- AgBioData-LIST - Main Bioinformatics Lab

Fwd: AG2PI training workshop: Plant Phenotyping Pipeline

by Darwin Campbell

Good morning. Passing this training opportunity along. I hope your day goes well. Darwin AgBioData Program Coordinator <><><><><><><><><><><><><><><><><><><><><><><><><><><><> Dear AG2PI member, Agricultural Genome to Phenome Initiative (AG2PI <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.ag2pi.org_&d=DwMFA…>) invites you to register for our next training workshop, “Phenomic Data Processing Using Machine Learning, Distributed Computing & Container Technology”, to be held July 22, 2021, from 1 PM to 3 PM (CDT; GMT -5). In this CyVerse-hosted workshop, the PhytoOracle team will show how to leverage their pipelines to process proximal and remote-sensing data for plant phenotyping. They will showcase two pipelines that leverage distributed computing, machine learning, and container technology. First, they will run through their thermal pipeline, which detects individual plants in thermal images and runs Kmeans clustering to collect individual plant temperature values. Then, they will run through their hyperspectral pipeline, which detects Spectralon reflectance reference targets and calculates plot-level reflectance values. You can access registration information for the workshop through the AG2PI website: https://www.ag2pi.org/workshops-and-activities/workshop-2021-07/ but you will need to register through CyVerse (if you don’t already have a free CyVerse account, you can create one here <https://cyverse.org/discovery-environment>). A recording will be made available on the AG2PI workshop webpage soon after the conclusion of the event. *This workshop will be limited to 50 participants*. Please share the attached 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 ***

4 years, 1 month

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AgBioData Consortium Virtual Booth Exhibit at ASPB 2021 -- FREE to you!

by Marcela K. Monaco

Dear All, Just a reminder that the AgBioData Consortium will have a virtual booth exhibit at Plant Biology 2021. Darwin Campbell has done a wonderful job setting this up with very basic info and links to the AgBioData website, which has in turn, links to all of our DBs/resources. We may not have the (wo)manpower to make a new video with summary slides for all resources but for now he has uploaded the intro video I recorded for the workshop. We can only list up to 4 contacts, so we may list AgBioData as one of them and forward any targeted inquiries to the relevant resource rep. Here is a screenshot of our v-booth: [image: image.png] If you would like to sign up for a time slot to (wo)man the booth, you will have the opportunity to schedule videochat meetings with general visitors and/or your users (we are part of the meeting's scavenger hunt so we can expect some traffic!). I believe that so far, only Asher and I have volunteered for this. *Show Hours: *Monday, Jul 19, 1:30 PM - 2:30 PM *Show Hours: *Tuesday, Jul 20, 1:30 PM - 2:30 PM *Show Hours: *Thursday, Jul 22, 1:30 PM - 2:30 PM *Show Hours: *Friday, Jul 23, 1:30 PM - 2:30 PM Other features we could take advantage of are: *- Upload up to 6 PDFs* (one will be the AgBioData brochure, and preference will be given to resources with a rep "on site", remember that exhibit-only registrations are FREE and it is only a 1-hour commitment to be on call at the booth!) *- Upload up to 6 images* (could consider slides combining various logos with pics/contact/availability of rep on site) *- A giveaway button*, if anyone is interested in offering some swag in exchange for, by example, filling a survey! (we will just need to provide a link to the form where details can be explained) *- List up to 4 reps with photo or DB logo, bio and contact details* - Again, I know Asher and I are confirmed for this, but could be mistaken... (if so, apologies) I will try to work some more on this next week, so anyone looking to participate and have your resource highlighted, please shoot us a line :) Minimum work for us, PLEASE, we're very tight! Happy weekend, Marcela -- Marcela Karey Tello-Ruiz, PhD The Ware Lab, USDA ARS / CSHL Computational Science Manager and Education, Outreach & Training Lead Cold Spring Harbor Laboratory One Bungtown Road, Williams #5 Cold Spring Harbor, NY 11724 Phone: 516-367-8893 Fax: 516-367-6851 E-mail: telloruiz(a)cshl.edu --- Facebook: https://www.facebook.com/Gramene Twitter: https://twitter.com/GrameneDatabase Blog: http://news.gramene.org/blog <http://news.gramene.org/blog/12>12 <telloruiz(a)cshl.edu> YouTube: https://goo.gl/ln9RLD

