- AgBioData-LIST - Main Bioinformatics Lab

REMINDER - Monthly Webinar TOMORROW, Dec. 6th, at 12 PM CT

by Annarita Marrano

Hi everybody, Join us TOMORROW, Dec. 6th, at 12 PM Central Time for our monthly webinar. This webinar will focus on single-cell data and metadata management in livestock and plants Benjamin Cole <https://jgi.doe.gov/our-science/scientists-jgi/benjamin-cole-genomics-of-pl…> , Christopher Tuggle <https://faculty.sites.iastate.edu/cktuggle/>, and Muskan Kapoorand <https://github.com/kapoormuskan>. I have included below more details about the webinar and the Zoom link to attend the webinar. I hope you will join us. Best, Annarita :-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-: *Abstracts:* *Benjamin Cole (Joint Genome Institute) on "Data management considerations for plant single-cell genomics."* While plants have arrived on the single-cell scene relatively late, the number and complexity of plant single-cell datasets have exploded over the past four years. With that massive increase in data has come a pressing need to ensure accurate documentation of the experimental provenance of plant single-cell datasets, not only for reproducibility but also for reusability in meta-analyses. During this presentation, I will discuss the current state of plant single-cell research as well as the most common practices for data storage. I will also argue for the need for better standards in the field, and what that could potentially enable. *Christopher Tuggle (Iowa State University) & Muskan Kapoor (Iowa State University) on "Single-Cell genomics data incorporation into agricultural G2P research by building a FAIR data ecosystem."* We will describe a pilot-scale project to determine if our current metadata standards for livestock and crops can be used to ingest scRNAseq datasets in a manner consistent with HCA DCP standards and if established resources (e.g., Terra) can be used to analyze the ingested data. Currently, the most comprehensive data ingestion portal for high throughput sequencing datasets from plants, fungi, protists, and animals/humans is Annotare (located at EMBL-European Bioinformatics Institute). For agricultural animal datasets, another EMBL-EBI portal, the FAANG portal, has been developed. scRNAseq data/metadata can be submitted to FAANG using a semi-automated process. We have extended this tool for scRNAseq data so that files can be validated using the HCA DCP metadata and data validation service. These files are incorporated using EMBL-EBI’s HCA DCP ingestion service and transferred to Terra for further analysis. We will also describe a Shiny-based web application, implemented in R and called Shiny-PIGGI, for the single cell-level transcriptomic study of pig immune tissues and peripheral blood mononuclear cells, which will be an important resource for improved annotation of porcine immune genes and cell types ( https://shinypiggi.ansci.iastate.edu). We intend to further build upon these existing tools to construct a scientist-friendly data resource and analytical ecosystem to facilitate single cell-level genomic analysis through data ingestion, storage, retrieval, re-use, visualization, and comparative annotation across agricultural species. *| 1P ET | 12P CT | 11A MT | 10A PT |* Find your local time here <https://www.timeanddate.com/worldclock/fixedtime.html?msg=AgBioData+Monthly…> Topic: AgBioData Monthly Webinar Time: This is a recurring meeting Meet anytime Join Zoom Meeting https://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09 Meeting ID: 820 3835 6125 Passcode: 160683 --- One tap mobile +19292056099,,82038356125#,,,,*160683# US (New York) +13017158592,,82038356125#,,,,*160683# US (Washington DC) --- Dial by your location • +1 929 205 6099 US (New York) • +1 301 715 8592 US (Washington DC) • +1 305 224 1968 US • +1 309 205 3325 US • +1 312 626 6799 US (Chicago) • +1 646 931 3860 US • +1 253 205 0468 US • +1 253 215 8782 US (Tacoma) • +1 346 248 7799 US (Houston) • +1 360 209 5623 US • +1 386 347 5053 US • +1 507 473 4847 US • +1 564 217 2000 US • +1 669 444 9171 US • +1 669 900 6833 US (San Jose) • +1 689 278 1000 US • +1 719 359 4580 US Meeting ID: 820 3835 6125 Passcode: 160683 Find your local number: https://us06web.zoom.us/u/kF3akiFg7

2 years, 1 month

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Board on Agriculture and Natural Resources Winter Meeting - Tomorrow, Dec. 5

by Annarita Marrano

Hi everybody, The Board on Agriculture and Natural Resources is holding a seminar on Access to Data *tomorrow, Dec. 5, at 11 AM ET.* The meeting will explore a range of topics of interest to the food, agriculture, and natural resources communities. The open sessions of the meeting will include a presentation on research priorities of the USDA Economic Research Service, a panel on disparities in access to data and journal publications, a briefing on a new National Academies report on Accelerating Decarbonization, and a presentation from Colorado State University researchers on a National Climate Change Roadmap: A Research Framework for U.S. Agriculture, Forestry, and Working Lands. You can find more information here <https://www.nationalacademies.org/event/41526_12-2023_board-on-agriculture-…> . Best, Annarita

