Greetings!
I hope you are doing well. Below are the details of the *May 5th AgBioData webinar*, we look forward to seeing you and hope your schedule allows you to join us *next* 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
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*Wednesday, May 5th, 2021*Hosted by Monica Poelchau 1 hour | 1P ET | 12P CT | 11A MT | 10A PT Find your local time: http://bit.ly/3856d6Y
https://iastate.zoom.us/j/91906292999?pwd=NlZrK0lUNjlPRVZxZ0JBSlB4ZXF0QT09 Or, go to https://iastate.zoom.us/join and enter meeting ID: 919 0629 2999 and password: 294711
Join from dial-in phone line: Dial: +1 312 626 6799 or +1 646 876 9923 Meeting ID: 919 0629 2999 +13126266799,,91906292999,,,,,,0#,,294711 +16468769923,,91906292999,,,,,,0#,,294711 Participant ID: Shown after joining the meeting International numbers available: https://iastate.zoom.us/u/aJkMOd9A
*Recommendations from the AgBioData GFF3 working group*
Over a year ago, AgBioData convened a discussion on GFF3 formatting issues, led by Scott Cain. This discussion led us to form the AgBioData GFF3 working group. Our goals are to 1) identify common problems with the GFF3 format; 2) recommend solutions for these problems; and 3) promote community adoption of these recommendations, so that data can be formatted in standard ways across databases. Members of AgBioData, the Alliance of Genome Resources, and NCBI have been working on these goals for the past year. We are now ready to receive feedback from the AgBioData community on our recommendations, in order to get traction on the final goal – community adoption of these solutions.
In this webinar, we will give an overview of our recommendations and will open up the floor for a stimulating discussion. If possible, please review our recommendations prior to the webinar: https://docs.google.com/document/d/180g1rfC5n_cR6sioG_LFGaUPNmQyDqTsPafVu4gM...
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Past webinars can be found here. https://www.youtube.com/channel/UCwMIJWOX7n_ZFoFpOsmCzgw/videos
Greetings!
A friendly reminder of the *May 5th AgBioData webinar*, we look forward to seeing you and hope your schedule allows you to join us *tomorrow*!
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
•• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• ••
*Wednesday, May 5th, 2021*Hosted by Monica Poelchau 1 hour | 1P ET | 12P CT | 11A MT | 10A PT Find your local time: http://bit.ly/3856d6Y
https://iastate.zoom.us/j/91906292999?pwd=NlZrK0lUNjlPRVZxZ0JBSlB4ZXF0QT09 Or, go to https://iastate.zoom.us/join and enter meeting ID: 919 0629 2999 and password: 294711
Join from dial-in phone line: Dial: +1 312 626 6799 or +1 646 876 9923 Meeting ID: 919 0629 2999 +13126266799,,91906292999,,,,,,0#,,294711 +16468769923,,91906292999,,,,,,0#,,294711 Participant ID: Shown after joining the meeting International numbers available: https://iastate.zoom.us/u/aJkMOd9A
*Recommendations from the AgBioData GFF3 working group*
Over a year ago, AgBioData convened a discussion on GFF3 formatting issues, led by Scott Cain. This discussion led us to form the AgBioData GFF3 working group. Our goals are to:
1) identify common problems with the GFF3 format; 2) recommend solutions for these problems; and 3) promote community adoption of these recommendations, so that data can be formatted in standard ways across databases.
Members of AgBioData, the Alliance of Genome Resources, and NCBI have been working on these goals for the past year. We are now ready to receive feedback from the AgBioData community on our recommendations, in order to get traction on the final goal – community adoption of these solutions.
In this webinar, we will give an overview of our recommendations and will open up the floor for a stimulating discussion. If possible, please review our recommendations prior to the webinar: https://docs.google.com/document/d/180g1rfC5n_cR6sioG_LFGaUPNmQyDqTsPafVu4gM...
•• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• ••
Past webinars can be found here. https://www.youtube.com/channel/UCwMIJWOX7n_ZFoFpOsmCzgw/videos
Greetings!
Over the past couple of months at the monthly webinars, we have been talking about and asking for input on two organizational documents; Code of Conduct https://www.agbiodata.org/code-of-conduct/, and a Privacy https://www.agbiodata.org/privacy/ statement. After careful review and consideration, both have been adopted by the Steering Committee and posted on the website.
With these two documents in place, the AgBioData Slack workspace is now open to all in the AgBioData community, and hope you will join us. The link to join can be found at https://www.agbiodata.org/ | Community | Join AgBioData Slack or by clicking here https://www.agbiodata.org/join-slack. Our hope is that this will become another avenue to connect you with other data professionals for thoughtful exchanges, and a forum to ask questions and engage on a real-time basis.
