- AgBioData-LIST - Main Bioinformatics Lab

AG2PI Field Day: Phenomic Prediction & Bioinformatic Workflows - AG2PI "Coconut" Grant Outcomes

by Scott, Nicole M [AGRON]

Dear AgBioData community members, The next Agricultural Genome to Phenome Initiative (AG2PI) Field Day will be "Phenomic Prediction & Bioinformatic Workflows - AG2PI "Coconut" Grant Outcomes" and will be on Wednesday, March 20 from 10:30 AM to 12:00 PM (CDT, UTC-5). In this field day, we will first hear from Dr. Daniel Runcie regarding how phenomic prediction can be used as a tool for plant breeding. Then, Dr. Fiona McCarthy will review new bioinformatic workflows her team has developed to support genomic analyses. Both of these presentations are outcomes from AG2PI "coconut" (large seed) grants. We invite you to register for this Zoom event at https://www.ag2pi.org/workshops-and-activities/field-day-2024-03-20/, where you will also find additional information. Upon registration, you will receive a confirmation email with information about joining the meeting. If you are unable to attend the live session, then you will be able to find a recording at ag2pi.org/<https://www.ag2pi.org/>, at a later date. You do not need to register to view the recording; it is readily available on the AG2PI website soon after the close of the event (generally within 24 hours). Please share the attached, digitally accessible flyer with your colleagues or students and encourage them to attend. Kind regards, Nicole ------------------------ Nicole Scott, PhD Program Specialist Agricultural Genome to Phenome Initiative Iowa State University 1111 WOI Rd Ames, IA 50011 office: 1077 Roy J. Carver Co-Lab phone: 515-294-3945 ag2pi.org<https://www.ag2pi.org/> *** If you no longer wish to receive messages from AG2PI, then please visit https://www.ag2pi.org/join-ag2pi/unsubscribe/ to unsubscribe *** Please note, you cannot unsubscribe if you are receiving this message through a third party ***

1 year

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REMINDER - Monthly Webinar TOMORROW at 12 PM CT

by Annarita Marrano

Hi everybody, Join us tomorrow, March. 6th, at 12 PM CDT, for our monthly webinar. Cyril Pommier <https://orcid.org/0000-0002-9040-8733> will talk about FAIR plant phenomics data management tools and guidelines from the ELIXIR and Emphasis European infrastructures. 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:* *FAIR Plant Phenomics Data Management Tools and Guidelines from ELIXIR and Emphasis European Infrastructures* Plant phenomics data has been greatly facilitated over the past ten years at several levels: data standards to organize and describe data, databases for the management of the experiments, data repositories to ensure long-term accessibility supplemented by data portals to maximise findability and finally, guidelines to ease their usage. We will review the recent advances from joint initiatives involving two European infrastructures: ELIXIR (Life science data) and EMPHASIS (Plant phenomics). First, we will update the current status of MIAPPE (www.miappe.org), a data standard interoperable with the Breeding API that enables not only phenotyping experiment formalisation but also their linking with genotyping. We will also give an overview of its usage in generic data repositories such as Dataverse or Zenodo and their relation with experimental databases such as PHIS. Finding the right documentation to use those tools and standards is not always straightforward. The RDMKit ( https://rdmkit.elixir-europe.org/) is a guidelines portal that has been built to help researchers find the information subset they need. Through a dedicated section, such as the plant domain page ( https://rdmkit.elixir-europe.org/), it shows the complementarity between standards and tools and provides the guidance needed for data management. Finally, we will also update the status of FAIDARE ( https://urgi.versailles.inrae.fr/faidare/), a global data portal that indexes 30 databases using either BrAPI or a generic minimal format. *| 1P ET | 12P CT | 11A MT | 10A PT |* Find your local time here <https://www.timeanddate.com/worldclock/fixedtime.html?msg=AgBioData+March+W…> *Join Zoom Meetinghttps://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09 <https://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09>* Meeting ID: 820 3835 6125 Passcode: 160683

1 year

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2024 AgBioData community workshop (VIRTUAL; 04/29-30, 05/02) - REGISTRATION FORM

by Annarita Marrano

Dear everyone, We are happy to announce that the registration for the *2024 AgBioData community workshop *(April 29-30; May 2) is now *OPEN*! This year's community workshop will be completely *VIRTUAL* and feature WG presentations and breakout room sessions from 9-11 AM CDT daily. We will soon share more details on the workshop agenda and other helpful information. *Please register for the community workshop by completing this form (https://forms.gle/MjLhMcw75YS3dWmcA <https://forms.gle/MjLhMcw75YS3dWmcA>) **by April 15*. I hope you will be able to join us! Please let me know if you have any questions. Have a lovely week. Annarita

