- Embrio-list - ecn.purdue.edu

NSF BII Meeting Agenda w/ Zoom link registration
by Ladd, Brent Thomas 11 Jan '24

11 Jan '24

Hello Everyone, NSF has shared the final agenda<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> for the Biology Integration Institutes Meeting taking place January 22-23. The link will require you register before receiving the actual zoom link for accessing the meeting sessions. You can use this link to register in advance: https://nsf.zoomgov.com/webinar/register/WN_u1fC5pxYTb65fBzA8O8HWQ<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fnsf.zoomg…> EMBRIO is slotted to present on day 1 at 11:15 (10 min) with Director Umulis. The Institute has three posters (day 1) and two flash talks (day 2) being presented by: Linlin Li Weiwei Zhang David Gazzo The following members will be at NSF in person representing EMBRIO. NSF invites everyone not in person to join via the zoom link. David Umulis Purdue Jeremy Zartman Notre Dame Brent Ladd Purdue David Gazzo Notre Dame Weiwei Zhang Purdue Linlin Li Purdue Janice Evans Purdue 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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End of Week Announcements: See draft data sharing policy for comments
by Ladd, Brent Thomas 10 Jan '24

10 Jan '24

Dear EMBRIOphytes, Data Sharing Policy for EMBRIO The Leadership team has been working on a data sharing policy for the Institute, drawing on the expertise of seasoned data managers and with other Institutes that have implemented such policies. A draft Data Sharing Policy<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> for EMBRIO has been designed to promote transparency, collaboration, and responsible data management within our research community. Please review the draft policy and provide comments by end of the year, either publicly associated with the online draft or your comments can be sent to me via email (laddb(a)purdue.edu) Ratifying a data sharing policy is a critical first step in an overall data management plan. Thanks in advance for everyone reading and commenting on this draft policy. Our next Institute seminar will take place January 8th, 3pm ET with an update from Thrust 4 leads and collaborators. The scheduling poll revealed no one requesting a different day or time, so we will march forward with Mondays at 3-4pm. We will stick with a "biweekly" schedule to the extent possible, with each month featuring an update from one of the research thrusts, along with guest speakers, ABIDES topic, and possible trainee topic sessions. Look for a calendar invite from me today with the series and zoom link. Note that due to university holidays, institute events, and speaker availability, it won't be a consistent biweekly schedule. with constraints of Outlook, the series invitation will initially include all weeks next semester, then I will "delete" the non-meeting occurrences from the calendar series. Mark your calendar for the NSF BII conference January 22-23. Calendar invite forthcoming from NSF with Zoom link. This year’s conference will be in a hybrid format, with most attending via zoom, and a smaller team in person at NSF headquarters. View the draft agenda<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…>. Final newsletter of the year will go out next Wednesday, December 13th. If you have any news or announcements you would like included please get those to me by next Tuesday. Wishing you all a good weekend, and smooth sailing with end of the semester, and if I don't see you again until January enjoy the holidays!!! 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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Monday Jan. 8th EMBRIO Thrust 4 presentation
by Ladd, Brent Thomas 08 Jan '24

08 Jan '24

Dear Embriophytes, Happy New Year! A reminder that we’ll be kicking off our first thrust level update this coming Monday, January 8th 3pm EST with Thrust 4 focused on pedagogical research, curriculum development, training, diversity, and outreach efforts. We will break Jan. 15th for celebrating MLK, Jr., and Jan 22nd is reserved for the NSF BII conference. January 29th will feature an ABIDES training session on developing your project management skills. View the all-hands thrust level seminar dates and plans for Spring semester below. See you all on Monday, 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 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 <https://www.purdue.edu/research/embrio/>

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Ca2+ Imaging Techniques Journal Club (2024)
by Perez Rosas, Norma Citlalcue 04 Jan '24

