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Modeling plants to create a 'digital twin'
  • Background
  • What we're looking for
  • What we can offer you
  • Who we are
  • Q&A
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Background

"Digital Twins” are digital representations of real world objects using structured, machine readable data.  

 

Isolated and targeted studies on plants investigate specific conditions, tissues, or species. We see promise in integrating the data from those studies with models in order to create a "Digital Twin", that would provide a holistic picture of plant physiology.  

 

Applications can include plant growth models, understanding of pesticide absorption, distribution, metabolism and excretion (ADME), mode of action, and understanding of resistance development.  

 

A "Digital Twin" solution would enable the creation of customized modeling pipelines over a unitary data and modeling architecture, for example, to identify the role a gene or a set of genes plays in combination with environmental conditions for the occurrence of a certain phenotype. 

 

A "Digital Twin" of a plant would incorporate data and information at different anatomic levels, including data from proteomics, metabolomics, genomics, transcriptomics, as well as comprehensive gene annotation, associated phenotypes, and known interactions with chemicals. This data can be sourced from public databases and literature, but also from internal experiments.  

 

Knowledge graphs excel at capturing the complexity of the real world, and they store information in a way that’s intuitive and are an ideal way to model "digital twin" data.

What we're looking for

BASF is seeking graph-based building and model-querying technologies that can be applied to model plants. We are also looking for large-language models and methods to integrate data from different physiological levels and different plants. We are open to partnering on earlier-stage research to achieve these objectives "from the ground up" or identifying partners with existing solutions.

Solutions of interest include:
  • Graph-based building and querying technologies that can be applied to model plants.
  • Methods to integrate data from different physiological levels and different conditions applicable to plants.
  • Algorithms that combine -omics data (proteomics, metabolomics, genomics, and transcriptomics) and labeled data over different physiological scales, that can be used for segregation of physiological effects in relation to effector or root cause.
  • Large-language models that interact with graph models, applicable to plant biology.
Our nice-to-have's are:
  • Proposals leveraging expertise and tools developed for other systems (human or animal models) that may be adapted to plant systems are welcome.
  • Methods to integrate data from different plants like duckweed (Lemna), Arabidopsis thaliana, Alopecurus myosuroides, Amaranthus palmeri, Glycine max, Brassica napus, and Triticum aestivum.
  • Methods to integrate -omics data (proteomics, metabolomics, genomics, and transcriptomics) from different plants by creating an unified gene ortholog system.
What's out of scope:
  • Human or animal specific models if they cannot be adapted to plants.
  • Models that cannot incorporate -omics (proteomics, metabolomics, genomics, and transcriptomics) data sets.
  • Models that cannot transfer learnings from one model plant to another.
Acceptable technology readiness levels (TRL):
Levels 1-6
What we can offer you
Eligible partnership models:
Sponsored research
Benefits:
Sponsored Research
Funding is proposal dependent, but an accepted proposal could expect support activities for up to one year and in the range of 50,000 - 200,000 USD (milestone dependent) with the potential for follow on funding.
Expertise
Partners will interact with a project lead to mutually develop a project plan and engage in regular meetings to ensure success. Partners will have access to BASF experts as appropriate.
Who we are

As a global chemical company, we operate in diverse markets with varying requirements. To ensure responsible conduct and maintain our license to operate, we are guided by our core values and standards. These values shape our daily actions and foster respectful relationships with colleagues, customers, and partners.

Our teams are committed to putting health and safety first, making sustainability a part of every decision, and meeting strict compliance and environmental standards. We embrace diversity—in people, perspectives, and experiences—and promote open feedback grounded in honesty, respect, and trust. We see setbacks as opportunities to learn and improve.

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Reviewers
Q&A with BASF

The Q&A is now closed.

