October 2023 - Embrio-list

Reminder: today no weekly - schedule your thrust level discussions instead
by Ladd, Brent Thomas 30 Oct '23

30 Oct '23

Dear EMBRIOphytes, A reminder of the biweekly dates remaining this semester that we won't hold the all-hands Weekly, and instead Thrust level meetings will be organized separately by the thrust leads are: Today, Oct. 30 Nov. 13 Nov. 27 Dec. 11 For Thrusts that don't already have a standing meeting, please consider using this bi-weekly blocked time of Monday 3-4pm ET. By request, the next All-hands online will be Nov. 6th , on Vcell by Dr. Michael Blinov, Center for Cell Analysis and Modeling, UConn Health. You are encouraged to check out the VCell website<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fvcell.org…>. "VCell (Virtual Cell) is a comprehensive platform for modeling cell biological systems that is built on a central database and disseminated as a web application." Next semester we will rotate the biweekly all-hands to feature a Thrust level progress/collab report-out once a month, with either a research seminar or professional development offering on the off weeks. This will allow everyone to hear each of the four research thrusts on progress, challenges, upcoming activities once per semester and offer more cross-thrust discussions. 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 <https://www.purdue.edu/research/embrio/>

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Reminders
by Ladd, Brent Thomas 24 Oct '23

24 Oct '23

Quick reminder to weigh in by end of today with your input regarding our Weekly meeting format and frequency. The survey consists of 3 Qs - takes a couple minutes. https://purdue.ca1.qualtrics.com/jfe/form/SV_2bq2CUWVQa3gPeS<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue.ca…> The primary purpose of the Weekly All-hands meeting has served as a platform for sharing insights and progress on research within the Institute, as well as getting to know each other as researchers. As the Institute has evolved, we want to best organize a regular All-hands meeting that reflects the diverse needs of our community; (needs that are not already being met through other regular research Thrust and project meetings). Regarding the All-hands weekly meeting frequency and format, we want to hear your opinions on this by end of today. The leadership team will use your input to make decisions on the format and frequency going forward. Cross BII Effort: Calling All BII Early Career Researchers (ECRs; students, postdocs, early-stage faculty, and anyone that considers themselves early career): During the last all-hands NSF BII Meeting, several groups of ECRs expressed interest in forming a cross-BII early career researcher community. Such a community can leverage the resources and professional development opportunities across the BII collective. The BII community has received an NSF Research Coordination Network grant to help support these activities, and they want to know about your priorities for such a community: https://forms.gle/fjJ43etC2ejZzaZLA<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fforms.gle…> 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 <https://www.purdue.edu/research/embrio/>

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Monday Announcements: Mentoring workshop today and Brief surveys capturing your input
by Ladd, Brent Thomas 23 Oct '23

23 Oct '23

Dear EMBRIO Community, Mentoring workshop today! Our ABIDES program will present an interactive mini workshop today at 3pm ET on cultural aspects of mentoring and teams via our regular Weekly zoom link. This mini workshop is for ALL EMBRIO members. Please plan to participate! Institute leadership requests your input on Weekly meeting format and frequency (by Tuesday, 10-24) https://purdue.ca1.qualtrics.com/jfe/form/SV_2bq2CUWVQa3gPeS<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue.ca…> The primary purpose of the Weekly All-hands meeting has served as a platform for sharing insights and progress on research within the Institute, as well as getting to know each other as researchers. As the Institute has evolved, we want to best organize a regular All-hands meeting that reflects the diverse needs of our community; (needs that are not already being met through other regular research Thrust and project meetings). Regarding the All-hands weekly meeting frequency and format, we want to hear your opinions on this by tomorrow Tuesday at the latest (Thanks to all who have submitted their responses.): Take the few minutes needed to fill the 3 question anonymous survey<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue.ca…>. Calling All BII Early Career Researchers (ECRs; students, postdocs, early-stage faculty, and anyone that considers themselves early career): During the last all-hands NSF BII Meeting, several groups of ECRs expressed interest in forming a cross-BII early career researcher community. Such a community can leverage the resources and professional development opportunities across the BII collective. The BII community has received an NSF Research Coordination Network grant to help support these activites, and they want to know about your priorities for such a community: https://forms.gle/fjJ43etC2ejZzaZLA<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fforms.gle…> Your responses will guide formation of the ECR community’s structure and opportunities - this is your chance to be heard! Participation is voluntary. And even if you’re interested in minimal engagement, or none at all, we’d very much value knowing that too - i.e. even if you’re not interested in participating in a Cross-BII ECR Community, we’d still value hearing that via this survey, to help quantify the portion of the overall ECR community such a group would serve. Any Qs about the survey can be directed to Brett Fredericksen at (frede368(a)umn.edu<mailto:frede368@umn.edu>). Thank you so much for engaging! ~The Cross-BII RCN Core Team 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 <https://www.purdue.edu/research/embrio/>