04 Jan '24

Dear all, In order to continue the work that JC did during 2023, here I send you the invitation for our meetings that will be held this year. The schedule is the same as the previous year, Monday from 11 AM to 12 PM. Since the group is currently drafting the manuscripts, our meeting will begin on January 8, 2024, and will end on February 12, 2024. Thank you all for your collaboration. Happy New Year! Norma ______________ Norma Citlalcue Perez Rosas is inviting you to a scheduled Zoom meeting. Topic: Ca2+ Imaging Techniques - Journal Club Time: Jan 8, 2024 11:00 AM Indiana (East) Every week on Mon, until Feb 12, 2024, 6 occurrence(s) Jan 8, 2024 11:00 AM Jan 15, 2024 11:00 AM Jan 22, 2024 11:00 AM Jan 29, 2024 11:00 AM Feb 5, 2024 11:00 AM Feb 12, 2024 11:00 AM Please download and import the following iCalendar (.ics) files to your calendar system. Weekly: https://purdue-edu.zoom.us/meeting/tJYkdeChqD4uHdZfifaQWg7M6qfFz7RTkZN8/ics…<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…> Join Zoom Meeting https://purdue-edu.zoom.us/j/92929965472?pwd=VDdTbXk5TTg2eitWYmEvelB1UjkvZz…<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…> Meeting ID: 929 2996 5472 Passcode: 607686 --- One tap mobile +13092053325,,92929965472#,,,,*607686# US +13126266799,,92929965472#,,,,*607686# US (Chicago) --- Dial by your location • +1 309 205 3325 US • +1 312 626 6799 US (Chicago) • +1 646 558 8656 US (New York) • +1 646 931 3860 US • +1 301 715 8592 US (Washington DC) • +1 305 224 1968 US • +1 669 900 6833 US (San Jose) • +1 689 278 1000 US • +1 719 359 4580 US • +1 253 205 0468 US • +1 253 215 8782 US (Tacoma) • +1 346 248 7799 US (Houston) • +1 360 209 5623 US • +1 386 347 5053 US • +1 507 473 4847 US • +1 564 217 2000 US • +1 669 444 9171 US Meeting ID: 929 2996 5472 Passcode: 607686 Find your local number: https://purdue-edu.zoom.us/u/amd3SzlNE --- Join by SIP • 92929965472(a)zoomcrc.com --- Join by H.323 • 162.255.37.11 (US West) • 162.255.36.11 (US East) Meeting ID: 929 2996 5472 Passcode: 607686 ____________________________

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EMERGENCE Newsletter Issue 28: December 18, 2023
by Ladd, Brent Thomas 18 Dec '23