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Q.
What IP requirements will be put on the outputs? Is it acceptable to produce a fully open source solution?
8
A.
Hello Tim, Thank you for your question, in short, the ability to publish depends upon regional requirements and negotiations, generally however, a model developed on public data can be published. Any model that has been developed on BASF confidential data would not be published.
LJ
Lauren Junker, Technology Scout, BASF
November 29, 2023
Is this response helpful?
1
0
A.
Thanks for the reply. What about the the tooling and architecture of the modelling framework and the conceptual design? I would think those would be the key IP for a project like this, rather than the data they run on. I would think that a well designed general solution should be as agnostic as possible to data for a particular species or domain.
1
A.
Hello Tim, You are correct regarding the architecture. Prior to engaging in sponsored research, IP terms would be negotiated and mutually agreed upon.
LJ
Lauren Junker, Technology Scout, BASF
December 1, 2023
Is this response helpful?
0
0
Q.
What staff costs can be included in a proposal? Applicants including PI, Co-I?
2
A.
Yes, staff costs can be included in the proposal.
LJ
Lauren Junker, Technology Scout, BASF
November 29, 2023
Is this response helpful?
0
0
Q.
Our platform (www.morf-db.org) integrates time-resolved microbial multi-omics data. Would you be interested in developing this for your plant data, in collaboration with a plant modelling expert?
2
A.
Hello Joyce, Thank you for your question, if you believe your platform can be efficiently adapted for multi- omic plant data, we would encourage you to submit a proposal to detail how you would approach this. Thank you for your consideration.
LJ
Lauren Junker, Technology Scout, BASF
October 19, 2023
Is this response helpful?
0
0
Q.
My specialty includes models that predict solubility & partitioning of molecules between complex phases, like biological structures and different cells. Would this be helpful as a collaborator in the larger project?
2
A.
Hello Steve, As you rightly point out, the interaction of a small molecule with plant structures and cells could be a piece of the larger model. Please consider submitting a proposal. Thank you, Lauren
LJ
Lauren Junker, Technology Scout, BASF
October 5, 2023
Is this response helpful?
0
0
Q.
I am currently working on different sorghum research projects in my lab, so can I use the "Sorghum" in my proposal too? It is not mentioned in this section: "Methods to integrate data from different plants like duckweed (Lemna), Arabidopsis thaliana, Alopecurus myosuroides, Amaranthus palmeri, Glycine max, Brassica napus, and Triticum aestivum."
1
A.
Hello Deepti, The focus of this RFP is to develop a digital twin for higher plants. As indicated, if you/ your team can leverage expertise. models and tools developed for sorghum that may be adapted to other plant species these proposals are welcome.
LJ
Lauren Junker, Technology Scout, BASF
November 13, 2023
Is this response helpful?
1
0
Q.
What deliverables do you expect in this project?
1
A.
Hello Christian, We would expect a software model, documentationand relevant algorithms to be delivered, including the source coding language in a popular programming language.
LJ
Lauren Junker, Technology Scout, BASF
November 29, 2023
Is this response helpful?
0
0
Q.
What is the timeframe for the proposed projects? Just to have an order of magnitude and adapt my proposal accordingly (especially if I will have enough time to generate experimental data.)
1
A.
Hello Carlos, We anticipate that the accepted proposal(s) could expect support activities for up to one year and in the range of 50,000 - 200,000 USD (milestone dependent) with the potential for follow on funding and extended duration.
LJ
Lauren Junker, Technology Scout, BASF
November 27, 2023
Is this response helpful?
0
0
Q.
This is for higher plants, yes? Will there likely be something similar for microalgae?
1
A.
Hello Kevin, The focus of this RFP is to develop a digital twin for higher plants. As indicated, if you/ your team can leverage expertise and tools developed for other systems that may be adapted to higher plant systems these proposals are welcome.
LJ
Lauren Junker, Technology Scout, BASF
November 10, 2023
Is this response helpful?
0
0
Q.
We consider a digital twin of wheat as a 3D representation of a wheat plot. So, the current TLR of the study does not include -omic data but has a high potential to be incorporated into the next steps. Will you consider?
1
A.
Hello Željana, We are interested in models which emphasize the integration of multi-omics and explore responses at the physiological level more so than at field level. We encourage you to submit a proposal.
LJ
Lauren Junker, Technology Scout, BASF
November 30, 2023
Is this response helpful?
1
0
Q.
Greetings, I am a Research Scientist currently affiliated with Dr. Jiao's research team at TTU. My current research focuses on a distinct Sorghum project that involves the utilization of machine learning techniques. I am inquiring whether it is permissible to utilize publicly accessible data for this particular project as part of my application process.
1
A.
Hello Deepti, Yes, leveraging public data is permissible. We look forward to reviewing your proposal.
LJ
Lauren Junker, Technology Scout, BASF
November 10, 2023
Is this response helpful?
1
0
Q.
My previous research identifies liquids using wireless signals. The ideas could be used to study leaf health, including the water level and drying of leaves. This could be used as part of digital twin. Will you consider?
1
A.
Hello Ashutosh, Thank you for your question and bringing awareness about your sensor technology. Through our RFP we are interested in gaining knowledge graph experience to inform the development of a digital twin. If you have experience with developing this with your sensors, please consider submitting a proposal. Thank you for your consideration.
LJ
Lauren Junker, Technology Scout, BASF
October 19, 2023
Is this response helpful?
0
0
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