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

EMBRIO Events Reminders + Action Items
by Ladd, Brent Thomas 23 May '25

23 May '25

Dear EMBRIO Members, Please see the action items below regarding our upcoming summer school and annual retreat. Please also act on the separate embrio-list email sent to you today on behalf of Soumi Mukerhjee in the Gardner Lab to schedule your follow up interview that is critical for Institute evaluation research and reporting. Soumi requests you fill out your schedule for a full hour of time. An FYI that I will be away from email 5/24 - 6/1. If you have questions regarding logistics for the events please contact Jennifer Goad at goad3(a)purdue.edu. Thank you, Brent EMBRIO Summer Events Items: The 2025 Summer School Schedule<https://www.purdue.edu/research/embrio/workforce-development/EMBRIO-summer-…> All-Hands Annual Retreat 2025 Schedule<https://www.purdue.edu/research/embrio/research/annual-retreat.php> Thrust Leaders (see the agenda at the above link for thrust project schedule) are asked to give a brief update on their project (10 min) spending the majority of their 30 minute talk to discuss what their goals/plans are for our Y5 and for the following five years if we are funded, while spending some time to discuss ideas to continue collaborations without NSF funding. For attendees at our upcoming Summer School (June 9-11), and Annual Retreat (June 12-13), there are items 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…> ) 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<mailto:goad3@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<mailto:sgardne@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 Members Please Schedule a Follow Up Interview with Soumi - Mandatory for all working on EMBRIO research projects for Institute Evaluation
by Ladd, Brent Thomas 23 May '25

23 May '25

Dear EMBRIO Community, Please see the message below regarding participation in a one-on-one interview to capture your experience in the Institute. This is a crucial part of our mandatory evaluation process in reporting to NSF. link to sign up is at the bottom of the message. “My name is Soumi Mukherjee, a graduate student in the Department of Biological Sciences at Purdue University. Along with my advisor, Dr. Stephanie Gardner, and lab mate, Emily Georgopoulos, I have been leading an institute-wide evaluation study as part of the EMBRIO Thrust 4 initiative. Our initial round of interviews and surveys has been instrumental in capturing your experiences as a member of EMBRIO. This work has informed formative evaluation reports submitted to the NSF and contributed to shaping the institute's competency framework. We are now entering the final phase of our evaluation study and would greatly value your participation in a follow-up interview. This round aims to capture how your collaborations have evolved over time and how these experiences have supported EMBRIO’s interdisciplinary and integrative mission. Your insights will also help us refine the institutional evaluation survey and better understand how EMBRIO’s structural changes have influenced both individual research trajectories and broader institute goals. The findings from this phase will be critical in guiding the evaluation design of EMBRIO 2.0 and ensuring our evaluation efforts continue to support a collaborative and innovative research environment. We truly appreciate your time and contribution to this important work. If you are a member of the EMBRIO institute currently doing a research project, we would like to invite you for participating in this study. Participation in the evaluation process is MANDATORY for all the members of the institute. As a part of the evaluation process, you will take part in an online session (via Zoom), which includes an interview and a brief survey, and the entire process should be completed in an hour. Interviews session would not exceed an hour and would be completed in a day. Everything will be similar to the interviews we did last time. Please fill in all the times you may be available for our interviews using the link below with either your name or email address. https://www.when2meet.com/?30690328-ExJqL<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.when2…> This information is requested so that we may contact you to set up an online session, but we will use a randomly generated 4-digit code in place of your name to identify all your information for the data collection and analysis. Your participation will not affect any aspect of your association with the EMBRIO institute. If you have any doubts regarding the evaluation process, please reach out to me at mukher42(a)purdue.edu<mailto:mukher42@purdue.edu>.” With Regards, Soumi Mukherjee PhD Candidate | Gardner Research Group Dept of Biology 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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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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