18 Dec '23

[cid:59cd6b21-3e3d-4bf2-82da-7af0e70c6474] Emergence: A biweekly newsletter of discovery, education, and outreach from the EMBRIO Institute Issue 28: December 18, 2023 DIRECTORS’ NOTE Winter (break) is here. With the Fall semester at an end, congrats to everyone on your collective and individual accomplishments, and thank you for your hard work and innovative research in the Institute! Check out a photo slide show of in-person highlights<https://www.purdue.edu/research/embrio/files/photo%20highlights%20movie%20w…> from 2023. We wish everyone a safe, enjoyable, and restful holiday season. Looking ahead to next year, we’ll be kicking off our first thrust update January 8th focused on pedagogical research, curriculum development, training, diversity, and outreach efforts from Thrust 4 leaders and collaborators. View the all-hands seminar dates and plans for Spring semester in this issue. The other all-hands date in January will be January 29th with an ABIDES training session on developing your project management skills (Jan. 15 holiday celebrates MLK, Jr., and Jan 22nd is reserved for the BII conference). Please remember to check out the draft agenda<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> and hold time on your calendars for the NSF Biology Integration Institutes conference happening January 22-23 (zoom link from NSF forthcoming). This year’s conference will be a hybrid, with most attending via zoom, and a smaller team from EMBRIO in person at NSF headquarters. A reminder that if you are new to EMBRIO or you have someone in your lab that is new or desires an introduction or refresher on EMBRIO, we recommend that you take a look at the resources on the shared Box account in the Orientation to EMBRIO<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> sub-folder. We will dedicate an all-hands session in the spring to this topic. This is our final newsletter issue of the year. Until 2024, Happy Holidays! David, Chris, Stephanie, Anjali, Janice, Jeremy, and Brent Notable Quote “Winter is coming.” ~ George R.R. Martin, A Game of Thrones QUICK LINKS BII Conference Agenda<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> SURF Post a Research Project Portal<https://engineering.purdue.edu/Engr/Research/EURO/SURF/Research/Y2024/add_r…> 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…> Undergraduate Researchers Opportunities for EMBRIO Labs and Students Note from Kay Kobak, Assoc. Dir., EURO, Purdue: Hello Undergraduate Research Allies, SURF Post a Research Project Portal<https://engineering.purdue.edu/Engr/Research/EURO/SURF/Research/Y2024/add_r…> is now open for faculty  Program Name Description Student Compensation In-Lab Time Commitment Funding provided by Call for applications* Summer Undergraduate Research Fellowships (SURF)<https://engineering.purdue.edu/Engr/Research/EURO/students/about-SURF> Summer program for both Purdue Internal and external students, full time research experience. A total of $6000 paid over 12 weeks. 30-40 hours/week Cost shared 1:1:1 between EURO, the College, and the lab. (EMBRIO Note: the Institute will pay the PI tab of $2K, plus the $1K housing stipend if a non-Purdue student) Summer 2024 project portal open now. Early deadline is Dec. 1st *if you have already identified a student you wish to work with for a given time period, we still ask you post the project so we can maintain that information for our records. We can expedite the selection process and then close the project to other applicants if you already have someone in mind. Additional opportunities if you're currently hosting undergraduate researchers: EURO Travel Grant<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue.ca…>: For Purdue affiliated undergraduates who will be presenting their research at a conference - $500 awarded by EURO OUR Fall Expo<https://www.purdue.edu/undergrad-research/conferences/fall/index.php>: While the abstract deadline has passed for those wishing to give a talk, undergraduate researchers can still request to present virtually or give a poster Nov. 14-21. Other undergrad researcher funding opportunities can be found here<https://www.purdue.edu/undergrad-research/scholarships/grants.php>, here<https://www.purdue.edu/undergrad-research/scholarships/ExtGrants.php>, and here<https://exed.purdue.edu/funding/student.php>. Please feel free to reach out if you have any questions, Kay Kobak, Ph.D. she, her, hers Associate Director, Engineering Undergraduate Research Office DUDL 2526 | o.765-496-2349 | 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 training session on project management is being planned for January 29th (details TBA). 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. 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 March 4 break 11 No Meeting: Spring Break 18 Thrust 2 Seminar 25 break April 1 Guest Speaker 8 break 15 Thrust 1 Seminar 22 break 29 Trainee topic or Speaker TBD May 6 Thrust 3 Seminar 13 break 20 Guest Speaker 27 No Meeting: Memorial Day January 2 – 6, 2024. BMES – CMBE Conference. San Juan, Puerto Rico. Conference details: https://www.bmes.org/cmbe2024<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.bmes.…> BII Annual Conference - January 22-23, 2024 . NSF is planning a hybrid one and 1/2 day meeting for all Biology Integration Institutes. Most attendees will be virtual, with a few of us in person at NSF headquarters. View the draft agenda<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…>. 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. 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 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 January 12th 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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Canceled: Ca2+ Imaging Techniques Journal Club (Invitation)
by Perez Rosas, Norma Citlalcue 17 Dec '23

17 Dec '23

Meeting cancelled due to the winter break. Happy holidays!