1 year

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Job alert: "Genomics Data Engineer (Joint Genome Institute)"

by Annarita Marrano

Hi everybody, Please see below for details about a position as "Genomic Data Engineer" in the Plant Comparative Analysis Group at the Joint Genome Institute: *http://phxc1b.rfer.us/LBLbNj9kY <http://phxc1b.rfer.us/LBLbNj9kY>* Best, Annarita

1 year, 1 month

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REMINDER - Monthly Webinar Next Wed, March. 6th, at 12 PM CT

by Annarita Marrano

Hi everybody, Join us next Wed, March. 6th, at 12 PM CDT, for our monthly webinar. Cyril Pommier <https://orcid.org/0000-0002-9040-8733> will talk about FAIR plant phenomics data management tools and guidelines from the ELIXIR and Emphasis European infrastructures. 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:* *FAIR Plant Phenomics Data Management Tools and Guidelines from ELIXIR and Emphasis European Infrastructures* Plant phenomics data has been greatly facilitated over the past ten years at several levels: data standards to organize and describe data, databases for the management of the experiments, data repositories to ensure long-term accessibility supplemented by data portals to maximise findability and finally, guidelines to ease their usage. We will review the recent advances from joint initiatives involving two European infrastructures: ELIXIR (Life science data) and EMPHASIS (Plant phenomics). First, we will update the current status of MIAPPE (www.miappe.org), a data standard interoperable with the Breeding API that enables not only phenotyping experiment formalisation but also their linking with genotyping. We will also give an overview of its usage in generic data repositories such as Dataverse or Zenodo and their relation with experimental databases such as PHIS. Finding the right documentation to use those tools and standards is not always straightforward. The RDMKit ( https://rdmkit.elixir-europe.org/) is a guidelines portal that has been built to help researchers find the information subset they need. Through a dedicated section, such as the plant domain page ( https://rdmkit.elixir-europe.org/), it shows the complementarity between standards and tools and provides the guidance needed for data management. Finally, we will also update the status of FAIDARE ( https://urgi.versailles.inrae.fr/faidare/), a global data portal that indexes 30 databases using either BrAPI or a generic minimal format. *| 1P ET | 12P CT | 11A MT | 10A PT |* Find your local time here <https://www.timeanddate.com/worldclock/fixedtime.html?msg=AgBioData+March+W…> *Join Zoom Meetinghttps://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09 <https://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09>* Meeting ID: 820 3835 6125 Passcode: 160683

1 year, 1 month

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Genome assembly graph resolution workshop at the AGBT-Ag conference

by Annarita Marrano

Forwarding this announcement from Timothy P.L. Smith (USDA-ARS, Meat Animal Research Center): ------------------------------------------------------------------------- We are pleased to announce that Drs. Arang Rhie and Sergey Koren, from the Center for Genomics and Data Science Research at the National Institutes of Health, have agreed to conduct an in-person hands- on workshop on inspecting and resolving genome assembly graphs in conjunction with the Advances in Genome Biology and Technology Agriculture conference (AGBT-Ag) in Phoenix on Sunday, April 14, 7-9 pm (following the RCN workshop). The workshop will be organized by Drs. Brenda Murdoch and Ben Rosen, and requires registration for the conference at www.agbt.org. Resolving assembly graphs is an important component of generating full haplotype separated diploid or polyploid assemblies in animals or plants, and particularly important in the context of “complete” telomere-to-telomere (T2T) assembly. The Ruminant T2T project aims to generate T2T assemblies of cetartiodactyla species and other species that can generate the appropriate data types but the graph resolution step is a manual process and additional trained personnel would be beneficial to speed progress and accelerate other T2T efforts. The training will cover evaluating assembly graphs in bandage, resolving tangles that are amenable to manual resolution, and generating assemblies with resolved sequence. Some easy and difficult graphs will be examined during the two hour workshop. We are very grateful that Arang and Sergey are willing to develop this tutorial and provide their expertise. Please email Kelsey McClure at kelsey.mcclure(a)usda.gov if you want to attend the workshop by March 5, so that we can make sure we can accommodate the number of interested participants. If you hope to attend but do not know if you will be able to by that deadline, please go ahead and email with a statement to that effect.