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Monday's Mini-Workshop 3pm ET
by Ladd, Brent Thomas 20 Oct '23

20 Oct '23

Dear EMBRIOnic People, Our ABIDES program will present a mini workshop on cultural aspects of mentoring and teams during the Weekly session this coming Monday, October 23rd . The session will be all online via our regular zoom link. This mini workshop is for ALL EMBRIO members. Please plan to participate! BTW, if you missed the previous “mentoring snack” that provides background for the upcoming workshop, check out the slides and resources in the ABIDES > Mentoring folder<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…>, and listen to “The Secret of Great Teams<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fhiddenbra…>” episode of The Hidden Brain podcast. Regarding the All-hands weekly meeting frequency and format, we need to hear your opinions on this by next Tuesday at latest: take the few minutes needed to fill the 4 question anonymous survey<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue.ca…>. Enjoy the Weekend! 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 <https://www.purdue.edu/research/embrio/>

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Emergence Issue 24: October 18, 2023
by Ladd, Brent Thomas 18 Oct '23

18 Oct '23

[cid:079b7edd-0aff-4c50-9b72-da80fa1832ad] Emergence: A biweekly newsletter of discovery, education, and outreach from the EMBRIO Institute Issue 24: October 18, 2023 DIRECTORS’ NOTE Welcome back to all who attended and presented at BMES in Seattle, and safe travels to all those who are attending other conferences. It is exciting to see EMBRIO research being disseminated and discussed in the broader scientific community! Please note that due to the final format of participatory exercises planned for the cultural aspects of mentoring and teams mini workshop (originally planned for a hybrid format), the ABIDES program needs to shift this Weekly session on Monday, October 23rd to be all online via our regular zoom link. This mini workshop is for ALL EMBRIO members. Please plan to participate! Regarding the All-hands weekly meeting frequency and format, we need to hear from you on this: asap, take the few minutes needed to fill the four question anonymous survey<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue.ca…>. BTW, if you missed the previous “mentoring snack” check out the slides and resources in the ABIDES > Mentoring folder<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…>, and listen to “The Secret of Great Teams<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fhiddenbra…>” episode of The Hidden Brain podcast. Learn more about your fellow EMBRIO member Abasiafak (Aby) Ndifreke Udosen in this issue. Aby is pursuing his doctorate in the Magana Lab at Purdue conducting research in Thrust 4 of the Institute focused on teamwork interactions and interdisciplinary learning. He’s also been collaborating with faculty on creating course project exercises for a new introductory EMBRIO course (more to come on this exciting development). We’ve heard from NSF regarding the next BII Annual Conference - January 22nd – Please hold the Date. Details on the agenda will be shared when available. NSF is planning a hybrid one day meeting. A few of us from the leadership team will attend in person at NSF headquarters as requested, with everyone else attending via zoom. For anyone wishing to learn and improve their use of the powerful data analysis tool fondly known as “R”, please take advantage of the bi-weekly series organized by Dr. Priyanka Baloni especially for EMBRIO trainees, staff, and faculty. The next session is tomorrow, Thursday afternoon, at 4pm (details below). The graduate students in biology education research at Purdue have organized a seminar series this fall and have a great slate of speakers lined up. The next speaker is this Friday, October 20th at 11:30 am ET in Zoom<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…>. Dr. Elli Theobald (U Washington) will be joining us virtually and her seminar is entitled: Mind the gap: Active learning improves equity in STEM classrooms. We want to hear about your news and announcements. Send them to Brent (laddb(a)purdue.edu) by October 27th for inclusion in the next issue of Emergence. David, Chris, Stephanie, Anjali, Janice, Jeremy, and Brent Notable Quote “Nothing we accomplish in life is totally free of the influence of spirit and community. We do nothing alone.”― Tricia Hersey, Rest Is Resistance: A Manifesto<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fthenapmin…> QUICK LINKS R Café session (Thursday, 4pm)<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…> All-hands Weekly (Monday, 3pm)<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…> ABIDES Culture and Mentoring resources<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> Survey: Your input on Weekly meeting frequency and format<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue.ca…> Summer workshop materials<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> Annual Retreat slides and posters<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> Weekly Update Meeting Recordings<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> EMBRIO ABIDES (Access, Belonging, Inclusion, Diversity, Equity, Support) Dr. Anjali Iyer-Pascuzzi, EMBRIO ABIDES Director and Professor at Purdue, leads activities for Institute members. A series of mentoring topics have been presented at the beginning of Weekly meetings, and a continuation of the Mentoring Panel topics from the annual retreat will be presented October 23rd during the EMBRIO Weekly with a deeper dive into how culture impacts our mentoring and team thinking. R CAFÉ SERIES – FALL SEMESTER Dr. Priyanka Baloni & Dr. Anke Tukker are hosting a bi-weekly session for those in EMBRIO interested in learning R and solving their research related questions. Participants only need to bring their laptop with R and R studio installed<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Frstudio-e…>. We