Below are the details of the *June 2nd AgBioData webinar*, we look forward to seeing you and hope your schedule allows you to join us *next* Wednesday.
All the best,
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
•• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• ••
*Wednesday, June 2nd, 2021*Hosted by Lisa Harper 1 hour | 1P ET | 12P CT | 11A MT | 10A PT Find your local time: https://bit.ly/3oUUkqK http://bit.ly/3856d6Y
https://iastate.zoom.us/j/91906292999?pwd=NlZrK0lUNjlPRVZxZ0JBSlB4ZXF0QT09 Or, go to https://iastate.zoom.us/join and enter meeting ID: 919 0629 2999 and password: 294711
Join from dial-in phone line: Dial: +1 312 626 6799 or +1 646 876 9923 Meeting ID: 919 0629 2999 +13126266799,,91906292999,,,,,,0#,,294711 +16468769923,,91906292999,,,,,,0#,,294711 Participant ID: Shown after joining the meeting International numbers available: https://iastate.zoom.us/u/aJkMOd9A
*Lisa Harper with MaizeGDB: Dealing with gene models from 50 different reference genomes. A progress report from MaizeGDB.* MaizeGDB now hosts over 50 reference quality genome assemblies and their associated gene model sets and metadata. We have started to use a “Pan-Gene” concept to group syntelogs. We define a pan-gene as the set of gene models from multiple genomes that appear to represent the same gene. After I show you how we are implementing this at MaizeGDB, let's have a discussion about how other databases are dealing with this gene model explosion.
•• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• ••
Past webinars can be found here. https://www.youtube.com/channel/UCwMIJWOX7n_ZFoFpOsmCzgw/videos
Greetings!
*This is a reminder of our monthly webinar happening tomorrow.*
Over the past couple of months at the monthly webinars, we have been talking about and asking for input on two organizational documents; Code of Conduct https://www.agbiodata.org/code-of-conduct/, and a Privacy https://www.agbiodata.org/privacy/ statement. After careful review and consideration, both have been adopted by the Steering Committee and posted on the website.
With these two documents in place, the AgBioData Slack workspace is now open to all in the AgBioData community, and hope you will join us. The link to join can be found at https://www.agbiodata.org/ | Community | Join AgBioData Slack or by clicking here https://www.agbiodata.org/join-slack. Our hope is that this will become another avenue to connect you with other data professionals for thoughtful exchanges, and a forum to ask questions and engage on a real-time basis.
Below are the details of the *June 2nd AgBioData webinar*, we look forward to seeing you and hope your schedule allows you to join us *tomorrow*.
All the best,
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
•• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• ••
*Wednesday, June 2nd, 2021*Hosted by Lisa Harper 1 hour | 1P ET | 12P CT | 11A MT | 10A PT Find your local time: https://bit.ly/3oUUkqK http://bit.ly/3856d6Y
https://iastate.zoom.us/j/91906292999?pwd=NlZrK0lUNjlPRVZxZ0JBSlB4ZXF0QT09 Or, go to https://iastate.zoom.us/join and enter meeting ID: 919 0629 2999 and password: 294711
Join from dial-in phone line: Dial: +1 312 626 6799 or +1 646 876 9923 Meeting ID: 919 0629 2999 +13126266799,,91906292999,,,,,,0#,,294711 +16468769923,,91906292999,,,,,,0#,,294711 Participant ID: Shown after joining the meeting International numbers available: https://iastate.zoom.us/u/aJkMOd9A
*Lisa Harper with MaizeGDB: Dealing with gene models from 50 different reference genomes. A progress report from MaizeGDB.* MaizeGDB now hosts over 50 reference quality genome assemblies and their associated gene model sets and metadata. We have started to use a “Pan-Gene” concept to group syntelogs. We define a pan-gene as the set of gene models from multiple genomes that appear to represent the same gene. After I show you how we are implementing this at MaizeGDB, let's have a discussion about how other databases are dealing with this gene model explosion.
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Past webinars can be found here. https://www.youtube.com/channel/UCwMIJWOX7n_ZFoFpOsmCzgw/videos
Greetings!
I hope you are doing well and in the full swing of summer. Not sure about you, but it's hard for me to believe we are knocking on the door of August.
Below are the details of the *August 4th AgBioData webinar*, we look forward to seeing you and hope your schedule allows you to join us *next* Wednesday!