1 year, 1 month

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AG2PI field day, new RFP, travel awards

by Scott, Nicole M [AGRON]

Dear AgBioData members, We, Agricultural Genome to Phenome Initiative (AG2PI), have three announcements to share: 1. AG2PI virtual field days are back! The next field day will be held February 21, 10:30 AM to 12:00 PM (CST, UTC-6) and will highlight the "coconut" (large seed) grant projects led by Dr. Pankaj Jaiswal on plant stress ontology and by Dr. Seth Murray on building a more connected unmanned aerial systems (UAS) community. For more information and to register, visit https://www.ag2pi.org/workshops-and-activities/field-day-2024-02-21/. 1. Reminder: AG2PI is offering student conference travel grants up to $1500 to any* undergraduate and graduate students attending an institution in the US. Details and instructions to apply can be found on the AG2PI website (https://www.ag2pi.org/seed-grants/student-conference-travel-awards-2023-11-…). These will be awarded on a rolling basis until all funds are committed, so apply soon! Application portal will close by June 1, 2024 and all travel must be completed by August 1, 2024. (*students must be engaged in AG2PI-related research, broadly, to apply) 1. A Request for Proposals has been released by USDA NIFA for FY2024 regarding the AG2PI program. There will be a NIFA Technical Assistance Webinar for the RFP on March 21, 2024. Registration details can be found here: https://www.nifa.usda.gov/events/technical-assistance-webinar-agricultural-…. Please share this message with anyone you think might be interested in either of these opportunities. Have a wonderful week, Nicole ------------------------ Nicole Scott, PhD Program Specialist Agricultural Genome to Phenome Initiative Iowa State University 1111 WOI Rd Ames, IA 50011 office: 1077 Roy J. Carver Co-Lab phone: 515-294-3945 ag2pi.org<https://www.ag2pi.org/> *** If you no longer wish to receive messages from AG2PI, then please visit https://www.ag2pi.org/join-ag2pi/unsubscribe/ to unsubscribe *** Please note, you cannot unsubscribe if you are receiving this message through a third party ***

1 year, 1 month

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REMINDER - Monthly Webinar, TODAY, at 12 PM CT - Zoom link

by Annarita Marrano

Hi everybody, Join us today* at 12 PM CT *for our monthly webinar. We will have Alex Ignatchenko and Paul Thomas talking about TreeGrafter, a method of predicting Gene Ontology annotations, and other tools implemented in InterProScan. *Zoom link: https://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09 <https://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09>.* Best, Annarita :-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-: *Abstracts:* *Alex Ignatchenko (EMBL-EBI):* Gene Ontology (GO) Annotation (GOA) project at EMBL-EBI aims to provide high-quality GO annotations to proteins in the UniProt Knowledgebase (UniProtKB), RNA molecules from RNACentral and protein complexes from the Complex Portal. Currently, the GOA database hosts 5 million manually curated GO annotations from over 70 research groups. This set is used as a foundation for 15 automatic GO annotation pipelines. The output data re-generated ever 2 month and commonly referred to as Inferred from Electronic Annotation (IEA). The IEA pipelines use range of statistical, rule-based and machine learning algorithms to enrich existing GO annotation coverage. The generated IEA set of over 1.1 billion GO annotations is subject to over 130 checks, constraints and filters to ensure the quality of predicted GO annotations. The GOA data is publicly available from GOA ftp and the GO annotation browser QuickGO. The GOA team is constantly looking for ways to improve the quality of GO annotations and gene product coverage. The TreeGrafter is a method of prediction of GO annotations based on PANTHER family/subfamily and the InterPro signatures. The project is a collaboration between PANTHER and the InterPro team at EMBL-EBI. The algorithm was published in 2019, and it was incorporated into the InterPro in the second half of 2023. The TreeGrafter mappings were processed and added to the GOA database for testing shortly after. This implementation resulted in about 301 million GO annotations after the GOA pipeline checks and filters. More importantly, the final set has over 200 million GO annotations, which is not predicted by any other IEA methods. The GOA team plans to intergrade TreeGrafter GO annotation pipeline into the GOA database and release it to public in a first half of 2024. *Paul D. Thomas (University of Southern California and Gene Ontology Consortium)Accurate annotation of protein sequences at large scale, using evolutionary modeling* Inferring (aka “annotating” or “predicting”) the functions of the vast numbers of known protein sequences has been a longstanding challenge in genomics. Over the last decade, a comprehensive system has been developed for addressing this challenge based on constructing and applying models of function evolution in protein families. The main components of the system– including PANTHER phylogenetic trees, Gene Ontology phylogenetic annotations and TreeGrafter software (now implemented in InterProScan)– work together in an integrated software and data suite that is now beginning to be broadly used to annotate the functions of protein-coding genes. I will describe each of these components, as well as how the tool can be easily used to annotate any set of protein-coding genes and how users can give feedback to help improve the annotations. *| 1P ET | 12P CT | 11A MT | 10A PT |* Find your local time here <https://www.timeanddate.com/worldclock/fixedtime.html?msg=AgBioData+Monthly…>