will have an interactive session where we try to solve coding related questions and learn new things related to data analysis and visualization using R. We invite everyone to work on their own R projects, ask questions and learn from each other. The first session was held Sept. 6th. Those interested in learning or brushing up on using R for data analysis, sessions of R Café will be on Thursdays. The next session will be Thursday, October 5th at 4pm ET. In person in DLR 323. These are the remaining dates: 10/5, 10/19, 11/2, 11/16, 11/30, and possibly 12/14. Virtual link for any that can join in person: https://purdue-edu.zoom.us/j/3998037199<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…> (please note this day and time change compared to previous announcements). JOURNAL CLUBS Journal Club on Calcium Imaging Techniques meets Monday’s 11am ET Due to the need within our EMBRIO community to process and analyze Ca2+ Images, Dr. Norma Perez Rosas (nperezro(a)purdue.edu<mailto:nperezro@purdue.edu> ) is helping lead this club in discussing papers regarding methods and tools for analyzing calcium imaging. The goal, beyond integrating these techniques, is to write a review paper. The Club is meeting weekly on Mondays at 11am. Please contact Norma about participating. Journal Club on Multimodal Functions of Calcium in Tuning and Regulating Cytoskeleton Networks Please contact Dr. Linlin Li (li2212(a)purdue.edu<mailto:li2212@purdue.edu> ) for information. The club is in the writing stage for organizing and publishing a review paper on the topic. It isn’t too late to join. Here is the link to the current working documents: https://docs.google.com/document/d/1Cpg77yjtioWiIuRmiDMCcAiAd4jNNX_J7s64RQk…<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.goog…> EMBRIO Member Spotlight [cid:d1364754-e81f-4baf-88fc-aa7ae73220a5] Abasiafak (“Aby”) Ndifreke Udosen Computer and Information Technology, Purdue University Advisor: Dr. Alejandra J. Magana, Ph.D Title of my EMBRIO project: “Characterizing Teamwork Interactions and Interdisciplinary Learning in the Context of Computational Modeling and Simulation Projects” Professional page: Linkedin<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.linke…> Magana research lab page: https://polytechnic.purdue.edu/rocketed/members What's your hometown, State, Country (and one thing you love, miss, remember, or want to tell others about it)? I am an indigene of Akwa Ibom State in Nigeria, where I spent the entirety of my childhood and most of my adult life. Throughout my formative years, one of my fondest memories was playing with homemade toys, both those I built myself and those given to me. My Dad observed my early affinity for hands-on experiences and believed that I would succeed in Engineering, and Technology Education, so he began teaching me Mathematics very early on as a kid. Thanks to my father I still have vivid memories of riding my bike to His office during the holidays, to seek his assistance in completing my high school projects and assignments. Fast forward to August 2022, I made one of the best decisions of my life by enrolling at Purdue University. My lovely wife, Faith, and our two little buddies, Shekinah and Shemaiah, joined me on this exciting journey. As a family, we are joyfully anticipating the arrival of our third child, Shalom. Glad to say our future is bright and full of promise! What are your hobbies? I love Faith-based activities, streaming action movies, watching narrated histories on YouTube, and hanging out with family and friends. What drew you into becoming a scientist or engineer (or both)? My academic and professional journey has been profoundly influenced by the invaluable contributions of my parents. My mother is a Full Professor of Educational Technology, while my father is a consultant Architect, Founder, and Building Engineer. They both provided me with invaluable mentorship and the encouragement I required to pursue my passion in the Engineering sciences. This led to my bachelor’s degree in mechanical engineering after which I proceeded to earn my master's degree in the same field, and my journey continued as I transitioned into the role of a junior lecturer, tutor, and researcher at the Department of Mechanical Engineering, University of Nigeria and the University of Cape Town, South Africa. Tell us the main point of your research as it relates to EMBRIO: My doctoral research broadly investigates teamwork interactions and interdisciplinary learning in computational modelling and simulation projects. It proposes to contribute research findings on how Engineering students, engaged in computational modelling-focused team-based projects can share metal models and learn to improve upon their model-based reasoning skills through effective collaboration and social interaction. My research ultimately falls into “Thrust 4” of the EMBRIO institute's goal which is aimed at identifying and implementing best practices in curriculum and training to support learning, meaningful engagement, and participation in integrative biology research. I am also actively engaged in the EMBRIO Innovation Hub Grant project, where I contribute to the design of a Team-Based transdisciplinary graduate course in Computational Understanding of Biological Systems and Data. Within this project, my specific role involves applying computational fluid dynamics methods in the development of partial differential equation (PDE) models to implement cell cytokinesis at a basic level in Python and MATLAB. You find yourself alone on an elevator with the president of your university – who knows very little about your field: They ask you to tell them about your research (15 seconds - go!): My research investigates teamwork dynamics in modeling and simulation processes within the context of a semester-long project undertaken in a Biomedical Engineering graduate course. What's on the horizon for you (research, career, personal, whatever you want to share)? I love interdisciplinary research, and I envision