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Events Reminders and Thrust 4 Seminar today 3pm, Magana Lab - "The Role of Teamwork in Computational Modeling: Opportunities for Interdisciplinary Learning"
by Ladd, Brent Thomas 19 May '25

19 May '25

Dear EMBRIOphytes, Thrust 4 Seminar Today 3pm EDT - Magana Lab - "The Role of Teamwork in Computational Modeling: Opportunities for Interdisciplinary Learning" Join us this afternoon for research updates from Thrust 4 Pedagogical Research, Training, and Outreach Zoom Link: https://purdue-edu.zoom.us/j/97946412458?pwd=YUurFKck0n1am07eA7b0O0TVKsVwpC…<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…> EMBRIO Summer Events Items: The 2025 Summer School Schedule<https://www.purdue.edu/research/embrio/workforce-development/EMBRIO-summer-…> Attendees - we have added a CompuCell3D Virtual Tissue Modeling (CC3D) Introductory mini-workshop and, in addition, may be able to offer a 2-hour Tissue Forge<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcompucell…> introductory mini-workshop on Day 3 of the School. Please reach out to me by EOB today (Brent: laddb(a)purdue.edu) if you would like to participate in the Tissue Forge session. Please Respond by the Deadlines: For attendees at our upcoming Summer School (June 9-11), and Annual Retreat (June 12-13), there are three related items that require your attention: Required by June 1st: Research Posters at Annual Retreat: For those who will present a research poster - upload your abstract with full citation, along with a 1-slide PowerPoint to use for your 1-min lightning talk to introduce your poster prior to the session: https://purdue.ca1.qualtrics.com/jfe/form/SV_6YxLsL2atyabFvo<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue.ca…> Entries for 2025 Best Scientific Figure or Live Video Awards https://purdue.ca1.qualtrics.com/jfe/form/SV_9X3KHxUUz0bg6Pk<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue.ca…> ) The annual retreat schedule will be finalized soon. We aim to start at 8:30am on June 9th for the Summer School, and the same 8:30am on June 12th for the Annual Retreat, ending at lunch on Friday the 13th. For those traveling to Purdue from our Partners, Jennifer Goad has been in touch with you regarding logistics with hotel, parking, etc. If you may have missed her email, you can reach Jen via email: goad3(a)purdue.edu EMBRIO Competencies Pilot: For those interested in working with the Gardner lab on implementing the Institute competencies for their use case, please contact Stephanie Gardner: sgardne(a)purdue.edu EMBRIO Trainees: 2025 CompuCell3D Virtual Tissue Modeling Workshop and Hackathon Our partners at I.U. in the Glazier Lab and Biocomplexity Institute have announced the 2025 CompuCell3D Virtual Tissue Modeling Workshop and Hackathon at Indiana University, Bloomington, July 28th to August 10th, 2025. Learn to model your biological system of interest with one-on-one help. Week 1 will cover CC3D basics. Week 2 will cover advanced topics in CC3D, followed by a 2-day model-building hackathon. Physicists, biologists, computer scientists, and modelers team up to build research-grade models of biological systems. All experience levels are welcome. For more information, email compucell3d.iu(a)gmail.com<mailto:compucell3d.iu@gmail.com> or visit www.compucell3d.org/Workshop25<https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.compuc…>. Register at: www.tinyurl.com/CC3D2025<https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.tinyur…>. 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(a)purdue.edu

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Thrust 4 Seminar Monday and Summer School/Annual Retreat Details
by Ladd, Brent Thomas 16 May '25

