February 2024 - Embrio-list

EMERGENCE newsletter issue 32: February 28, 2024
by Ladd, Brent Thomas 28 Feb '24

28 Feb '24

[cid:20cd9def-65e5-47c7-97b8-9c429532253a] Emergence: A biweekly newsletter of discovery, education, and outreach from the EMBRIO Institute Issue 32: February 28, 2024 DIRECTORS’ NOTE As we march toward spring (and spring break), we’ll have to cope with an extra day in February tomorrow, apparently the 2nd least favorite month next to January. Take heart, there are many signs that spring is just around the corner. The local weather czar near Purdue predicts we’ll hit 70F on Sunday. Thanks to all who tuned in on Monday for the Directors update. If you missed it, you could watch the recording on Box (All-Hands Meeting Recordings > 2024 > 2024-02-28_All-Hands_Directors-Update<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> ). Following spring break(s), our next all-hands seminar on March 18th will feature Dr. Jeremy Zartman presenting the research in Thrust 2b. It was announced that our third annual Summer School (previously referred to as Training Workshop) will be held July 8th – 10th, followed by our All-Hands Annual Meeting, July 11th-12th, both hosted in-person at Purdue. Please complete this RSVP<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue.ca…> for either/ both events. Calendar invites have been emailed to all members. The theme for the Summer School will benefit all Institute members (more in this issue). The Gardner lab is conducting the third annual evaluation survey supporting Thrust 4 research into the interdisciplinary nature of the Institute, as well as supporting continual improvement and feedback for the structure and functioning of EMBRIO. Individual emails were delivered to each active member’s inbox on Monday via the Qualtrics Survey System. Please complete this mandatory survey by March 8th at the latest! In addition, an NSF BII-wide effort that is supported with an RCN grant, is gearing up to develop targeted mentoring resources and trainings for everyone engaged in interdisciplinary research. The working group has requested that EMBRIO members participate in this input survey RCN interdisciplinary mentorship survey<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcolostate…>. A reminder that there are still members who have not yet signed the Institute’s Data Sharing Policy. PI’s make sure those in your lab working on EMBRIO research use this URL to review and sign<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue.ca…> (you can use your mouse to sign, or if using phone/tablet your finger). On Wednesday, March 6th, Dr. Elsje Pienaar and the BME Dept. at Purdue is hosting Dr. Melissa Kemp<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbme.gatec…>, who is the Carol Ann and David D. Flanagan Professor of BME at Georgia Tech/Emory for our BME department seminar. (9:30 a.m. in MRGN 121, Zoom link TBD). She is a leader in systems biology and analytical methods to study how cell populations respond metabolically to oxidative stress, and how inter-cellular variability and protein networks affect these responses in stem cells, cancer cells and other systems. She has also led several multi-site NSF centers and won multiple graduate mentoring awards. If you are interested in meeting with her on March 5th, during the day or for a meal, please add your name to this schedule document<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.goog…> (available spots or highlighted in yellow). Jeremy Zartman, Greg Reeves, and Linlin Li have organized an EMBRIO workshop during The Allied Genetics Conference (TAGC24), March 9th 2-4pm, in Washington D.C. (Genetics Society of America). https://genetics-gsa.org/tagc-2024/<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgenetics-…> . Titled Advancing Computational Developmental Biology: Integrating Experimental and Computational Systems Approaches. Speakers include Drs. Zartman, Reeves, Kumar, Deng, W. Zhang, Glazier, Brubaker, and Li. A description and full schedule are in this issue. We will endeavor to share the slide decks from the workshop. Take advantage of related outside professional development opportunities including the Chicago Cytoskeleton Lightning Talks and Poster Session on March 15 (details in this issue), a series at Purdue on open science and research data management<https://blogs.lib.purdue.edu/news/2024/01/26/empowering-research-a-trio-of-…> (next up is on March 1st “Introduction to the Open Science Framework: A platform to facilitate open research and scholarship” with Dr. Reid Boehm), and a future mentors program for graduate students<https://honors.purdue.edu/current-students/Undergraduate-Research/mentorshi…>. Stay tuned for an announcement of the 2024 CompuCell3D<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcompucell…> summer workshop dates (typically in late July and early August) that EMBRIO members have benefited from the last few years. David, Chris, Anjali, Janice, Jeremy, Alejandra, and Brent Notable Quote "Never be limited by other people's limited imaginations." - Dr. Mae Jemison, first African American female astronaut. February is Black History Month.<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.black…> QUICK LINKS Sign the Data Sharing Policy Agreement<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue.ca…> RSVP: EMBRIO Summer School & Annual Meeting<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue.ca…> All-Hands Meetings Recordings<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> RCN interdisciplinary mentorship survey<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcolostate…> Orientation to EMBRIO<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> ABIDES Culture and Mentoring resources<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> EMBRIO SUMMER SCHOOL July 8-10, 2024. Summer School (followed by the Annual Meeting, July 11-12th). Hosted at Purdue, Please complete this RSVP<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue.ca…> asap. All Institute members are encouraged to participate. There may be room for graduate TA’s at Purdue outside of EMBRIO to also participate. EMBRIO INSTITUTE’S 3rd ANNUAL SUMMER SCHOOL: Communicating your research with novice audiences through computational media. Participants will identify a topic of their research (or teaching) that they want to make accessible to novice audiences. Following best practices of learning design or mentoring, participants will create a product (e.g., a computational Colab notebook, a digital poster, a Prezi presentation, or similar) to teach or communicate their selected topic to broader audiences. The products will be broadly disseminated through the Institute. EMBRIO Institute's 2nd Annual Summer Training Workshop took place July 10-12, 2023. 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 EMBRIO INSTITUTE’S 3rd ANNUAL ALL-HANDS MEETING: July 11-12, 2024, at Purdue University. Please complete this RSVP<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue.ca…> asap. Last year the annual meeting brought more than sixty EMBRIO members engaging in research talks, poster presentations, programmatic discussions, and informal gatherings. A call for posters and talks will be forthcoming. EMBRIO WORKSHOP AT TAGC24 Title: Advancing Computational Developmental Biology: Integrating Experimental and Computational Systems Approaches Date/Time: Saturday, March 9, 2:00-4:00 pm Description :This workshop delves into the integration of experimental and computational approaches in systems developmental biology, with talks covering the majority of model systems included in TAGC including Drosophila, zebrafish, mammalian cells, and plants. Participants will explore computational modeling approaches, including mechanistic models that are calibrated or tested through a combination of optogenetics, live tissue imaging, and genetics. The workshop aims to foster a synergy between modeling and experiments, providing attendees with transferable skills and knowledge to advance their research in developmental biology through the application of mechanistic and data-driven computational approaches. The focus on computational modeling, including ODE and PDE models differentiates this workshop from other platform sessions. Organizers : Dr. Jeremiah Zartman, Dr. Gregory Reeves Dr. Linlin Li Schedule: Time: 2:00 pm, Dr. Jeremiah Zartman, University of Notre Dame, Title: Introductory remarks Time: 2:05 pm, Dr. Gregory Reeves, Texas A&M University, Title: Can We Make Developmental Biology as Quantitative as Chemical Engineering? Time: 2:20 pm, Dr. Nilay Kumar, University of Notre Dame, Title: Piezo regulates epithelial topology and promotes precision in organ size control Time: 2:35 pm, Dr. Qing Deng, Purdue University, Title: Modeling immediate calcium wave after tailfin amputation in zebrafish Time: 2:50 pm, Dr. WeiWei Zhang, Purdue University, Title: Decoding Ca2+ signatures and signaling to the actin cytoskeleton in plant immune response. Time: 3:05 pm, Dr. James Glazier, Indiana University Bloomington Title: Using Virtual Tissue Computer Simulations to Explore Biological Mechanisms Across Scales Time: 3:25 pm, Dr. Douglas Brubaker, Case Western Reserve University, Title: Bridging Animal and Human Biology via Computational Systems Biology Approaches Time: 3:45 pm, Dr. Linlin Li, Purdue University, Title: Modeling the BMP patterning formation of Zebrafish Embryo with Quantitative Analysis of Imaging Data 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) incoming president, 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 ABIDES (Access, Belonging, Inclusion, Diversity, Equity, Support) Dr. Anjali Iyer-Pascuzzi, EMBRIO ABIDES Director and Professor at Purdue, leads activities for Institute members. A session on mentorship and project management<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> was presented January 29th. A series of mentoring topics were presented at the beginning of Weekly meetings this past Fall, and a continuation of the Mentoring Panel topics from the annual retreat was presented October 23rd , 2023 during the EMBRIO Weekly with a deeper dive into how culture impacts our mentoring and team thinking. BTW, if you missed “The role of culture and communication in mentoring” mini-workshop – view it here,<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> or the previous “mentoring snacks” 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. 