conducting future research in the areas of Computing and Engineering Education, Computational Modelling of thermo-fluid processes in biological systems and Integrating AI and Machine Learning approaches in these areas. After my PhD education, I look forward to collaborating with research teams in academia or industry. One of my life goals is to leverage my research experiences to make meaningful and impactful contributions to society. What’s your various URL/social media handles that others can follow (prof. website, twitter, LinkedIn, blog, etc)? Kindly follow me on LinkedIn @ Linkedin<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.linke…> STUDENT LEADERSHIP COUNCIL CORNER The SLC is recruiting new officers to represent your university and your perspective for EMBRIO. Reach out to David Gazzo (dgazzo(a)nd.edu) Feyisayo Akande (fakande(a)purdue.edu) and Jazzmin Owens (jazzmin.owens(a)morehouse.edu) for more information, and log your ideas for future topics or events<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.goog…> that the SLC could organize. Access SLC slides and documents<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…>, and consider signing up to give or receive mentoring<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.goog…> for/from EMBRIO trainees in helping support and orient to the EMBRIO mission and interdisciplinary framework. EMBRIO SUMMER WORKSHOP RESOURCES EMBRIO Institute's 2nd Annual Summer Training Workshop took place July 10-12. Workshop Schedule of Sessions<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.goog…>. Hosted by Dr. Jeremiah Zartman at the University of Notre Dame with a theme of Image Acquisition, Processing, and Analysis, tutorials and hands-on sessions were specifically aimed at benefiting trainees from both computational and experimental domains. Slides, handouts, and video recordings from this workshop are available on our shared Box account: https://app.box.com/s/mzo5ihlqiq4tfeig2psx2l6rmmdxto0c<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> EMBRIO ALL-HANDS ANNUAL RETREAT MATERIALS EMBRIO Institute’s Annual Retreat was hosted in the Weldon School of Biomedical Engineering on the Purdue University West Lafayette Campus, July 13-14, 2023. The annual retreat brought together the large majority of EMBRIO members in one physical place, with more than 60 of us engaging in research talks, poster presentations, programmatic discussions, and informal gatherings. Slide decks and posters from the annual retreat can be accessed here: https://app.box.com/s/rmsiuvydlsccexzhugyjp2b5v72xlg9l<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> UPCOMING DEADLINES, IMPORTANT DATES, & INFO EMBRIO Weekly Meeting, Monday’s 3-4pm ET. Zoom link<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…>. Aug 14 Benchling Workshop - SLC (Feyisayo) Aug 21 Student Leadership Council - Grads and Postdocs Only Session Aug 28 Faculty Investigators Only Sept 4 Labor Day no meeting Sept 11 Dr. Linlin Li: Part I: Solving mathematical modeling with ODE or PDE in MatLab or Python (Google Colab) Sept 18 Dr. Linlin Li: Part II: Solving mathematical modeling with ODE or PDE in MatLab or Python (Google Colab) Sept 25 Dr. Adrian Buganza Tepole: Part I: Physics informed machine learning Oct 2 Dr. Adrian Buganza Tepole: Part II: Physics informed machine learning Oct 9 Fall Break - no meeting Oct 16 Open Discussion and Thrust Project Breakout Rooms Oct 23 ABIDES: Culture, Mentoring, & Teams Mini Workshop Oct 30 TBD Nov 6 VCell talk by Dr. Michael Blinov, Center for Cell Analysis and Modeling, UConn To make them as relevant and useful as possible, we need your input on frequency and format for future "Weekly" all-hands meetings. Please take a few minutes to let us know your thoughts via this anonymous 4 question survey: https://purdue.ca1.qualtrics.com/jfe/form/SV_2bq2CUWVQa3gPeS<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue.ca…> October 20, 2023. Biology Education Research Seminar Series. The graduate students in biology education research at Purdue have organized a seminar series this fall and have a great slate of speakers lined up. The first speaker is Friday, October 20th at 11:30am ET in Zoom. Dr. Elli Theobald (U Washington) will be joining us virtually and her seminar is entitled: Mind the gap: Active learning improves equity in STEM classrooms. Zoom: https://purdue-edu.zoom.us/j/91764754503<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…> October 23, 2023. The October 23rd Weekly will be dedicated to a mini workshop on the cultural aspects of mentoring led by our ABIDES program. October 27 – 2024 Hertz Fellowship<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fhertzfoun…> Application deadline for doctoral students. January 2 – 6, 2024. BMES – CMBE Conference. San Juan, Puerto Rico. Accepting abstracts – deadline September 12. Conference details: https://www.bmes.org/cmbe2024<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.bmes.…> BII Annual Conference - January 22nd - Hold the Date. Details on the agenda will be shared when available. NSF is planning a hybrid one day meeting. Expecting most will be virtual, with a few of us possibly in person at NSF headquarters. Hot Off the Press: New EMBRIO Journal Papers Let us know about new papers you want to highlight for the EMBRIO community! 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.” Awards Congrats to Dr. Krishna Jayant being awarded by DoD for his project grant entitled “A Traveling Wave Basis for Coding Touch: Unraveling recurrent and translaminar circuit contributions to sensory-evoked traveling waves”. Read the Story<https://engineering.purdue.edu/Engr/AboutUs/News/Spotlights/2023/2023-1004-…>. Open Positions 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://app.box.com/s/frd9275xc069gmgtbe3y1osoz1j7ssk7<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> ) Submit your items for the next newsletter by Oct. 27th to Brent (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 <https://www.purdue.edu/research/embrio/>

