[cid:3142e24a-928b-4048-8438-62862b8c6bda] Dear EMBRIOphytes, I hope everyone has settled into the new semester and has been enjoying the new student energy back on campus. Monday afternoon, we'll continue with our biweekly All-Hands Lab meeting with Session II of The Biological Modeling Workflow: A Brief Introduction (details and links below). Thanks to all who developed and submitted figures and videos in consideration for Annual Best Scientific Figure and to those who voted. Results will be announced early next week. Check out the new paper recently published from the Umulis lab on digital cousins as a single optimized model across species! Please see details below from Qing Deng about an opportunity to meet with renowned cell biologist, Dr. Denise Montell, in October, as well as earlier reminders and announcements on the new CalciumInsights tool and making sure your experimental and computational data published as part of EMBRIO projects is properly uploaded and shared to EMBRIO repositories. New Paper on Digital Cousins as single optimized model across species 🧬🐟🪰 “Digital cousins: Simultaneous optimization of one model for BMP signaling in distant relatives reveals essential core” in Computational and Structural Biotechnology from EMBRIO authors Linlin Li and David Umulis: [https://www.csbj.org/cms/10.1016/j.csbj.2025.08.021/asset/f93cec71-7113-47ec...] 📖 Read the full paper: https://doi.org/10.1016/j.csbj.2025.08.021<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.1016%2Fj.csbj.2025.08.021&data=05%7C02%7Cembrio-list%40ecn.purdue.edu%7C57f52913441c4e75f60508ddecb150a2%7C4130bd397c53419cb1e58758d6d63f21%7C1%7C0%7C638926968483789842%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=brSemrsdPUchg0ZGmzRQiMSg1Ddg3HUPvyZq1500UBE%3D&reserved=0> The paper explores how a single mathematical model can capture the conserved and divergent dynamics of BMP signaling in zebrafish and Drosophila. Using multi-objective optimization and introducing the novel concept of Utopian fronts, the team reveals how minimal changes in diffusion-related parameters can reconcile species-specific differences in morphogen gradients. 🔍 Key insights: •A shared core model can fit wild-type data across species. •Mutant conditions require species-specific regulatory extensions. •Diffusion and processing parameters are key drivers of divergence. •The framework enhances cross-species model interpretability and translational relevance. Opportunity to meet with Dr. Montell October 6 - 7 at Purdue (note from Qing Deng) Dear EMBRIO investigators, I am hosting Dr. Denise Montell, a world-renowned cell biologist, in the fall. She will deliver our department's Karling Lecture on Oct 7, 12:30-1:30 pm. She would have some time to meet faculty and students on the 7th and possibly the 6th. Please let me know if you would like to meet her. Each meeting slot will likely be 25-30 minutes. I have attached her Wikipedia page FYI: https://en.wikipedia.org/wiki/Denise_Montell<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fen.wikipedia.org%2Fwiki%2FDenise_Montell&data=05%7C02%7Cembrio-list%40ecn.purdue.edu%7C57f52913441c4e75f60508ddecb150a2%7C4130bd397c53419cb1e58758d6d63f21%7C1%7C0%7C638926968483813411%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=ukPB1%2FJer3F5FrEx5h5kr%2BJnLn6dBpw%2BVa%2FVDn5gvHE%3D&reserved=0> Best, Qing qingdeng@purdue.edu https://www.denglab.us<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.denglab.us%2F&data=05%7C02%7Cembrio-list%40ecn.purdue.edu%7C57f52913441c4e75f60508ddecb150a2%7C4130bd397c53419cb1e58758d6d63f21%7C1%7C0%7C638926968483827488%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=7BTcFqJy%2BzWRUYE27bRKwwMwuavSADE0yJD9q468C9U%3D&reserved=0> EMBRIO All-Hands "Lab Meeting" Session II of The Biological Modeling Workflow: A Brief Introduction Monday, September 8th 3-4pm EDT Zoom link for the semester: https://purdue-edu.zoom.us/j/92061591849?pwd=wclgpzLpzWKsZ9M2XYwM7Kbumaabr3.1&from=addon<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-edu.zoom.us%2Fj%2F92061591849%3Fpwd%3DwclgpzLpzWKsZ9M2XYwM7Kbumaabr3.1%26from%3Daddon&data=05%7C02%7Cembrio-list%40ecn.purdue.edu%7C57f52913441c4e75f60508ddecb150a2%7C4130bd397c53419cb1e58758d6d63f21%7C1%7C0%7C638926968483840934%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=MC2ReTTitcK5R8Jaza1bQrjd8WIk%2BNwv7FhrxbChy8o%3D&reserved=0> Hayden Fennell, Postdoc Fellow at IU in Biocomplexity Institute of the Glazier lab, will continue with session II of The Biological Modeling Workflow: A Brief Introduction. All who are interested are encouraged to check out the modeling template and other resources from Session I on our Box account<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.com%2Fs%2Fvmoaq3w216ye0c78vxhyzmhh0j4vr8mx&data=05%7C02%7Cembrio-list%40ecn.purdue.edu%7C57f52913441c4e75f60508ddecb150a2%7C4130bd397c53419cb1e58758d6d63f21%7C1%7C0%7C638926968483854359%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=ALORPzD4FO0RVnq%2BfYYQvME3Lm3p4eofKOQRn75jJUY%3D&reserved=0> (EMBRIO Institute > All-Hands Meetings Recordings > 2025). If you would like to get input and help in thinking through your biological problem of interest, please reach out to Hayden (haydenfennell@gmail.com) and James Glazier (jaglazier@gmail.com). Description: Computational modeling is becoming more and more ubiquitous in essentially all fields of scientific study. Biology is no exception, although the usefulness of computation in biology can sometimes be less obvious, given the methodological "distance" from practices in wet-lab experimentation. This seminar will discuss the benefits and challenges of computational modeling in biology, as well as provide a computational modeling workflow that can be applied to a wide variety of biological problems. Session II will focus on examples to illustrate the workflow in practice, and a template has been provided for participants to brainstorm how to apply the workflow to their own biological problems of interest. View the materials on Box<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.com%2Fs%2Fvmoaq3w216ye0c78vxhyzmhh0j4vr8mx&data=05%7C02%7Cembrio-list%40ecn.purdue.edu%7C57f52913441c4e75f60508ddecb150a2%7C4130bd397c53419cb1e58758d6d63f21%7C1%7C0%7C638926968483867515%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=vd8ZdSqPV7Xhx6C2%2B3T%2FEu4%2BHYbbBsv%2FvDgHUtJzN6M%3D&reserved=0>. The second part of the lab meeting will offer continued Q&A on the main topic, with potential breakout rooms for small groups wanting to get started on their own modeling template. If you would like to get input and help in thinking through your biological problem of interest before Sept. 8th, please reach out to Hayden Fennell (haydenfennell@gmail.com) and James Glazier (jaglazier@gmail.com). Please see the previous reminders below on the CalciumInsights tool and complying with our data management plan. 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@purdue.edu ________________________________ From: Embrio-list <embrio-list-bounces@ecn.purdue.edu> on behalf of Brent Thomas Ladd <laddb@purdue.edu> Sent: Wednesday, September 3, 2025 4:12 PM To: embrio-list@ecn.purdue.edu <embrio-list@ecn.purdue.edu> Subject: [Embrio-list] Reminders: Vote for Best Sci. Fig., All-Hands Lab next Monday, CalciumInsights on GitHub, Data Management [cid:da855d1d-c6a7-472b-a037-2aa5490c490a] Dear EMBRIO Community, * Open voting ends tomorrow night (Thursday) for choosing the EMBRIO Best Scientific Figure 2025. (view the webpage<https://www.purdue.edu/research/embrio/research/sci-fig-comp.php>) * All-Hands Lab Meeting Monday, September 8th, "Session II: The Biological Modeling Workflow" (Materials for Session I and II<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.com%2Fs%2Fvmoaq3w216ye0c78vxhyzmhh0j4vr8mx&data=05%7C02%7Cembrio-list%40ecn.purdue.edu%7C57f52913441c4e75f60508ddecb150a2%7C4130bd397c53419cb1e58758d6d63f21%7C1%7C0%7C638926968483880988%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=Oz8d3gOXmgtcxrvyAgN6sHp%2FszyG7xODQtvhXbNnmb4%3D&reserved=0>) * CalciumInsights