April 2025 - Embrio-list - ecn.purdue.edu

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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EMBRIO Seminar T2A Today 3pm Staiger + Iyer-Pascuzzi labs, Best Paper Award Submission Due April 9th
by Ladd, Brent Thomas 07 Apr '25

07 Apr '25

Dear EMBRIOphytes, Thrust 2A Seminar, Today, 3-4PM EDT Plan to join us for the Institute’s next all-hands seminar 3PM EDT today with the Staiger lab and Iyer-Pascuzzi lab leading the presentation for Thrust 2A. Zoom Link: https://purdue-edu.zoom.us/j/97946412458?pwd=YUurFKck0n1am07eA7b0O0TVKsVwpC…<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…>. If you've missed any previous seminars, recordings are available 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 Best Paper Award Submissions - Due April 9th Submission online.<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue.ca…> Grads, Postdocs, and Staff Research Scientists: If you've published EMBRIO research as a first author or first co-author, you are invited and encouraged to submit your paper in the EMBRIO Best Paper Award competition. The deadline is this Wednesday, April 9th. Submission online.<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue.ca…> There will be a division for Grads and a division for postdocs and staff research scientists. Details attached, along with the Best Scientific Figure competition (deadline June 1). Sloan Mentorship Community of Practice Workshop: Rubrics for Holistic Competitive Decisions, April 22nd, 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<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. EMBRIO is participating in the Q-Bio Symposium: “Harnessing Complexity, Revealing Simplicity” happening this Friday, April 11th at University of Notre Dame. The symposium, planned and hosted by the quantitative biology student committee – including the Zartman Lab at the University of Notre Dame, will feature EMBRIO speakers and posters. Q-Bio Symposium RSVP and Schedule<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.goog…> 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 Reminders - T2A Seminar Monday, Best Paper Submissions, Mentorship CoP wkshp, Q-Bio Symposium
by Ladd, Brent Thomas 04 Apr '25

04 Apr '25

Dear EMBRIOphytes, Thrust 2A Seminar, Monday April 7th , 2-3PM EDT Plan to join us for the Institute’s next all-hands seminar Monday, April 7th, 3PM EDT with the Staiger lab and Iyer-Pascuzzi lab leading the presentation for Thrust 2A. Zoom Link: https://purdue-edu.zoom.us/j/97946412458?pwd=YUurFKck0n1am07eA7b0O0TVKsVwpC…<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…>. If you missed any previous seminars, recordings are available 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 Best Paper Award Submissions - Due April 9th Grads, Postdocs, and Staff Research Scientists: If you've published EMBRIO research as a first author or first co-author, you are invited and encouraged to submit your paper in the Best EMBRIO Paper Award competition. The deadline is next Wednesday, April 9th. Submission online<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue.ca…>. Details attached, along with the Best Scientific Figure competition (deadline June 1). Sloan Mentorship Community of Practice Workshop: Rubrics for Holistic Competitive Decisions, April 22nd, 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<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. EMBRIO is participating in the Q-Bio Symposium: “Harnessing Complexity, Revealing Simplicity” happening on Friday, April 11th at University of Notre Dame. The symposium, planned and hosted by the quantitative biology student committee – including the Zartman Lab at the University of Notre Dame, will feature EMBRIO speakers and posters. Q-Bio Symposium RSVP and Schedule<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.goog…> 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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