1 year, 1 month

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REMINDER - Monthly Webinar TOMORROW, Feb. 7th, at 12 PM CT

by Annarita Marrano

Hi everybody, This is a friendly reminder of our monthly webinar *tomorrow, Feb. 7th, at 12 PM CT*. Alex Ignatchenko and Paul Thomas will talk about TreeGrafter, a method of predicting Gene Ontology annotations, and other tools implemented in InterProScan. 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:* *Alex Ignatchenko (EMBL-EBI):* Gene Ontology (GO) Annotation (GOA) project at EMBL-EBI aims to provide high-quality GO annotations to proteins in the UniProt Knowledgebase (UniProtKB), RNA molecules from RNACentral and protein complexes from the Complex Portal. Currently, the GOA database hosts 5 million manually curated GO annotations from over 70 research groups. This set is used as a foundation for 15 automatic GO annotation pipelines. The output data re-generated ever 2 month and commonly referred to as Inferred from Electronic Annotation (IEA). The IEA pipelines use range of statistical, rule-based and machine learning algorithms to enrich existing GO annotation coverage. The generated IEA set of over 1.1 billion GO annotations is subject to over 130 checks, constraints and filters to ensure the quality of predicted GO annotations. The GOA data is publicly available from GOA ftp and the GO annotation browser QuickGO. The GOA team is constantly looking for ways to improve the quality of GO annotations and gene product coverage. The TreeGrafter is a method of prediction of GO annotations based on PANTHER family/subfamily and the InterPro signatures. The project is a collaboration between PANTHER and the InterPro team at EMBL-EBI. The algorithm was published in 2019, and it was incorporated into the InterPro in the second half of 2023. The TreeGrafter mappings were processed and added to the GOA database for testing shortly after. This implementation resulted in about 301 million GO annotations after the GOA pipeline checks and filters. More importantly, the final set has over 200 million GO annotations, which is not predicted by any other IEA methods. The GOA team plans to intergrade TreeGrafter GO annotation pipeline into the GOA database and release it to public in a first half of 2024. *Paul D. Thomas (University of Southern California and Gene Ontology Consortium)Accurate annotation of protein sequences at large scale, using evolutionary modeling* Inferring (aka “annotating” or “predicting”) the functions of the vast numbers of known protein sequences has been a longstanding challenge in genomics. Over the last decade, a comprehensive system has been developed for addressing this challenge based on constructing and applying models of function evolution in protein families. The main components of the system– including PANTHER phylogenetic trees, Gene Ontology phylogenetic annotations and TreeGrafter software (now implemented in InterProScan)– work together in an integrated software and data suite that is now beginning to be broadly used to annotate the functions of protein-coding genes. I will describe each of these components, as well as how the tool can be easily used to annotate any set of protein-coding genes and how users can give feedback to help improve the annotations. *| 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 - SC bi-weekly meeting Time: This is a recurring meeting Meet anytime Join Zoom Meeting https://us06web.zoom.us/j/83731466263?pwd=Q2ZZbHB2UEcrRHAvNzZxV3BRRlBuUT09 Meeting ID: 837 3146 6263 Passcode: 827841 --- One tap mobile +15642172000,,83731466263#,,,,*827841# US +16469313860,,83731466263#,,,,*827841# US --- Dial by your location • +1 564 217 2000 US • +1 646 931 3860 US • +1 669 444 9171 US • +1 669 900 6833 US (San Jose) • +1 689 278 1000 US • +1 719 359 4580 US • +1 929 205 6099 US (New York) • +1 253 205 0468 US • +1 253 215 8782 US (Tacoma) • +1 301 715 8592 US (Washington DC) • +1 305 224 1968 US • +1 309 205 3325 US • +1 312 626 6799 US (Chicago) • +1 346 248 7799 US (Houston) • +1 360 209 5623 US • +1 386 347 5053 US • +1 507 473 4847 US Meeting ID: 837 3146 6263 Passcode: 827841 Find your local number: https://us06web.zoom.us/u/kekUSg0LV1