2 years, 1 month

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REMINDER - Monthly Webinar Next Wed, Nov 1st, at 12 PM CT

by Annarita Marrano

Hi everybody, Join us next Wed, Dec. 6th, at 12 PM CT for our monthly webinar. This webinar will focus on single-cell data and metadata management in livestock and plants Benjamin Cole <https://jgi.doe.gov/our-science/scientists-jgi/benjamin-cole-genomics-of-pl…> , Christopher Tuggle <https://faculty.sites.iastate.edu/cktuggle/>, and Muskan Kapoorand <https://github.com/kapoormuskan>. I have included below more details about the webinar and the Zoom link to attend the webinar. I hope you will join us. Best, Annarita :-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-: *Abstracts:* *Benjamin Cole (Joint Genome Institute) on "Data management considerations for plant single-cell genomics."* While plants have arrived on the single-cell scene relatively late, the number and complexity of plant single-cell datasets have exploded over the past four years. With that massive increase in data has come a pressing need to ensure accurate documentation of the experimental provenance of plant single-cell datasets, not only for reproducibility but also for reusability in meta-analyses. During this presentation, I will discuss the current state of plant single-cell research as well as the most common practices for data storage. I will also argue for the need for better standards in the field, and what that could potentially enable. *Christopher Tuggle (Iowa State University) & Muskan Kapoor (Iowa State University) on "Single-Cell genomics data incorporation into agricultural G2P research by building a FAIR data ecosystem."* We will describe a pilot-scale project to determine if our current metadata standards for livestock and crops can be used to ingest scRNAseq datasets in a manner consistent with HCA DCP standards and if established resources (e.g., Terra) can be used to analyze the ingested data. Currently, the most comprehensive data ingestion portal for high throughput sequencing datasets from plants, fungi, protists, and animals/humans is Annotare (located at EMBL-European Bioinformatics Institute). For agricultural animal datasets, another EMBL-EBI portal, the FAANG portal, has been developed. scRNAseq data/metadata can be submitted to FAANG using a semi-automated process. We have extended this tool for scRNAseq data so that files can be validated using the HCA DCP metadata and data validation service. These files are incorporated using EMBL-EBI’s HCA DCP ingestion service and transferred to Terra for further analysis. We will also describe a Shiny-based web application, implemented in R and called Shiny-PIGGI, for the single cell-level transcriptomic study of pig immune tissues and peripheral blood mononuclear cells, which will be an important resource for improved annotation of porcine immune genes and cell types ( https://shinypiggi.ansci.iastate.edu). We intend to further build upon these existing tools to construct a scientist-friendly data resource and analytical ecosystem to facilitate single cell-level genomic analysis through data ingestion, storage, retrieval, re-use, visualization, and comparative annotation across agricultural species. *| 1P ET | 12P CT | 11A MT | 10A PT |* Find your local time here <https://www.timeanddate.com/worldclock/fixedtime.html?msg=AgBioData+Monthly…> Topic: AgBioData Monthly Webinar Time: This is a recurring meeting Meet anytime Join Zoom Meeting https://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09 Meeting ID: 820 3835 6125 Passcode: 160683 --- One tap mobile +19292056099,,82038356125#,,,,*160683# US (New York) +13017158592,,82038356125#,,,,*160683# US (Washington DC) --- Dial by your location • +1 929 205 6099 US (New York) • +1 301 715 8592 US (Washington DC) • +1 305 224 1968 US • +1 309 205 3325 US • +1 312 626 6799 US (Chicago) • +1 646 931 3860 US • +1 253 205 0468 US • +1 253 215 8782 US (Tacoma) • +1 346 248 7799 US (Houston) • +1 360 209 5623 US • +1 386 347 5053 US • +1 507 473 4847 US • +1 564 217 2000 US • +1 669 444 9171 US • +1 669 900 6833 US (San Jose) • +1 689 278 1000 US • +1 719 359 4580 US Meeting ID: 820 3835 6125 Passcode: 160683 Find your local number: https://us06web.zoom.us/u/kF3akiFg7

2 years, 1 month

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Sign-Up for New AgBioData Working Groups OPEN!!!