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RSVP for Monday Oct. 23 and your input for future Weekly meetings
by Ladd, Brent Thomas 13 Oct '23

13 Oct '23

Dear EMBRIOnic Folk, To make them as relevant and useful as possible, we need your input on frequency and format for future "Weekly" all-hands meetings, as well as to get a count of people planning to attend in person for the mentoring workshop on October 23rd. Please take a few minutes to let us know via this anonymous 5 question survey: https://purdue.ca1.qualtrics.com/jfe/form/SV_2bq2CUWVQa3gPeS<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue.ca…> Thank you! 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 <https://www.purdue.edu/research/embrio/>

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Today's Weekly canceled + announcements
by Ladd, Brent Thomas 09 Oct '23

09 Oct '23

Dear EMBRIOphytes, A reminder that there will be no Weekly meeting today due to Fall break at Purdue. It is also Indigenous Peoples Day today (statement<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.white…> from the White House). We are planning to have an all-hands meeting during the Weekly zoom for October 16th with open discussion and breakout rooms per thrust area. The October 23rd Weekly will be dedicated to a mini workshop on mentoring led by our ABIDES program, with in-person participation requested of those at Purdue (the regular zoom link for web participation for our members off-campus can also be used). Stay tuned for a pre-workshop prep and RSVP. Everyone, please plan to join these Weekly sessions. The graduate students in biology education research at Purdue have organized a seminar series this fall and have a great slate of speakers lined up. The first speaker is this Friday, October 13th at 11:30am ET in Zoom (meeting link<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…>). Dr. Justin Shaffer will be joining us virtually and his seminar is entitled: The impact of high structure course design across courses, disciplines, and universities. We’ve heard from NSF regarding the next BII Annual Conference - January 22nd - Hold the Date. Details on the agenda will be shared when available. NSF is planning a hybrid one day meeting. We are anticipating that most of us will connect virtually, with a few of us possibly in person at NSF headquarters. 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 <https://www.purdue.edu/research/embrio/>

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Canceled: Ca2+ Imaging Techniques Journal Club (Invitation)
by Perez Rosas, Norma Citlalcue 09 Oct '23

09 Oct '23

Due to the Fall break at Purdue, there will be no Journal club meeting today. We will resume the following Monday 10/16. Thank you.

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EMERGENCE newsletter issue 23: October 4, 2023
by Ladd, Brent Thomas 04 Oct '23