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…> UPCOMING DEADLINES, IMPORTANT DATES, & INFO EMBRIO All-hands Meeting Schedule, Monday’s 3-4pm ET. Zoom<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…>. All Hands Zoom Meeting Recordings<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> Jan 8 Thrust 4 Seminar 15 No Meeting: MLK Day 22 BII Conference - NSF Headquarters and Zoom 29 ABIDES topic: Project Management Feb 5 break 12 postponed 19 break 26 Open Forum: State of the Institute and open discussion March 4 break 11 No Meeting: Spring Break 18 Thrust 2b Seminar 25 break April 1 TBD: “Promoting Reproducible Science: How to manage and share your research data”. 8 break 15 Thrust 1 Seminar 22 break 29 Thrust 1 Seminar May 6 Thrust 3a Seminar 13 break 20 Thrust 3b Seminar 27 No Meeting: Memorial Day March 5-6, 2024. Dr. Elsje Pienaar and the BME Dept. at Purdue is hosting Dr. Melissa<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbme.gatec…> <https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbme.gatec…> Kemp<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbme.gatec…>, who is the Carol Ann and David D. Flanagan Professor of BME at Georgia Tech/Emory for our BME department seminar. (9:30 a.m. in MRGN 121, Zoom link TBD). She is a leader in systems biology and analytical methods to study how cell populations respond metabolically to oxidative stress, and how inter-cellular variability and protein networks affect these responses in stem cells, cancer cells and other systems. She has also led several multi-site NSF centers and won multiple graduate mentoring awards. If you are interested in meeting with her on March 5th, during the day or for a meal, please add your name to this schedule document<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.goog…> (available spots or highlighted in yellow). March 6-10, 2024. The Allied Genetics Conference (TAGC24). Washington D.C. (Genetics Society of America). https://genetics-gsa.org/tagc-2024/<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgenetics-…> See details above. March 15, 2024. Chicago Cytoskeleton Lightning Talks and Poster Session, Northwestern University, Feinberg School of Medicine. (see details below) July 8-12, 2024. Summer School & Annual Meeting. Hosted at Purdue, Summer School will be July 8th – 10th, followed by our All-Hands Annual Meeting, July 11th-12th. Please complete this RSVP<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue.ca…> asap. See details above. Spring Semester Series on Empowering Research: A Trio of Open Science Workshops to Ignite Innovation. (in person only) Website<https://blogs.lib.purdue.edu/news/2024/01/26/empowering-research-a-trio-of-…> Workshop #2: Unleashing Open Research Potential with Reid Boehm, Ph.D. “Introduction to the Open Science Framework: A platform to facilitate open research” Date: March 1, 2024 Time: 10:00 to 11:15 AM Location: WALC 2051 On March 1st, explore the Open Science Framework (OSF) with Dr. Reid Boehm, Research Data Systems Manager. The OSF is a free platform that supports researchers in managing, sharing, and collaborating on projects. Gain insights into its features, functions, and flexible utilities that cater to diverse aspects of the open research process. This workshop is your gateway to harnessing the benefits of OSF as a Purdue University affiliate. Workshop #3: Navigating Open Access Publishing with Nina Collins, M.L.I.S. “Open Access Publishing: Opportunities and pathways for wider dissemination of your scholarship” Date: April 1, 2024 Time: 10:00 to 11:15 AM Location: WALC 2051 Join Nina Collins, an advocate for Open Access, to navigate the world of Open Access publishing. This workshop will delve into the challenges researchers face and uncover the multitude of pathways available for Purdue authors. Learn how Open Access Publishing Partnerships can remove financial barriers, providing opportunities for broader dissemination, use, and impact of your scholarly work. Don’t miss this chance to explore ethical publishing practices and increase your scholarly impact. Embark on this comprehensive exploration of Open Science and equip yourself with the tools and knowledge to drive your research forward. We invite you to attend these workshops, engage with experts, and contribute to the vibrant culture of openness and collaboration in our academic community. Course – HONR 59901 Future Mentors Program Research Mentorship Training for Graduate Students (at Purdue, in person only). More info and to apply<https://honors.purdue.edu/current-students/Undergraduate-Research/mentorshi…>. Purpose of the Program Effective mentorship requires specific skillsets and approaches. Implementation of these strategies can lead to mutually beneficial experiences for both mentors and mentees. The Future Mentors program offers research mentorship training for graduate students who are or would like to begin mentoring undergraduates in STEM research. This program is ideal for doctoral students who plan to pursue a career in academia or leadership roles in industry. The March Chicago Cytoskeleton meeting and poster contest is coming up soon, Friday March 15. Contact Holly Goodson (hgoodson(a)nd.edu<mailto:hgoodson@nd.edu>) with questions or concerns! At this meeting, we will have four regular (20 +10 minute) talks, plus the yearly CC poster session. And, as last year, we are holding an associated lightning talk contest to determine who are the four trainees who will speak April 19th alongside our plenary speaker Dan Fletcher (UC Berkeley). The winners of this contest will be announced at the March 15 meeting. Speakers March 15 will be: Noah Mitchell (KITP; incoming faculty member at University of Chicago) Katie Drerup (University of Wisconsin - Madison) Dileep Varma (Northwestern Feinberg School of Medicine) Greg Smith. (Northwestern Feinberg School of Medicine) Titles to come soon! Key points about the lightning talk contest and poster session: Did you or someone in your lab present a lightning talk or poster at ASCB, Biophysics, or another conference? Give that presentation a new life through Chicago Cytoskeleton! Or perhaps you want to put together a new presentation? CC is a great place to try it out! • If you want to compete for an April 19 speaker slot: please submit (details below) a pre-recorded 3-5 minute lightning talk that will be viewed and judged by the Steering Committee. > The Deadline for submitting your recording is Wednesday March 6. • If you just want to present a poster without competing: please simply submit an abstract by the same deadline (Wednesday March 6). More information about the poster session and associated competition is provided below. CC Meeting Place and time: Sessions are held in the Lurie Medical Research Center at the Feinberg School of Medicine. For the March 15 meeting, talks will start at 3:00 and continue until ~5:00, followed by the poster session with refreshments. There is no registration fee - just join us! Parking: If you would like a parking coupon, please fill out this form (coupons will be distributed at the meeting): https://forms.feinberg.northwestern.edu/view.php?id=2879544<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fforms.fei…> We look forward to seeing you Friday March 15! -Holly Goodson and the Chicago Cytoskeleton Steering Committee ****** LIGHTNING TALK AND POSTER ABSTRACT SUBMISSION INFO******** If you want to participate in the lightning talk competition: 1) Please ASAP send an email to me (hgoodson(a)nd.edu<mailto:hgoodson@nd.edu>) with the subject line "CC lightning talk competition." I'll then email you a non-public Google Drive link into which you can submit your e-poster talk as well your abstract and (recommended but not required) a PDF of the associated poster. The only people with access to this link will be the poster submitters and the Steering Committee. 2) Please create in this Google Drive a folder with you name, and put in this folder: i) your pre-recorded lightning talk (3-5 minutes) ii) the abstract for the associated poster (we will put this along with the other abstracts in the ebooklet for the March 15 meeting) iii) a PDF of your poster (helpful but not required for following along with your talk; if you prefer, you can submit slides instead of a poster). >> Please upload all this information by the deadline of Wednesday March 6. If you simply want to present a poster March 15: By Wednesday March 6, please send an email to me (hgoodson(a)nd.edu<mailto:hgoodson@nd.edu>) with the subject line "CC poster abstract", and attach your abstract in .docx format > Please be sure to include the title (!), authors, and affiliations in your file. > Please be sure to use .docx and not PDF. Other notes: • For your recording, please use Zoom or a similar method, presenting your poster via presenter mode. Alternatively, you could prepare and present separate slides. Either works. • Please keep the talk and poster to reasonable sizes - less than 25MB if possible. • Please let me (hgoodson(a)nd.edu<mailto:hgoodson@nd.edu>) know if you have any questions or concerns! Hot Off the Press: New EMBRIO Journal Papers 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…> 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 Let us know about your grants and other awards! 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> ) Submit your items for the next newsletter by March 15th 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

