- Embrio-list - ecn.purdue.edu

EMBRIO Summer Training Workshop - Registration Open (deadline June 19th)
by Ladd, Brent Thomas 09 Jun '23

09 Jun '23

The EMBRIO Institute's 2nd Annual Summer Training Workshop Registration<https://cvent.me/04V231> is now open! The hard deadline to register is June 19th. Please register only if you are committed to attending! 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 are specifically aimed at benefiting trainees from both computational and experimental domains. Sessions will begin Monday, July 10th at 9am and conclude mid-day Wednesday, July 12th. Goals of the Workshop: * Participants will increase their capacity to connect and converse with each other across the experimental and computational disciplines. * Participants will increase their knowledge, know-how, and confidence using image acquisition, processing, and analysis modalities crucial for advancing research outcomes in the Institute. * Participants will deepen their connections and broaden their personal networks within the Institute. Primary Sessions (will include tutorials and hands-on): * Unit 1: Dr. Sara Cole (Notre Dame) - Microscopy basics, sample preparation, and data acquisition, w/ planned session on using a light sheet microscope * Unit 2: Professor Krishna Jayant and Lab (Purdue) - Fundamentals of image processing, including in-depth sessions on calcium signaling * Unit 3: Professor Gregory Reeves (TAMU) - Raster image correlation spectroscopy (RICS). RICS is a new and novel technique for measuring molecular dynamics and concentrations from fluorescence confocal images. * Unit 4: Dr. Scott Howard (Notre Dame) - Super resolution microscopy techniques and tools * Unit 5: Professor Elsje Pienaar (Purdue) – Data-driven model calibration Detailed workshop itinerary available soon. Logistics: Students and postdocs will stay on the Notre Dame campus with dorm rooms and meals provided (lodging available starting evening of Sunday, July 9th). Faculty and outside guest instructors have the option of making a reservation at nearby hotels<https://www.visitsouthbend.com/notre-dame/hotels/?view=list&sort=qualitySco…>. Carpool and/or shuttle transport will be organized for those traveling from Purdue campus. Please register only if you are committed to attending! Note that this workshop is limited to EMBRIO members only. Brent T. Ladd, Senior Research Program Manager, EMBRIO Institute<https://www.purdue.edu/research/embrio/> Weldon School of Biomedical Engineering Purdue University laddb(a)purdue.edu <https://www.purdue.edu/research/embrio/>

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End of Week Reminders
by Ladd, Brent Thomas 09 Jun '23

09 Jun '23

Dear EMBRIO Members, A reminder that on Monday the 12th during our Weekly Update at 3pm ET we have David Gazzo and Mayesha Mim (Zartman Lab) leading an introduction to scientific figure creation employing BioRender. In advance of the workshop, sign-up and create a BioRender account for free at www.biorender.com<http://www.biorender.com/> so that you can follow along. You will be receiving additional emails specifically about our two main summer events. * EMBRIO Institute's 2nd Annual Summer Training Workshop * EMBRIO Annual Retreat Thanks, Brent ps. I will be away from the office next week w/o reliable internet, back on June 19th Brent T. Ladd, Senior Research Program Manager, EMBRIO Institute<https://www.purdue.edu/research/embrio/> Weldon School of Biomedical Engineering Purdue University laddb(a)purdue.edu <https://www.purdue.edu/research/embrio/>

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EMBRIO Announcements
by Ladd, Brent Thomas 05 Jun '23

05 Jun '23

Dear EMBRIO, Our next Weekly Update takes place Monday June 12th at 3pm ET. David Gazzo and Mayesha Mim (Zartman Lab) will lead an introduction to scientific figure creation employing BioRender. In advance of the workshop, sign-up and create a BioRender account for free at www.biorender.com<http://www.biorender.com/> so that you can follow along during the demo. We are working on finalizing the schedule and registration will be open very soon for the EMBRIO Summer Workshop hosted by the Zartman Lab at Notre Dame July 10-12, followed by our Annual All-Hands Retreat at Purdue July 13-14. See a draft schedule for the workshop (attached) and please complete our RSVP poll<https://purdue.ca1.qualtrics.com/jfe/form/SV_1HcnKhD5uxVQIbs> so that we can best plan the two events, get your input and ideas for additional training this year, and select your size preference on a new EMBRIO T-shirt. Greg Reeves is guest editor for the upcoming special issue of IEEE Transactions on Molecular, Biological, and Multi-scale Communications entitled "Seeing Through the Crowd: Molecular Communication in Crowded and Multi-Cellular Environments". Submissions are invited now - deadline 9/15 (see full message below). Dear Colleagues, We are pleased to invite submissions to the upcoming special issue in IEEE Transactions on Molecular, Biological, and Multi-scale Communications entitled "Seeing Through the Crowd: Molecular Communication in Crowded and Multi-Cellular Environments". You can find the full CFP on the T-MBMC website<https://urldefense.com/v3/__https://www.comsoc.org/publications/journals/ie…>. Please consider submitting and sharing this call with your collaborators. We do welcome contributions from authors outside of IEEE/ComSoc. To facilitate this, initial submissions do not need to follow the IEEE formatting guidelines, as long as the scientific and technical ideas are conveyed clearly. The aim of this Special Issue is to raise a spotlight on the diversity of complex environments and the tools that are needed to describe molecular signaling and communication in these systems. We have a particular interest in biophysical models that have not yet been subject to extensive molecular communication analysis, but contributions using any models that are appropriate for “large” cellular systems are welcome. The list of invited topics includes (but is not limited to) research articles and surveys on the following: * Signal propagation models designed for intercellular environments such as organoids, tissues, organs, tumors, and biofilms * Signal propagation models designed for intracellular environments such as cytoplasm, nuclei, and organelles * Signal propagation models designed for crowded environments (biological or non-biological) such as porous media * Unconventional diffusion modeling, including anisotropic diffusion, anomalous diffusion (superdiffusion or subdiffusion), fractional Brownian motion, and multi-phase diffusion * Biophysical flow modelling, including turbulent and laminar flow * Multi-cellular chemical reaction networks * Design of synthetic or natural communication systems in multi-cellular environments * Communication system analysis in multi-cellular environments * Decentralized cellular decision-making and computation * Experimental methods to apply or detect signals in multi-cellular environments, either in aggregate or at single-cell resolution Manuscript Submission Deadline: 15 September 2023 Publication Date: March 2024 Guest Editors Adam Noel (Lead Guest Editor) University of Warwick, UK Andrew Eckford York University, Canada Radek Erban University of Oxford, UK Matteo Icardi University of Nottingham, UK Gregory Reeves Texas A&M University, USA If you have any questions about this Special Issue, please get in touch with me or any of the other SI Guest Editors (cc'd). Best Regards, Adam On behalf of the SI Guest Editors Dr Adam Noel<https://urldefense.com/v3/__https://warwick.ac.uk/fac/sci/eng/people/adam_n…> | Associate Professor | School of Engineering<https://urldefense.com/v3/__https://warwick.ac.uk/fac/sci/eng/__;!!KwNVnqRv…> (D205) University of Warwick<https://urldefense.com/v3/__https://www2.warwick.ac.uk/__;!!KwNVnqRv!Dqknrs…> | Coventry, UK | CV4 7AL<https://urldefense.com/v3/__https://warwick.ac.uk/about/visiting/maps/inter…> adam.noel(a)warwick.ac.uk<mailto:adam.noel@warwick.ac.uk> | Internal: 74566 | M: 07391 100 137 Hide message history Brent T. Ladd, Senior Research Program Manager, EMBRIO Institute<https://www.purdue.edu/research/embrio/> Weldon School of Biomedical Engineering Purdue University laddb(a)purdue.edu <https://www.purdue.edu/research/embrio/>

