[Embrio-list] EMBRIO all-hands today 3pm "Maximize the Information Content of Experiments" + Biological Sciences seminar at 11:30am

[Ladd, Brent Thomas]

Dear EMBRIO,

Don't miss our EMBRIO all-hands seminar today at 3PM ET featuring Alexander Dowling, Ph.D., Chemical and Biomolecular Engineering (primary), Applied & Computational Mathematics & Statistics (concurrent), University of Notre Dame. Alex's talk, "Maximize the Information Content of Experiments" will present modern mathematical and computational tools to optimize experiments, leveraging these methods in systems biology contexts (Abstract and zoom link below). Please check out the recommended reading resources listed below the abstract!

Also, check out the Biological Sciences Seminar, Purdue University this morning at 11:30AM ET on "Using Systems and Systems Thinking to Unify Biology Education" with Jennifer Momsen, Ph.D.., North Dakota State University (abstract  and zoom link below).

Cheers,
Brent

Brent T. Ladd, Senior Research Program Manager, EMBRIO Institute<https://www.purdue.edu/research/embrio/>
Weldon School of Biomedical Engineering, Purdue University
Office: Hall for Discovery Learning and Research, Ste. 203
207 S. Martin Jischke Drive
West Lafayette, IN 47907
laddb at purdue.edu
-----------------------------------


Title: Maximize the Information Content of Experiments

Alexander Dowling, Ph.D., University of Notre Dame
EMBRIO Institute Fall Seminar Series
November 11th, 3PM ET
Join Zoom Meeting:
https://purdue-edu.zoom.us/j/99105530025?pwd=wPuFZtASboXSfD8Y9e4vsbKpcrKl5j.1&from=addon<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-edu.zoom.us%2Fj%2F99105530025%3Fpwd%3DwPuFZtASboXSfD8Y9e4vsbKpcrKl5j.1%26from%3Daddon&data=05%7C02%7Cembrio-list%40ecn.purdue.edu%7C4e639c8b0c5540d7e38a08dd02599f18%7C4130bd397c53419cb1e58758d6d63f21%7C0%7C0%7C638669306129291930%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=au67bCrsu94kSOE01dOhRe7%2FFHKBklfBwGSRuleUmhs%3D&reserved=0>

Meeting ID: 991 0553 0025
Passcode: 469678


Abstract: In this talk, I will present modern mathematical and computational tools to optimize experiments. I will overview methods for different modeling paradigms, ranging from Bayesian optimization using purely data-driven models, optimal experiment design using science-based mathematical models, and hybrid approaches that use data-driven components (e.g., Gaussian processes) to correct model-form uncertainty in mechanistic models. While most of the examples we will discuss focus on energy and manufacturing applications, the computational approaches are generalized and domain agnostic. I will conclude by describing some ongoing collaborative work with Prof. Jeremy Zartman and colleagues at Notre Dame to leverage these methods in systems biology contexts.

Recommended Reading (organized by topic):

Bayesian Optimization (purely data-driven):
https://www.sciencedirect.com/science/article/pii/S2211339821000605<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.sciencedirect.com%2Fscience%2Farticle%2Fpii%2FS2211339821000605&data=05%7C02%7Cembrio-list%40ecn.purdue.edu%7C4e639c8b0c5540d7e38a08dd02599f18%7C4130bd397c53419cb1e58758d6d63f21%7C0%7C0%7C638669306129448195%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=aeZwMkeU1Tann3xjZy%2FljgWGWZ5qIL0T%2FaC6Vg2L208%3D&reserved=0>
https://pubs.rsc.org/en/content/articlelanding/2022/EE/D2EE01844F<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpubs.rsc.org%2Fen%2Fcontent%2Farticlelanding%2F2022%2FEE%2FD2EE01844F&data=05%7C02%7Cembrio-list%40ecn.purdue.edu%7C4e639c8b0c5540d7e38a08dd02599f18%7C4130bd397c53419cb1e58758d6d63f21%7C0%7C0%7C638669306129448195%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=SGWe%2BxIqEmATVbNUVEjkYUGtC1rurEXX1YkPJDDh%2FFk%3D&reserved=0>
https://doi.org/10.1002/adma.202212230<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.1002%2Fadma.202212230&data=05%7C02%7Cembrio-list%40ecn.purdue.edu%7C4e639c8b0c5540d7e38a08dd02599f18%7C4130bd397c53419cb1e58758d6d63f21%7C0%7C0%7C638669306129448195%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=ZchtO6R1PygYGwf3yNpJcbUUh11WWCdclqxngVn%2FceY%3D&reserved=0>
https://pubs.rsc.org/en/content/articlelanding/2024/ee/d4ee00866a<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpubs.rsc.org%2Fen%2Fcontent%2Farticlelanding%2F2024%2Fee%2Fd4ee00866a&data=05%7C02%7Cembrio-list%40ecn.purdue.edu%7C4e639c8b0c5540d7e38a08dd02599f18%7C4130bd397c53419cb1e58758d6d63f21%7C0%7C0%7C638669306129604400%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=EyrqdIPuBu0qakmIEpKNXKqVBl0diinbnZVYOqYzHM4%3D&reserved=0>
https://pubs.acs.org/doi/10.1021/acsami.4c07936<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpubs.acs.org%2Fdoi%2F10.1021%2Facsami.4c07936&data=05%7C02%7Cembrio-list%40ecn.purdue.edu%7C4e639c8b0c5540d7e38a08dd02599f18%7C4130bd397c53419cb1e58758d6d63f21%7C0%7C0%7C638669306129604400%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=UwWkww3wpr0pd%2FxaMsudeElOXoYGkRMQe3ciUnx%2B0LE%3D&reserved=0>