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Today's All-hands Session at 3pm ET
by Ladd, Brent Thomas 26 Feb '24

26 Feb '24

Dear EMBRIO Members, Our all-hands session this afternoon at 3 has been slated as an overall State of the Institute session. We'll also have a short presentation from SLC President, David Gazzo, and we'll cover upcoming Institute events and deadlines, with time for questions/discussions. See you there! 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 Institute Evaluation Survey
by Gardner, Stephanie M 22 Feb '24

22 Feb '24

Dear Members of the EMBRIO Institute, As part of our Institute evaluation for our own continuous improvement, reporting to NSF, and research you will be receiving individual invitations through Qualtrics to complete an institutional survey for the year 3 evaluation. Please remember to check your spam and junk folders and it is best to complete this survey on your desktop/table/laptop computer. Participation in the evaluation is required, and the deadline for submitting your responses is 8th March 2024. You will only be required to complete this survey once a year and the survey should not take you more than 20 minutes to complete. Your feedback is invaluable in shaping activities and contributing to the ongoing improvement of the institute Thanks, Stephanie and Soumi -- Stephanie M. Gardner Associate Professor Associate Head for Curriculum, Teaching, and Learning Faculty Director for the Undergraduate Science Scholars Program Department of Biological Sciences 915 Mitch Daniels Blvd, Lilly 2-226 Purdue University West Lafayette, IN 47907 (765) 496-2936 Lab website: https://www.bio.purdue.edu/lab/gardner/ my Pronouns: She | Her | Hers |

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Emergence Newsletter Issue 31, February 14, 2024
by Ladd, Brent Thomas 14 Feb '24

