to migrate AnVIL data workspaces from multi-region to US-central1 region due to the changes in pricing structure for multi-region buckets. The benefits of AnVIL making this change to single-region storage are: * Avoid data transfer fees: GCP pricing changes means some operations that were previously free would now incur costs, which will be avoided with this downtime procedure. * Use Autoclass feature: This is also an opportunity to take advantage of Google’s Autoclass feature, which automatically moves files to colder storage, saving on storage costs. To date, the feature has not been available for existing buckets, but since this migration process recreates the bucket, the Autoclass feature is enabled at the time of migration. More information on this migration and how it impacts workspaces can be found in this Terra article<https://support.terra.bio/hc/en-us/articles/19677261508507-Workspace-multi-…>. Additionally, you’ll find resources for migrating your own workspaces in this article. This scheduled downtime for AnVIL data housing workspaces may impact AnVIL users. During this time: * Users will not be able to reference or access all AnVIL data storage workspaces which includes all released workspaces to researchers, consortium access workspaces, and submission workspaces. * If users are in the process of referencing or accessing these workspaces, then their processes that are running will fail or not complete. All operations associated with accessing these workspaces can be resumed upon completion of the migration. If users know the source workspace, they can confirm if it has been migrated if the region is us-central1 and not US multi-region. We recommend that all active Terra workspaces migrate to us-central1. However, users need to do their own risk assessment and work with their cloud provider representatives to ensure there will be no charges. Please see here<https://support.terra.bio/hc/en-us/articles/19677261508507-Workspace-multi-…> for a support article with more information. We appreciate your patience and understanding. As always, if you have questions or issues, please write to help(a)lists.anvilproject.org<mailto:help@lists.anvilproject.org>. Thank you, The AnVIL Team See this post on the AnVIL Support Forum: https://help.anvilproject.org/t/scheduled-downtime-for-anvil-data-storage-w…. -- Natalie Kucher / Project Manager Johns Hopkins University, Department of Biology Krieger School of Arts & Sciences e: nkucher3(a)jhu.edu<mailto:nkucher3@jhu.edu> / AnVIL<https://anvilproject.org/> / Galaxy<https://galaxyproject.org/> / GDSCN<https://www.gdscn.org/>

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[AnVIL-mailing-list] Register for AnVIL Demo and Q&A: Collecting and subsetting SRA data on December 14
by Natalie Kucher 27 Nov '23

27 Nov '23

Join our next AnVIL Demo! Collecting and subsetting SRA data December 14, 2023 at 11:00 AM ET (your time zone<https://www.timeanddate.com/worldclock/fixedtime.html?msg=AnVIL+Demo&iso=20…>) on Zoom 11:00 AM - 11:30 AM ET – Demo on AnVIL In this demo, Ava Hoffman from the Fred Hutch 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. 11:30 AM - 12:00 PM ET – Q&A We’ll open up the floor to questions about the demo presented, and will have AnVIL and Terra support on call to answer any questions about AnVIL you might have! ✏️ Sign up: <https://urldefense.com/v3/__https:/forms.gle/7CcaLE9AM7FrYqpP7__;!!GuAItXPz…> https://forms.gle/7CcaLE9AM7FrYqpP7 Future Demos Sign up for the 2024 schedule! Topics are to be announced. What are AnVIL Demos? AnVIL Demos are a monthly, virtual meeting where we highlight what you can do on the NHGRI<https://www.genome.gov/> Analysis, Visualization, and Informatics Lab-space (AnVIL<https://anvilproject.org/>), a cloud-based computing platform for genomic data science! AnVIL Demos will start out with a 30-minute demonstration on the platform followed by open time for Q&A and user support. The demos will highlight a range of topics, from a capability of the platform to a scientific analysis powered by AnVIL. If you’re interested in showcasing how you use AnVIL at a future AnVIL Demos session, reach out to Natalie Kucher (nkucher3(a)jhu.edu<mailto:nkucher3@jhu.edu>). After the demo, we’ll open up the floor to answer questions about the demo and to answer any general questions you might have about AnVIL. Watch our past Demos from our YouTube playlist<https://www.youtube.com/playlist?list=PL6aYJ_0zJ4uC978C57P3TgAAfB38uy58E>! ✏️ Sign up for more demos: <https://urldefense.com/v3/__https:/forms.gle/7CcaLE9AM7FrYqpP7__;!!GuAItXPz…> https://forms.gle/7CcaLE9AM7FrYqpP7 Resources * AnVIL Getting Started Guide. An opinionated guide on how to get set up and start your work on AnVIL. Get started here<https://jhudatascience.org/AnVIL_Book_Getting_Started/>. * AnVIL YouTube Channel. Learn about AnVIL capabilities and features with our “AnVIL in 2 minutes” videos. Watch AnVIL in 2 minutes here<https://www.youtube.com/playlist?list=PL6aYJ_0zJ4uCABkMngSYjPo_3c-nUUmio> or watch past AnVIL Demos here<https://www.youtube.com/playlist?list=PL6aYJ_0zJ4uC978C57P3TgAAfB38uy58E>. * AnVIL Support Forum. Join the conversation at help.anvilproject.org<http://help.anvilproject.org/>. Upcoming Events Sign up to hear about future AnVIL Demos and announcements at lists.anvilproject.org<https://lists.anvilproject.org/lists/anvil-mailing-list.lists.anvilproject.…> and learn about upcoming events at https://anvilproject.org/events! Best, Natalie -- Natalie Kucher | Project Manager Johns Hopkins University Department of Biology Krieger School of Arts & Sciences nkucher3(a)jhu.edu<mailto:nkucher3@jhu.edu> https://anvilproject.org/