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EMBRIO bi-weekly meeting schedule
by Ladd, Brent Thomas 05 Dec '23

05 Dec '23

Dear EMBRIO Members, For the spring semester we intend to continue with the bi-weekly schedule for our all-hands online meetings, starting on January 8th with a presentation from the Thrust 4 leads and collaborators. We've had the established time of 3-4pm on Mondays for some time now and will most likely continue with that schedule. (a calendar invite with new zoom link is forthcoming) However, if this day and time is not available for you during spring semester, please let me. know by end of this Thursday the 7th via this one question survey<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue.ca…>. Thank you! Brent Brent T. Ladd, Senior Research Program Manager, EMBRIO Institute<https://www.purdue.edu/research/embrio/> Weldon School of Biomedical Engineering, Purdue University Office: Hall for Discovery Learning and Research, Ste. 203 207 S. Martin Jischke Drive West Lafayette, IN 47907 laddb(a)purdue.edu

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EMBRIO Research Seminar Today: Systems Modeling for Multiomics Analysis Integration in Inflammatory Bowel Disease
by Ladd, Brent Thomas 04 Dec '23

04 Dec '23

Good Morning EMBRIO Members: Today our all-hands EMBRIO research seminar, 3-4pm EST, features Ph.D. candidate Javier Muñoz (Brubaker/Green Lab) presenting Systems Modeling for Multiomics Analysis Integration in Inflammatory Bowel Disease (abstract below). Check out the online training opportunity by the creators of Imaris happening Dec. 7th, 11AM ET, "Trainable AI Image Analysis for Everyone!". Details and Registration link below. Purdue labs planning for undergraduate researchers next summer (and our partner institutions who have students who want to come to Purdue for a summer research experience), the SURF REU project portal<https://engineering.purdue.edu/Engr/Research/EURO/SURF/Research/Y2024/add_r…> <https://engineering.purdue.edu/Engr/Research/EURO/SURF/Research/Y2024/add_r…> is open for faculty to submit your projects. Please indicate your project as affiliated with EMBRIO Institute. EMBRIO will cover the PI portion of the cost. Mark your calendar for the NSF BII conference January 22-23. This year’s conference will be a hybrid, with most attending via zoom, and a smaller team in person at NSF headquarters. View the draft agenda<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…>. EMBRIO Research Seminar - Monday Dec. 4th, 3PM EST: ZoomMeeting<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…> Systems modeling for Multiomics AnalysisIntegration in Inflammatory Bowel Disease. Javier Munoz-Briones and Doug Brubaker Crohn’s disease and ulcerative colitis are chronic inflammatory bowel diseases (IBD) with a rising global prevalence, influenced by clinical and demographics factors. The pathogenesis of IBD involves complexinteractions between gut microbiome dysbiosis, epithelial cell barrierdisruption, and immune hyperactivity, which are poorly understood. This necessitates the development of novel approaches to integrate and model multiple clinical and molecular data modalities from patients, animal models, and in vitro systems to discover