14 Feb '24

[cid:d7c6f108-4390-4677-beed-c519bc44ada0] Emergence: A biweekly newsletter of discovery, education, and outreach from the EMBRIO Institute Issue 31: February 14, 2024 DIRECTORS’ NOTE EMBRIO held its second annual Winter Science Retreat last week in Indianapolis, with thrust and site leaders and key investigators of the Institute together in person. Marking the middle of year three of our Institute, thrust leaders presented recent research findings, along with updates to research goals, insights into challenges and existing gaps, with plans for remaining NSF period three activity. Open discussions and input took place on updating integration goals of our strategic plan<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.goog…>, the use of generative AI in science writing, and authorship guidelines. The leadership team is currently discussing an Institute policy regarding generative AI use for written and science products produced under support of EMBRIO Institute funding. With respect to authorship, please note that EMBRIO agreed in our NSF awarded proposal to adhere to the International Committee of Medical Journal Editors for authorship credit. Refer to ICMJE for authorship guidelines<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.icmje…>, with all involved in collaborations to have authorship discussions early and often. Our third annual Summer School (previously referred as Training Workshop) will be held July 8th – 10th, followed by our All-Hands Annual Meeting, July 11th-12th, both hosted in-person at Purdue. Please complete this RSVP<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue.ca…> for either/ both events asap. Calendar invites were emailed to all members. The theme for the Summer School will be: Communicating your research with novice audiences through computational media Participants will identify a topic of their research (or teaching) that they want to make accessible to novice audiences. Following best practices of learning design or mentoring, participants will create a product (e.g., a computational Colab notebook, a digital poster, a Prezi presentation, or similar) to teach or communicate their selected topic to broader audiences. The products will be broadly disseminated through the Institute. Jeremy Zartman, Greg Reeves, and Linlin Li have organized an EMBRIO workshop during the The Allied Genetics Conference (TAGC24), March 9th 2-4pm, in Washington D.C. (Genetics Society of America). https://genetics-gsa.org/tagc-2024/<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgenetics-…> . Titled Advancing Computational Developmental Biology: Integrating Experimental and Computational Systems Approaches, speakers include Drs. Zartman, Reeves, Kumar, Deng, W. Zhang, Glazier, Brubaker, and Li. A description and full schedule are in this issue. For those yet to sign the Data Sharing Policy, use this URL (you can use your mouse to sign, or if using phone/tablet your finger): https://purdue.ca1.qualtrics.com/jfe/form/SV_25Zs5169Rs1MCNg<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue.ca…> Our next all-hands session is planned for February 26th as an open forum, where the leadership team will provide an update on the state of the Institute with open discussion and feedback, plus a brief overview of Student Leadership Council opportunities. Take advantage of related outside professional development opportunities including the Chicago Cytoskeleton Lightning Talks and Poster Session, March 15 (details in this issue), a series at Purdue on open science and research data management<https://blogs.lib.purdue.edu/news/2024/01/26/empowering-research-a-trio-of-…> (next up is on March 1st “Introduction to the Open Science Framework: A platform to facilitate open research and scholarship” with Dr. Reid Boehm), and a future mentors program for graduate students<https://honors.purdue.edu/current-students/Undergraduate-Research/mentorshi…>. David, Chris, Stephanie, Anjali, Janice, Jeremy, and Brent Notable Quote "Darkness cannot drive out darkness: only light can do that. Hate cannot drive out hate: only love can do that." ~Rev. Dr. Martin Luther King, Jr. February is Black History Month.<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.black…> QUICK LINKS Sign the Data Sharing Policy Agreement<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue.ca…> RSVP: EMBRIO Summer School & Annual Meeting<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue.ca…> All-Hands Meetings Recordings<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> Orientation to EMBRIO<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> ABIDES Culture and Mentoring resources<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> EMBRIO SUMMER SCHOOL July 8-10, 2024. Summer School (followed by the Annual Meeting, July 11-12th). Hosted at Purdue, Please complete this RSVP<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue.ca…> asap. EMBRIO INSTITUTE’S 3rd ANNUAL SUMMER SCHOOL: Communicating your research with novice audiences through computational media. Participants will identify a topic of their research (or teaching) that they want to make accessible to novice audiences. Following best practices of learning design or mentoring, participants will create a product (e.g., a computational Colab notebook, a digital poster, a Prezi presentation, or similar) to teach or communicate their selected topic to broader audiences. The products will be broadly disseminated through the Institute. EMBRIO Institute's 2nd Annual Summer Training Workshop took place July 10-12, 2023. 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 EMBRIO INSTITUTE’S 3rd ANNUAL ALL-HANDS MEETING: July 11-12, 2024, at Purdue University. Please complete this RSVP<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue.ca…> asap. Last year the annual meeting brought more than sixty EMBRIO members engaging in research talks, poster presentations, programmatic discussions, and informal gatherings. A call for posters and talks will be forthcoming. EMBRIO WORKSHOP AT TAGC24 Title: Advancing Computational Developmental Biology: Integrating Experimental and Computational Systems Approaches Date/Time: Saturday, March 9, 2:00-4:00 pm Description :This workshop delves into the integration of experimental and computational approaches in systems developmental biology, with talks covering the majority of model systems included in TAGC including Drosophila, zebrafish, mammalian cells, and plants. Participants will explore computational modeling approaches, including mechanistic models that are calibrated or tested through a combination of optogenetics, live tissue imaging, and genetics. The workshop aims to foster a synergy between modeling and experiments, providing attendees with transferable skills and knowledge to advance their research in developmental biology through the application of mechanistic and data-driven computational approaches. The focus on computational modeling, including ODE and PDE models differentiates this workshop from other platform sessions. Organizers : Dr. Jeremiah Zartman, Dr. Gregory Reeves Dr. Linlin Li Schedule: Time: 2:00 pm, Dr. Jeremiah Zartman, University of Notre Dame, Title: Introductory remarks Time: 2:05 pm, Dr. Gregory Reeves, Texas A&M University, Title: Can We Make Developmental Biology as Quantitative as Chemical Engineering? Time: 2:20 pm, Dr. Nilay Kumar, University of Notre Dame, Title: Piezo regulates epithelial topology and promotes precision in organ size control Time: 2:35 pm, Dr. Qing Deng, Purdue University, Title: Modeling immediate calcium wave after tailfin amputation in zebrafish Time: 2:50 pm, Dr. WeiWei Zhang, Purdue University, Title: Decoding Ca2+ signatures and signaling to the actin cytoskeleton in plant immune response. Time: 3:05 pm, Dr. James Glazier, Indiana University Bloomington Title: Using Virtual Tissue Computer Simulations to Explore Biological Mechanisms Across Scales Time: 3:25 pm, Dr. Dougla Brubaker, Case Western Reserve University, Title: Bridging Animal and Human Biology via Computational Systems Biology Approaches Time: 3:45 pm, Dr. Linlin Li, Purdue University, Title: Modeling the BMP patterning formation of Zebrafish Embryo with Quantitative Analysis of Imaging Data 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) incoming president, 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 ABIDES (Access, Belonging, Inclusion, Diversity, Equity, Support) Dr. Anjali Iyer-Pascuzzi, EMBRIO ABIDES Director and Professor at Purdue, leads activities for Institute members. A session on mentorship and project management<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> was presented January 29th. A series of mentoring topics were presented at the beginning of Weekly meetings this past Fall, and a continuation of the Mentoring Panel topics from the annual retreat was presented October 23rd during the EMBRIO Weekly with a deeper dive into how culture impacts our mentoring and team thinking. BTW, if you missed “The role of culture and communication in mentoring” mini-workshop – view it here,<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> or the previous “mentoring snacks” 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. 