16 May '25

Dear EMBRIOphytes, Thrust 4 Seminar Monday May 19th - Magana Lab - "The Role of Teamwork in Computational Modeling: Opportunities for Interdisciplinary Learning" Next Monday, May 19th 3-4PM EDT, we wrap up the spring semester seminar series with a presentation led by the Magana lab on Thrust 4 projects. Zoom Link: https://purdue-edu.zoom.us/j/97946412458?pwd=YUurFKck0n1am07eA7b0O0TVKsVwpC…<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…> EMBRIO Summer Events Items The 2025 Summer School Schedule<https://www.purdue.edu/research/embrio/workforce-development/EMBRIO-summer-…> Attendees - we have added a CompuCell3D Virtual Tissue Modeling (CC3D) Introductory mini-workshop and, in addition, may be able to offer a 2-hour Tissue Forge<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcompucell…> introductory mini-workshop on Day 3 of the School. Please reach out to me by early next week (Brent: laddb(a)purdue.edu) if you definitely would like to participate in the Tissue Forge session. Please Respond by the Deadlines: For attendees at our upcoming Summer School (June 9-11), and Annual Retreat (June 12-13), there are three related items that require your attention: By EOB Today: If you have a dietary restriction or disability for which you request accommodations - we need this information returned by this Friday, May 16th via this quick survey (if you don't have either, there is no need to complete the survey): https://purdue.ca1.qualtrics.com/jfe/form/SV_db7D8ZNLmHL7cJo<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue.ca…> Required by June 1st: Research Posters at Annual Retreat: For those who will present a research poster - upload your abstract with full citation, along with a 1-slide PowerPoint to use for your 1-min lightning talk to introduce your poster prior to the session: https://purdue.ca1.qualtrics.com/jfe/form/SV_6YxLsL2atyabFvo<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue.ca…> Entries for 2025 Best Scientific Figure or Live Video Awards (see attached for details. submission here: https://purdue.ca1.qualtrics.com/jfe/form/SV_9X3KHxUUz0bg6Pk<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue.ca…> ) Annual Retreat schedule will be finalized soon. We aim to start at 8:30am on June 9th for the Summer School, and the same 8:30am on June 12th for the Annual Retreat, ending at lunch on Friday the 13th. For those traveling to Purdue from our Partners, Jennifer Goad has been in touch with you regarding logistics with hotel, parking, etc. If you may have missed her email, you can reach her via email: goad3(a)purdue.edu EMBRIO Competencies Pilot: For those interested in working with the Gardner lab on implementing the Institute competencies for their use case, please contact Stephanie Gardner: sgardne(a)purdue.edu EMBRIO Trainees: 2025 CompuCell3D Virtual Tissue Modeling Workshop and Hackathon Our partners at I.U. in the Glazier Lab and Biocomplexity Institute have announced the 2025 CompuCell3D Virtual Tissue Modeling Workshop and Hackathon at Indiana University, Bloomington, July 28th to August 10th, 2025. Learn to model your biological system of interest with one-on-one help. Week 1 will cover CC3D basics. Week 2 will cover advanced topics in CC3D, followed by a 2-day model-building hackathon. Physicists, biologists, computer scientists, and modelers team up to build research-grade models of biological systems. All experience levels are welcome. For more information, email compucell3d.iu(a)gmail.com<mailto:compucell3d.iu@gmail.com> or visit www.compucell3d.org/Workshop25<https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.compuc…>. Register at: www.tinyurl.com/CC3D2025<https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.tinyur…>. 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(a)purdue.edu

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EMBRIO Announcements - Thrust 4 Magana Lab May 19th, Summer Events Deadlines, Competencies Pilot
by Ladd, Brent Thomas 12 May '25