effectivebiomarkers for diseaseprogression and drug response. For this presentation, my focus is on the lack of understanding of regarding the composition and functional interactions of the gut microbiome in IBD. As sequencing technologies advance, the amount of molecular and compositional data from pairedmeasurements of host and microbiome systems is exploding. While it is become routine to generate such rich, deep datasets, tools for their interpretation lag behind. Here, I presenta computational framework for integrative modelingof microbiome multi-omics data: Latent Interacting Variable Effects (LIVE) modeling. LIVE combines various types of microbiome multi-omics data using single-omic latent variables (LV) into a structured meta-model to determine the most predictive combinations of multi-omics features predicting an outcome, patient group, or phenotype. I implemented and tested LIVE using publicly available metagenomic and metabolomics data set from Crohn’s Disease(CD) and ulcerative colitis (UC) status patients in the PRISM and LLDeep cohorts. The findings show that LIVE reduced the number of features interactions from the originaldatasets for CD to tractable numbers and facilitated prioritization of biological associations between microbes, metabolites, enzymes, clinical variables, and a disease status outcome. LIVE modeling makes a distinct and complementary contribution to the current methods to integrate microbiome data to predict IBD status because of its flexibility to adapt to different types of microbiome multi-omics data, scalability for large and small cohort studies via reliance on latent variables and dimensionality reduction, and the intuitive interpretability of the meta-model integrating -omic data types. ============================================================ WEBINAR: IMARIS 10.1 - TRAINABLE AI IMAGE ANALYSIS FOR EVERYONE! ============================================================ Date: 7th December 2023 Time: 4PM GMT | 11AM ET | 9AM PT Speaker: Anna Paszulewicz Imaris 10.1 optimizes your image analysis workflows using AI Trainable Segmentation (Machine Learning). The AI Segmentation is very easy, because the user only needs to define the interesting object and the background with a few brush strokes, which Imaris uses to learn the patterns and segment the data accordingly. The user interface is very straightforward, and users can immediately see what Imaris has learned from their brush strokes, and correct if necessary. Imaris AI segmentation is a very robust tool, which can be applied to segment microscopy data representing samples from multiple disciplines from cell biology, organoid studies to neuroscience. Learning Objectives * Best practices in training the AI Segmentation Tool * Applications for the AI Segmentation * How to re-train your AI Segmentation model to apply it on multiple images. Register Here >><https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsmc-link.…> [Andor Technology Logo] Imaris, An Oxford Instruments Company 7 Millennium Way, Springvale Business Park, Belfast, BT12 7AL, UK 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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End of Week Announcements
by Ladd, Brent Thomas 01 Dec '23