application, led by our members at University of Puerto Rico at Mayagüez, is now available on the Institute's central GitHub (of which we'll be forking more projects, publications, and materials soon): https://github.com/orgs/EMBRIOInstitute/repositories<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Forgs%2FEMBRIOInstitute%2Frepositories&data=05%7C02%7Cembrio-list%40ecn.purdue.edu%7C57f52913441c4e75f60508ddecb150a2%7C4130bd397c53419cb1e58758d6d63f21%7C1%7C0%7C638926968483894257%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=ku1U1zqvJ2t5asA72vMjTmpDBNjx6mNSoXwhG4nUpw0%3D&reserved=0> * Reminder to have your EMBRIO published experimental data uploaded to our central repository (contact Scott Bolton: boltons@purdue.edu<mailto:boltons@purdue.edu>) * For those new(ish) to EMBRIO who would like more details of what our Institute is about, check out our orientation materials on our shared Box Account: https://app.box.com/s/om3brzae0z3o9s3c7x2fhxw6n2h1ipjt<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.com%2Fs%2Fom3brzae0z3o9s3c7x2fhxw6n2h1ipjt&data=05%7C02%7Cembrio-list%40ecn.purdue.edu%7C57f52913441c4e75f60508ddecb150a2%7C4130bd397c53419cb1e58758d6d63f21%7C1%7C0%7C638926968483907496%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=aNORCNcdmjb6GdLV%2BGbD%2BTTarsYSqjpi7%2BuiHwxb%2BiA%3D&reserved=0> Vote for your selections in the 2025 EMBRIO Best Scientific Figure or Video (view the webpage<https://www.purdue.edu/research/embrio/research/sci-fig-comp.php>) It's time to vote on the best scientific figure or video from member submissions. The webpage link above contains the instructions and PowerPoint file of the submissions. Thanks to the graduate students, postdocs, and research scientists who have developed these figures and videos and submitted them for consideration. Voting will be open through next Thursday, September 4th. Division Name ID Slide# Thrust Type II Nilay Kumar/Linlin Li/Chang Ding/David Gazzo/Naomi Ross/Maria Unger PD1 2 CORE + 2 + 3 Figure II Sharon Minsuk PD2 3 CORE + 3 Video II Maria Unger PD3 4 2 Figure I Bakary Samasa G1 5 3 Video I David Gazzo G2 6 2 Figure I Agnes Doszpoly G3 7 1 Figure I Boyu Jiang G4 8 CORE Figure EMBRIO All-Hands "Lab Meeting" Session II of The Biological Modeling Workflow: A Brief Introduction Monday, September 8th 3-4pm EDT Zoom link for the semester: https://purdue-edu.zoom.us/j/92061591849?pwd=wclgpzLpzWKsZ9M2XYwM7Kbumaabr3.1&from=addon<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-edu.zoom.us%2Fj%2F92061591849%3Fpwd%3DwclgpzLpzWKsZ9M2XYwM7Kbumaabr3.1%26from%3Daddon&data=05%7C02%7Cembrio-list%40ecn.purdue.edu%7C57f52913441c4e75f60508ddecb150a2%7C4130bd397c53419cb1e58758d6d63f21%7C1%7C0%7C638926968483925389%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=wNoboVwpMHfv6jJQQXindh%2F3UcWsgPVW1r8lCgAa7LI%3D&reserved=0> Hayden Fennell, Postdoc Fellow at IU in Biocomplexity Institute of the Glazier lab, will continue with session II of The Biological Modeling Workflow: A Brief Introduction. All who are interested are encouraged to check out the modeling template and other resources from Session I on our Box account<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.com%2Fs%2Fvmoaq3w216ye0c78vxhyzmhh0j4vr8mx&data=05%7C02%7Cembrio-list%40ecn.purdue.edu%7C57f52913441c4e75f60508ddecb150a2%7C4130bd397c53419cb1e58758d6d63f21%7C1%7C0%7C638926968483943875%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=WnFzlY%2FmI4VVTHcVeLQ%2B26FCQrZLBPfTVSkOAFVH7oY%3D&reserved=0> (EMBRIO Institute > All-Hands Meetings Recordings > 2025). If you would like to get input and help in thinking through your biological problem of interest, please reach out to Hayden (haydenfennell@gmail.com) and James Glazier (jaglazier@gmail.com). Description: Computational modeling is becoming more and more ubiquitous in essentially all fields of scientific study. Biology is no exception, although the usefulness of computation in biology can sometimes be less obvious, given the methodological "distance" from practices in wet-lab experimentation. This seminar will discuss the benefits and challenges of computational modeling in biology, as well as provide a computational modeling workflow that can be applied to a wide variety of biological problems. Session II will focus on examples to illustrate the workflow in practice, and a template has been provided for participants to brainstorm how to apply the workflow to their own biological problems of interest. View the materials on Box<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.com%2Fs%2Fvmoaq3w216ye0c78vxhyzmhh0j4vr8mx&data=05%7C02%7Cembrio-list%40ecn.purdue.edu%7C57f52913441c4e75f60508ddecb150a2%7C4130bd397c53419cb1e58758d6d63f21%7C1%7C0%7C638926968483961199%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=yd8OECPb8C4gUU2D2UY7YoI4EDqbRsnlUxnivMMfQi0%3D&reserved=0>. The second part of the lab meeting will offer continued Q&A on the main topic, with potential breakout rooms for small groups wanting to get started on their own modeling template. If you would like to get input and help in thinking through your biological problem of interest before Sept. 8th, please reach out to Hayden Fennell (haydenfennell@gmail.com) and James Glazier (jaglazier@gmail.com). Check Out CalciumInsights Application [image] EMBRIO members at University of Puerto Rico at Mayagüez, in collaboration with labs in the Institute, developed CalciumInsights, an interactive application built in R that is designed to analyze tissue-agnostic calcium traces. The tool is now available on the Institute's central GitHub (of which we'll be forking more projects and materials soon): https://github.com/orgs/EMBRIOInstitute/repositories<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Forgs%2FEMBRIOInstitute%2Frepositories&data=05%7C02%7Cembrio-list%40ecn.purdue.edu%7C57f52913441c4e75f60508ddecb150a2%7C4130bd397c53419cb1e58758d6d63f21%7C1%7C0%7C638926968483978303%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=ciPVY8iDFJQ%2BYlkRzXEXSNj1nqrducvGcKcSCepL7jQ%3D&reserved=0> For details, please contact Deiver Suarez (deiver.suarez@upr.edu ), Mauricio Cabrerra (mauricio.cabrera1@upr.edu ) and Clara Isaza (clara.isaza@upr.edu ). EMBRIO Labs: Get Your Experimental Data Associated with EMBRIO Publications Ready and Connected with our Data Management System We have an obligation to make our published data accessible to the broader scientific community. With the fall semester starting up again, now is a great opportunity to begin using OMERO to store your experimental data taken at the microscope. You can store your data with detailed experimental text to keep your images organized with context. This will benefit your science because: * Identifying experiments no longer requires searching image filenames written in your notebook * Original data is stored in a viewable format in a central location * Data can be reviewed by everyone in the lab without downloading a local copy and opening in ImageJ * Comments, tags, and keywords can be annotated at any time that stays with the image(s) * Support for Fiji (ImageJ) is built-in – you can use a plugin to work with the image data directly in OMERO * Image data can be published as a persistent link in PURR for your publications Thanks to the labs who are already adopting OMERO into their workflow. We encourage everyone in EMBRIO who performs microscopy experiments to take advantage of this new tool. We hope it will improve your workflow and make the management of your microscopy data easier. For more information and help getting started, please contact Scott Bolton at boltons@purdue.edu<mailto:boltons@purdue.edu>. 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@purdue.edu