04 Oct '23

[cid:85d06175-6747-442e-a57e-08b0ea57f66e] Emergence: A biweekly newsletter of discovery, education, and outreach from the EMBRIO Institute Issue 23: October 4, 2023 DIRECTORS’ NOTE Thanks to Dr. Linlin Li and Dr. Adrian Buganza Tepole for leading hands-on mini workshops during our recent all-hands Weekly sessions. These sessions have helped provide insights into solving ODEs and PDEs and using artificial neural networks to approximate different functions that arise in ODE and PDE solutions. The session recordings are available on our shared Box drive in the Weekly Updates sub folder<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…>. A reminder that there will be no Weekly meeting Monday, October 10th due to Fall break at Purdue. We are planning to have an all-hands meeting during the Weekly for October 16th with open discussion and breakout rooms per thrust area. The October 23rd Weekly will be dedicated to a mini workshop on mentoring led by our ABIDES program. Everyone, please plan to join the Weekly sessions. Thank you to Dr. Priyanka Baloni who has organized a bi-weekly series on using R for anyone in the Institute to learn and improve their use of this powerful data analysis tool. The next session is this Thursday afternoon at 4pm (details below). The graduate students in biology education research at Purdue have organized a seminar series this fall and have a great slate of speakers lined up. The first speaker is Friday, October 13th at 11:30am ET in Zoom. Dr. Justin Shaffer will be joining us virtually and his seminar is entitled: The impact of high structure course design across courses, disciplines, and universities. Please see the attached flyer. We’ve heard from NSF regarding the next BII Annual Conference - January 22nd - Hold the Date. Details on the agenda will be shared when available. NSF is planning a hybrid one day meeting. We are anticipating that most of us will connect virtually, with a few of us possibly in person at NSF headquarters. We want to hear about your news and announcements. Send them to Brent (laddb(a)purdue.edu) by October 13th for inclusion in the next issue of Emergence. David, Chris, Stephanie, Anjali, Janice, Jeremy, and Brent Notable Quote "It's only when you risk failure that you discover things. When you play it safe, you're not expressing the utmost of your human experience."― Lupita Nyong'o, Academy Award winning Mexican-Kenyon actress. QUICK LINKS Summer workshop materials<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> Annual Retreat slides and posters<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> Weekly Update Meeting Recordings<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> Student Leadership Council Slides and Documents<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> JOURNAL CLUBS Journal Club on Calcium Imaging Techniques meets Monday’s 11am ET Due to the need within our EMBRIO community to process and analyze Ca2+ Images, Dr. Norma Perez Rosas (nperezro(a)purdue.edu<mailto:nperezro@purdue.edu> ) is helping lead this club in discussing papers regarding methods and tools for analyzing calcium imaging. The goal, beyond integrating these techniques, is to write a review paper. The Club is meeting weekly on Mondays at 11am. Please contact Norma about participating. Journal Club on Multimodal Functions of Calcium in Tuning and Regulating Cytoskeleton Networks Please contact Dr. Linlin Li (li2212(a)purdue.edu<mailto:li2212@purdue.edu> ) for information. The club is in the writing stage for organizing and publishing a review paper on the topic. It isn’t too late to join. Here is the link to the current working documents: https://docs.google.com/document/d/1Cpg77yjtioWiIuRmiDMCcAiAd4jNNX_J7s64RQk…<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.goog…> R CAFÉ SERIES – FALL SEMESTER Dr. Priyanka Baloni & Dr. Anke Tukker are hosting a bi-weekly session for those in EMBRIO interested in learning R and solving their research related questions. Participants only need to bring their laptop with R and R studio installed<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Frstudio-e…>. We will have an interactive session where we try to solve coding related questions and learn new things related to data analysis and visualization using R. We invite everyone to work on their own R projects, ask questions and learn from each other. The first session was held Sept. 6th. Those interested in learning or brushing up on using R for data analysis, sessions of R Café will be on Thursdays. The next session will be Thursday, October 5th at 4pm ET. In person in DLR 323. These are the remaining dates: 10/5, 10/19, 11/2, 11/16, 11/30, and possibly 12/14. Virtual link for any that can join in person: https://purdue-edu.zoom.us/j/3998037199<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…> (please note this day and time change compared to previous announcements). EMBRIO ABIDES (Access, Belonging, Inclusion, Diversity, Equity, Support) Dr. Anjali Iyer-Pascuzzi, EMBRIO ABIDES Director and Professor at Purdue, leads activities for Institute members. A series of mentoring topics have been presented at the beginning of Weekly meetings, and a continuation of the Mentoring Panel topics from the annual retreat will be presented in-person October 23rd during the EMBRIO Weekly in DLR 221. A zoom link will be provided for those unable to be in person. STUDENT LEADERSHIP COUNCIL CORNER The SLC is recruiting new officers to represent your university and your perspective for EMBRIO. Reach out to David Gazzo (dgazzo(a)nd.edu) Feyisayo Akande (fakande(a)purdue.edu) and