4 years, 1 month

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Fwd: Next AG2PI Field Day on FAANG

by Darwin Campbell

Greetings! This may be of interest to some of you in case you are not subscribed to their mailing list. All the best, have a great weekend. Darwin <><><><><><> Dear AG2PI community member, The next AG2PI Field Day is on Wednesday, June 16 from 10:30 AM to 12:00 PM (Central Time, -5 GMT). This field day will focus on Functional Annotation of ANimal Genomes (FAANG). During this event, three members of FAANG will share the consortium’s goals and its aspirations to provide resources for understanding the genome of all livestock and aquaculture species. The speakers will discuss how the consortium was envisioned, the foundations that were laid, its current activities, and future plans, providing an example of a successful consortium in the agricultural genomics space. We invite you to register for this Zoom event at https://tinyurl.com/AG2PI-FD8. Upon registration, you will receive a confirmation email with information about joining the meeting. A link to join the meeting will also be provided the day of the event on the AG2PI website <http://ag2pi.org>. 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. Space IS limited, so register soon. Feel free to share this message and the attached flyer with colleagues at your institution. 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/>

4 years, 2 months

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ASPB and code of conduct information

by Darwin Campbell

Greetings! In the webinar presented Wednesday by Monica Poelchau, (link to the webinar recording: https://youtu.be/nFskgT23pnY), she mentioned a couple of things in the announcements portion that I wanted to follow up on. - Through the generous support of Dorrie Main, AgBioData will have a workshop and virtual booth at 2021 ASPB. The video ( https://youtu.be/nFskgT23pnY?t=30) has details about and booth and the URL to sign up for space at the booth can be found here: https://docs.google.com/spreadsheets/d/1RlLXxEF992PNByzRTclKqrTTdg1wF26tTrR…. Marcela K. Monaco sent an email to this list group on Fri, Apr 30, with the subject: *Plant Bioinformatics Resources Workshop & Virtual Booth Exhibit at ASPB 2021* that has additional details. I'm sure we'll have additional information to share as this process moves forward. - The AgBioData Consortium steering committee is working toward the adoption of a *Code of Conduct* (https://youtu.be/nFskgT23pnY?t=155). We invite you to provide your thoughts and input on the content in this google document: https://tinyurl.com/yf263q7h before its adoption. With your browser in "suggesting mode", feel free to make changes or add comments as you wish. If you have any questions or comments that you would rather not post in a public document but want to share, send an email to me at darwin(a)iastate.edu. *The commenting period will close at Noon CT on May 13th (next Wednesday)*. *** *The Steering Committee is looking for one or two people that would serve as Ombudsperson to AgBioData community. This could be a person outside of the organization that one could report inappropriate activity to the Steering Committee without engaging them directly *if* the need arises. It is expected that their services would be seldom needed or used. Contact me at darwin(a)iastate.edu if you or someone you know might be interested in this opportunity. All the best, and I hope you have a safe and great weekend! Darwin Campbell, AgBioData coordinator on behalf of the AgBioData steering committee Jacqueline Campbell Ethalinda Cannon Laurel Cooper Lisa Harper Sook Jung Monica Poelchau Meg Staton Leonore Reiser Marcela K. Tello-Ruiz