Optimal Experiment Design (mechanistic models):
https://aiche.onlinelibrary.wiley.com/doi/abs/10.1002/aic.17813<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Faiche.onlinelibrary.wiley.com%2Fdoi%2Fabs%2F10.1002%2Faic.17813&data=05%7C02%7Cembrio-list%40ecn.purdue.edu%7C4e639c8b0c5540d7e38a08dd02599f18%7C4130bd397c53419cb1e58758d6d63f21%7C0%7C0%7C638669306130229461%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=5tTlSpN65QwbX1Yv8bk7wzIK8F%2F6%2Fi4j67a%2FRQcSYc8%3D&reserved=0>
https://www.sciencedirect.com/science/article/pii/S0378381223001139<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.sciencedirect.com%2Fscience%2Farticle%2Fpii%2FS0378381223001139&data=05%7C02%7Cembrio-list%40ecn.purdue.edu%7C4e639c8b0c5540d7e38a08dd02599f18%7C4130bd397c53419cb1e58758d6d63f21%7C0%7C0%7C638669306130229461%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=TkyjThMLr41BlkHYeDo8iNxDbf08wVSVomzeuZZvd%2FE%3D&reserved=0>
https://www.sciencedirect.com/science/article/pii/S0098135424002047<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.sciencedirect.com%2Fscience%2Farticle%2Fpii%2FS0098135424002047&data=05%7C02%7Cembrio-list%40ecn.purdue.edu%7C4e639c8b0c5540d7e38a08dd02599f18%7C4130bd397c53419cb1e58758d6d63f21%7C0%7C0%7C638669306130385730%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=LB0VD7OM3qkkfhhsvLwyglLhkVUBNo6WAaJZT5E2Xbk%3D&reserved=0>
https://pubs.acs.org/doi/abs/10.1021/acsami.4c11749<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpubs.acs.org%2Fdoi%2Fabs%2F10.1021%2Facsami.4c11749&data=05%7C02%7Cembrio-list%40ecn.purdue.edu%7C4e639c8b0c5540d7e38a08dd02599f18%7C4130bd397c53419cb1e58758d6d63f21%7C0%7C0%7C638669306130385730%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=em4dVemlZ5bh1YY7yuXDczQGdR5d%2FQyllcotGhQbuhQ%3D&reserved=0>

Hybrid Models (mechanistic + data driven):
https://www.sciencedirect.com/science/article/abs/pii/S0098135423003009<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.sciencedirect.com%2Fscience%2Farticle%2Fabs%2Fpii%2FS0098135423003009&data=05%7C02%7Cembrio-list%40ecn.purdue.edu%7C4e639c8b0c5540d7e38a08dd02599f18%7C4130bd397c53419cb1e58758d6d63f21%7C0%7C0%7C638669306130385730%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=wNHFu4UpK65e%2FsdsKfuWEfW83dCVrxypvcRn1bKs93I%3D&reserved=0>


Alexander Dowling, Ph.D.
Associate Professor
Chemical and Biomolecular Engineering (primary)
Applied & Computational Mathematics & Statistics (concurrent)
University of Notre Dame

===========


"Using Systems and Systems Thinking to Unify Biology Education"
Jennifer Momsen, Ph.,D., North Dakota State University
Biological Sciences Seminar Series
November 11th, 11:30AM ET
Join Zoom Meeting:
https://purdue-edu.zoom.us/j/98381460464?pwd=15M68qC6HT9PdEbYE3E13IGAuZqK7z.1&from=addon<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-edu.zoom.us%2Fj%2F98381460464%3Fpwd%3D15M68qC6HT9PdEbYE3E13IGAuZqK7z.1%26from%3Daddon&data=05%7C02%7Cembrio-list%40ecn.purdue.edu%7C4e639c8b0c5540d7e38a08dd02599f18%7C4130bd397c53419cb1e58758d6d63f21%7C0%7C0%7C638669306130385730%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=ZWDs3XW2dqphVYP3jiwL9iHvwm3BJAMJ9v%2F3igVzNUo%3D&reserved=0>

Meeting ID: 983 8146 0464
Passcode: 293433

In-person: Lilly Hall 1-117, Purdue University

Abstract: Thinking in terms of systems is a foundational practice throughout biology but is rarely taught as an explicit objective. Although systems feature prominently in national reports informing life sciences education, there is minimal guidance about specific objectives for systems thinking, relevant strategies for assessing evidence of systems thinking, or instructional approaches that foster the competencies and conceptual knowledge necessary for reasoning about systems. Following a review of interdisciplinary literature on systems and systems thinking, we developed the Biology Systems Thinking (BST) framework, which identifies and describes the requisite skills for thinking about biological systems. In this talk, I will introduce the BST framework and share how this framework can be used to design an integrated introductory biology curriculum and what it reveals about students’ reasoning about biological phenomena.




Brent T. Ladd, Senior Research Program Manager, EMBRIO Institute<https://www.purdue.edu/research/embrio/>
Weldon School of Biomedical Engineering, Purdue University
Office: Hall for Discovery Learning and Research, Ste. 203
207 S. Martin Jischke Drive
West Lafayette, IN 47907
laddb at purdue.edu

-------------- next part --------------
An HTML attachment was scrubbed...
URL: </ECN/mailman/archives/embrio-list/attachments/20241111/3dec199a/attachment-0001.htm>