01 Dec '23

Dear EMBRIOphytes, * This coming Monday plan to tune in for EMBRIO research seminar, December 4th, by Javier Muñoz (Brubaker/Green Lab) titled Systems modeling for Multiomics Analysis Integration in Inflammatory Bowel Disease (abstract below). * Purdue labs looking/planning for undergraduate researchers next summer (and our partner institutions who have students who want to come to Purdue for a summer research experience), the SURF REU project portal<https://engineering.purdue.edu/Engr/Research/EURO/SURF/Research/Y2024/add_r…> <https://engineering.purdue.edu/Engr/Research/EURO/SURF/Research/Y2024/add_r…> is open for faculty to submit your projects. Please indicate your project as affiliated with EMBRIO Institute. EMBRIO will cover the PI portion of the cost. * Check out the online training opportunity by the creators of Imaris happening Dec. 7th, 11AM ET, "Trainable AI Image Analysis for Everyone!". Details and Registration link are below. * Please hold January 22-23 for the annual NSF BII conference. This year’s conference will be a hybrid, with most attending via zoom, and a smaller team in person at NSF headquarters. View the draft agenda<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…>. EMBRIO Research Seminar - Monday Dec. 4th: Systems modeling for Multiomics AnalysisIntegration in Inflammatory Bowel Disease. Javier Munoz-Briones and Doug Brubaker Crohn’s disease and ulcerative colitis are chronic inflammatory bowel diseases (IBD) with a rising global prevalence, influenced by clinical and demographics factors. The pathogenesis of IBD involves complex interactions betweengut microbiome dysbiosis, epithelial cell barrierdisruption, and immune hyperactivity, which are poorly understood. This necessitates the development of novel approaches to integrate and model multiple clinical and molecular data modalities from patients, animal models, and in vitro systems to discover effectivebiomarkers for diseaseprogression and drug response. For this presentation, my focus is on the lack of understanding of regarding the composition and functional interactions of the gut microbiome in IBD. As sequencing technologies advance, the amount of molecular and compositional data from pairedmeasurements of host and microbiome systems is exploding. While it is become routine to generate such rich, deep datasets, tools for their interpretation lag behind. Here, I presenta computational framework for integrative modelingof microbiome multi-omics data: Latent Interacting Variable Effects (LIVE) modeling. LIVE combines various types of microbiome multi-omics data using single-omic latent variables (LV) into a structured meta-model to determine the most predictive combinations of multi-omics features predicting an outcome, patient group, or phenotype. I implemented and tested LIVE using publicly available metagenomic and metabolomics data set from Crohn’s Disease(CD) and ulcerative colitis (UC) status patients in the PRISM and LLDeep cohorts. The findings show that LIVE reduced the number of features interactions from the originaldatasets for CD to tractable numbers and facilitated prioritization of biological associations between microbes, metabolites, enzymes, clinical variables, and a disease status outcome. LIVE modeling makes a distinct and complementary contribution to the current methods to integrate microbiome data to predict IBD status because of its flexibility to adapt to different types of microbiome multi-omics data, scalability for large and small cohort studies via reliance on latent variables and dimensionality reduction, and the intuitive interpretability of the meta-model integrating -omic data types. ============================================================ WEBINAR: IMARIS 10.1 - TRAINABLE AI IMAGE ANALYSIS FOR EVERYONE! ============================================================ Date: 7th December 2023 Time: 4PM GMT | 11AM ET | 9AM PT Speaker: Anna Paszulewicz Imaris 10.1 optimizes your image analysis workflows using AI Trainable Segmentation (Machine Learning). The AI Segmentation is very easy, because the user only needs to define the interesting object and the background with a few brush strokes, which Imaris uses to learn the patterns and segment the data accordingly. The user interface is very straightforward, and users can immediately see what Imaris has learned from their brush strokes, and correct if necessary. Imaris AI segmentation is a very robust tool, which can be applied to segment microscopy data representing samples from multiple disciplines from cell biology, organoid studies to neuroscience. Learning Objectives * Best practices in training the AI Segmentation Tool * Applications for the AI Segmentation * How to re-train your AI Segmentation model to apply it on multiple images. Register Here >><https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsmc-link.…> [Andor Technology Logo] Imaris, An Oxford Instruments Company 7 Millennium Way, Springvale Business Park, Belfast, BT12 7AL, UK 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 issue 27: Nov. 29, 2023
by Ladd, Brent Thomas 29 Nov '23