4 years, 3 months

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Plant Bioinformatics Resources Workshop & Virtual Booth Exhibit at ASPB 2021

by Marcela K. Monaco

Dear All, Once again, Shabari (TAIR) and myself (Marcela, CSHL) are in charge of the organization of the Plant Bioinformatics Resources Workshop at the Virtual 2021 ASPB Plant Biology meeting. We were allotted a total of 2 hours on the Sunday prior to the official kick off of the meeting. So, we would like to get an idea of how many resources would be interested in participating in the workshop. Plant Bioinformatics Resources Workshop Sunday July 18, 2021 4:45 PM – 6:45 PM EDT If you are planning on attending the meeting and are interested in giving a talk, please fill out the table below with your contact info and tentative title (topic) of your talk to help us decide on how to best accommodate all interested speakers or if we need to set forth selection metrics in a minimum rubric (e.g., topics of interests from last survey, impact on the plant community, interconnectivity with other resources, target users, etc.). https://docs.google.com/spreadsheets/d/1RlLXxEF992PNByzRTclKqrTTdg1wF26tTrR… (WORKSHOP page) Our deadline to finalize the list of speakers is May 19, so we will close this table by May 10. Again, if there is a similar number of resources as last year, we are likely to follow the same format of short pre-recorded talks. However, if we have a larger number, we might need to select a subset of representative topics/resources. VIRTUAL BOOTH EXHIBIT The AgBioData Steering Committee is pleased to announce that all members of the consortium will have the opportunity to have a virtual presence in the AgBioData Virtual Booth Exhibit. The booth will have premium features including the ability to virtually interact live and text chat with visiting users, get analytic data of views/clicks, scan visitors via a scavenger hunt, and other perks. If you are interested in participating, I may be asking you for a logo of your resource and a summary slide to include in an automated slideshow that will be uploaded in our booth. The best part is that even if you are not attending the meeting, there are free exhibit hall-only registrations, which would allow us to split duties to "wo/man" the booth at prime times, and set up 1-on-1 meetings with our users. Anyhow, if you are interested in having your resource participate in the booth, please sign up in the same doc: https://docs.google.com/spreadsheets/d/1RlLXxEF992PNByzRTclKqrTTdg1wF26tTrR… (BOOTH page) Also, do not forget the reduced group registration rates (regardless of membership status and affiliation), before June 19: 5-9 People, per person $219 10-24 people, per person $159 Looking forward to having a strong AgBioData presence at the next ASPB meeting! Marcela On behalf of the AgBioData Steering Committee

4 years, 3 months

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Conference: BOSC 2021, part of ISMB/ECCB Online!

by Monica Munoz-Torres

Dear colleagues, I hope it is okay for me to share this message with the community. I would like to kindly invite all of you to consider joining us at BOSC 2021. I believe that this event offers a brilliant opportunity for many in the AgBioData community to share the fruits of your work. The 2021 Bioinformatics Open Source Conference <https://www.open-bio.org/events/bosc-2021> (BOSC) is a forum for developers and users to interact and share research results and ideas in open source bioinformatics and open science. Topics include software development practices that promote open science standards and sharing of biological data and code, as well as approaches for building diverse communities. BOSC is a track of the conference on Intelligent Systems in Molecular Biology / European Conference on Computational Biology 2021 <https://www.iscb.org/ismbeccb2021> (ISMB/ECCB), and it will be held online on July 29-30. *The main abstract deadline is May 6th*. Please see our announcement on the BOSC website for complete details at https://www.open-bio.org/2021/03/24/join-us-at-bosc-2021 *Requesting registration fee assistance*: We realize that the cost of ISMB/ECCB may be prohibitive for some. If you are submitting an abstract to BOSC and would have difficulty covering the cost of registration, you can request registration fee assistance during abstract submission. *Increasing diversity in participation*: Please share this announcement with other people and groups who might be interested. We are particularly interested in reaching out to communities who may not yet be aware of BOSC! *Key Dates* - May 6, 2021: Deadline for submitting one-page talk/poster abstracts at https://www.open-bio.org/events/bosc/submit/ - May 27: Talk/poster acceptance notifications - June 3: Late poster and Late-Breaking Lightning Talk (LBLT) submission deadline - June 10: Late poster / LBLT acceptance notifications - July 29-30: BOSC 2021 Online <https://www.open-bio.org/events/bosc/> (part of ISMB/ECCB 2021 Online) - July 31-Aug 1: CollaborationFest <https://www.open-bio.org/events/bosc-2021/collaborationfest/> (CoFest) We hope to see you online at BOSC 2021! Sincerely, ~moni, *on behalf of the BOSC 2021 Organizing Committee: Nomi Harris (chair), Karsten Hokamp (co-chair), Peter Cock, Chris Fields, Jessica Maia, Monica Munoz-Torres, Malvika Sharan, Jason Williams* <https://www.open-bio.org/events/bosc/> *--Moni Munoz-Torres, PhDAssistant Professor, Oregon State UniversityAffiliate Professor, Lawrence Berkeley National LaboratoryDirector of Operations, Center for Cancer Data Harmonization (CCDH)*