12 May '25

Dear EMBRIOphytes, Hope that everyone's semesters have crossed the finish line. As we enter summer session, please give your attention to several announcements for upcoming events: Thrust 4 Seminar Monday May 19th Next Monday, May 19th 3-4PM EDT, we wrap up the spring semester seminar series with a presentation led by the Magana lab on Thrust 4 projects. If you missed last week's seminar on the Thrust 4 research into the EMBRIO Community of Practice and Institute Competencies, or any of our previous seminars you can access those on our shared Box account under All Hands Meeting Recordings and select the year you are looking for. (2025 seminars: https://app.box.com/s/ml2ftp0oyj7cthx12p0uq1krvypruydh<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> ). EMBRIO Summer Events Items - Please Respond by the Deadlines: For attendees at our upcoming Summer School (June 9-11), and Annual Retreat (June 12-13), there are three related items that require your attention: By today, May 12th: If you have not RSVP, please do so via this link: https://purdue.ca1.qualtrics.com/jfe/form/SV_d5oR3KzZcHjj7Ui<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue.ca…> . By May 16th: If you have a dietary restriction or disability for which you request accommodations - we need this information returned by this Friday, May 16th via this quick survey (if you don't have either, there is no need to complete the survey): https://purdue.ca1.qualtrics.com/jfe/form/SV_db7D8ZNLmHL7cJo<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue.ca…> Required by June 1st: Research Posters at Annual Retreat: For those who will present a research poster - upload your abstract with full citation, along with a 1-slide PowerPoint to use for your 1-min lightning talk to introduce your poster prior to the session: https://purdue.ca1.qualtrics.com/jfe/form/SV_6YxLsL2atyabFvo<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue.ca…> Entries for 2025 Best Scientific Figure or Live Video Awards (see attached for details. submission here: https://purdue.ca1.qualtrics.com/jfe/form/SV_9X3KHxUUz0bg6Pk<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue.ca…> ) The Summer School and Annual Retreat Full schedules will be finalized soon. We aim to start at 8:30am on June 11th for the Summer School, and the same 8:30am on June 12th for the Annual Retreat, ending at lunch on Friday the 13th. For those traveling to Purdue from our Partners, Jennifer Goad, has been in touch with you regarding logistics with hotel, parking, etc. If you may have missed her email, you can reach her via email: goad3(a)purdue.edu EMBRIO Competencies Pilot: For those interested in working with the Gardner lab on implementing the Institute competencies for their use case, please contact Stephanie Gardner: sgardne(a)purdue.edu EMBRIO Trainees: 2025 CompuCell3D Virtual Tissue Modeling Workshop and Hackathon Our partners at I.U. in the Glazier Lab and Biocomplexity Institute have announced the 2025 CompuCell3D Virtual Tissue Modeling Workshop and Hackathon at Indiana University, Bloomington, July 28th to August 10th, 2025. Learn to model your biological system of interest with one-on-one help. Week 1 will cover CC3D basics. Week 2 will cover advanced topics in CC3D, followed by a 2-day model-building hackathon. Physicists, biologists, computer scientists, and modelers team up to build research-grade models of biological systems. All experience levels are welcome. For more information, email compucell3d.iu(a)gmail.com<mailto:compucell3d.iu@gmail.com> or visit www.compucell3d.org/Workshop25<https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.compuc…>. Register at: www.tinyurl.com/CC3D2025<https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.tinyur…>. 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(a)purdue.edu

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General start and end times for EMBRIO Summer School and Annual Retreat
by Ladd, Brent Thomas 09 May '25

09 May '25

Dear EMBRIOphytes, I hope this finds everyone doing well and your respective semesters are wrapping up positively. A quick note on planning for general start and end times for our summer events at Purdue during June 9-13. The summer school we'll start early on Monday morning, and wrap up on Wednesday at lunch or just after lunch for a break before annual retreat starts. Annual retreat we'll start early Thursday - probably 8:30, and we aim to end at lunch time on Friday. I'm finalizing sessions and schedules next week. Stay tuned for those. For our Partners traveling into Purdue: Jennifer Goad has been/will be in contact with you to arrange those logistics for lodging, etc. Thanks! 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(a)purdue.edu

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EMBRIO Thrust 4 seminar 3PM EDT today - Institute Competencies
by Ladd, Brent Thomas 05 May '25

05 May '25

Dear EMBRIOphytes, Join us this afternoon at 3pm EDT for our all-hands seminar focused on Institute competencies and their implementation as part of Thrust 4 research and practice led by the Gardner lab: Zoom link: https://purdue-edu.zoom.us/j/97946412458?pwd=YUurFKck0n1am07eA7b0O0TVKsVwpC…<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…> Best, 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(a)purdue.edu

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May 5th Institute Competencies Seminar led by the Gardner Lab
by Ladd, Brent Thomas 02 May '25