Darwin Campbell, AgBioData coordinator on behalf of the AgBioData steering committee
Jacqueline Campbell Ethalinda Cannon Laurel Cooper Lisa Harper Eva Huala Sook Jung Dorrie Main Monica Poelchau Meg Staton Leonore Reiser Marcela K. Tello-Ruiz
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*Wednesday, August 4th, 20211 hour | 1P ET | 12P CT | 11A MT | 10A PT*Find your local time: https://bit.ly/3acKzjB
https://iastate.zoom.us/j/91906292999?pwd=NlZrK0lUNjlPRVZxZ0JBSlB4ZXF0QT09 Or, go to https://iastate.zoom.us/join and enter meeting ID: 919 0629 2999 and password: 294711
Join from dial-in phone line: Dial: +1 312 626 6799 or +1 646 876 9923 Meeting ID: 919 0629 2999 +13126266799,,91906292999,,,,,,0#,,294711 +16468769923,,91906292999,,,,,,0#,,294711 Participant ID: Shown after joining the meeting International numbers available: https://iastate.zoom.us/u/aJkMOd9A
*Interactions between the phenomics and database communities*
Noah Fahlgren and Malia Gehan Donald Danforth Plant Science Center
High-throughput phenotyping has emerged as a promising area in plant, animal, and agricultural sciences that brings together researchers from life sciences, engineering, computer science, data science, mathematics, and other research fields to develop technologies for rapidly and accurately measuring phenotypes using robotics, imaging, and other tools. High-throughput phenotyping can be done at different scales, from cellular to ecological, typically using image-based approaches for data collection and analysis. The development of computer vision and machine learning approaches to extract biologically meaningful measurements from images, including physical, physiological, morphological, and qualitative properties of crops and livestock, is a major activity within the field. Phenotype datasets can be used for a variety of purposes, but in conjunction with large genomic datasets, are a powerful tool for linking phenotype to genotype, training genomic prediction models, and other approaches that integrate genetic, phenotypic, and environmental datasets.
We will introduce our efforts to develop PlantCV ( https://plantcv.danforthcenter.org/), an open-source platform for image-based plant phenotyping, and discuss opportunities for collaboration between the phenomics and database communities.
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Past webinars can be found here. https://www.youtube.com/channel/UCwMIJWOX7n_ZFoFpOsmCzgw/videos
A friendly reminder of the AgBioData Webinar tomorrow. I hope your schedule allows you to join us, other wise you can catch the video on YouTube after it's posted.
All the best!
Darwin
•• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• Greetings!
I hope you are doing well and in the full swing of summer. Not sure about you, but it's hard for me to believe we are knocking on the door of August.
Below are the details of the *August 4th AgBioData webinar*, we look forward to seeing you and hope your schedule allows you to join us *next* Wednesday!
Darwin Campbell, AgBioData coordinator on behalf of the AgBioData steering committee
Jacqueline Campbell Ethalinda Cannon Laurel Cooper Lisa Harper Eva Huala Sook Jung Dorrie Main Monica Poelchau Meg Staton Leonore Reiser Marcela K. Tello-Ruiz
•• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• ••
*Wednesday, August 4th, 20211 hour | 1P ET | 12P CT | 11A MT | 10A PT*Find your local time: https://bit.ly/3acKzjB
https://iastate.zoom.us/j/91906292999?pwd=NlZrK0lUNjlPRVZxZ0JBSlB4ZXF0QT09 Or, go to https://iastate.zoom.us/join and enter meeting ID: 919 0629 2999 and password: 294711
Join from dial-in phone line: Dial: +1 312 626 6799 or +1 646 876 9923 Meeting ID: 919 0629 2999 +13126266799,,91906292999,,,,,,0#,,294711 +16468769923,,91906292999,,,,,,0#,,294711 Participant ID: Shown after joining the meeting International numbers available: https://iastate.zoom.us/u/aJkMOd9A
*Interactions between the phenomics and database communities*
Noah Fahlgren and Malia Gehan Donald Danforth Plant Science Center
High-throughput phenotyping has emerged as a promising area in plant, animal, and agricultural sciences that brings together researchers from life sciences, engineering, computer science, data science, mathematics, and other research fields to develop technologies for rapidly and accurately measuring phenotypes using robotics, imaging, and other tools. High-throughput phenotyping can be done at different scales, from cellular to ecological, typically using image-based approaches for data collection and analysis. The development of computer vision and machine learning approaches to extract biologically meaningful measurements from images, including physical, physiological, morphological, and qualitative properties of crops and livestock, is a major activity within the field. Phenotype datasets can be used for a variety of purposes, but in conjunction with large genomic datasets, are a powerful tool for linking phenotype to genotype, training genomic prediction models, and other approaches that integrate genetic, phenotypic, and environmental datasets.
We will introduce our efforts to develop PlantCV ( https://plantcv.danforthcenter.org/), an open-source platform for image-based plant phenotyping, and discuss opportunities for collaboration between the phenomics and database communities.
•• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• ••
Past webinars can be found here. https://www.youtube.com/channel/UCwMIJWOX7n_ZFoFpOsmCzgw/videos
agbiodata-list@bioinfo.wsu.edu
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Darwin Campbell