Jazzmin Owens (jazzmin.owens(a)morehouse.edu) for more information, and log your ideas for future topics or events<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.goog…> that the SLC could organize. Access SLC slides and documents<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…>, and consider signing up to give or receive mentoring<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.goog…> for/from EMBRIO trainees in helping support and orient to the EMBRIO mission and interdisciplinary framework. EMBRIO SUMMER WORKSHOP RESOURCES EMBRIO Institute's 2nd Annual Summer Training Workshop took place July 10-12. Workshop Schedule of Sessions<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.goog…>. Hosted by Dr. Jeremiah Zartman at the University of Notre Dame with a theme of Image Acquisition, Processing, and Analysis, tutorials and hands-on sessions were specifically aimed at benefiting trainees from both computational and experimental domains. Slides, handouts, and video recordings from this workshop are available on our shared Box account: https://app.box.com/s/mzo5ihlqiq4tfeig2psx2l6rmmdxto0c<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> EMBRIO ALL-HANDS ANNUAL RETREAT MATERIALS EMBRIO Institute’s Annual Retreat was hosted in the Weldon School of Biomedical Engineering on the Purdue University West Lafayette Campus, July 13-14, 2023. The annual retreat brought together the large majority of EMBRIO members in one physical place, with more than 60 of us engaging in research talks, poster presentations, programmatic discussions, and informal gatherings. Slide decks and posters from the annual retreat can be accessed here: https://app.box.com/s/rmsiuvydlsccexzhugyjp2b5v72xlg9l<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> UPCOMING DEADLINES, IMPORTANT DATES, & INFO EMBRIO Weekly Meeting, Monday’s 3-4pm ET. Zoom link<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…>. Aug 14 Benchling Workshop - SLC (Feyisayo) Aug 21 Student Leadership Council - Grads and Postdocs Only Session Aug 28 Faculty Investigators Only Sept 4 Labor Day no meeting Sept 11 Dr. Linlin Li: Part I: Solving mathematical modeling with ODE or PDE in MatLab or Python (Google Colab) Sept 18 Dr. Linlin Li: Part II: Solving mathematical modeling with ODE or PDE in MatLab or Python (Google Colab) Sept 25 Dr. Adrian Buganza Tepole: Part I: Physics informed machine learning Oct 2 Dr. Adrian Buganza Tepole: Part II: Physics informed machine learning Oct 9 Fall Break - no meeting Oct 16 Open Discussion and Thrust Project Breakout Rooms Oct 23 ABIDES: Mentoring Workshop (in person, DLR 221) followed by EMBRIO Image Analysis Workstation Open House DLR 203 Oct 30 Open Discussion and Thrust Project Breakout Rooms (extra credit for Halloween outfits) The EMBRIO Weekly will adapt to a new format the second half of the semester. The intention is to focus more time for research thrust projects to meet with cross talk between the thrusts, while dedicating one week a month to a trainee topic, and periodic research talks. Twice a month, the ABIDES program will feature a “10-minute mentoring snack” at the beginning of the Weekly. No Weekly meeting on October 10th due to Fall break at Purdue. We are planning to have an all-hands meeting during the Weekly for October 16th with open discussion and breakout rooms per thrust area. The October 23rd Weekly will be dedicated to a mini workshop on mentoring led by our ABIDES program. October 11-14, 2023. The 2023 BMES Annual Meeting will be held in Seattle, WA. Thousands of biomedical engineers will attend this year’s meeting to learn, collaborate, and network. https://www.bmes.org/annualmeeting<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.bmes.…> October 13, 2023. Biology Education Research Seminar Series. The graduate students in biology education research at Purdue have organized a seminar series this fall and have a great slate of speakers lined up. The first speaker is Friday, October 13th at 11:30am ET in Zoom. Dr. Justin Shaffer will be joining us virtually and his seminar is entitled: The impact of high structure course design across courses, disciplines, and universities. Zoom: https://purdue-edu.zoom.us/j/91764754503<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…> October 27 – 2024 Hertz Fellowship<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fhertzfoun…> Application deadline for doctoral students. January 2 – 6, 2024. BMES – CMBE Conference. San Juan, Puerto Rico. Accepting abstracts – deadline September 12. Conference details: https://www.bmes.org/cmbe2024<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.bmes.…> BII Annual Conference - January 22nd - Hold the Date. Details on the agenda will be shared when available. NSF is planning a hybrid one day meeting. Expecting most will be virtual, with a few of us possibly in person at NSF headquarters. Hot Off the Press: New EMBRIO Journal Papers Let us know about new papers you want to highlight for the EMBRIO community! 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.” Awards Congrats to Dr. Krishna Jayant being awarded by DoD for his project grant entitled “A Traveling Wave Basis for Coding Touch: Unraveling recurrent and translaminar circuit contributions to sensory-evoked traveling waves” Open Positions 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://app.box.com/s/frd9275xc069gmgtbe3y1osoz1j7ssk7<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> ) Submit your items for the next newsletter by Oct. 13th to Brent (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 <https://www.purdue.edu/research/embrio/>