02 May '25

Dear EMBRIOphytes, Join us next Monday, May 5th at 3pm EDT for our all-hands seminar focused on Institute competencies and their implementation as part of Thrust 4 research and practice led by the Gardner lab: https://purdue-edu.zoom.us/j/97946412458?pwd=YUurFKck0n1am07eA7b0O0TVKsVwpC…<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…> BTW, Congrats to Stephanie Gardner for being promoted to Full Professor in Department of Biological Sciences, Purdue University!! EMBRIO Investigators, Trainees, and Research Scientists: Get your entries in for the EMBRIO Best Paper Competition (first author/co-author as EMBRIO graduate student, postdoc, or staff research scientist - papers published between 9/1/2021 and now are eligible). We ask that you submit your nominations by this weekend at the latest. Details are attached. Best Paper Nomination submission: https://purdue.ca1.qualtrics.com/jfe/form/SV_0GUgolkEbJKjm2W<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue.ca…> Entries for Best Scientific Figure are also now open! (deadline June 1) Please see the attached for details and submission link. Summer School & Annual Retreat Thanks to all who have submitted your RSVP for the upcoming Summer School and Annual Meeting. We will be in touch next week with those of you traveling to Purdue regarding lodging, parking, and other logistics. Those planning to present a poster, stay tuned for instructions in the next two weeks. EMBRIO Trainees: 2025 CompuCell3D Virtual Tissue Modeling Workshop and Hackathon Our partners at I.U. in the Glazier Lab and Biocomplexity Institute have announced the 2025 CompuCell3D Virtual Tissue Modeling Workshop and Hackathon at Indiana University, Bloomington, July 28th to August 10th, 2025. Learn to model your biological system of interest with one-on-one help. Week 1 will cover CC3D basics. Week 2 will cover advanced topics in CC3D, followed by a 2-day model-building hackathon. Physicists, biologists, computer scientists, and modelers team up to build research-grade models of biological systems. All experience levels are welcome. For more information, email compucell3d.iu(a)gmail.com<mailto:compucell3d.iu@gmail.com> or visit www.compucell3d.org/Workshop25<https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.compuc…>. Register at: www.tinyurl.com/CC3D2025<https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.tinyur…>. 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(a)purdue.edu

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EMBRIO Announcements - Nominations for Best Paper, RSVP Summer Events, Institute Competencies Seminar May 5th
by Ladd, Brent Thomas 28 Apr '25

28 Apr '25

Dear EMBRIO Members, Join us next Monday, May 5th at 3pm EDT for our all-hands seminar focused on Institute Competencies and their implementation as part of Thrust 4 research and practice led by the Gardner lab. We will wrap up the spring semester seminar series on May 19th with Thrust 4 research led by the Magana lab. If you missed any previous seminars you can find the recording on our shared Box drive in the All-Hands Meetings Recordings folder<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…>. EMBRIO Investigators, Trainees, and Research Scientists: There is still time to nominate EMBRIO peer-reviewed published papers for the Best Paper Competition (first author/co-author as EMBRIO graduate student, postdoc, or staff research scientist - papers published between 9/1/2021 and now are eligible). We ask that you submit your nominations by this Friday at the latest. Details are attached. Best Paper Nomination submission: https://purdue.ca1.qualtrics.com/jfe/form/SV_0GUgolkEbJKjm2W<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue.ca…> We will open nominations for Best Scientific Figure award later this week. Thanks for completing the RSVP survey for input on this year’s summer school and annual meeting, along with a quick self-assessment of the Institute’s twelve competency areas. If you haven't yet done so, reminder emails are being sent. Please complete this survey asap so that we can best plan for an impactful week June 9-13 for the EMBRIO Summer School (Mon-Wed) and Annual Meeting (Thurs-Fri) hosted at Purdue University. EMBRIO Trainees: 2025 CompuCell3D Virtual Tissue Modeling Workshop and Hackathon (workshop flyer attached) Our partners at I.U. in the Glazier Lab and Biocomplexity Institute have announced the 2025 CompuCell3D Virtual Tissue Modeling Workshop and Hackathon at Indiana University, Bloomington, July 28th to August 10th, 2025. Learn to model your biological system of interest with one-on-one help. Week 1 will cover CC3D basics. Week 2 will cover advanced topics in CC3D, followed by a 2-day model-building hackathon. Physicists, biologists, computer scientists, and modelers team up to build research-grade models of biological systems. All experience levels are welcome. For more information, email compucell3d.iu(a)gmail.com<mailto:compucell3d.iu@gmail.com> or visit www.compucell3d.org/Workshop25<https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.compuc…>. Register at: www.tinyurl.com/CC3D2025<https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.tinyur…>. 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(a)purdue.edu