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[AnVIL-mailing-list] AnVIL Demo: Epigenetics in AnVIL on September 21, 2023
by Natalie Kucher 14 Sep '23

14 Sep '23

Join our next AnVIL Demo! [A blue and white logo Description automatically generated] Epigenetics in AnVIL September 21, 2023 at 11:00 AM ET (your time zone<https://www.timeanddate.com/worldclock/fixedtime.html?msg=September+AnVIL+D…>) on Zoom 11:00 AM - 11:30 AM ET – Demo on AnVIL In this demo, we'll introduce fundamentals of epigenetic data analysis and show how you can use RStudio to look at Chip-seq experiment results on AnVIL. We'll also briefly touch on other resources for doing epigenetics research on AnVIL. 11:30 AM - 12:00 PM ET – Q&A We’ll open up the floor to questions about the demo presented, and will have AnVIL and Terra support on call to answer any questions about AnVIL you might have! ✏️ Sign up: <https://urldefense.com/v3/__https:/forms.gle/7CcaLE9AM7FrYqpP7__;!!GuAItXPz…> https://forms.gle/7CcaLE9AM7FrYqpP7 What are AnVIL Demos? AnVIL Demos are a monthly, virtual meeting where we highlight what you can do on the NHGRI<https://www.genome.gov/> Analysis, Visualization, and Informatics Lab-space (AnVIL<https://anvilproject.org/>), a cloud-based computing platform for genomic data science! AnVIL Demos will start out with a 30-minute demonstration on the platform followed by open time for Q&A and user support. The demos will highlight a range of topics, from a capability of the platform to a scientific analysis powered by AnVIL. If you’re interested in showcasing how you use AnVIL at a future AnVIL Demos session, reach out to Natalie Kucher (nkucher3(a)jhu.edu<mailto:nkucher3@jhu.edu>). After the demo, we’ll open up the floor to answer questions about the demo and to answer any general questions you might have about AnVIL. Watch our past Demos from our YouTube playlist<https://www.youtube.com/playlist?list=PL6aYJ_0zJ4uC978C57P3TgAAfB38uy58E>! Future Demos September 21, 2023 – Epigenetics in AnVIL October 26, 2023 – DUOS - A tour of the AnVIL's innovative data sharing platform, and how it can help your research November 16, 2023 – Machine Learning with Bioconductor December 14, 2023 – Collecting and subsetting SRA data ✏️ Sign up for more demos: <https://urldefense.com/v3/__https:/forms.gle/7CcaLE9AM7FrYqpP7__;!!GuAItXPz…> https://forms.gle/7CcaLE9AM7FrYqpP7 Resources * AnVIL Getting Started Guide. An opinionated guide on how to get set up and start your work on AnVIL. Get started here<https://jhudatascience.org/AnVIL_Book_Getting_Started/>. * AnVIL YouTube Channel. Learn about AnVIL capabilities and features with our “AnVIL in 2 minutes” videos. Watch AnVIL in 2 minutes here<https://www.youtube.com/playlist?list=PL6aYJ_0zJ4uCABkMngSYjPo_3c-nUUmio> or watch past AnVIL Demos here<https://www.youtube.com/playlist?list=PL6aYJ_0zJ4uC978C57P3TgAAfB38uy58E>. * AnVIL Support Forum. Join the conversation at help.anvilproject.org<http://help.anvilproject.org/>. Upcoming Events Sign up to hear about future AnVIL Demos and announcements at lists.anvilproject.org<https://lists.anvilproject.org/lists/anvil-mailing-list.lists.anvilproject.…> and learn about upcoming events at https://anvilproject.org/events! Best, Natalie -- Natalie Kucher | Project Manager Johns Hopkins University Department of Biology Krieger School of Arts & Sciences nkucher3(a)jhu.edu<mailto:nkucher3@jhu.edu> https://anvilproject.org/