29 Nov '23

[cid:61f8178c-fbed-472b-9120-0650a04d4dea] Emergence: A biweekly newsletter of discovery, education, and outreach from the EMBRIO Institute Issue 27: November 29, 2023 DIRECTORS’ NOTE As we enter the home stretch of the semester, we hope everyone had an enjoyable Thanksgiving break. This coming Monday don’t miss our next EMBRIO seminar, December 4th, by Javier Muñoz (Brubaker/Green Lab) titled Systems modeling for Multiomics Analysis Integration in Inflammatory Bowel Disease (abstract in this issue). If you missed the all-hands session last time featuring Dr. Weiwei Zhang presenting a thrust 2 seminar titled Decoding Ca2+ signatures and signaling to the actin cytoskeleton during the plant innate immune response, you can access the video in our Box account under the “All-Hands Meetings Recordings” folder. Purdue labs looking/planning for undergraduate researchers now or next summer (and our partner institutions who have students who want to come to Purdue for a summer research experience), the SURF REU program portal is open for faculty to submit your projects, with an early deadline of this Friday, Dec. 1st. See the info from Kay Kobak, their new Assoc. Director in this issue. When submitted your project, please indicate it is attached to the EMBRIO Institute, and note that EMBRIO will cover the PI’s portion of the SURF program cost. Please hold January 22-23 for the annual NSF BII conference. This year’s conference will be a hybrid, with most attending via zoom, and a smaller team in person at NSF headquarters. View the draft agenda<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…>. A reminder that if you are new to EMBRIO (or want a refresher), we recommend that you take a look at the resources on the shared Box account in the Orientation to EMBRIO<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> sub-folder. We will dedicate an all-hands session in the spring to this topic. We want to hear about your news and announcements. Send them to Brent (laddb(a)purdue.edu) by December 8th for inclusion in the next issue of Emergence. David, Chris, Stephanie, Anjali, Janice, Jeremy, and Brent Notable Quote "The real problem has far less to do with what is really out there than it does with our resistance to finding out what is really out there." ~ Barbara Brown Taylor, Learning to Walk in the Dark. QUICK LINKS BII Conference Agenda<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> SURF Post a Research Project Portal<https://engineering.purdue.edu/Engr/Research/EURO/SURF/Research/Y2024/add_r…> 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…> Undergraduate Researchers Opportunities for EMBRIO Labs and Students Note from Kay Kobak, Assoc. Dir., EURO, Purdue: Hello Undergraduate Research Allies, SURF Post a Research Project Portal<https://engineering.purdue.edu/Engr/Research/EURO/SURF/Research/Y2024/add_r…> is now open for faculty  Program Name Description Student Compensation In-Lab Time Commitment Funding provided by Call for applications* Summer Undergraduate Research Fellowships (SURF)<https://engineering.purdue.edu/Engr/Research/EURO/students/about-SURF> Summer program for both Purdue Internal and external students, full time research experience. A total of $6000 paid over 12 weeks. 30-40 hours/week Cost shared 1:1:1 between EURO, the College, and the lab. (EMBRIO Note: the Institute will pay the PI tab of $2K, plus the $1K housing stipend if a non-Purdue student) Summer 2024 project portal open now. Early deadline is Dec. 1st *if you have already identified a student you wish to work with for a given time period, we still ask you post the project so we can maintain that information for our records. We can expedite the selection process and then close the project to other applicants if you already have someone in mind. Additional opportunities if you're currently hosting undergraduate researchers: EURO Travel Grant<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue.ca…>: For Purdue affiliated undergraduates who will be presenting their research at a conference - $500 awarded by EURO OUR Fall Expo<https://www.purdue.edu/undergrad-research/conferences/fall/index.php>: While the abstract deadline has passed for those wishing to give a talk, undergraduate researchers can still request to present virtually or give a poster Nov. 14-21. Other undergrad researcher funding opportunities can be found here<https://www.purdue.edu/undergrad-research/scholarships/grants.php>, here<https://www.purdue.edu/undergrad-research/scholarships/ExtGrants.php>, and here<https://exed.purdue.edu/funding/student.php>. Please feel free to reach out if you have any questions, Kay Kobak, Ph.D. she, her, hers Associate Director, Engineering Undergraduate Research Office DUDL 2526 | o.765-496-2349 | 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 series of mentoring topics have been presented at the beginning of Weekly meetings, and a continuation of the Mentoring Panel topics from the annual retreat 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 link<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…>.Weekly Update Meeting Recordings<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…> Aug 14 Benchling Workshop - SLC (Feyisayo) Aug 21 Student Leadership Council - Grads and Postdocs Only Session Aug 