by Annarita Marrano

Hello AgBioData community, We are happy to announce that the sign-up for AgBioData working groups is now OPEN! *Please complete this form <https://forms.gle/MeZZrCeSvUywxkQo6> by November 22 at 12 p.m. ET to join one or more of our working groups.* We will have two new working groups starting from January 2023, which are the "*Phenotypic Data Standardization and Management*" and the "*scRNAseq BIOCURATION*" working groups. Two current working groups (i.e., the *DEI Recruiting* and *FAIR Scientific Literature WGs*) are also recruiting new members to join their incredible efforts. You can find more details about them in the form. *We anticipate the commitment will generally be between 2-6 hours per month*, including meeting attendance and offline work (e.g., literature, writing, etc.). This is your opportunity to shape the future of our research community by contributing to developing best practices of data archiving and management that can benefit you and all the other stakeholders. Participating in the AgBioData working groups will also offer you opportunities for - professional networking - leadership skill development - authorship in impactful manuscripts Please share the registration link with anybody that you think can be interested. Thanks, Annarita

2 years, 2 months

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Nomination for a new AgBioData steering committee member due to Nov. 3rd

by Annarita Marrano

Hi everybody, The AgBioData steering committee (SC) is calling for nominations for new SC members! The SC is a vibrant, collaborative, and inclusive environment that offers opportunities to expand your leadership skills, network with agricultural research community stakeholders, and help achieve a FAIR agricultural data ecosystem. *We are looking for candidates to serve as members of the AgBioData SC willing to commit a proportion of time to AgBioData activities (approximately 2 hours/week) for a term of 3 years. * *Nominate yourself or somebody you think might fit the position by this Friday, November 3rd at https://forms.gle/jVN6GZvbhS5QnJkB7 <https://forms.gle/jVN6GZvbhS5QnJkB7>.* Best, Annarita

2 years, 2 months

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REMINDER - Monthly Webinar TOMORROW, Nov. 1st, at 12 PM CT

by Annarita Marrano

Hi everybody, Join us *TOMORROW, Nov. 1st, at 12 PM CT* for our monthly webinar. We will host Ben Rosen <https://www.ars.usda.gov/northeast-area/beltsville-md-barc/beltsville-agric…>, who will talk about telomere-to-telomere genome assemblies of ruminant species and how they will help answer important evolutionary questions. I have included below more details about the webinar and the Zoom link to attend the webinar. I hope you will join us. Best, Annarita :-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-: *Presenters: * Ben Rosen, USDA-ARS *Abstract:* *The Ruminant T2T Consortium* The first draft of the human genome assembly was released over twenty years ago. However, a gapless telomere-to-telomere (T2T) “complete” assembly remained elusive until last year. The highly repetitive nature of pericentromeric, subtelomeric, and duplicated gene families, such as rRNA arrays, made them impossible to assemble. It was only with advances in long-read sequencing technologies and new bioinformatic tools that these structures were resolved. Recently, we proposed the application of these new resources, tools, and knowledge in support of a “Ruminant T2T Consortium.” Our goal is to generate complete genomes for the ruminant evolutionary lineage. The ruminant Suborder comprises six Families and 66 living genera. These species are found in geographically dispersed areas and have adapted to a wide variety of environments. They have also been subjected to both natural and artificial selection. Our hypothesis is that T2T assemblies of ruminant species with relatedness varying from those capable of interbreeding to higher evolutionary distances (up to the estimated 25 million years ago last common ancestor) will inform our understanding of the underpinnings of ruminant evolution. It will also shed light on the genomic consequences of domestication and enhance our knowledge of the functional roles of heterochromatin and other repeat regions of the genome. *| 1P ET | 12P CT | 11A MT | 10A PT |* Find your local time here <https://www.timeanddate.com/worldclock/fixedtime.html?msg=AgBioData+Monthly…> Topic: AgBioData Monthly Webinar Time: This is a recurring meeting Meet anytime Join Zoom Meeting https://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09 Meeting ID: 820 3835 6125 Passcode: 160683 --- One tap mobile +19292056099,,82038356125#,,,,*160683# US (New York) +13017158592,,82038356125#,,,,*160683# US (Washington DC) --- Dial by your location • +1 929 205 6099 US (New York) • +1 301 715 8592 US (Washington DC) • +1 305 224 1968 US • +1 309 205 3325 US • +1 312 626 6799 US (Chicago) • +1 646 931 3860 US • +1 253 205 0468 US • +1 253 215 8782 US (Tacoma) • +1 346 248 7799 US (Houston) • +1 360 209 5623 US • +1 386 347 5053 US • +1 507 473 4847 US • +1 564 217 2000 US • +1 669 444 9171 US • +1 669 900 6833 US (San Jose) • +1 689 278 1000 US • +1 719 359 4580 US Meeting ID: 820 3835 6125 Passcode: 160683 Find your local number: https://us06web.zoom.us/u/kF3akiFg7