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Model Competition - Ext Deadline this Friday - 2025 OpenVT Reproducible Agent-Based Multicellular Model Competition
by Ladd, Brent Thomas 21 Apr '25

21 Apr '25

[cid:a93a0a24-baad-4107-9b34-93e41e619e75] >From the Glazier Lab: Announcing the 2025 OpenVT Reproducible Agent-Based Multicellular Model Competition EXTENDED deadline for submissions: Friday April 25, 2025 We are pleased to announce the inaugural 2025 OpenVT Reproducible Agent-Based Multicellular Model Competition promoting FAIR, reproducible, and reusable multicellular simulations. Models must be published in a refereed journal on or after January 1, 2023 and publicly distributed. For detailed instructions and to submit your model visit: https://forms.gle/7u7tNj2mE5p9yytd8<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fforms.gle…>. Deadline for submissions has been extended April 25, 2025. For questions about the competition contact: openvtprize(a)gmail.com<mailto:openvtprize@gmail.com> . Winners will be invited to present in the GLIMPRINT’s virtual seminar series.

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EMBRIO Seminar Today Mullins Lab Thrust 3A + Summer School-Annual Meeting RSVP survey
by Ladd, Brent Thomas 21 Apr '25

21 Apr '25

Dear EMBRIO Members, Join us this afternoon at 3pm EDT for our all-hands seminar with the Mullins lab leading the presentation for Thrust 3A. Our May 5th seminar will focus on Institute Competencies and their implementation as part of Thrust 4 research and practice led by the Gardner lab. We will wrap up the spring semester seminar series on May 19th with Thrust 4 research led by the Magana lab. If you missed any previous seminars you can find the recording on our shared Box drive in the All-Hands Meetings Recordings folder<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…>. All EMBRIO members have been sent an RSVP survey by email for input on this year’s summer school and annual meeting, along with a quick self-assessment of the Institute’s twelve competency areas. Please complete this survey asap so that we can best plan for an impactful week June 9-13 for the EMBRIO Summer School (Mon-Wed) and Annual Meeting (Thurs-Fri) hosted at Purdue University. Sloan Mentorship Community of Practice Workshop: Rubrics for Holistic Competitive Decisions (flyer attached) will be held tomorrrow, April 22nd, with leadership from EMBRIO Investigator Stephanie Gardner. Please consider registering in advance for this meeting: https://purdue-edu.zoom.us/meeting/register/UvqM_3QWTdacKoLsbGk0Sg<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…> After registering, you will receive a confirmation email containing information about joining the meeting. 2025 CompuCell3D Virtual Tissue Modeling Workshop and Hackathon (workshop flyer attached) Our partners at I.U. in the Glazier Lab and Biocomplexity Institute have announced the 2025 CompuCell3D Virtual Tissue Modeling Workshop and Hackathon at Indiana University, Bloomington, July 28th to August 10th, 2025. Learn to model your biological system of interest with one-on-one help. Week 1 will cover CC3D basics. Week 2 will cover advanced topics in CC3D, followed by a 2-day model-building hackathon. Physicists, biologists, computer scientists, and modelers team up to build research-grade models of biological systems. All experience levels are welcome. For more information, email compucell3d.iu(a)gmail.com<mailto:compucell3d.iu@gmail.com> or visit www.compucell3d.org/Workshop25<https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.compuc…>. Register at: www.tinyurl.com/CC3D2025<https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.tinyur…>. 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(a)purdue.edu