28 Faculty Investigators Only Sept 4 Labor Day no meeting Sept 11 Dr. Linlin Li: Part I: Solving mathematical modeling with ODE or PDE in MatLab or Python (Google Colab) Sept 18 Dr. Linlin Li: Part II: Solving mathematical modeling with ODE or PDE in MatLab or Python (Google Colab) Sept 25 Dr. Adrian Buganza Tepole: Part I: Physics informed machine learning Oct 2 Dr. Adrian Buganza Tepole: Part II: Physics informed machine learning Oct 9 Fall Break - no meeting Oct 16 Open Discussion and Thrust Project Breakout Rooms Oct 23 ABIDES: Culture, Mentoring, & Teams Mini Workshop Oct 30 No meeting. Thrust Leads organize own meetings Nov 6 VCell tutorial by Dr. Michael Blinov, Center for Cell Analysis and Modeling, UConn Nov 13 No meeting. Thrust Leads organize own meetings Nov 20 Dr. Weiwei Zhang, Staiger Lab, Thrust 2 Integrations Nov 27 No meeting. Thrust Leads organize own meetings Dec 4 Javier Muñoz (Brubaker/Green Lab) Dec 11 No meeting. Thrust Leads organize own meetings Winter Break December 4, 2023. EMBRIO All-Hands. Systems modeling for Multiomics Analysis Integration in Inflammatory Bowel Disease. This work in the CORE thrust is presented by Javier Muñoz from the Brubaker/Green Lab. Systems modeling for Multiomics AnalysisIntegration in Inflammatory Bowel Disease. Javier Munoz-Briones and Doug Brubaker Crohn’s disease and ulcerative colitis are chronic inflammatory bowel diseases (IBD) with a rising global prevalence, influenced by clinical and demographics factors. The pathogenesis of IBD involves complex interactions betweengut microbiome dysbiosis, epithelial cell barrierdisruption, and immune hyperactivity, which are poorly understood. This necessitates the development of novel approaches to integrate and model multiple clinical and molecular data modalities from patients, animal models, and in vitro systems to discover effectivebiomarkers for diseaseprogression and drug response. For this presentation, my focus is on the lack of understanding of regarding the composition and functional interactions of the gut microbiome in IBD. As sequencing technologies advance, the amount of molecular and compositional data from pairedmeasurements of host and microbiome systems is exploding. While it is become routine to generate such rich, deep datasets, tools for their interpretation lag behind. Here, I presenta computational framework for integrative modelingof microbiome multi-omics data: Latent Interacting Variable Effects (LIVE) modeling. LIVE combines various types of microbiome multi-omics data using single-omic latent variables (LV) into a structured meta-model to determine the most predictive combinations of multi-omics features predicting an outcome, patient group, or phenotype. I implemented and tested LIVE using publicly available metagenomic and metabolomics data set from Crohn’s Disease(CD) and ulcerative colitis (UC) status patients in the PRISM and LLDeep cohorts. The findings show that LIVE reduced the number of features interactions from the originaldatasets for CD to tractable numbers and facilitated prioritization of biological associations between microbes, metabolites, enzymes, clinical variables, and a disease status outcome. LIVE modeling makes a distinct and complementary contribution to the current methods to integrate microbiome data to predict IBD status because of its flexibility to adapt to different types of microbiome multi-omics data, scalability for large and small cohort studies via reliance on latent variables and dimensionality reduction, and the intuitive interpretability of the meta-model integrating -omic data types. January 2 – 6, 2024. BMES – CMBE Conference. San Juan, Puerto Rico. Conference details: https://www.bmes.org/cmbe2024<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.bmes.…> BII Annual Conference - January 22-23, 2024 . NSF is planning a hybrid one and 1/2 day meeting for all Biology Integration Institutes. Most attendees will be virtual, with a team of us in person at NSF headquarters. View the draft agenda<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapp.box.c…>. 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-…> Note: EMBRIO is organizing a workshop for this conference. More TBA. Hot Off the Press: New EMBRIO Journal Papers Let us know about new papers you want to highlight for the EMBRIO community! REMINDER: EMBRIO Acknowledgement for Scholarly Papers and Posters. For EMBRIO related research publications, NSF requires acknowledgement of EMBRIO NSF funding for our Institute to claim the work in our reporting back to NSF. Please include the following acknowledgement in your journal and conference papers and posters: “This work is based upon efforts supported by EMBRIO Institute, contract #2120200, a National Science Foundation (NSF) Biology Integration Institute.” Awards Congrats to Feyisayo Akande (Staiger Lab, Purdue) for passing her thesis defense: Investigating the role of atpiezo as a possible mechanoreceptor during plant defense. Feyisayo will be continuing her research career at the University of Missouri in the plant sciences Ph.D. program. We wish you continued success, Feyi! 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 Dec. 8 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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