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Today's Weekly: Part II of Physics Informed Machine Learning and a 'Mentoring Snack'
by Ladd, Brent Thomas 02 Oct '23

02 Oct '23

Today's Weekly will feature Part II of Physics Informed Machine Learning hands-on led by Dr. Adrian Buganza Tepole. Our session will begin with a "mentoring snack"; insights on mentoring best practices from the ABIDES program. Don't miss it! Google Colab for today's session: https://colab.research.google.com/drive/1wloCgDIItT_BxDp4Gs5xvntNkshzCnAV?u…<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcolab.res…> [https://colab.research.google.com/img/colab_favicon_256px.png]<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcolab.res…> Google Colaboratory<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcolab.res…> colab.research.google.com Last week's Part I video recording<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> is available on Box under the Weekly Meeting Recordings folder. Mini workshop: Physics informed machine learning Machine learning has impacted all fields of engineering. Artificial neural networks are universal function approximators. Thus, it is not surprising that they can be used to represent the types of functions that arise as solution of ordinary or partial differential equations (ODEs or PDEs respectively). ODEs and PDEs are natural mathematical models for many physical phenomena such as diffusion, heat transfer, and mechanical equilibrium. Previous workshops as part of EMBRIO have already focused on the solution of ODEs and PDEs with more traditional methods, namely finite differences. This workshop builds on that knowledge and explores the use of artificial neural networks for the solution of the same kinds of problems. We will introduce JAX, a numerical linear algebra package which is an alternative to other, perhaps more popular machine learning tools such as pytorch. The reason to do the workshop around JAX is that this library allows for just-in-time compilation of code and vectorization which make it very efficient. Additionally, if attendees are familiar with the standard python packages numpy and scipy then JAX will hopefully require a less steep learning curve. Using JAX we will show that the PDEs of interest can be used as part of the loss function such that minimization of this objective yields the PDE solution. 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 <https://www.purdue.edu/research/embrio/>

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