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[AnVIL-mailing-list] AnVIL Demos: Learn how to use data across multiple AnVIL workspaces on June 22
by Natalie Kucher 08 Jun '23

08 Jun '23

Upcoming AnVIL Demos ✏️ Sign up: https://forms.gle/7CcaLE9AM7FrYqpP7 What are AnVIL Demos? AnVIL Demos are a monthly, virtual meeting where we highlight what you can do on the NHGRI<https://www.genome.gov/> Analysis, Visualization, and Informatics Lab-space (AnVIL<https://anvilproject.org/>), a cloud-based computing platform for genomic data science! AnVIL Demos will start out with a 30-minute demonstration on the platform followed by open time for Q&A and user support. The demos will highlight a range of topics, from a capability of the platform to a scientific analysis powered by AnVIL. If you’re interested in showcasing how you use AnVIL at a future AnVIL Demos session, reach out to Natalie Kucher (nkucher3(a)jhu.edu<mailto:nkucher3@jhu.edu>). After the demo, we’ll open up the floor to answer questions about the demo and to answer any general questions you might have about AnVIL. Watch our past Demos from our YouTube playlist<https://www.youtube.com/playlist?list=PL6aYJ_0zJ4uC978C57P3TgAAfB38uy58E>! June Demo: How to use data across multiple AnVIL workspaces When: June 22, 2023 at 11:00 AM ET (your time zone<https://www.timeanddate.com/worldclock/fixedtime.html?msg=AnVIL+Demos&iso=2…>) on Zoom<https://zoom.us/j/98431880835?pwd=ZDVSMGcyak54dnZKNUE1Tm50WE4vUT09> 11:00 AM - 11:30 AM ET – Demo on AnVIL In this demo, Frederick Tan will highlight a key benefit of using a cloud-based platform for data storage and compute: you can access and analyze the data right in the cloud, without having to move it around or download it! He will demonstrate how to bring together data that are stored in different workspaces to analyze them together. 11:30 AM - 12:00 PM ET – Q&A We’ll open up the floor to questions about the demo presented, and will have AnVIL and Terra support on call to answer any questions about AnVIL you might have! ✏️ Sign up for more demos: https://forms.gle/7CcaLE9AM7FrYqpP7<https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefens…> Future Demos July 20, 2023 – Interactive Genomic Data Science with Bioconductor August 24, 2023 – Galaxy on AnVIL September 21, 2023 – Epigenetics in AnVIL Resources * AnVIL Getting Started Guide. An opinionated guide on how to get set up and start your work on AnVIL. Get started here<https://jhudatascience.org/AnVIL_Book_Getting_Started/>. * AnVIL YouTube Channel. Learn about AnVIL capabilities and features with our “AnVIL in 2 minutes” videos. Watch AnVIL in 2 minutes here<https://www.youtube.com/playlist?list=PL6aYJ_0zJ4uCABkMngSYjPo_3c-nUUmio>. * AnVIL Support Forum. Join the conversation at help.anvilproject.org<http://help.anvilproject.org>. Upcoming Events Sign up to hear about future AnVIL Demos and announcements at lists.anvilproject.org<https://lists.anvilproject.org/lists/anvil-mailing-list.lists.anvilproject.…> and learn about upcoming events at https://anvilproject.org/events! Best, Natalie -- Natalie Kucher | Project Manager Johns Hopkins University Department of Biology Krieger School of Arts & Sciences nkucher3(a)jhu.edu<mailto:nkucher3@jhu.edu> https://anvilproject.org/

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