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EMBRIO end of week announcements and reminders
by Ladd, Brent Thomas 02 Jun '23

02 Jun '23

Dear EMBRIO Community, Our next Weekly Update takes place Monday June 12th at 3pm ET. David Gazzo and Mayesha Mim (Zartman Lab) will lead an introduction to scientific figure creation employing BioRender. In advance of the workshop, sign-up and create a BioRender account for free at www.biorender.com<http://www.biorender.com/> so that you can follow along during the demo. We are working on finalizing the schedule and registration will be open very soon for the EMBRIO Summer Workshop hosted by the Zartman Lab at Notre Dame July 10-12, followed by our Annual All-Hands Retreat at Purdue July 13-14. See a draft schedule for the workshop (attached) and please complete our RSVP poll<https://purdue.ca1.qualtrics.com/jfe/form/SV_1HcnKhD5uxVQIbs> so that we can best plan the two events, get your input and ideas for additional training this year, and select your size preference on a new EMBRIO T-shirt. Thanks to all who completed the updated demographics survey that NSF asks us to collect and report. If you haven’t yet completed the anonymous survey, it takes about one minute. You can access it here: EMBRIO Demographics Survey 2023<https://purdue.ca1.qualtrics.com/jfe/form/SV_dninhzrnl1EH8Tc>. We've welcomed to campus and into EMBRIO labs at Purdue 12 undergraduates who will be advancing their research skills as they engage in EMBRIO projects throughout the summer (see attached table for names and host investigator labs). We also welcomed Iván Sierra, graduate student in the Cabrera and Isaza lab at UPRM, to Purdue campus last week. He'll be working primarily with the Staiger lab this summer. We submitted our 2nd Annual Report to NSF yesterday, making the new deadline (which was 3 months earlier than the normal Sept. 1 date 😅 ). Thank you to everyone for your timely progress reports and edits along the way. You can access the report on our shared Box account; EMBRIO Institute > Annual Reporting > BII NSF Annual Report 2023: https://app.box.com/s/rxkobfwat4gg4errnvdq1oy0q5xx7zh1 Have a great weekend, Brent Brent T. Ladd, Senior Research Program Manager, EMBRIO Institute<https://www.purdue.edu/research/embrio/> Weldon School of Biomedical Engineering Purdue University laddb(a)purdue.edu <https://www.purdue.edu/research/embrio/>

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EMERGENCE issue 19: May 31, 2023
by Ladd, Brent Thomas 31 May '23