1 year, 1 month

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REMINDER - Monthly Webinar Next Wed, Feb. 7th, at 12 PM CT

by Annarita Marrano

Hi everybody, After the holiday break and PAG 31, we are ready to restart our monthly webinar series! Join us next Wed, Feb. 7th, at 12 PM CT for our monthly webinar. Alex Ignatchenko and Paul Thomas will talk about TreeGrafter, a method of predicting Gene Ontology annotations, and other tools implemented in InterProScan. 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:* *Alex Ignatchenko (EMBL-EBI):* Gene Ontology (GO) Annotation (GOA) project at EMBL-EBI aims to provide high-quality GO annotations to proteins in the UniProt Knowledgebase (UniProtKB), RNA molecules from RNACentral and protein complexes from the Complex Portal. Currently, the GOA database hosts 5 million manually curated GO annotations from over 70 research groups. This set is used as a foundation for 15 automatic GO annotation pipelines. The output data re-generated ever 2 month and commonly referred to as Inferred from Electronic Annotation (IEA). The IEA pipelines use range of statistical, rule-based and machine learning algorithms to enrich existing GO annotation coverage. The generated IEA set of over 1.1 billion GO annotations is subject to over 130 checks, constraints and filters to ensure the quality of predicted GO annotations. The GOA data is publicly available from GOA ftp and the GO annotation browser QuickGO. The GOA team is constantly looking for ways to improve the quality of GO annotations and gene product coverage. The TreeGrafter is a method of prediction of GO annotations based on PANTHER family/subfamily and the InterPro signatures. The project is a collaboration between PANTHER and the InterPro team at EMBL-EBI. The algorithm was published in 2019, and it was incorporated into the InterPro in the second half of 2023. The TreeGrafter mappings were processed and added to the GOA database for testing shortly after. This implementation resulted in about 301 million GO annotations after the GOA pipeline checks and filters. More importantly, the final set has over 200 million GO annotations, which is not predicted by any other IEA methods. The GOA team plans to intergrade TreeGrafter GO annotation pipeline into the GOA database and release it to public in a first half of 2024. *Paul D. Thomas (University of Southern California and Gene Ontology Consortium)Accurate annotation of protein sequences at large scale, using evolutionary modeling* Inferring (aka “annotating” or “predicting”) the functions of the vast numbers of known protein sequences has been a longstanding challenge in genomics. Over the last decade, a comprehensive system has been developed for addressing this challenge based on constructing and applying models of function evolution in protein families. The main components of the system– including PANTHER phylogenetic trees, Gene Ontology phylogenetic annotations and TreeGrafter software (now implemented in InterProScan)– work together in an integrated software and data suite that is now beginning to be broadly used to annotate the functions of protein-coding genes. I will describe each of these components, as well as how the tool can be easily used to annotate any set of protein-coding genes and how users can give feedback to help improve the annotations. *| 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 +15642172000,,82038356125#,,,,*160683# US +16469313860,,82038356125#,,,,*160683# US --- Dial by your location • +1 564 217 2000 US • +1 646 931 3860 US • +1 669 444 9171 US • +1 669 900 6833 US (San Jose) • +1 689 278 1000 US • +1 719 359 4580 US • +1 929 205 6099 US (New York) • +1 253 205 0468 US • +1 253 215 8782 US (Tacoma) • +1 301 715 8592 US (Washington DC) • +1 305 224 1968 US • +1 309 205 3325 US • +1 312 626 6799 US (Chicago) • +1 346 248 7799 US (Houston) • +1 360 209 5623 US • +1 386 347 5053 US • +1 507 473 4847 US Meeting ID: 820 3835 6125 Passcode: 160683 Find your local number: https://us06web.zoom.us/u/kF3akiFg7

1 year, 2 months

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