2 years, 2 months

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REMINDER - Monthly Webinar Next Wed, Nov 1st, at 12 PM CT

by Annarita Marrano

Hi everybody, Join us next Wed, Nov. 1st, at 12 PM CT for our monthly webinar. We will host Ben Rosen <https://www.ars.usda.gov/northeast-area/beltsville-md-barc/beltsville-agric…>, who will talk about telomere-to-telomere genome assemblies of ruminant species and how they will help answer important evolutionary questions. I have included below more details about the webinar and the Zoom link to attend the webinar. I hope you will join us. Best, Annarita :-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-: *Presenters: * Ben Rosen, USDA-ARS *Abstract:* *The Ruminant T2T Consortium * The first draft of the human genome assembly was released over twenty years ago. However, a gapless telomere-to-telomere (T2T) “complete” assembly remained elusive until last year. The highly repetitive nature of pericentromeric, subtelomeric, and duplicated gene families, such as rRNA arrays, made them impossible to assemble. It was only with advances in long-read sequencing technologies and new bioinformatic tools that these structures were resolved. Recently, we proposed the application of these new resources, tools, and knowledge in support of a “Ruminant T2T Consortium.” Our goal is to generate complete genomes for the ruminant evolutionary lineage. The ruminant Suborder comprises six Families and 66 living genera. These species are found in geographically dispersed areas and have adapted to a wide variety of environments. They have also been subjected to both natural and artificial selection. Our hypothesis is that T2T assemblies of ruminant species with relatedness varying from those capable of interbreeding to higher evolutionary distances (up to the estimated 25 million years ago last common ancestor) will inform our understanding of the underpinnings of ruminant evolution. It will also shed light on the genomic consequences of domestication and enhance our knowledge of the functional roles of heterochromatin and other repeat regions of the genome. *| 1P ET | 12P CT | 11A MT | 10A PT |* Find your local time here <https://www.timeanddate.com/worldclock/fixedtime.html?msg=AgBioData+Monthly…> Annarita Marrano is inviting you to a scheduled Zoom meeting. Topic: AgBioData Monthly Webinar Time: This is a recurring meeting Meet anytime Join Zoom Meeting https://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09 Meeting ID: 820 3835 6125 Passcode: 160683 --- One tap mobile +19292056099,,82038356125#,,,,*160683# US (New York) +13017158592,,82038356125#,,,,*160683# US (Washington DC) --- Dial by your location • +1 929 205 6099 US (New York) • +1 301 715 8592 US (Washington DC) • +1 305 224 1968 US • +1 309 205 3325 US • +1 312 626 6799 US (Chicago) • +1 646 931 3860 US • +1 253 205 0468 US • +1 253 215 8782 US (Tacoma) • +1 346 248 7799 US (Houston) • +1 360 209 5623 US • +1 386 347 5053 US • +1 507 473 4847 US • +1 564 217 2000 US • +1 669 444 9171 US • +1 669 900 6833 US (San Jose) • +1 689 278 1000 US • +1 719 359 4580 US Meeting ID: 820 3835 6125 Passcode: 160683 Find your local number: https://us06web.zoom.us/u/kF3akiFg7

2 years, 2 months

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INFO - Subscription to the AgBioData mailing list

by Annarita Marrano

Dear everyone, We are excited to announce that we will soon reactivate the quarterly AgBioData newsletter with past and future events and valuable resources for this community. We will use Mailchimp as a newsletter platform. *Since you already subscribe to our mailing list, we will add your contact to our newsletter list in Mailchimp. If you prefer opting out, you will find instructions on how to unsubscribe at the bottom of the Mailchimp newsletter.* Please let us know if you have any questions. Have a lovely week, Annarita

2 years, 2 months

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DEI Recruiting WG Open Meeting: "Establishing relationships with the 1890’s Land Grant Community"