31 May '23

[cid:c7386884-bbba-47b5-ae74-6fa16e3cdf41] Emergence: A biweekly newsletter of discovery, education, and outreach from the EMBRIO Institute Issue 19: May 31, 2023 DIRECTORS’ NOTE Thank you to Nissa Larson (Umulis lab) for presenting her Ph.D. research project during our last meeting: Multiscale Modeling of BMP Signaling Pathway during Zebrafish Embryogenesis. If you missed the presentation, you may access the recording on Box > Weekly Meeting Recordings (recording_Larson_N.)<https://app.box.com/s/vjlm1n394buvt629aox4u23lhaq4kgqt> On June 12th during our Weekly Update David Gazzo and Mayesha Mim (Zartman Lab) will lead an introduction to scientific figure creation employing BioRender (details below). In advance of the workshop, sign-up and create a BioRender account for free at www.biorender.com<http://www.biorender.com/> so that you can follow along. We are working on finalizing the schedule and registration for the EMBRIO Summer Workshop hosted by the Zartman Lab at Notre Dame July 10-12, followed by our Annual All-Hands Retreat at Purdue July 13-14. Please see the entry in this issue for the draft schedule of the workshop and link to an RSVP poll<https://purdue.ca1.qualtrics.com/jfe/form/SV_1HcnKhD5uxVQIbs> so that we can better plan the events, get your input and ideas for additional training, and your size preference on a new EMBRIO t-shirt – a shout out to Shelly Tan in the Deng Lab for her deft design and illustration skills! Check out the training opportunity later this summer with the Glazier Lab & Biocomplexity Institute at IU are offering a two week online live course in basic and advanced CompuCell3D July 31 - August 13. Details to participate are below. Thanks to all who completed the updated demographics survey that NSF asks us to collect and report. If you haven’t yet completed the anonymous survey, it takes about one minute. You can access it here: EMBRIO Demographics Survey 2023<https://purdue.ca1.qualtrics.com/jfe/form/SV_dninhzrnl1EH8Tc>. As we prepare for presentations and posters at conferences, and manuscripts for publication please remember to acknowledge our NSF award:“This work is based upon efforts supported by EMBRIO Institute, contract #2120200, a National Science Foundation (NSF) Biology Integration Institute.” This is necessary in order for us to include your publications and conference papers in our NSF reporting. Find recommended poster and PowerPoint templates, along with EMBRIO and NSF logos on our Box account in the “Poster and Presentation Templates & Logos” folder. Direct Link<https://app.box.com/s/agkalrgrarb7yv1mskiqb5imuxkdtgej>. We want to hear about your news and announcements. Send them to Brent (laddb(a)purdue.edu) by June 16th for inclusion in the next issue of Emergence. David, Chris, Stephanie, Anjali, and Brent Notable Quote “Since all models are wrong, it is very important to know what to worry about; or, to put it in another way, what models are likely to produce procedures that work in practice (where exact assumptions are never true)." ~ George Box (1919 – 2013), Statistician (see “All models are wrong”)<https://en.wikipedia.org/wiki/All_models_are_wrong> QUICK LINKS Please complete the EMBRIO Events RSVP and Training poll: online survey<https://purdue.ca1.qualtrics.com/jfe/form/SV_1HcnKhD5uxVQIbs> Compucell3D School and Hackathon July 31 – August 13<http://www.compucell3d.org/Workshop23> Schedule Your One-on-One Interview with Soumi<https://www.when2meet.com/?18327719-shNWM> Weekly Update Meeting Recordings<https://app.box.com/s/48uqgrgoy5ygp1tsj2l3lafoy8ubgkop> BioRender Mini-Workshop During regular EMBRIO Weekly on June 12th . Led by David Gazzo and Mayesha Mim (Zartman Lab), with support from EMBRIO Student Leadership Council. ALL EMBRIO MEMBERS WELCOME!! Are you exhausted spending hours, days, and countless meetings pouring over PowerPoint, Illustrator, or Inkscape figure designs? Well, we're here to help you change that! Join our BioRender-ing workshop for a crash course on how to create professional, beautiful scientific images in a fraction of the time. But what is BioRender . . . ? BioRender<https://www.biorender.com/> is the easy friendly-to-use illustration platform geared for scientific use that is quickly taking over research and academic institutions around the world! We will be showing you the tips, tricks, and amazing aspects that we have learned through our own use of BioRender. Mainly focusing on figure design and creation, but also covering BioRender’s slide/presentation and poster design aspects as well. You can sign-up and create a BioRender account for free at www.biorender.com<http://www.biorender.com/> and follow along with us as we show you a new world. JOURNAL CLUBS CALCIUM IMAGING TECHNIQUES Meets Monday’s 11am ET via Zoom<https://purdue-edu.zoom.us/j/92929965472?pwd=VDdTbXk5TTg2eitWYmEvelB1UjkvZz…> (use this link through June 26th ) Due to the need within our EMBRIO community to process and analyze Ca2+ Images, Director Umulis has proposed to discuss papers regarding methods and tools for analyzing calcium imaging as part of a new journal club. The goal, beyond integrating these techniques, is to write a review paper. Norma Perez (nperezro(a)purdue.edu<mailto:nperezro@purdue.edu> ), EMBRIO Postdoc with the Buganza-Tepole and Umulis Labs has been leading the effort with this journal club, please contact her about participating in the club. The club is currently discussing the following papers: https://docs.google.com/document/d/1uESi45Zv_kGL369NW8sPW60GByOAXme7-vr1XKB… ONGOING CLUB: 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 currently entering 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… EMBRIO SUMMER WORKSHOP – Notre Dame, July 10-12. Registration opening soon. Please complete our events RSVP poll: online survey<https://purdue.ca1.qualtrics.com/jfe/form/SV_1HcnKhD5uxVQIbs> 2nd Annual EMBRIO Workshop DRAFT schedule Theme: Image Acquisition, Processing, Analysis Dates: July 10-12, 2023 (options to stay overnight on the 9th) Location: University of Notre Dame, South Bend, Indiana Organizer and contact: Prof. Jeremiah Zartman, Department of Chemical and Biomolecular Engineering, University of Notre Dame 7/10 Monday morning. Start time 9:00-9:30 Jeremiah Zartman. Introductions and announcements. 9:30-12:00 (with break) Dr. Sara Cole Unit 1: Microscopy basics, sample preparation, and data acquisition Two sessions 9:30 am -12:00 pm and 1:00 pm -2 pm 1. Fixation 2. Sectioning? or not. 3. Labeling 3a. intrinsic (fluorescence proteins) 3b. immunocytochemistry/immunohistochemistry 3c. genetic probes 3d. fluorogenic/photoconvertible probes 3e. others? 4. Controls and why are they important? 