Computomics: Discussions On Machine Learning Algorithms For Plant Breeding Challenges

In this episode, we talk to Jim Schwartz, Director of Research, Agronomy and PFR and Jason Gahimer, PFR Manager, both working for Beck’s Hybrids about the Practical Farm Research (PFR) program. Learn what the PFR program is, why it is important, and how farmers can get involved. Dive into the origins of the Practical Farm Research (PFR) program, tracing its roots back to 1964 when Sonny Beck started this unbiased research program to help farmers succeed by providing them with reliable information on agronomic practices, equipment, and other inputs.

Jason Gahimer, PFR Manager at Beck’s Hybrids grew up on a small family farm in Milroy, IN. He attended Ball State University and graduated with a degree in Computer Technology. Jason has been with Beck‘s for over 12 years and served in many different roles within the Practical Farm Research department.
Jim Schwartz, Director of Research, Agronomy, and PFR at Beck’s grew up in Southern Indiana and went to Purdue University. His career in the seed business for 38 years has included a 17 year stent with Monsanto. Jim‘s last role there was as the U.S. agronomy lead for the regional brands. He was also a partner and co-owner in a seed company called Icorn that he eventually sold to Monsanto. Jim has been at Beck's for 6 1/2 years.

Links:
https://www.beckshybrids.com/research/practical-farm-research

In this episode Brent Atthill, managing director of RMI Analytics GmbH delves into the fascinating world of barley. Explore the entire supply chain, uncovering the challenges and emerging trends within the industry. Brent provides valuable insights into why having the best quality barley is crucial for the malting process in the brewing industry and gain a better understanding of the role of technology and data in this sector. With his dedication to fostering exchange and sharing best practices, Brent takes the lead in engaging with all stakeholders in the barley network, ensuring a collaborative and thriving industry.

Brent Atthil is an accomplished global professional with over 25 years experience in the grain, malting, and brewing industries, with a proven track record in strategic procurement, team leadership, and business integration. In his current position as principal owner, board member, and managing director for RMI Analytics GmbH, he focuses on driving RMI’s content delivery through their Journal publication, webinars, and global Insights Tours. He is a leader in the development of extensive supply chain strategies designed to deliver continuous, real business value through optimization and a constant challenge to the status quo. Brent is absolutely passionate about agriculture and sustainability!

https://www.rmi-analytics.com/

Hannah Senior is CEO of PBS International, President of NAPB (National Association of Plant Breeders) and a podcast creator. In this episode you will get a glimpse into Hannah’s broad experience. Learn about the process of developing new solutions within PBS International for plant breeding.
On top of that, Hannah shares her story on how she became the first president of the NAPB from outside North America. During her period as president of the NAPB Hannah is focusing on 3 themes: Putting more structure into the organization, fostering exchange with other international plant breeding organizations and communication and advocacy.
Last but not least get to know what made her become a podcast creator and host of the Plant Breeding Stories podcast.

Hannah Senior grew up in a farming community but followed a career into corporate life working with multinational companies, including 5 years with Tesco. She completed an MBA at Stanford University before returning to the UK and agriculture when she acquired PBS International, a company which makes specialist pollination control products for plant breeders and seed producers around the globe.
Hannah’s business career brought her into plant breeding but her contribution to this discipline goes further than PBS International. She has championed communication about plant breeding and highlighting the diversity of perspectives through activities like the podcast series she created called Plant Breeding Stories, and as President of the National Association of Plant Breeders (NAPB).
Hannah’s interest in plant breeding sits alongside her interest in AgriTech entrepreneurship more generally.[nbsp] She holds Board and advisory positions with several AgriTech companies including Crop Health and Protection, the UK’s government-backed Agritech centre for Crops.

PBS International: https://www.pbsinternational.com/

NAPB: https://www.plantbreeding.org/

Podcast - Plant Breeding Stories: https://www.pbsinternational.com/podcast/

Book recommendation: Braiding Sweetgrass from Robin Wall Kimmerer

In this episode Stefan Schmitz, Executive Director of the Crop Trust, gives comprehensive insights on the background, history and purpose of the Crop Trust. Learn how conserving seeds works and how it is ensured that the seeds are safe and secure. What is the difference between seed banks in general and the Svalbard Global Seed Vault? Why is the Global Seed Vault located in Svalbard and what is so extraordinary about it?

Stefan Schmitz joined the Crop Trust as Executive Director in January 2020. He previously worked as Deputy Director-General and Commissioner for the “One World – No Hunger” Initiative at the German Federal Ministry for Economic Cooperation and Development (BMZ). He also chaired the Steering Committee of the Global Agriculture and Food Security Program (GAFSP). For more than 10 years, Stefan was leading the food security, agriculture and rural development work at BMZ. From 2007 until 2009 he worked as senior advisor to the Secretariat of the Organization for Economic Cooperation and Development (OECD) in Paris. Before joining the BMZ in 2001, Stefan held various posts in the German federal administration in the fields of geographical information systems, regional planning and international cooperation on urban issues. He received scholarships of the McCloy Fellowship of the American Council on Germany and of the German Academic Exchange Service. After studying in Bonn and St. Andrews, he graduated from Bonn University in geography and mathematics and received a doctorate in geosciences from the Free University of Berlin in 2000.