by Annarita Marrano

Hi everybody, The DEI Recruiting WG will have an open meeting this *Monday, Oct. 16, at 3 PM ET* about *establishing relationships with the 1890’s Land Grant Community*. We will host Dr. Louis Whitesides <https://louiswhitesides.com/about-me>, Vice President and Executive Director of the 1890 Land Grant Programs, Dr. Alton Thompson <https://foundationfar.org/about/people/alton-thompson-ph-d/>, Executive Director, Association of 1890 Research Directors (ARD), and Dr. Pat Millner <https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.linke…>, Research Microbiologist at the USDA-ARS. You can find the abstract and the Zoom link to join at the bottom of this email. I hope you will join us! Best, Annarita -------------------------------------------------------------------------------------------- *Session Abstract:*The 1890 land-grant institutions are historically black universities established under the Second Morrill Act of 1890. The 1890’s institutions provide significant contributions in research; and provide access to college, graduate programs and professional schools for African American, low income, and first-generation students. One of the goals of the AgBioData community is to diversify both the species represented in our data repositories and to increase participation by underrepresented communities in our community.We welcome presentations and discussion with Drs. Alton Thompson and Louis Whitesides representatives of the 1890’s land grant research community and Dr. Pat Millner, Agricultural Research Service. The discussions will focus on methods to establish successful relationships with the 1890 land grant community. Drs. Whitesides and Thompson will provide their advice and guidance in connecting with researchers and educators in their community, by articulating the priorities and needs of the community. Dr. Pat Millner provides her on-the-ground experience in successfully working with the 1890 community. In 2020, Dr. Pat Millner was recognized, by the USDA, Agricultural Research Service, with the Agency-level award for Outreach, Diversity, and Equal Opportunity in the Supervisory/Managerial Category, “For outstanding accomplishments in coordinating, conducting, and fostering collaborative food safety research and experiential training opportunities for students and faculty between ARS scientist and 1890 land-grant institutions.” Topic: Recruiting WG Time: This is a recurring meeting Meet anytime Join Zoom Meeting https://us06web.zoom.us/j/89060768261?pwd=TC9EOWR3UVdQS3UxNGZWQTEvWDFaZz09 Meeting ID: 890 6076 8261 Passcode: 733778 --- One tap mobile +13052241968,,89060768261#,,,,*733778# US +13092053325,,89060768261#,,,,*733778# US --- Dial by your location • +1 305 224 1968 US • +1 309 205 3325 US • +1 312 626 6799 US (Chicago) • +1 646 931 3860 US • +1 929 205 6099 US (New York) • +1 301 715 8592 US (Washington DC) • +1 669 900 6833 US (San Jose) • +1 689 278 1000 US • +1 719 359 4580 US • +1 253 205 0468 US • +1 253 215 8782 US (Tacoma) • +1 346 248 7799 US (Houston) • +1 360 209 5623 US • +1 386 347 5053 US • +1 507 473 4847 US • +1 564 217 2000 US • +1 669 444 9171 US Meeting ID: 890 6076 8261 Passcode: 733778 Find your local number: https://us06web.zoom.us/u/kbdn4ZqlK2

2 years, 3 months

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REMINDER - Monthly Webinar TOMORROW, Oct 4th, at 12 PM CT

by Annarita Marrano

Hi everybody, Due to the great interest in tomorrow's webinar, I am resharing the details and Zoom link again. Thanks, everyone, and welcome to the new members. Best, Annarita :-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-: Presenters: Pascal Neveu, UMR MISTEA, INRAE (France) Abstract: *PHIS, an ontology-based Information System for Plant Phenotyping* The European EMPHASIS infrastructure aims to enable researchers to use facilities, resources, and services for high-throughput phenotyping of plants. Within the infrastructure, we are leading actions to help scientists better understand plant performance and translate this knowledge into applications. This presentation will look at some examples of data management and implementation of data standards carried out in this context to add value to the phenotyping data. In particular, we will look at PHIS, an ontology-based information system based on the OpenSILEX framework. *| 1P ET | 12P CT | 11A MT | 10A PT |* Find your local time here <https://www.timeanddate.com/worldclock/fixedtime.html?msg=AgBioData+Monthly…> Topic: AgBioData Monthly Webinar Time: This is a recurring meeting Meet anytime Join Zoom Meeting https://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09 Meeting ID: 820 3835 6125 Passcode: 160683 --- One tap mobile +19292056099,,82038356125#,,,,*160683# US (New York) +13017158592,,82038356125#,,,,*160683# US (Washington DC) --- Dial by your location • +1 929 205 6099 US (New York) • +1 301 715 8592 US (Washington DC) • +1 305 224 1968 US • +1 309 205 3325 US • +1 312 626 6799 US (Chicago) • +1 646 931 3860 US • +1 253 205 0468 US • +1 253 215 8782 US (Tacoma) • +1 346 248 7799 US (Houston) • +1 360 209 5623 US • +1 386 347 5053 US • +1 507 473 4847 US • +1 564 217 2000 US • +1 669 444 9171 US • +1 669 900 6833 US (San Jose) • +1 689 278 1000 US • +1 719 359 4580 US Meeting ID: 820 3835 6125 Passcode: 160683 Find your local number: https://us06web.zoom.us/u/kF3akiFg7

2 years, 3 months

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AgBioData-LIST