12:00 -1:00 Lunch break (boxed lunches) 1:00 - 2:30 Dr. Sara Cole 5. Microscopy 5a. brightfield, fluorescence 5b. contrast imaging 5c. reflectance/polarized 5d. large sample imaging (2photon, lightsheet, oct, tissue clearing prep) 5e. quantitative imaging (photon counting) 5f. enhanced/super resolution 5g. fluorescence lifetime imaging 2:30-3:00 Break 3:00 - 4:30 TBD. Possibilities: Bruker / Imaris presentations 7/10 Evening - EMBRIO student council - evening activities 7/11 Tuesday 9:00-9:30 Krishna Jayant (kjayant(a)purdue.edu) Tuesday July 11 Unit 2: Fundamentals of image processing module 9:00-9:30 Overview by Professor Krishna Jayant (kjayant(a)purdue.edu) (Via zoom) 9:30-10:45 Part 1 9:30-10:45 Shulan Xiao - Building image processing pipelines, tools and techniques 11:00 - 12:00 Hamad Khan - Walking through a specific Ca2+ imaging Pipeline 1:00 - 2:00 Part 2 1:00-2:00 Saumitra Yadav - Point spread functions Unit 3: RICS workshop. Prof. Gregory Reeves, TAMU 2:30-4:30 RICS is a tool for measuring absolute concentrations and mobilities (which includes determining the fraction of fluorescent molecules bound to immobile structures). In addition, we could use cross-correlation RICS to measure the fraction of GFP-tagged molecules bound to an RFP-tagged molecule. Specific learning objectives: 1. Describe the relationship between fluctuations in intensity and molecule number in a confocal voxel 2. Describe the background of how an autocorrelation function is calculated from fluctuations in intensity 3. Describe the relationship between the shape of the autocorrelation function, the decay in correlations in fluctuations with increasing time shifts, and the diffusivity of the molecule 4. Choose appropriate microscope parameters to acquire high quality RICS images 5. Practice acquisition of RICS images 7/12 Wednesday Morning (in process) 9:00-10:30 Dr. Elsje Pienaar Unit 4: Data driven model calibration 10:30 -12:00 Group modeling exercise Afternoon: Depart for Purdue University, West Lafayette July 13-14 EMBRIO Annual Retreat, Hosted with Weldon School of Biomedical Engineering, Purdue University, West Lafayette Campus. (Full schedule TBD) Thursday July 13 9am – 5pm Friday July 14 9am – 12pm (potential afternoon workshop or activity). EMBRIO ABIDES (Access, Belonging, Inclusion, Diversity, Equity, Support) Dr. Anjali Iyer-Pascuzzi, EMBRIO ABIDES Director and Associate Professor at Purdue, leads activities for Institute members. Stay tuned for ABIDES activities later this summer and Fall semester. UPCOMING DEADLINES, IMPORTANT DATES, & INFO Weekly Research & Education Zoom Meetings Spring & Summer, Monday’s 3 – 4 pm. Recordings: EMBRIO Box account > Weekly Update Meeting. Direct URL<https://app.box.com/s/48uqgrgoy5ygp1tsj2l3lafoy8ubgkop>. Spring & Summer Zoom link<https://purdue-edu.zoom.us/j/99819751005?pwd=UVlvWVpxRDB0cDVXbmxBU1NUTEZGZz…>: * January 9 – Krishna Jayant, Asst. Prof., BME, Purdue * January 16 – Martin Luther King, Jr. Day – No Meeting, please volunteer locally * January 23 – Trainee Professional Development, Grants Series Session #2 * January 30 – Anjali Iyer-Pascuzzi, Assoc. Prof., BPP, Purdue, DEI Director, EMBRIO * February 6 – Thrust & Site Leads Update Meeting * February 13 – Priyanka Baloni, Asst. Prof, HHS, Purdue * February 20 – Trainee Professional Development, Grants Series Session #3 * February 27 – Bakary Samasa, Mary Mullins Lab * March 6 – Thrust & Site Leads Update Meeting – NSF site visit debrief, next steps * March 13 – Spring break, no meeting * March 20 – NSF site visit debrief and trainee orientation to the Institute * March 27 – Nilay Kumar, Ph.D. Candidate, Zartman Lab, Notre Dame * April 3 – Thrust & Site Leads Update Meeting * April 10 – Manager Meets * April 17 – Project Discussions * April 24 – Project Discussions * May 1 – No meeting. Integrated and Enabling Project Proposals Due. * May 8 – No Meeting * May 15 – Leopold Green, Assist. Prof. BME, Purdue * May 22 – Nissa Larson, Ph.D. Student, Umulis Lab, BME, Purdue * May 29 – No meeting, Memorial Day * June 5 – TBD * June 12 – BioRender mini-workshop (organized by David Gazzo, Mayesha Mim, and EMBRIO Student Leadership Council). June 1, 2023. NSF Annual Report Due. June 8, 2023. Quantitative Biology Symposium, Hosted by the Department of Cell and Developmental Biology, Northwestern University, 8am – 6pm CT. https://planitpurple.northwestern.edu/event/590383 June 12, 2023. BioRender Mini-Workshop. During regular EMBRIO Weekly, 3-4pm ET. July 10-12, 2023. EMBRIO Trainees Summer Workshop, Notre Dame University. Details above. July 13-14, 2023. EMBRIO All-Hands Annual Meeting, Purdue University. More information forthcoming. July 31 - August 13, 2023. 2023 Multicell Virtual-Tissue Modeling Online Summer School and Hackathon Learn to model your biological system of interest with one-on-one help. Week 1 will cover CC3D basics. Week 2 will cover advanced topics in CC3D, followed by a 2-day model-building hackathon. Physicists, biologists, computer scientists, and modelers team up to build research-grade models of biological systems. All experience levels are welcome. For more information, email compucell3d.iu(a)gmail.com<mailto:compucell3d.iu@gmail.com> or visit www.compucell3d.org/Workshop23<http://www.compucell3d.org/Workshop23>. Register at: www.tinyurl.com/CC3D2023<http://www.tinyurl.com/CC3D2023>. INSTITUTE EVALUATION: SIGN UP FOR YOUR ONE-ON-ONE INTERVIEW (hint: it’s mandatory) If you are a member of the EMBRIO institute currently doing a research project, we would like to invite you for participating in this study. Participation in the evaluation process is MANDATORY for all the members of the institute. As a part of the evaluation process, you will take part in an online session (via Zoom), which includes an interview and a brief survey, and the entire process should be completed in less than an hour. Interviews will be conducted annually for the total duration of your participation in the institute and the session would not exceed an hour and would be completed in a day. Please fill in all the times you may be available for our interviews using the link below with either your name or email address. This information is requested so that we may contact you to set up an online session, but we will use a randomly generated 4-digit code in place of your name to identify all your information for the data collection and analysis. https://www.when2meet.com/?18327719-shNWM Your participation will not affect any aspect of your association with the EMBRIO institute. If you have any doubts regarding the evaluation process, please reach out to Soumi at mukher42(a)purdue.edu<mailto:mukher42@purdue.edu>.” Hot Off the Press: New EMBRIO Journal and Conference Papers Let us know about new papers you want to highlight for the EMBRIO community! REMINDER: EMBRIO Acknowledgement for Scholarly Papers. 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.” Conference Presentations: Let us know about your conference presentations. Awards Congratulations to Priyanka Baloni, Asst. Prof., Health & Human Sciences; her proposal entitled, "Identifying metabolic signatures associated with PFAS exposure and their role in neurotoxicity" was selected by the external Showalter Trust Selection Committee to receive a 2023 Showalter Trust Research Award. Open Positions Two Open-Rank Professor Positions in Technology and Research Related to Next-Generation Biomedical Digital Twins The Department of Intelligent Systems Engineering at Indiana University is pleased to announce a search to fill Two Open-Rank Professor Positions in Technology and Research Related to Next-Generation Biomedical Digital Twins. Appointments can be at Full, Associate or Assistant Professor level and two-person cluster hires are possible. Appointments can begin as early as August 1, 2023. This search is part of a broad collaborative initiative to create key hardware and software components of next-generation digital twins for research, bioengineering and clinical application. To learn more about Luddy School, ISE, and to apply online, please visit https://indiana.peopleadmin.com/postings/16811 For more details see attached full announcement. Questions, nominations, and confidential inquiries may be sent to Prof. James A. Glazier (jaglazier(a)gmail.com<mailto:jaglazier@gmail.com>) 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 ), 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 June 16th to Brent (laddb(a)purdue.edu<mailto:laddb@purdue.edu>) <https://www.purdue.edu/research/embrio/>

