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<p style="margin: 0in; font-family: Aptos, sans-serif; font-size: 11pt;"><span style="font-family: "Times New Roman", serif; font-size: 12pt;">Hello all,</span></p>
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<p style="margin: 0in; font-family: Aptos, sans-serif; font-size: 11pt;"><span style="font-family: "Times New Roman", serif; font-size: 12pt;">I hope your summer is going well! ~</span></p>
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<span style="font-family: "Times New Roman", serif; font-size: 12pt;">This email is to inform you of an exciting new course offered this Fall 2024 for both undergraduate and graduate students!</span></p>
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<span style="font-family: "Times New Roman", serif; font-size: 12pt;">The course is PLS 481/581 Computational Plant Science taught by Dr. Alexander Bucksch.</span></p>
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<b>Description of Course</b></div>
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Introduction to imaging and simulation in the computational plant sciences using Python.</div>
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<b>Course Prerequisites or Corequisites</b></div>
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No formal prerequisites. Basic programming experience, the fundamentals of linear algebra, introductory statistics, or some basic plant biology are helpful during the course, but not required.</div>
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Informal prerequisites. The course is not a competition between students but an opportunity to improve from where you are at. Therefore, you must be comfortable to fail often with every task in the course until you succeed.</div>
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<span style="font-family: "Times New Roman", serif; font-size: 12pt; color: rgb(0, 0, 0);"><b>Long- Course Description:</b></span></p>
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<span style="font-family: "Times New Roman", serif;">The course introduces mathematical background and computational techniques to explore plant biology for students that are new to programming or do not regularly program. In doing so, the course introduces
basic techniques that allow the simulation of plant growth from the cellular to the organismal level and the imaging analysis of plant morphology. In contrast to other courses that focus on syntax, existing algorithms and data structures, the computational
Plant Science course is problem-oriented and teaches hands-on algorithm development under guidance.</span></p>
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<span style="font-family: "Times New Roman", serif;">The first 6 weeks cover basic python programming (for-loop, while-loop, if statement, variables data types, functions and a little bit of object-oriented programming) by extending existing code step-by-step
and basics of source code management with GitHub. In doing so, we will learn diffusion limited aggregation as a basic stochastic process to grow structures like lichen, leaf veins or corals. The course code is commented in a way that students can learn from
it and have a weekly learning goal defined.</span></p>
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<span style="font-family: "Times New Roman", serif;">In the second part of the class, we spend 4 weeks of procedural programming, basic data analysis and introduction to image processing and file handling by investigating the diffusion-reaction models that
produce pattern observed in looping vein structures, the shoot apical meristem, and initiate root hair growth. The second module of the course uses existing code from the internet and simulates a typical science scenario where code must be understood and adapted
to each student/group’s problem.</span></p>
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<span style="font-family: "Times New Roman", serif;">We finish the course with 3 weeks L-system modeling to generate branching patterns of plants that have a fractal structure. This graph-rewriting technique introduces students to graphs as a method to represent
growth-processes along with abstract graph grammars. The L-system module will be taught in a playful manner using the python turtle module and intuitive use of graph-grammars. We will not require the underlying group theoretical aspects as part of the homework,
but we want to introduce the concept to a point that a biology student can communicate their needs effectively in collaborations.</span></p>
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<span style="font-family: "Times New Roman", serif;">In week 7, the real fun begins, and the class becomes more interest driven. The students will select mini projects depending on their level of programming and needs for their research projects. This project
is presented during the final exam time.</span></p>
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<span style="font-family: "Times New Roman", serif;">What makes this class different in its setting is that your instructor is part of the class and often becomes your student at the end. During the class you will become more and more self-sufficient in proposing
and solving challenges with more than just a handful of solutions. Therefore, you might implement ideas your instructor or classmate cannot solve the same way.</span></p>
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<span style="font-family: "Times New Roman", Times, serif; font-size: 12pt; color: rgb(0, 0, 0);"><b>Instructor Research Interests:</b></span></p>
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<p style="margin-right: 0in; margin-bottom: 12pt; margin-left: 0.5in;"><span style="font-family: "Times New Roman", serif; font-size: 12pt; color: rgb(0, 0, 0);">Alexander Bucksch develops innovative computational methods to study plant organizational levels
from a computational and mathematical perspective. He expands to plant science the mathematical concept of “shape descriptors,” which reveal the state and growth of complex structures. Using imaging instruments and simulation models, Bucksch captures spatial
arrangements of branches, roots, and other organs that together form complex morphological phenotypes. His interdisciplinary methods have led to discoveries of phenotypes on scales ranging from populations to gene regulatory elements, that had been hidden
to classically trained biologists. Bucksch’s work increases understanding of plant adaptions to changing environments, which could benefit crop yield and public health. More than 700 researchers use his methods through the world’s largest root phenotyping
platform, <u><a href="http://dirt.cyverse.org" id="OWAffd79416-d9ee-2a86-42dd-9dd648bdac49" class="OWAAutoLink" data-auth="NotApplicable" data-loopstyle="linkonly" style="color: rgb(0, 0, 0); margin-top: 0px; margin-bottom: 0px;">Digital Imaging of Root Traits</a></u>.</span></p>
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<span style="font-family: "Times New Roman", serif; font-size: 12pt; color: rgb(0, 0, 0);"><i>We hope to see you there! </i></span></p>
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<span style="font-family: "Times New Roman", serif; font-size: 12pt; color: rgb(0, 0, 0);"><i>Have a wonderful summer! 🙂</i></span></p>
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<p style="margin-top: 0px; margin-bottom: 0px;"><span style="font-family: "Sitka Text", Cochin, serif; font-size: 16pt; color: rgb(23, 78, 134);"><img id="image_0" width="162" height="89" style="width: 162px; height: 89px; margin-top: 0px; margin-bottom: 0px;" data-outlook-trace="F:1|T:1" src="cid:447fb272-40c0-451d-804f-4cb5a386a1ac"></span></p>
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<p style="margin-top: 0px; margin-bottom: 0px;"><span style="font-family: "Sitka Text", Cochin, serif; font-size: 16pt; color: rgb(0, 0, 0);"><b>Keenia Shinagawa, M.Ed.