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Emergence Newsletter Issue 41, April 17, 2025
by Ladd, Brent Thomas 17 Apr '25

17 Apr '25

[cid:9a731071-3037-4566-8a04-7bf5d6c01017] Emergence: A newsletter of discovery, education, and outreach from the EMBRIO Institute Issue 41: April 17, 2025 DIRECTORS’ NOTE Plan to join us for the Institute’s next all-hands seminar Monday, April 21st, 3PM EDT with the Mullins lab leading the presentation for Thrust 3A. Following in the seminar schedule on May 5th a focus on Institute Competencies and their implementation as part of Thrust 4 research and practice will be led by the Gardner lab. We will wrap up the spring semester seminar series on May 19th with Thrust 4 research led by the Magana lab. If you missed any previous seminars you can find the recording on our shared Box drive in the All-Hands Meetings Recordings folder<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…>. All EMBRIO members have been sent an RSVP survey by email for input on this year’s summer school and annual meeting, along with a quick self-assessment of the Institute’s twelve competency areas. Please complete this survey asap so that we can best plan for an impactful week June 9-13 for the EMBRIO Summer School (Mon-Wed) and Annual Meeting (Thurs-Fri) hosted at Purdue University. With NSF reporting season and progress updates in full swing, thanks to all the EMBRIO investigators and labs for submitting your progress reports and budget requests this week! The Institute participated in an engaging day of research exchange during the Joint Quantitative Biology Symposium: “Harnessing Complexity, Revealing Simplicity”<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsites.nd.…> last Friday, April 11th hosted by University of Notre Dame. EMBRIO researchers presenting talks included Co-Directors David Umulis and Jeremy Zartman, along with Research Scientists Linlin Li, Nilay Kumar, and Weiwei Zhang. EMBRIO poster presenters included David Gazzo, Mayesha Mim, Maria Unger, Stephen Cini, and Brent Ladd. Also participating throughout the day Elsje Pienaar and Himabindu Kovvali. The symposium was planned and hosted by the quantitative biology student committee – including David Gazzo and Mayesha Mim from the Zartman Lab. (View photos on our LinkedIn posts: here<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.linke…> and here<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.linke…>). Other Opportunities and Workshops for EMBRIO Members 2025 CompuCell3D Virtual Tissue Modeling Workshop and Hackathon (workshop flyer attached) Our partners at I.U. in the Glazier Lab and Biocomplexity Institute have announced the 2025 CompuCell3D Virtual Tissue Modeling Workshop and Hackathon at Indiana University, Bloomington, July 28th to August 10th, 2025. Learn to model your biological system of interest with one-on-one help. Week 1 will cover CC3D basics. Week 2 will cover advanced topics in CC3D, followed by a 2-day model-building hackathon. Physicists, biologists, computer scientists, and modelers team up to build research-grade models of biological systems. All experience levels are welcome. For more information, email compucell3d.iu(a)gmail.com<mailto:compucell3d.iu@gmail.com> or visit www.compucell3d.org/Workshop25<https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.compuc…>. Register at: www.tinyurl.com/CC3D2025<https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.tinyur…>. Sloan Mentorship Community of Practice Workshop: Rubrics for Holistic Competitive Decisions (flyer attached) will be held April 22nd, with leadership from EMBRIO Investigator Stephanie Gardner. Please consider registering in advance for this meeting: https://purdue-edu.zoom.us/meeting/register/UvqM_3QWTdacKoLsbGk0Sg After registering, you will receive a confirmation email containing information about joining the meeting. David, Jeremy, Chris, Anjali, Janice, Alejandra, Elsje, and Brent QUICK LINKS All-Hands Meetings Recordings<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> Materials from Summer School & Annual Retreat<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> Institute Skills and Strengths Sharing Platform<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.goog…> Orientation to EMBRIO<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> Sign the Data Sharing Policy Agreement<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue.ca…> EMBRIO Personnel