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Reminder! NSF demographics survey by Friday
by Iyer-Pascuzzi, Anjali 24 May '23

24 May '23

Hi everyone, Thank you to the 48 people who have completed the survey so far! If you haven't yet, please do so by the end of the day on Friday, May 26. Here's the anonymous link: https://purdue.ca1.qualtrics.com/jfe/form/SV_dninhzrnl1EH8Tc Anjali Anjali Iyer-Pascuzzi, Ph.D. Associate Professor Department of Botany and Plant Pathology Center for Plant Biology Purdue University 915 Mitch Daniels Blvd West Lafayette, IN 47907-2054 Phone: 765-494-4653 (office), 765-496-7799 (lab) Website: https://www.purdue.edu/btny/iyer-pascuzzilab/ Google Scholar profile: Anjali Iyer-Pascuzzi Twitter: @Anjali_IP Pronouns: she, her, hers

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EMBRIO Demographics survey for NSF reporting
by Iyer-Pascuzzi, Anjali 22 May '23

22 May '23

Hi All, Our annual NSF report is due soon, and as part of that we're asking everyone to please (please please) fill out a short demographics survey. It's 9 questions and should only take you 1 or 2 minutes. The anonymous link is here: https://purdue.ca1.qualtrics.com/jfe/form/SV_dninhzrnl1EH8Tc Many thanks, Anjali Anjali Iyer-Pascuzzi, Ph.D. Associate Professor Department of Botany and Plant Pathology Center for Plant Biology Purdue University 915 Mitch Daniels Blvd West Lafayette, IN 47907-2054 Phone: 765-494-4653 (office), 765-496-7799 (lab) Website: https://www.purdue.edu/btny/iyer-pascuzzilab/ Google Scholar profile: Anjali Iyer-Pascuzzi Twitter: @Anjali_IP Pronouns: she, her, hers

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Today's Talk: Nissa Larson, Umulis Lab
by Ladd, Brent Thomas 22 May '23

22 May '23

Dear EMBRIO Members, Join us for our meeting today at 3 pm ET featuring Nissa Larson (Umulis Lab) presenting her Ph.D. research project: Multiscale Modeling of BMP Signaling Pathway during Zebrafish Embryogenesis. Please note that we won't meet the following Monday on the 29th in observance of Memorial Day. See you all this afternoon! Brent Brent T. Ladd, Senior Research Program Manager, EMBRIO Institute<https://www.purdue.edu/research/embrio/> Weldon School of Biomedical Engineering Purdue University laddb(a)purdue.edu <https://www.purdue.edu/research/embrio/>

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EMERGENCE: Issue 18 "Graduation Issue", May 18, 2023
by Ladd, Brent Thomas 18 May '23