More information about the Crop Trust: https://www.croptrust.org/

In this episode, Patrizia Ricca from Computomics gives us comprehensive insights into xSeedScore – a breeders’ tool to develop new crop varieties adjusted to future climates. Learn about how to work with xSeedScore, about the benefits of using machine learning, and how it differs from conventional methods. What data is needed to apply xSeedScore? What role does the interaction between genetics and temperature play for future varieties?

Patrizia Ricca joined Computomics 4 years ago as Bioinformatics Analyst. She studied Plant Molecular Biology and Bioinformatics at the University of Tübingen, graduating at the Center for Plant Molecular Biology and the Max Planck Institute for Developmental Biology, Tübingen. Patrizia has worked in industry and academia in multiple fields. She has comprehensive and unique knowledge in plant biology, genomics, metagenomics, transcriptomics and machine learning. Since beginning of the year 2022, Patrizia is the Scientific Product Manager for xSeedScore – Computomics’ predictive plant breeding technology.

Details xSeedScore: https://computomics.com/services/innovative-plant-breeding.html

In this episode Thomas Lübberstedt a professor of agronomy from Iowa State University shares his research goals focusing on doubled haploid technology in maize breeding. What are the challenges, what did they achieve already and what are the further research plans? How can doubled haploid speed up the process of getting homozygous lines?
A second focus area is on the organic farming industry. Within 2 organic projects, Thomas is working with a sweet corn breeder and a popcorn breeder on different research goals ranging from the use of natural traits instead of GMO to inbred performance under weedy conditions.

Thomas Lübberstedt is Professor and K.J. Frey Chair at the Department of Agronomy, Iowa State University (ISU). Thomas serves as Director of the R.F. Baker Center for Plant Breeding, and the Distance M.S. in Plant Breeding program. He is founder of the Doubled Haploid (DH) Facility, and Faculty Scholar of Plant Sciences Institute at ISU. Thomas served as chair of the Plant Breeding Coordinating Committee (PBCC) in 2016/17. He continued to contribute to the PBCC education objective and was co-host of the 2022 NAPB meeting at ISU.

In this episode Prof. Dr. Dominik Grimm from TUM Campus Straubing and Weihenstephan-Triesdorf University of Applied Sciences gives us insights into CropML, a BMBF funded project. The project evaluates new machine learning techniques for more accurate plant breeding by integrating heterogeneous external factors.  Different phenotype prediction models, including basic genomic selection methods to more advanced deep learning-based techniques have been compared. Learn why advanced models are the future and where the challenges are.

Dominik is heading the Bioinformatics department at TUM Campus Straubing. He received his PhD from Max-Planck-Institute for Intelligent Systems & Max-Planck-Institute for Developmental Biology Tübingen in 2015. Dominik did his PostDoc at ETH Zürich. From there he moved on to TUM where is now Head of Bioinformatics. He receved a prize for Excellence in Teaching two years in a row.

Publication: https://www.frontiersin.org/articles/10.3389/fpls.2022.932512/full

git: https://github.com/grimmlab/easyPheno

In this episode, listen to Anne Buchwalder, an experienced plant breeder for different crops ranging from pea, cantaloupe, sweet and hot pepper to cocoa. Anne shares her view on sustainable agricultural production, what it implies for the consumer but also the impact on the producing country. Learn about the value chain from farmer to customer. The second part of this episode covers the role technology plays for plant breeding and how it can help plant breeders breed forward. Technology has improved over the last 25 years and plant breeders have much more tools in their [nbsp]toolbox available today.

After her graduation in agronomy, Anne started her career as commercial plant breeder. During 13 years she had been in charge of several vegetable breeding programs for different seed companies: processing pea, cantaloup sweet and hot pepper, in Europe and Middle East. In 2010 Anne joined Nestlé group to support the Global sustainable sourcing of cocoa beans -Nestlé Cocoa Plan. In 2018 she took the head of a research institute center specialized in perfume and medicinal plants. Since the pandemic Anne started a freelance consultancy activity. Today she is helping companies in the horticultural sector to structure their R[&]D teams and to broaden their expertise to achieve their goals to support more sustainable practices and resilient cropping systems.

To shorten the summer break we take a quick look back what we covered in the last season and give a preview of what to expect in season 4. We already have a great line-up for the next season, stay tuned and don't miss any episode! If there is anyone out there you would like to listen to with interesting stories in agriculture and technology, let us know. Just send us a short message to podcast@computomics.com.

In this episode, Karsten Borgwardt gives insights into his current research projects. In two examples, Karsten explains how machine learning algorithms are being developed specifically in the medical sector. Learn about the importance of massive amounts of data, and how this data is used to train a machine learning model to predict the probability of a sepsis of individual patients. Understand the various challenges, the importance of big datasets, the importance of validation, and why it’s a huge undertaking to make machine learning in medicine work. Apart from the Sepsis Study hear how Karstens career started in plant genetics and how the field has grown in importance.