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…> UPCOMING DEADLINES, IMPORTANT DATES, & INFO EMBRIO All-hands Meeting Schedule, Monday’s 3-4pm ET. Zoom<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…>. All Hands Zoom Meeting Recordings<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> Jan 8 Thrust 4 Seminar 15 No Meeting: MLK Day 22 BII Conference - NSF Headquarters and Zoom 29 ABIDES topic: Project Management Feb 5 break 12 postponed 19 break 26 Open Forum: State of the Institute and open discussion March 4 break 11 No Meeting: Spring Break 18 Thrust 2 Seminar 25 break April 1 Guest Speaker TBD 8 break 15 Thrust 1 Seminar 22 break 29 Trainee topic or Speaker TBD May 6 Thrust 3 Seminar 13 break 20 Speaker TBD 27 No Meeting: Memorial Day March 6-10, 2024. The Allied Genetics Conference (TAGC24). Washington D.C. (Genetics Society of America). https://genetics-gsa.org/tagc-2024/<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgenetics-…> See details above. March 15, 2024. Chicago Cytoskeleton Lightning Talks and Poster Session, Northwestern University, Feinberg School of Medicine. (see details below) July 8-12, 2024. Summer School & Annual Meeting. Hosted at Purdue, Summer School will be July 8th – 10th, followed by our All-Hands Annual Meeting, July 11th-12th. Please complete this RSVP<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue.ca…> asap. See details above. Spring Semester Series on Empowering Research: A Trio of Open Science Workshops to Ignite Innovation. (in person only) Website<https://blogs.lib.purdue.edu/news/2024/01/26/empowering-research-a-trio-of-…> Workshop #2: Unleashing Open Research Potential with Reid Boehm, Ph.D. “Introduction to the Open Science Framework: A platform to facilitate open research” Date: March 1, 2024 Time: 10:00 to 11:15 AM Location: WALC 2051 On March 1st, explore the Open Science Framework (OSF) with Dr. Reid Boehm, Research Data Systems Manager. The OSF is a free platform that supports researchers in managing, sharing, and collaborating on projects. Gain insights into its features, functions, and flexible utilities that cater to diverse aspects of the open research process. This workshop is your gateway to harnessing the benefits of OSF as a Purdue University affiliate. Workshop #3: Navigating Open Access Publishing with Nina Collins, M.L.I.S. “Open Access Publishing: Opportunities and pathways for wider dissemination of your scholarship” Date: April 1, 2024 Time: 10:00 to 11:15 AM Location: WALC 2051 Join Nina Collins, an advocate for Open Access, to navigate the world of Open Access publishing. This workshop will delve into the challenges researchers face and uncover the multitude of pathways available for Purdue authors. Learn how Open Access Publishing Partnerships can remove financial barriers, providing opportunities for broader dissemination, use, and impact of your scholarly work. Don’t miss this chance to explore ethical publishing practices and increase your scholarly impact. Embark on this comprehensive exploration of Open Science and equip yourself with the tools and knowledge to drive your research forward. We invite you to attend these workshops, engage with experts, and contribute to the vibrant culture of openness and collaboration in our academic community. Course – HONR 59901 Future Mentors Program Research Mentorship Training for Graduate Students (at Purdue, in person only). More info and to apply<https://honors.purdue.edu/current-students/Undergraduate-Research/mentorshi…>. Purpose of the Program Effective mentorship requires specific skillsets and approaches. Implementation of these strategies can lead to mutually beneficial experiences for both mentors and mentees. The Future Mentors program offers research mentorship training for graduate students who are or would like to begin mentoring undergraduates in STEM research. This program is ideal for doctoral students who plan to pursue a career in academia or leadership roles in industry. The March Chicago Cytoskeleton meeting and poster contest is coming up soon, Friday March 15. Contact Holly Goodson (hgoodson(a)nd.edu<mailto:hgoodson@nd.edu>) with questions or concerns! At this meeting, we will have four regular (20 +10 minute) talks, plus the yearly CC poster session. And, as last year, we are holding an associated lightning talk contest to determine who are the four trainees who will speak April 19th alongside our plenary speaker Dan Fletcher (UC Berkeley). The winners of this contest will be announced at the March 15 meeting. Speakers March 15 will be: Noah Mitchell (KITP; incoming faculty member at University of Chicago) Katie Drerup (University of Wisconsin - Madison) Dileep Varma (Northwestern Feinberg School of Medicine) Greg Smith. (Northwestern Feinberg School of Medicine) Titles to come soon! Key points about the lightning talk contest and poster session: Did you or someone in your lab present a lightning talk or poster at ASCB, Biophysics, or another conference? Give that presentation a new life through Chicago Cytoskeleton! Or perhaps you want to put together a new presentation? CC is a great place to try it out! • If you want to compete for an April 19 speaker slot: please submit (details below) a pre-recorded 3-5 minute lightning talk that will be viewed and judged by the Steering Committee. > The Deadline for submitting your recording is Wednesday March 6. • If you just want to present a poster without competing: please simply submit an abstract by the same deadline (Wednesday March 6). More information about the poster session and associated competition is provided below. CC Meeting Place and time: Sessions are held in the Lurie Medical Research Center at the Feinberg School of Medicine. For the March 15 meeting, talks will start at 3:00 and continue until ~5:00, followed by the poster session with refreshments. There is no registration fee - just join us! Parking: If you would like a parking coupon, please fill out this form (coupons will be distributed at the meeting): https://forms.feinberg.northwestern.edu/view.php?id=2879544<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fforms.fei…> We look forward to seeing you Friday March 15! -Holly Goodson and the Chicago Cytoskeleton Steering Committee ****** LIGHTNING TALK AND POSTER ABSTRACT SUBMISSION INFO******** If you want to participate in the lightning talk competition: 1) Please ASAP send an email to me (hgoodson(a)nd.edu<mailto:hgoodson@nd.edu>) with the subject line "CC lightning talk competition." I'll then email you a non-public Google Drive link into which you can submit your e-poster talk as well your abstract and (recommended but not required) a PDF of the associated poster. The only people with access to this link will be the poster submitters and the Steering Committee. 2) Please create in this Google Drive a folder with you name, and put in this folder: i) your pre-recorded lightning talk (3-5 minutes) ii) the abstract for the associated poster (we will put this along with the other abstracts in the ebooklet for the March 15 meeting) iii) a PDF of your poster (helpful but not required for following along with your talk; if you prefer, you can submit slides instead of a poster). >> Please upload all this information by the deadline of Wednesday March 6. If you simply want to present a poster March 15: By Wednesday March 6, please send an email to me (hgoodson(a)nd.edu<mailto:hgoodson@nd.edu>) with the subject line "CC poster abstract", and attach your abstract in .docx format > Please be sure to include the title (!), authors, and affiliations in your file. > Please be sure to use .docx and not PDF. Other notes: • For your recording, please use Zoom or a similar method, presenting your poster via presenter mode. Alternatively, you could prepare and present separate slides. Either works. • Please keep the talk and poster to reasonable sizes - less than 25MB if possible. • Please let me (hgoodson(a)nd.edu<mailto:hgoodson@nd.edu>) know if you have any questions or concerns! 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 Phase II Grant Proposal Award: Design and Instruction of a Team-Based Transdisciplinary Cross-Listed Course in Computational Understanding of Biological Systems and Data. (Ladd, B., Evans, J., Magana, A., Pienaar, E.). $43,448. Issued by Purdue University Innovation Hub · Jan 2024 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 Feb. 23 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

