[Embrio-list] ODEs & PDEs Workshop @ EMBRIO Weekly today

[Ladd, Brent Thomas]

At today's Weekly we kick off a two-part workshop led by Dr. Linlin Li of the Umulis Lab September 11th and 18th for Solving Ordinary Differential Equations (ODEs) and Partial Differential Equations (PDEs) using Google Colab. Linlin will use this Colab site<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcolab.research.google.com%2Fdrive%2F1DZBf7LVK58xr0E0CR7Ub4evblMY7qZe9%3Fusp%3Dsharing&data=05%7C01%7Cembrio-list%40ecn.purdue.edu%7C2d739cfe1ed44025209808dbb2d5b092%7C4130bd397c53419cb1e58758d6d63f21%7C0%7C0%7C638300403101795371%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=GENjtkiQpejBysq%2BM3%2FVnwhtvcpUJ%2BngrKEcCAMgZd8%3D&reserved=0> for the workshop. The meeting will start with a 10-min mentoring topic "snack" from the ABIDES program.



The two-session workshop will primarily focus on introducing participants to basic numerical methods for solving Ordinary Differential Equations (ODEs) and Partial Differential Equations (PDEs) using Google Colab. During the first section, we will provide an overview of fundamental concepts related to ODEs and PDEs, followed by a practical demonstration of ODE solvers in Python, including a specific example involving the modeling of Ca2+ oscillations.


In the second section of the workshop, we will focus on solving simple PDE models within a regular domain, using the finite difference method. The primary goal of this workshop is to facilitate the understanding of mathematical modeling techniques among entry-level students and those who may not have prior modeling experience. Hopefully, by the end of the workshop, participants will be equipped with the skills necessary to tackle basic mathematical modeling challenges using Python and Google Colab.





Purdue BME/EMBRIO Seminar Wednesday 9/13: “Imaging Genetics: Dynamic Gene Control in Space and Time” by Dr. Bomyi Lim

Dr. Bomyi Lim from the University of Pennsylvania will be on the Purdue campus Wednesday 9/13, presenting a seminar 9:30 - 10:30 am. in BME Department, rm MJIS 1001. BME students should attend in person. Those further away or off-campus can join via Zoom<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-edu.zoom.us%2Fj%2F5593290378%3Fpwd%3DeFBOZFlNTU50ZDA2S2gwcnpyOWIwUT09&data=05%7C01%7Cembrio-list%40ecn.purdue.edu%7C2d739cfe1ed44025209808dbb2d5b092%7C4130bd397c53419cb1e58758d6d63f21%7C0%7C0%7C638300403101795371%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=cKNaPhZ2X177suL0j2eWiifFrOfqT%2BrRUs3Q0rop%2BpY%3D&reserved=0>. Faculty interested in meeting with Dr. Lim, please contact Lee Hua Chiang chiang47 at purdue.edu<mailto:chiang47 at purdue.edu> or 765-496-1339.


Abstract: Proper gene control across space and time is crucial for the seamless execution of various cellular functions, as too much or too little gene expression in the wrong place or time leads to developmental defects and disease phenotypes. While the importance of gene regulation is well acknowledged, systematic characterization of dynamic gene control is lacking. What is the “normal” range of gene expression, and how does transcriptional kinetics play a role? We employ quantitative live imaging to examine the structure-function relationships of genome topology and gene activity and ultimately relate it to phenotypes. We first systematically varied the distance and orientation between an enhancer and the target promoter and analyzed the changes in transcriptional dynamics. To gain further insights into the kinetics of E-P interactions, we employed the trans-activation (transvection) assay and utilized the DNA and RNA labeling to measure the long-range E-P interaction kinetics and its relationship with transcription. Our study provides a comprehensive characterization of the E-P interaction dynamics required for transcription and normal development.

Check out additional news and opportunities in the Emergence newsletter<https://www.purdue.edu/research/embrio/newsletters/index.php>.



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 at purdue.edu

<https://www.purdue.edu/research/embrio/>
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