4 years, 4 months

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Reminder: AgBioData webinar - Wednesday April 7th

by Darwin Campbell

Greetings! I hope this email finds you well. Spring is in full swing in the midwest, the crocus and hyacinth are now in full bloom and sharing their most awesome aroma. Perhaps, unless you have allergies, it doesn't get much better than this. Below are the details of the *April 7th AgBioData webinar*, we look forward to seeing you online with us, and hope your schedule allows you to join us *this* Wednesday! Darwin Campbell, AgBioData coordinator on behalf of the AgBioData steering committee Jacqueline Campbell Ethalinda Cannon Laurel Cooper Lisa Harper Sook Jung Dorrie Main Monica Poelchau Meg Staton Leonore Reiser Marcela K. Tello-Ruiz •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• *PhyloGenese helps users explore precomputed gene family trees with known functions for individual family members, and assists users with inferring gene functions.* *Presented by: Peifen Zhang* *Wednesday, April 7, 2021* Hosted by Leonore Reiser https://iastate.webex.com/iastate/j.php?MTID=m09b0d3589ee14b82e68915eb31f41… 1 hour | 1P ET | 12P CT | 11A MT | 10A PT Find your local time: http://bit.ly/37WzH6I Meeting number: 120 906 4216 Password: mMTNB2ZkE23 PhyloGenes (phylogenes.org) presents precomputed phylogenetic trees of plant gene families along with known functions for individual family members. By displaying experimentally validated gene functions associated to individual genes within a tree, PhyloGenes enables functional inference for genes of uncharacterized function, based on their evolutionary relationships to experimentally studied genes, in a visually traceable manner. For the many families containing genes that have evolved to perform different functions, PhyloGenes also facilitates the study of function evolution. The current PhyloGenes release (version 2.2) includes 40 plant genomes covering a broad taxonomic range and including all major crops, along with 10 non-plant model organisms represented in over 8,000 gene families. Over two-thirds of the families have at least one member with a validated known function as GO terms. To increase the predictive power of PhyloGenes, future work will involve community contribution and emphasize on incorporating new functional annotations of family members across families and subfamilies, and also adding complimentary functional datasets such as gene expression and mutant phenotype Join by video system Dial 1209064216(a)iastate.webex.com You can also dial 173.243.2.68 and enter your meeting number. Join by phone +1-312-535-8110 United States Toll (Chicago) Access code: 120 582 0206

4 years, 4 months

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AgBioData webinar - February 3rd - tomorrow!

by Darwin Campbell

Greetings! This is a reminder of the *February 3rd* AgBioData webinar (tomorrow) we look forward to seeing you, and hope you can join us! Darwin Campbell, AgBioData coordinator on behalf of the AgBioData steering committee •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• *Global Biodata Coalition - Chuck Cook * Host: Leonore Reiser Global Biodata Coalition (GBC) is working with funders to encourage more efficient collaboration in funding data resources and to sustain funding for critical data resources. Much of this is relevant to the themes you list below. More info, including pdfs of past talks: www.globalbiodata.org https://iastate.webex.com/iastate/j.php?MTID=mfae1dbfdf166f57b58d8c258f6f73… *Wednesday, Feb 3, 2021 *| 1 hour | 1P ET | 12P CT | 11A MT | 10A PT | Find your local time: https://bit.ly/34aHm0e Meeting number: 120 582 0206 Password: 25inNd3JfT5 Join by video system Dial 1205820206(a)iastate.webex.com You can also dial 173.243.2.68 and enter your meeting number. Join by phone +1-312-535-8110 United States Toll (Chicago) Access code: 120 582 0206