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Monday Announcements (today's seminar session is canceled)
by Ladd, Brent Thomas 12 Feb '24

12 Feb '24

Dear EMBRIO, Due to several conflicts, we must cancel our session this afternoon. We will move it to our next scheduled session Feb. 26th for our Institute-wide updates/feedback/open discussion along with an intro to plans from the SLC. Please note: we'll resume all online attendance for these all-hands sessions and won't attempt to meet in person for these going forward. Thank you to all thrust and site leaders and key investigators that joined together in-person last week for our Winter Science Retreat in Indianapolis where a noticeable increase in integration activity at the Thrust levels was highlighted (EMBRIO made the Purdue News<https://www.purdue.edu/newsroom/purduetoday/releases/2023/Q4/embrio-institu…>). Thrust leaders also presented updates to research goals, insights into challenges, gaps existing, with plans for remaining Y3 activity. Open discussions and input took place on updating our stratetic plan, the use of generative AI in science writing, and authorship guidelines. Please note that in our NSF awarded proposal, EMBRIO agreed to adhere to the International Committee of Medical Journal Editors for authorship credit: ICMJE for authorship guidelines<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.icmje…>. A reminder that all EMBRIO members should read<https://www.purdue.edu/research/embrio/research/DSP.php> and sign<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Foutlook.o…> the recently ratified Data Sharing Policy (Future EMBRIO funding is tied to the policy. PIs make sure your lab members working on EMBRIO projects read and sign the policy.) We have dates for our Summer Training Workshop on July 8th – 10th, followed by our All-Hands Annual Meeting, July 11th-12th, hosted in-person at Purdue. Please complete this RSVP<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue.ca…> asap. A calendar invite was emailed to all members. EMBRIO is leading an in-person workshop, March 6-10, 2024, during the Allied Genetics Conference (TAGC24) in Washington D.C. (Genetics Society of America). https://genetics-gsa.org/tagc-2024/<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgenetics-…> . Contact Dr. Jeremiah Zartman for additional details. Take advantage of outside professional development opportunities including the attached Chicago Cytoskeleton Lightning Talks and Poster Session, March 15; a series at Purdue on open science and research data management<https://blogs.lib.purdue.edu/news/2024/01/26/empowering-research-a-trio-of-…>; mentorship workshop for faculty, and a future mentors program for graduate students<https://honors.purdue.edu/current-students/Undergraduate-Research/mentorshi…>. 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

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EMBRIO Data Mng-Sci Position discussion next Leadership Meet?
by Ladd, Brent Thomas 02 Feb '24

02 Feb '24

Dear Team, Following up from David and Tami talking with Scott Bolton, I had a helpful discussion with Scott about the data manager position and was able to answer most of his questions. He is very interested and said the kinds of things this position can undertake in combination with the science and imaging work being done align well with his skill set and interests. However, I don't think he is interested in only doing the data curation/workflow/management pieces, although he understood those need to come first. From the 45 min discussion with him, I think he does bring most of what we are looking for, though he does have questions about the position (esp. pursuing use of AI tools and technologies (he would like to do this), and room to do some grant writing) that I think are better discussed with this team as a whole. He did say that he has Tami's support to pursue this and can commit to 50% of his time to focus on it. I propose we schedule at least the first or second half of the next Leadership meeting (Feb. 8th 8:30, or 9:00) to have Scott come in to discuss the position with us. Is this doable for you all next week? To what extent can we meet in person for this? (We'll all have just seen each other for two straight glorious days - up for a third morning? Jeremy, you could stay over in West Lafayette Wed night and we can go to breakfast Thurs. morn if you like😀 ) David: summary from yesterday's meeting - Nilay is on board and ready to go. He, Linlin, and Weiwei will all three participate in the retreat next week. Discussion focused on the need to formalize this coordination team to help address some of the growing pains and gaps the Institute needs to address. I think all are in agreement, though Linlin had some input /questions on how to balance everything she's currently doing. Next week's retreat will help a lot to get this started ( could consider mentioning this during your State of the Institute welcome on Tuesday 🙂 ). Everyone, please add on to this with your assessment and thoughts. 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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Recall: EMBRIO Data Mng-Sci Position discussion next Leadership Meet?
by Ladd, Brent Thomas 02 Feb '24

02 Feb '24

laddb(a)purdue.edu would like to recall the message, "EMBRIO Data Mng-Sci Position discussion next Leadership Meet?".