18 May '23

[cid:583d5023-6584-47ec-addc-1b0c82d53362] Emergence: A biweekly newsletter of discovery, education, and outreach from the EMBRIO Institute Issue 18: May 18, 2023 “Graduation Issue” DIRECTORS’ NOTE Much deserved congratulations to all EMBRIO graduates, mentors, as well as those on the “green light” side of qualification exams! View a list of graduates and their thesis titles with available links below, as well as those passing prelim exams, and those receiving promotions. Thank you to Dr. Leo Green for presenting his research at our most recent Weekly Update meeting (recording available<https://app.box.com/s/m6lyb2ow0qqv97j2eau7k9x660g38fp8>). Our upcoming meeting on Monday, May 22nd will feature Nissa Larson presenting her EMBRIO Ph.D. research project Multiscale Modeling of BMP Signaling Pathway during Zebrafish Embryogenesis. Learn more about Nissa in the Member Spotlight of this issue. David Gazzo and Mayesha Mim (Zartman Lab) will lead an introduction to scientific figure creation employing BioRender during our June 12th Weekly (details below). As the summer session gets started, we are working on the schedule and registration for the EMBRIO summer training workshop hosted by the Zartman Lab at Notre Dame July 10-12, followed by our Annual All-Hands meeting at Purdue July 13-14. The Glazier Lab & Biocomplexity Institute at IU are offering a two week online live course in basic and advanced CompuCell3D July 31 - August 13. Details below. As members prepare for presentations and posters at conferences, and manuscripts for publication please remember to acknowledge our NSF award: “This work is based upon efforts supported by EMBRIO Institute, contract #2120200, a National Science Foundation (NSF) Biology Integration Institute.” Find recommended poster and PowerPoint templates, along with EMBRIO and NSF logos on our Box account in the “Poster and Presentation Templates & Logos” folder. Direct Link<https://app.box.com/s/agkalrgrarb7yv1mskiqb5imuxkdtgej>. We want to hear about your news and announcements. Send them to Brent (laddb(a)purdue.edu) by April 28th for inclusion in the next issue of Emergence. David, Chris, Stephanie, Anjali, and Brent Notable Quote “Fall in love with some activity and do it! Nobody ever figures out what life is all about, and it doesn't matter. Explore the world. Nearly everything is really interesting if you go into it deeply enough.” ~ Richard Feynman<https://en.wikipedia.org/wiki/Richard_Feynman>, Theoretical Physicist and Nobel Prize in Physics (1965). QUICK LINKS Journal Club – Calcium Imaging Techniques: Monday’s 11am Zoom<https://purdue-edu.zoom.us/j/92929965472?pwd=VDdTbXk5TTg2eitWYmEvelB1UjkvZz…>, papers to be discussed<https://docs.google.com/document/d/1uESi45Zv_kGL369NW8sPW60GByOAXme7-vr1XKB…> Compucell3D School and Hackathon July 31 – August 13<http://www.compucell3d.org/Workshop23> Schedule Your One-on-One Interview with Soumi<https://www.when2meet.com/?18327719-shNWM> Weekly Update Meeting Recordings<https://app.box.com/s/48uqgrgoy5ygp1tsj2l3lafoy8ubgkop> CELEBRATING GRADUATES, PRELIMS, & PROMOTIONS A shout out to EMBRIO trainees who have graduated recently (or anytime in the past year)! And congratulations to all those passing your prelims/quals, as well as those receiving promotions [Let me (laddb(a)purdue.edu ) know if I’ve missed someone]. Recent EMBRIO Graduates CORE: Adebowale, Joan (2022). MS Thesis. Advisor: J. Mendenhall. Rocha Clavijo, Daniel (2023). Towards a rapid estimation system in calcium signaling. MS Thesis. Co-Advisors: M. Cabrera and C. Isaza. EMBRIO Committee members: D. Umulis, C. Staiger. Thompson, Matthew J (2022): Precision of Positional Information Along the Developing Cochlea Radial Axis: Linear BMP Activity Helps Set the Stage. Purdue University Graduate School. Thesis. (Advisor: D. Umulis. EMBRIO Committee members: T. Kinzer-Ursem) https://doi.org/10.25394/PGS.21301113.v1 Matt is now a Data Scientist with The Ohio State University. Weathered, Catherine (2022): Multiscale Spatiotemporal Modeling For Human Disease: Agent Based Models For Nontuberculous Mycobacterium Infections And Alzheimer’s Disease. Purdue University Graduate School. Thesis. https://doi.org/10.25394/PGS.21298182.v1. (Advisor: E. Pienaar. EMBRIO Committee members: T. Kinzer-Ursem). Catherine is a Postdoctoral Researcher in Quantitative Systems Pharmacology at Pfizer Thrust 2, Project 2B: Kumar, Nilay. (2023). Reverse Engineering Epithelial Morphogenesis: A Systems Biology Approach. University of Notre Dame. (Advisor: J.J. Zartman) Nilay is joining EMBRIO as a Sr. Research Scientist in October. Soundarrajan, Dharsan. K. (2022). Dynamics of Calcium Signaling in Multicellular Systems: Quantitative Experiments and Computational Modelling. University of Notre Dame. (Advisor: J.J. Zartman) https://doi.org/10.7274/dj52w379b8f Dharsan is a Mathematical Modeler at Immunetrics Vijay Kumar Naidu, Velagala. (2023). Mechanisms of Crosstalk and Signal Integration of Calcium Signaling in Epithelial Tissues. University of Notre Dame. (Advisor: J.J. Zartman) https://doi.org/10.7274/sq87br89z23 Velagala is a Data Scientist at Zifo Thrust 3, Project 3B Wang, Yueyang (2022): Mitofusin 2 regulates actin cytoskeleton and cell migration. Purdue University Graduate School. Thesis. (Advisor: Q. Deng) https://doi.org/10.25394/PGS.19661556.v1 Yueyang is a Research Fellow with Harvard Medical School Thrust 4. Lyon, Joseph Alan (2022): Characterizing Computational Thinking Through The Use Of Modeling And Simulation Activities Within The Engineering Classroom. Purdue University Graduate School. Thesis. (Advisor: A. Magana) https://doi.org/10.25394/PGS.19692784.v1 Joseph is an instructor at Purdue University in the Engineering Honors/Goss Scholars program Preliminary/Qualifying Exams Passed: Chang Ding, Purdue University PI: Qing Deng (Thrust 3B) Project: “ROS relax wounds to allow healing and regrowth” David Gazzo, Notre Dame University, PI. Jeremy Zartman (Thrust 2B) “Reverse Engineering Calcium Signaling Crosstalk and Integration Responses to Pathogen and Cellular Damage Cues” Nissa Larson, Purdue University PI: David M. Umulis (CORE) “Multiscale Modeling of BMP Signaling Pathway during Zebrafish Embryogenesis” Mayesha Mim, Notre Dame PI: Jeremy Zartman (Thrust 2B) Project: “Calcium-Mediated Morphogenesis: Forward Engineering Organ Development with Optogenetics and Mechanosensation” Soumi Mukherjee, Purdue University PI: Stephanie Gardner (Thrust 4) Project: “Investigating the nature and development of interdisciplinary competencies, identity formation and collaboration amongst members participating in a Biology Integration Institute” Dhulika Ravinuthala, Purdue University PI: Janice Evans (Thrust 1B) Project: “Influence of Calcium Signaling in Mammalian Eggs on the Actomyosin Cytoskeleton in the Cortex and its Role in the Prevention