In this episode we talk to Tom Koch, research manager at Beck’s Hybrids. Tom talks about the challenges of a mid-size breeding company and gives insights into how technology helps Beck’s stay ahead of competition. Apart from technology, learn what else is important in corn breeding and what role data plays especially for phenotyping.

Learn from Cyrille about the hot topics in consumer foods from food inflation, the shift in consumer behaviour, the long term story of climate change and the reduction of emissions. What is the cause for food inflation and how does geo politics and labor affect the supply chain and with that food inflation? How does the shift in consumer behaviour impact food companies? What is quick commerce? And what role does plant breeding play in consumer foods?

Get to know Dr. Alisa-Noemi Sieber and gain insights into the Wheat Initiative in this episode of the Computomics podcast. What is the idea behind the Wheat Initiative, who is part of it and what are first results? Additionally, learn what a pre-breeders work is and what role the Swabian specialty "Spätzle" played in the work life of Alisa. Last but not least understand what role plant breeding plays to support the UN Sustainability Goals (SDG).

In this episode Sebastian Schultheiss, Managing Director of Computomics, is talking about the new investment of BVC and Amathaon, the impact it has, the technology and why entrepreneurial independence is of highest importance to Computomics.

In this first episode of season 3 we are speaking with Andy LaVigne, the President and CEO of the American Seed Trade Association (ASTA). He tells us how he ended up in agriculture, gives insights on the focus and main challenges of ASTA, explains how the pandemic changed and impacted the seed industry, shares ASTA’s plans for the setup of the CSS & Seed Expo 2021 and much more.

Miguel Rapela talks to us about his career in bridging the divide between intellectual IP and agricultural development in Argentina as well as about the collaboration between UBATEC and Computomics.

In this episode we chat with our Director of Global Business Strategy, Ruth Mayes, on the ways we can support our clients on their journey to success.

Kevin Falk is a recent PhD graduate of Iowa State University where he focused on soybean breeding, plant phenomics and image analytics. In 2019 he started with Corteva Agriscience as an Integrated Field Sciences Research Scientist where he sits on the IFS Global Innovation team. Kevin is also on the National Association of Plant Breeders education committee, has a passion for science communication and enjoys bringing his camera with them wherever he goes. This week we talk about the field of agriculture and innovation and the role that "Big-Ag" plays in driving that innovation.

In this episode we discuss the need to integrate environmental data into phenotype predictions. Our Computomics xSeedScore Scientist Björn leads us through what type of data is needed to untangle complex traits and how a focus on the client's needs is integral in providing data that is actionable and useful.

VITO is an international research organization with the mission of accelerating our path to a more sustainable world through research in the applied technology domain and by utilizing human creativity. We discuss their products for translating remote sensing data to actionable insights for the agricultural sector.

In this podcast we follow up on the questions we received during our December Webinar titled Innovation in Plant Breeding: Advanced machine learning for predictive plant breeding. If interested, please download the webinar: https://computomics.com/webinar-2020.html or listen to the replay https://seedworld.com/seed-world-innovation-webinar-series-advanced-machine-learning-for-predictive-plant-breeding/

Contact Ruth Mayes for further information: rm@computomics.com

Detlef Weigel, Computomics co-founder and Managing Director at the MPI for Developmental Biology discusses his scientific career and where he sees scientific discovery headed in the future. 

In this end of the year episode we look back on lessons from 2020 and look forward to 2021.

This episode dives into a discussion on human psychology and dealing with the instability in our world while moving technology forward.

Max from ConstellR discusses the challenges of integrating and homogenizing earth observation data and the need to make it accessible and usable for agricultural purposes. 

Prof. Dr. Albrecht Melchinger provides a primer on maize breeding and how machine learning capabilities can improve accuracy and prediction capability for complex traits. 

This week we talk to Saskia Biskup, the co-founder of CeGaT, a diagnostic company that's moving the field of human health forward. Their microbiome analysis tools utilize MEGAN6 to bring patients improved understanding of what their metagenomics results really mean.

The final episode in our series on Metagenomics analysis concludes with an interview with Computomics Co-Founder and MEGAN6 author Daniel Huson. We discuss how MEGAN came about, what long-reads sequencing has meant to Metagenomics, and the way forward. 

Dr. Oliver Deusch from Computomics will talk about interactive and reproducible metagenomics data analysis with MORPHEUS. MORPHEUS enables comparative data analysis and storage of hundreds of samples without the need for your own high performance compute infrastructure. It offers interactive and reproducible analysis of taxonomy and function. 

We interview Simone Graef-Hoenninger who is head of CANNABIS-NET on the benefits of international collaborations in agricultural challenges around cannabis and hemp production.

Volkmar is Head of the Department of Photonics and the Environment at the Fraunhofer UMSICHT and he tells us about their guiding principles in making urban farms as efficient as possible. 

Find their most recent project here: https://www.altmarktgarten-oberhausen.de