4 years, 4 months

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watching picture-a-scientist

by Sushma Naithani

Please feel free to circulate this info in agbiodata mailing list. Hi all, The international society of Biocurators is hosting a screening of this movie. The movie is free of charge for biocurators/ members of ISB and others who contribute to data curation. The registration is on first-come-to-first-basis. If you have time, you can get registered for watching pictureascientist. Save the date! March 12-14 screening of the amazing https:// pictureascientist.com/media <https://t.co/R9FdjoodJH?amp=1> sponsored by ISB. Register here: https://surveymonkey.com/r/HSMLY3Z <https://t.co/lvCU0WUsYs?amp=1> *#WomeninScience, #DiversityMatters, #BlackinSTEM* Best regards Sushma -- *Sushma Naithani* (she/her) Associate Professor Senior Research Editor-in chief, Current Plant Biology Dept. of Botany and Plant Pathology Center for Genome Research & Biocomputing *Oregon State University*, Corvallis, OR, 97331 Phone: +1-541-737-8022 Fax: +1-541-737-3573 e-mail: sushma.naithani(a)oregonstate.edu <sushma.naithani(a)oregonstate.edu> e-mail: naithans(a)science.oregonstate.edu <naithans(a)science.oregonstate.edu> webpage: https://agsci.oregonstate.edu/users/sushma-naithani “*He is an emissary of pity, and science, and progress, and devil knows what else.”— Heart of Darkness, Joseph Conrad*

4 years, 5 months

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Fwd: AG2PI seed grant applications open!

by Darwin Campbell

Greetings! Forwarding this on in the event you are interested to apply. Please note there is a mini conference on 2/24 to discuss the Seed Grant Mechanism and Team-Building Opportunity. Darwin Campbell, AgBioData coordinator on behalf of the AgBioData steering committee ---------- Forwarded message --------- From: Scott, Nicole M [AGRON] <nmscott(a)iastate.edu> Date: Tue, Feb 2, 2021 at 4:22 PM Subject: AG2PI seed grant applications open! To: Scott, Nicole M [AGRON] <nmscott(a)iastate.edu> Dear Colleagues and AG2PI Community Members, A major goal of the Agricultural Genome to Phenome Initiative (AG2PI <https://ag2pi.org/>) is to bring together agricultural scientists across disciplines to work together in addressing shared challenges in genome-to-phenome. As such, we have launched a *seed grant program* to foster first steps towards the development of community solutions to research needs and opportunities, as well as gaps in physical infrastructure and data management. The AG2PI seed grant program aims to fund around six (6) awards, each up to $20,000. Applications will be due by 5pm CST on Friday, March 19th. The anticipated start date for funded projects is May 15, 2021 and each project may be 6-12 months in duration. Further details regarding the request for proposals, application and review can be found at the AG2PI website ( https://ag2pi.org). AG2PI will be hosting a Seed Grant Conference on February 24 from 10:30am-12:30pm CST. This conference will provide an overview of the seed grant mechanism, examples of how seed grants have improved or advanced a scientific endeavor or community and will provide an opportunity to ask questions regarding the seed grants. Additionally, there will be a “teaming” event which will create the virtual space to discuss your seed grant idea with like-minded researchers with whom you may want to work. For the full conference agenda, please see the “Workshops & Activities” page of the AG2PI website. We invite you to register for this mini-conference at https://www.ag2pi.org/workshops-and-activities/conference-2021-02-24/. Upon registration, you will receive a confirmation email with information about joining the meeting. A link to join the meeting will also be provided the day of the event on the AG2PI website. If you are unable to attend the live session, then you will be able to find a recording at ag2pi.org/ <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.ag2pi.org_&d=DwMFA…>, at a later date. Space IS limited, so register soon. Feel free to share this message with colleagues at your institution. If you have any questions regarding the mini-conference or seed grants, please direct them to Nicole Scott at nmscott(a)iastate.edu. 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/>

4 years, 6 months

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