of Polyspermy” Promotions: Anjali S. Iyer-Pascuzzi, (ABIDES Director, and Thrust 2A Investigator) was promoted from Assoc. Prof. to Professor of Botany and Plant Pathology, Purdue University David M. Umulis, (EMBRIO Director, CORE Investigator) has been promoted to Sr. Vice Provost for Purdue in Indianapolis. Congrats Anjali and David! MEMBER SPOTLIGHT [cid:f7f9041a-a537-4820-9dff-c141dea91361] [cid:b8ee51dd-697e-4fd1-994c-ef8f301312ed] Nissa Larson, 2nd year Graduate Research Assistant, BME, Purdue University PI: David M. Umulis Multiscale Modeling of BMP Signaling Pathway during Zebrafish Embryogenesis https://engineering.purdue.edu/UmulisLab What's your hometown, State, Country (and one thing you love, miss, remember, or want to tell others about it) I am from Charleston, Illinois – a small town in central Illinois. I go back every now and then to see my family and the animals. I also brought a couple of cats to West Lafayette with me. I really miss having fresh eggs. What are your hobbies? I walk my cats a couple of times a week and play on a few intramural sports teams. I also play a few instruments (primarily flute & piccolo) in both a Purdue concert band and the Lafayette Citizens’ Band. And the strawberries have started blooming on my community garden plot at Cumberland Park! What drew you into becoming a scientist or engineer (or both)? I think the cross-section of disciplines is such an important place to be. Each person in the institute is doing incredible work, but the implications cannot be realized without bringing things together. This requires being able to think both as an engineer and as a scientist. Tell us the main point of your research as it relates to EMBRIO: I am building a multiscale model of the BMP network that drives dorsoventral cell differentiation during zebrafish embryogenesis. Working both computationally and experimentally, I’m investigating the origins of noise throughout the signal transduction process as well as mechanisms of robustness and resulting phenotypic variability. 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!): Every cell in your body contains the same information in the form of DNA, so where does the information come from to tell them all specifically what to do? The bone morphogenetic protein network is known to provide some of this information in similar pathways throughout the animal kingdom. The network is extremely complex however, so I’m trying to elucidate what mechanisms allow it to be so good at what it does. What's on the horizon for you (research, career, personal, whatever you want to share)? I’m writing this the day before my qualifying exam – so hopefully that goes well. Then I’m looking forward to getting some optogenetics experimentation completed this summer along with image quantification and use of the light sheet microscope. What’s your various URL/social media handles that others can follow (prof. website, twitter, LinkedIn, blog, etc)? linkedin.com/in/nissa-larson-234b9923a JOURNAL CLUBS CALCIUM IMAGING TECHNIQUES Meets Monday’s 11am ET via Zoom<https://purdue-edu.zoom.us/j/92929965472?pwd=VDdTbXk5TTg2eitWYmEvelB1UjkvZz…> (use this link through June 26th ) Due to the need within our EMBRIO community to process and analyze Ca2+ Images, Director Umulis has proposed to discuss papers regarding methods and tools for analyzing calcium imaging as part of a new journal club. The goal, beyond integrating these techniques, is to write a review paper. Norma Perez ( nperezro(a)purdue.edu ), EMBRIO Postdoc with the Buganza-Tepole and Umulis Labs, is leading the effort with this journal club, please contact her about participating in the club. The club is currently discussing the following papers: https://docs.google.com/document/d/1uESi45Zv_kGL369NW8sPW60GByOAXme7-vr1XKB… ONGOING CLUB: Multimodal Functions of Calcium in Tuning and Regulating Cytoskeleton Networks Please contact Dr. Linlin Li ( li2212(a)purdue.edu ) for information. The club is currently entering 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… BioRender Mini-Workshop During regular EMBRIO Weekly on June 12th . Led by David Gazzo and Mayesha Mim (Zartman Lab), with support from EMBRIO Student Leadership Council. ALL EMBRIO MEMBERS WELCOME!! Are you exhausted spending hours, days, and countless meetings pouring over PowerPoint, Illustrator, or Inkscape figure designs? Well, we're here to help you change that! Join our BioRender-ing workshop for a crash course on how to create professional, beautiful scientific images in a fraction of the time. But what is BioRender . . . ? BioRender<https://www.biorender.com/> is the easy friendly-to-use illustration platform geared for scientific use that is quickly taking over research and academic institutions around the world! We will be showing you the tips, tricks, and amazing aspects that we have learned through our own use of BioRender. Mainly focusing on figure design and creation, but also covering BioRenders slide/presentation and poster design aspects as well. You can sign-up and create a BioRender account for free at www.biorender.com<http://www.biorender.com/> and follow along with us as we show you a new world. Calcium: An EMBRIO Course in the Basics Norma C. Perez Rosas, Postdoc Fellow in the Buganza Tepole and Umulis labs, has designed and delivered a minicourse on the basics of understanding calcium in different systems. Perez first delivered this course live over eight sessions to the UPRM group who are working on incorporating calcium data from biological experiments into optimized models. The initial course material is now available to all EMBRIO members via our shared Box file system: “EMBRIO Courses_Modules > Calcium: An EMBRIO Course in the Basics (Norma Perez Rosas)”. Norma is updating the materials periodically with a potential live series being offered during Fall semester. Direct link: https://app.box.com/s/79nzu1br18c4g33t1c9z45zb4krbecs2 EMBRIO ABIDES (Access, Belonging, Inclusion, Diversity, Equity, Support) Dr. Anjali Iyer-Pascuzzi, EMBRIO ABIDES Director and Associate Professor at Purdue, leads activities for Institute members. Stay tuned for ABIDES activities for this summer and Fall semester. UPCOMING DEADLINES, IMPORTANT DATES, & INFO Weekly Research & Education Zoom Meetings Spring & Summer, Monday’s 3 – 4 pm. Recordings: EMBRIO Box account > Weekly Update Meeting. Direct URL<https://app.box.com/s/48uqgrgoy5ygp1tsj2l3lafoy8ubgkop>. Spring & Summer Zoom link<https://purdue-edu.zoom.us/j/99819751005?pwd=UVlvWVpxRDB0cDVXbmxBU1NUTEZGZz…>: * January 9 – Krishna Jayant, Asst. Prof., BME, Purdue * January 16 – Martin Luther King, Jr. Day – No Meeting, please volunteer locally * January 23 – Trainee Professional Development, Grants Series Session #2 * January 30 – Anjali Iyer-Pascuzzi, Assoc. Prof., BPP, Purdue, DEI Director, EMBRIO * February 6 – Thrust & Site Leads Update Meeting * February 13 – Priyanka Baloni, Asst. Prof, HHS, Purdue * February 20 – Trainee Professional Development, Grants Series Session #3 * February 27 – Bakary Samasa, Mary Mullins Lab * March 6 – Thrust & Site Leads Update Meeting – NSF site visit debrief, next steps * March 13 – Spring break, no meeting * March 20 – NSF site visit debrief and trainee orientation to the Institute * March 27 – Nilay Kumar, Ph.D. Candidate, Zartman Lab, Notre Dame * April 3 – Thrust & Site Leads Update Meeting * April 10 – Manager Meets * April 17 – Project Discussions * April 24 – Project Discussions * May 1 – No meeting. Integrated and Enabling Project Proposals Due. * May 8 – No Meeting * May 15 – Leopold Green, Assist. Prof. BME, Purdue * May 22 – Nissa Larson, Ph.D. Student, Umulis Lab, BME, Purdue * May 29 – No meeting, Memorial Day * June 5 – Thrust and Site Leads Meet * June 12 – BioRender mini-workshop (organized by EMBRIO Student Leadership Council). June 1, 2023. NSF Annual Report Due. June 8, 2023. Quantitative Biology Symposium, Hosted by the Department of Cell and Developmental Biology, Northwestern University, 8am – 6pm CT. https://planitpurple.northwestern.edu/event/590383 June 12, 2023. BioRender Mini-Workshop. During regular EMBRIO Weekly, 3-4pm ET. July 10-12, 2023. EMBRIO Trainees Summer Workshop, Notre Dame University. Details forthcoming. July 13-14, 2023. EMBRIO All-Hands Annual Meeting, Purdue University. More information forthcoming. July 31 - August 13, 2023. 2023 Multicell Virtual-Tissue Modeling Online Summer School and Hackathon Learn to model your biological system of interest with one-on-one help. Week 1 will cover CC3D basics. Week 2 will cover advanced topics in CC3D, followed by a 2-day model-building hackathon. Physicists, biologists, computer scientists, and modelers team up to build research-grade models of biological systems. All experience levels are welcome. For more information, email compucell3d.iu(a)gmail.com or visit www.compucell3d.org/Workshop23<http://www.compucell3d.org/Workshop23>. Register at: www.tinyurl.com/CC3D2023<http://www.tinyurl.com/CC3D2023>. INSTITUTE EVALUATION: SIGN UP FOR YOUR ONE-ON-ONE INTERVIEW (hint: it’s mandatory) If you are a member of the EMBRIO institute currently doing a research project, we would like to invite you for participating in this study. Participation in the evaluation process is MANDATORY for all the members of the institute. As a part of the evaluation process, you will take part in an online session (via Zoom), which includes an interview and a brief survey, and the entire process should be completed in less than an hour. Interviews will be conducted annually for the total duration of your participation in the institute and the session would not exceed an hour and would be completed in a day. Please fill in all the times you may be available for our interviews using the link below with either your name or email address. This information is requested so that we may contact you to set up an online session, but we will use a randomly generated 4-digit code in place of your name to identify all your information for the data collection and analysis. https://www.when2meet.com/?18327719-shNWM Your participation will not affect any aspect of your association with the EMBRIO institute. If you have any doubts regarding the evaluation process, please reach out to Soumi at mukher42(a)purdue.edu.xn--ivg With Regards Soumi Hot Off the Press: New EMBRIO Journal and Conference Papers Let us know about new papers you want to highlight for the EMBRIO community! REMINDER: EMBRIO Acknowledgement for Scholarly Papers. 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.” Conference Presentations: Let us know about your conference presentations. Awards Congrats to Weiwei Zhang. She received a professional development award at Purdue: https://www.purdue.edu/newsroom/purduetoday/releases/2023/Q2/mapsac-awards-… Open Positions Two Open-Rank Professor Positions in Technology and Research Related to Next-Generation Biomedical Digital Twins The Department of Intelligent Systems Engineering at Indiana University is pleased to announce a search to fill Two Open-Rank Professor Positions in Technology and Research Related to Next-Generation Biomedical Digital Twins. Appointments can be at Full, Associate or Assistant Professor level and two-person cluster hires are possible. Appointments can begin as early as August 1, 2023. This search is part of a broad collaborative initiative to create key hardware and software components of next-generation digital twins for research, bioengineering and clinical application. To learn more about Luddy School, ISE, and to apply online, please visit https://indiana.peopleadmin.com/postings/16811 For more details see attached full announcement. Questions, nominations, and confidential inquiries may be sent to Prof. James A. Glazier (jaglazier(a)gmail.com) 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 ), or they have graduated, let Brent know their names and email contacts (laddb(a)purdue.edu ) Submit your items for the next newsletter by May 26th to Brent (laddb(a)purdue.edu) Brent T. Ladd, Senior Research Program Manager, EMBRIO Institute<https://www.purdue.edu/research/embrio/> Weldon School of Biomedical Engineering Purdue University laddb(a)purdue.edu <https://www.purdue.edu/research/embrio/>

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Quantitative Biology Symposium - June 8, Chicago, IL
by Ladd, Brent Thomas 17 May '23

17 May '23

EMBRIO Members, A one-day symposium of interest hosted by the Department of Cell and Developmental Biology, Northwestern University, 8am – 6pm CT.: (flyer attached) June 8, 2023. Quantitative Biology Symposium, https://planitpurple.northwestern.edu/event/590383 The Quantitative Biology Symposium will showcase the power that quantitative and computational methodologies offer to open questions in cell and developmental biology. The day-long event includes lectures by scientists seamlessly treading the boundaries between biology and other disciplines, interactive activities between experimental and computational participants, and hands-on workshops covering a range of topics. The collective goals for the event are to catalyze interactions between cell and developmental biologists and mathematicians / physicists / statisticians / engineers and unveil the potential of quantitative methodologies to trainees across the broader Chicagoland area. Purdue people, let me know if you're interested in going - we can likely arrange a carpool. Best, Brent Brent T. Ladd, Senior Research Program Manager, EMBRIO Institute<https://www.purdue.edu/research/embrio/> Weldon School of Biomedical Engineering Purdue University laddb(a)purdue.edu <https://www.purdue.edu/research/embrio/>

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