[Plsgs] Fwd: New Course! PLS 481/581 Computational Plant Science

Thu Aug 15 16:02:43 MST 2024

Happy summer everyone!

I wanted to send a reminder about my new course “Computational Plant Science” just before the start of the new semester.
There is still time to register if you haven’t done so, missed the first announcements or still need a course.

The course is designed for both undergraduate and graduate students and no previous programming expierience is necessary.

Cheers and I am excited for the new semester,

Alex

P.S.: Below is Keenia’s original email with all details and I attach a quick flyer with an overview.

—————————————————————————————————————————————————————————

[cid:8582f225-3809-478c-9514-a73b142f86a0 at namprd19.prod.outlook.com]

Dr. Alexander Bucksch
Associate Professor - School of Plant Sciences
BIO5 member
GIDP Faculty in Data Science & Statistics and Applied Mathematics

e: bucksch at arizona.edu
w: http://www.computational-plant-science.org
LinkedIn: https://www.linkedin.com/in/abucksch/

[cid:86e4c267-e6bb-4469-9f8b-60a7c038d023 at namprd19.prod.outlook.com]

http://www.ipps8.org/

We respectfully acknowledge the University of Arizona is on the land and territories of Indigenous peoples. Today, Arizona is home to 22 federally recognized tribes, with Tucson being home to the O’odham and the Yaqui. Committed to diversity and inclusion, the University strives to build sustainable relationships with sovereign Native Nations and Indigenous communities through education offerings, partnerships, and community service.

Begin forwarded message:

From: "Shinagawa, Keenia Alejandra Ibarra - (kshinagawa)" <kshinagawa at arizona.edu>
Subject: New Course! PLS 481/581 Computational Plant Science
Date: June 4, 2024 at 11:23:32 AM MST
To: "plsugs at list.cals.arizona.edu" <plsugs at list.cals.arizona.edu>, "plsgs at list.cals.arizona.edu" <Plsgs at list.cals.arizona.edu>
Cc: "Bucksch, Alexander - (bucksch)" <bucksch at arizona.edu>

Hello all,

I hope your summer is going well! ~

This email is to inform you of an exciting new course offered this Fall 2024 for both undergraduate and graduate students!
The course is PLS 481/581 Computational Plant Science taught by Dr. Alexander Bucksch.

[cid:6f431495-41d4-4b69-800f-ce3cf3deceb5 at namprd19.prod.outlook.com]

Description of Course

Introduction to imaging and simulation in the computational plant sciences using Python.

Course Prerequisites or Corequisites

  *
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.
  *
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.

Long- Course Description:

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.

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.

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.

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.

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.

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.

Instructor Research Interests:

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, Digital Imaging of Root Traits<http://dirt.cyverse.org/>.

We hope to see you there!

Have a wonderful summer! 🙂

[cid:b452d60d-a122-41b6-b6a3-49621b11cd35 at namprd19.prod.outlook.com]

Keenia Shinagawa, M.Ed. she/her
Student Support | Graduate Coordinator
THE UNIVERSITY OF ARIZONA
School of Plant Sciences (SPLS)
College of Ag., Life & Environ. Sci (CALES)
Office: Forbes, 317
O: (520) 621-1336

Student Resources:
Click here for mental health/stress, etc. support -> CALS Life Management Counselors<https://cals.arizona.edu/life-management-services>
Click here for academic support ->CALS Learning Lab<https://cals.arizona.edu/learning-lab>
Click here for grad path form instructions/help -> Grad Path User Guides<https://grad.arizona.edu/gsas/gradpath/gradpath-user-guides>
Let me know if you need any other resources!

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://list.cals.arizona.edu/pipermail/plsgs/attachments/20240815/af8b69bc/attachment-0001.htm>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: attachment.png
Type: image/png
Size: 9761 bytes
Desc: attachment.png
URL: <https://list.cals.arizona.edu/pipermail/plsgs/attachments/20240815/af8b69bc/attachment-0002.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image002.jpg
Type: image/jpeg
Size: 8946 bytes
Desc: image002.jpg
URL: <https://list.cals.arizona.edu/pipermail/plsgs/attachments/20240815/af8b69bc/attachment-0002.jpg>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image001.png
Type: image/png
Size: 568747 bytes
Desc: image001.png
URL: <https://list.cals.arizona.edu/pipermail/plsgs/attachments/20240815/af8b69bc/attachment-0003.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Outlook-40wy1q3s.jpg
Type: image/jpeg
Size: 41406 bytes
Desc: Outlook-40wy1q3s.jpg
URL: <https://list.cals.arizona.edu/pipermail/plsgs/attachments/20240815/af8b69bc/attachment-0003.jpg>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: PLS 481581 Bucksch .pdf
Type: application/pdf
Size: 395186 bytes
Desc: PLS 481581 Bucksch .pdf
URL: <https://list.cals.arizona.edu/pipermail/plsgs/attachments/20240815/af8b69bc/attachment-0001.pdf>