</b></span><span style="font-family: "Times New Roman", serif; font-size: 10pt; color: rgb(73, 80, 87);">she/her</span></p>
<p style="margin-top: 0px; margin-bottom: 0px;"><span style="font-family: "Times New Roman", serif; font-size: 10pt; color: rgb(23, 78, 134); background-color: rgb(255, 255, 255);"><b>Student Support | Graduate Coordinator</b></span></p>
<p style="margin-top: 0px; margin-bottom: 0px;"><span style="font-family: "Times New Roman", serif; font-size: 9pt; color: rgb(200, 38, 19); background-color: rgb(255, 255, 255);"><b>THE UNIVERSITY OF ARIZONA</b></span></p>
<p style="text-align: left; background-color: rgb(255, 255, 255); margin: 0in;"><span style="font-family: "Times New Roman", serif; font-size: 10pt; color: rgb(111, 192, 64);"><b><i>School of Plant Sciences (SPLS)</i></b></span><span style="font-family: "Times New Roman", serif; font-size: 11pt; color: rgb(0, 36, 81);"><br>
</span><span style="font-family: "Times New Roman", serif; font-size: 10pt; color: rgb(0, 0, 0);"><b><i>College of Ag., Life & Environ. Sci (CALES)</i></b></span><span style="font-family: "Times New Roman", serif; font-size: 11pt; color: rgb(0, 36, 81);"><br>
</span><span style="font-family: "Times New Roman", serif; font-size: 10pt; color: rgb(23, 78, 134);">Office:
<b>Forbes, 317</b></span></p>
<p style="text-align: left; background-color: rgb(255, 255, 255); margin: 0in;"><span style="font-family: "Times New Roman", serif; font-size: 10pt; color: rgb(118, 62, 155);"><i>O: (520) 621-1336</i></span></p>
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<p style="text-align: left; background-color: rgb(255, 255, 255); margin: 0in;"><span style="font-family: "Times New Roman", serif; font-size: 10pt; color: rgb(196, 0, 164);"><b>Student Resources:</b></span></p>
<p style="text-align: left; background-color: rgb(255, 255, 255); margin: 0in;"><span style="font-family: "Times New Roman", serif; font-size: 10pt; color: rgb(0, 0, 0);">Click here for mental health/stress, etc. support ->
<a href="https://cals.arizona.edu/life-management-services" style="margin: 0px;">
CALS Life Management Counselors</a> </span></p>
<p style="text-align: left; background-color: rgb(255, 255, 255); margin: 0in;"><span style="font-family: "Times New Roman", serif; font-size: 13px;">Click here for academic support -></span><span style="font-family: "Times New Roman", serif; font-size: 10pt; color: rgb(0, 0, 0);"><a href="https://cals.arizona.edu/learning-lab" style="margin: 0px;">CALS
Learning Lab</a> </span></p>
<p style="text-align: left; background-color: rgb(255, 255, 255); margin: 0in;"><span style="font-family: "Times New Roman", serif; font-size: 10pt; color: rgb(0, 0, 0);">Click here for grad path form instructions/help ->
<a href="https://grad.arizona.edu/gsas/gradpath/gradpath-user-guides" title="https://grad.arizona.edu/gsas/gradpath/gradpath-user-guides" style="margin-top: 0px; margin-bottom: 0px;">
Grad Path User Guides</a></span></p>
<p style="text-align: left; background-color: rgb(255, 255, 255); margin: 0in;"><span style="font-family: "Times New Roman", Times, serif; font-size: 10pt; color: rgb(190, 91, 23);"><i>Let me know if you need any other resources!</i></span></p>
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