List<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> Hot Off the Press: New & Recent EMBRIO Journal Papers and Preprints Let us know about new papers you want to highlight for the EMBRIO community! Check out our Google Scholar Page<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fscholar.g…> See a more complete list of Scholarly Products produced under support of EMBRIO Institute<https://www.purdue.edu/research/embrio/research/scholarly-products.php> EMBRIO currently has 32 published peer-reviewed journal papers, and 19 pre-print or in submission phase manuscripts, with more on the way! REMINDER: EMBRIO Acknowledgement for Scholarly Papers and Posters. For EMBRIO related research publications, NSF requires acknowledgement of EMBRIO NSF funding for our Institute to claim the work in our reporting back to NSF. Please include the following acknowledgement in your journal and conference papers and posters: “This work is based upon efforts supported by EMBRIO Institute, contract #2120200, a National Science Foundation (NSF) Biology Integration Institute.” UPCOMING DEADLINES, IMPORTANT DATES, OPPORTUNITIES & INFO EMBRIO All-hands Meeting Schedule, Monday’s 3-4pm ET. Zoom Link: https://purdue-edu.zoom.us/j/97946412458?pwd=YUurFKck0n1am07eA7b0O0TVKsVwpC…<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…> Previous All Hands Recordings<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> Trainees and collaborators encouraged to co-present during the Thrust seminars this semester. Month Day Spring Semester 2025 Jan 13 Denise Driscoll, Purdue (ABIDES Invited Scholar) Jan 27 Scott Howard, Notre Dame Feb 10 Krishna Jayant Lab; Thrust 1A Feb 24 Janice Evans Lab; Thrust 1B Mar 10 Qing Deng Lab; Thrust 3B Mar 24 Jeremiah Zartman Lab; Thrust 2B Apr 7 Chris Staiger and Anjali Iyer-Pascuzzi Labs; Thrust 2A Apr 21 Mary Mullins Lab; Thrust 3A May 5 Stephanie Gardner Lab; Thrust 4 May 19 Ale Magana Lab; Thrust 4 April 22, 2025. Sloan Mentorship Community of Practice Virtual Workshop: Rubrics for Holistic Competitive Decisions, with leadership from EMBRIO Investigator Stephanie Gardner. Please see the attached flyer for details and QR code for the zoom link, but consider registering in advance for this meeting: https://purdue-edu.zoom.us/meeting/register/UvqM_3QWTdacKoLsbGk0Sg After registering, you will receive a confirmation email containing information about joining the meeting. June 9-13, 2025. EMBRIO Summer School and Annual Meeting, Purdue University. Additional Details forthcoming. July 9-13, 2025. International Zebrafish Conference<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.izfs.…>. Madison, WI, USA. July 28 – August 10, 2025. CompuCell3D Virtual Tissue Modeling Workshop and Hackathon (workshop flyer attached) Our partners at I.U. in the Glazier Lab and Biocomplexity Institute have announced the 2025 CompuCell3D Virtual Tissue Modeling Workshop and Hackathon at Indiana University, Bloomington, July 28th to August 10th, 2025. Learn to model your biological system of interest with one-on-one help. Week 1 will cover CC3D basics. Week 2 will cover advanced topics in CC3D, followed by a 2-day model-building hackathon. Physicists, biologists, computer scientists, and modelers team up to build research-grade models of biological systems. All experience levels are welcome. For more information, email compucell3d.iu(a)gmail.com<mailto:compucell3d.iu@gmail.com> or visit www.compucell3d.org/Workshop25<https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.compuc…>. Register at: www.tinyurl.com/CC3D2025<https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.tinyur…>. Awards Congrats to EMBRIO members receiving faculty promotions (Purdue University): Deva Chan, associate professor of biomedical engineering, Xiaoqian (Joy) Wang, associate professor of electrical and computer engineering, and Jacqueline Linnes, professor of biomedical engineering New Lab Members? Did you recently have new students or staff members join your EMBRIO projects? We want to add them to the listserv, Box account, demographics survey, and Personnel List for ensuring their inclusion in communications and participation. If they are not already on our Personnel spreadsheet<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> , or they have graduated, let Brent know their names and email contacts (laddb(a)purdue.edu<mailto:laddb@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(a)purdue.edu

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