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End of Week Reminders
by Ladd, Brent Thomas 02 Feb '24

02 Feb '24

Dear EMBRIO Folk, A few items here - if you missed yesterday's newsletter, check it out for all the deets and opportunities: Emergence Newsletter Issues<https://www.purdue.edu/research/embrio/newsletters/index.php> We have dates for our Summer Training Workshop on July 8th – 10th, followed by the All-Hands Annual Meeting, July 11th-12th, hosted in-person at Purdue. Please complete this RSVP<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue.ca…> asap. A calendar invite was emailed to all members. Additional details will be shared soon. A reminder that all EMBRIO members should read<https://www.purdue.edu/research/embrio/research/DSP.php> and sign<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Foutlook.o…> the recently ratified Data Sharing Policy (deadline was Jan. 31st, however only half of our members have signed the policy. Future EMBRIO funding is tied to the policy. PIs make sure your lab members working on EMBRIO projects read and sign the policy.) Take advantage of several outside professional development opportunities including a terrific series on open science and research data management<https://blogs.lib.purdue.edu/news/2024/01/26/empowering-research-a-trio-of-…>, mentorship workshop for faculty (see yesterday's newsletter), and a future mentors program for graduate students<https://honors.purdue.edu/current-students/Undergraduate-Research/mentorshi…>. Our next All-hands seminar will be February 12th (in-person for Purdue people) where the leadership team will provide a summary of the PIs Retreat outcomes, as well as covering an orientation to the big picture of EMBRIO<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…>, plus a brief overview of Student Leadership Council opportunities. Thrust and site leaders and key investigators are planning to be together in-person for a two-day collaborative science retreat taking place next week Feb. 6-7th in Indianapolis. Outcomes of the retreat will be shared institute wide. This retreat is focused on in-depth exchanges to foster what is working well, address what isn’t working, share key results and outcomes to date, identify gaps, and plan for higher levels of integration as we enter the second half of year 3 of our NSF funding and begin strategizing for funding renewal. 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

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Emergence Newsletter Issue 30: Feb 1, 2024
by Ladd, Brent Thomas 01 Feb '24

01 Feb '24

[cid:63b7f160-fa2f-41b8-a73b-8b8290f7a33d] Emergence: A biweekly newsletter of discovery, education, and outreach from the EMBRIO Institute Issue 30: February 1, 2024 DIRECTORS’ NOTE The EMBRIO Community has a LOT happening, and upcoming (read this Directors' Note so you are not left out). We have dates for our Summer Training Workshop on July 8th – 10th, followed by our All-Hands Annual Meeting, July 11th-12th, hosted in-person at Purdue. Please complete this RSVP<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue.ca…> asap. A calendar invite was emailed to all members. Additional details will be shared soon. We learned important information and engaged in insightful scientific exchanges during the recent NSF BII Meeting in D.C., and will be sharing those insights, along with a call during our PIs Retreat next week with our NSF Program Officer, Wilson Francisco. We also welcome Nilay Kumar<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.linke…>, whose first day with EMBRIO is today, as a Sr. Research Scientist. Nilay received his Ph.D. with the Zartman lab at Notre Dame and will be working closely with the Pienaar and Buganza Tepole labs, as well as helping to coordinate efforts with the other Research Scientists in EMBRIO. A reminder that all EMBRIO members should read<https://www.purdue.edu/research/embrio/research/DSP.php> and sign<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Foutlook.o…> the recently ratified Data Sharing Policy (deadline was yesterday, however only half of our members have signed the policy. Future EMBRIO funding is tied to the policy. PIs make sure your lab members working on EMBRIO projects read and sign the policy.) Check out the Journal Papers section at the end of this issue for recent publications from the Magana and Pienaar labs, and the Iyer-Pascuzzi and Staiger labs, along with a new book by Alejandra Magana on Teaching and Learning in STEM with Computation, Modeling, and Simulation Practices. Our next All-hands seminar will be February 12th (in-person for Purdue people) where the leadership team will provide a summary of the PIs Retreat outcomes, as well as covering an orientation to the big picture of EMBRIO<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…>, plus a brief overview of the Student Leadership Council opportunities. Our previous seminar<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> , organized by our ABIDES program and led by Javier Muñoz, focused on how mentees can take a leadership role in their mentorship, and an effective method to project management for researchers. Please take advantage of the several outside professional development opportunities shared in this issue, include a terrific series on open science and research data management<https://blogs.lib.purdue.edu/news/2024/01/26/empowering-research-a-trio-of-…>, mentorship workshop for faculty, and a future mentors program for graduate students<https://honors.purdue.edu/current-students/Undergraduate-Research/mentorshi…>. As mentioned above, thrust and site leaders and key investigators are planning to be together in-person for a two-day collaborative science retreat taking place on Feb. 6-7th in Indianapolis. Outcomes of the retreat will be shared institute wide. This retreat is focused on in-depth exchanges to foster what is working well, address what isn’t working, share key results and outcomes to date, identify gaps, and plan for higher levels of integration as we enter the second half of year 3 of our NSF funding and begin strategizing for funding renewal. Today kicks off Black History Month<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.black…> “celebrating the achievements and paying tribute to the generations of African Americans that have struggled against systemic adversity to achieve full citizenship in American society”. Today is also known as Imbolc<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fen.wikipe…> a Celtic calendar cross-quarter day half-way between the winter solstice and the spring equinox, also called St. Brighid’s Day in Ireland (the 1500th anniversary of her death this year). David, Chris, Stephanie, Anjali, Janice, Jeremy, and Brent Notable Quote “Being in a band is always a compromise. Provided that the balance is good, what you lose in compromise, you gain by collaboration.” Michael John Cloete Crawford Rutherford: English guitarist, bassist, songwriter and singer, best known as co-founder of the rock band Genesis. QUICK LINKS RSVP: EMBRIO Summer Workshop & Annual Meeting<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue.ca…> All-Hands Meetings Recordings<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> Orientation to EMBRIO<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> ABIDES Culture and Mentoring resources<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%2Foutlook.o…> 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) incoming president, 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 ABIDES (Access, Belonging, Inclusion, Diversity, Equity, Support) Dr. Anjali Iyer-Pascuzzi, EMBRIO ABIDES Director and Professor at Purdue, leads activities for Institute members. A session on mentorship and project management<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> was presented January 29th. A series of mentoring topics were presented at the beginning of Weekly meetings this past Fall, and a continuation of the Mentoring Panel topics from the annual retreat was presented October 23rd during the EMBRIO Weekly with a deeper dive into how culture impacts our mentoring and team thinking. BTW, if you missed “The role of culture and communication in mentoring” mini-workshop – view it here,<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> or the previous “mentoring snacks” 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. 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 SUMMER WORKSHOP RESOURCES EMBRIO Institute's 2nd Annual Summer Training Workshop took place July 10-12, 2023. 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 All-hands Meeting Schedule, Monday’s 3-4pm ET. Zoom<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…>. All Hands Zoom Meeting Recordings<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> Jan 8 Thrust 4 Seminar 15 No Meeting: MLK Day 22 BII Conference - NSF Headquarters and Zoom 29 ABIDES topic: Project Management Feb 5 break 12 Orientation to EMBRIO/State of the Institute and open discussion (debrief PI’s Retreat) 19 break 26 Guest Speaker TBD March 4 break 11 No Meeting: Spring Break 18 Thrust 2 Seminar 25 break April 1 Guest Speaker TBD 8 break 15 Thrust 1 Seminar 22 break 29 Trainee topic or Speaker TBD May 6 Thrust 3 Seminar 13 break 20 Guest Speaker TBD 27 No Meeting: Memorial Day February 6-7, 2024. EMBRIO Thrust & Site Leads Retreat. Thrust and site leads, and key investigators, will engage in two days of thrust and project working sessions in person (and yes, actual retreat social activity, as well). Logistics have been shared with all involved. March 6-10, 2024. The Allied Genetics Conference (TAGC24). Washington D.C. (Genetics Society of America). https://genetics-gsa.org/tagc-2024/<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgenetics-…> EMBRIO is organizing an in-person workshop at this conference. July 8-12, 2024. Summer Training Workshop & Annual Meeting. Hosted at Purdue, Workshop will be July 8th – 10th, followed by our All-Hands Annual Meeting, July 11th-12th. Please complete this RSVP<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue.ca…> asap. Spring Semester Series on Empowering Research: A Trio of Open Science Workshops to Ignite Innovation. (in person only) Website<https://blogs.lib.purdue.edu/news/2024/01/26/empowering-research-a-trio-of-…> Workshop #1: Maximizing Research Reproducibility with Chao Cai, Ph.D. “Promoting Reproducible Science: How to manage and share your research data” Date: February 12, 2024 Time: 2:00 to 3:30 PM Location: WALC 2088 Reproducibility of research is a key scientific practice gaining attention from funding agencies. Join Dr. Chao Cai, an Assistant Professor and Plant Sciences Information Specialist, on February 12th, as he provides hands-on experience and knowledge for managing quantitative data to maximize research reproducibility. Learn about the principles of FAIR data and effective practices for sharing research data through a data repository. Workshop #2: Unleashing Open Research Potential with Reid Boehm, Ph.D. “Introduction to the Open Science Framework: A platform to facilitate open research” Date: March 1, 2024 Time: 10:00 to 11:15 AM Location: WALC 2051 On March 1st, explore the Open Science Framework (OSF) with Dr. Reid Boehm, Research Data Systems Manager. The OSF is a free platform that supports researchers in managing, sharing, and collaborating on projects. Gain insights into its features, functions, and flexible utilities that cater to diverse aspects of the open research process. This workshop is your gateway to harnessing the benefits of OSF as a Purdue University affiliate. Workshop #3: Navigating Open Access Publishing with Nina Collins, M.L.I.S. “Open Access Publishing: Opportunities and pathways for wider dissemination of your scholarship” Date: April 1, 2024 Time: 10:00 to 11:15 AM Location: WALC 2051 Join Nina Collins, an advocate for Open Access, to navigate the world of Open Access publishing. This workshop will delve into the challenges researchers face and uncover the multitude of pathways available for Purdue authors. Learn how Open Access Publishing Partnerships can remove financial barriers, providing opportunities for broader dissemination, use, and impact of your scholarly work. Don’t miss this chance to explore ethical publishing practices and increase your scholarly impact. Embark on this comprehensive exploration of Open Science and equip yourself with the tools and knowledge to drive your research forward. We invite you to attend these workshops, engage with experts, and contribute to the vibrant culture of openness and collaboration in our academic community. Course – HONR 59901 Future Mentors Program Research Mentorship Training for Graduate Students (at Purdue, in person only). More info and to apply<https://honors.purdue.edu/current-students/Undergraduate-Research/mentorshi…>. Purpose of the Program Effective mentorship requires specific skillsets and approaches. Implementation of these strategies can lead to mutually beneficial experiences for both mentors and mentees. The Future Mentors program offers research mentorship training for graduate students who are or would like to begin mentoring undergraduates in STEM research. This program is ideal for doctoral students who plan to pursue a career in academia or leadership roles in industry. Faculty Session (Purdue, in person): My Voice, My Story: Understanding the Untold Lived Experiences of Graduate and Professional Students: 2/6 | 10:00 AM - 12:00 PM | YONG 175 | Lunch Provided My Voice, My Story pairs video monologues - constructed from the experiences of real graduate students - with facilitated discussion. The primary objective is to utilize the power of narrative to achieve a greater understanding of the depth and breadth of the lived experiences of graduate and professional students. Through stories and discussion, participants explore a more inclusive and supporting research and mentoring environments. RSVP to Alli Loy at Loy2(a)purdue.edu<mailto:Loy2@purdue.edu> Listening to and discussing the stories of the characters portrayed in the My Voice, My Story monologues provides participants with opportunities for learning through: * Listening for understanding, especially when we think we are different from one another. * Understanding intent versus impact and the possible implications when the two don’t align. * Developing awareness and understanding of experiences of exclusion and inclusion in research and mentoring environments. * Establishing respect for our mutual similarities and differences. * Experiencing empathy for and identification with all of the characters portrayed in the video monologues. * Recognizing instances of implicit bias. * Learning and sharing strategies on how one can contribute to improving the climate of research and mentoring environments. Hot Off the Press: New EMBRIO Journal Papers Let us know about new papers you want to highlight for the EMBRIO community! J ARIGYE, JA LYON, AJ MAGANA, E PIENAAR. 2024. The Reflective Modeling Practitioner: Promoting Self-regulation and Self-confidence in Computational Modeling and Simulation Practices<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fscholar.g…>. International Journal of Engineering Education 40 (1), 179-195. Magana, A.J. 2024. Teaching and Learning in STEM with Computation, Modeling, and Simulation Practices: A Guide for Practitioners and Researchers. Purdue University Press. Hiles, Rachel; Rogers, Abigail; Jaiswal, Namrata; Zhang, Weiwei; Butchacas, Jules; Merfa, Marcus; Klass, Taylor; Kaser, Erica; Jacobs, Jonathan M; Staiger, Christopher J; Matthew J Helm, Iyer-Pascuzzi, Anjali S. A Ralstonia solanacearum type III effector alters the actin and microtubule cytoskeleton to promote bacterial virulence in plants, bioRxiv, https://www.biorxiv.org/content/10.1101/2023.11.01.565113v1<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.biorx…> , 2023, Cold Spring Harbor Laboratory. 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 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 Feb. 9 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

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