Cheminformatics Online Chemistry Course (OLCC): A Community Effort to Introduce Cheminformatics Content into the Undergraduate Chemistry Curriculum

Presented at the American Chemical Society (ACS) Spring 2021 National Meeting (Virtual, April 16, 2021).

==== Abstract ====
Computer and informatics skills to handle an ever-increasing amount of chemical information are considered important for students pursuing STEM careers in the age of big data. However, many schools do not offer a cheminformatics course or alternative training opportunities. The Cheminformatics Online Chemistry Course (OLCC) is a community effort to introduce cheminformatics content into the undergraduate chemistry curriculum. It is a highly collaborative teaching project involving instructors at multiple schools as well as external cheminformatics experts recruited across sectors, including academia, government, and industry. Three Cheminformatics OLCCs were offered in the Fall 2015, Spring 2017, and Fall 2019 semesters. In each OLCC, the instructors at participating schools would meet face-to-face with the students, while external cheminformatics experts engaged through online discussions across campuses with both the instructors and students. All the material created in the course has been made available at the open education repositories of LibreTexts and CCCE websites for other institutions to adapt to their future needs. This presentation describes the instructional approaches of the Cheminformatics OLCC project and the lessons learned from this community effort. We also discuss future directions for this project as well as cheminformatics education in general, including pedagogy, resources, and course content.

1. Cheminformatics Online Chemistry Course (OLCC):
A Community Effort to Introduce Cheminformatics
Content into the Undergraduate Chemistry Curriculum
Sunghwan Kim
1
, Ehren C. Bucholtz
2
& Robert E. Belford
3
1
U.S. National Library of Medicine, National Institutes of Health
2
University of Health Sciences and Pharmacy in St. Louis
3
University of Arkansas at Little Rock

2. Kimetal.,J.Chem.Educ.,2021, 98(2),416-425

3. Why Teach Cheminformatics?
Ever-increasing amount of chemical information
(Google, Wikipedia, PubChem, SciFinder, Reaxys, …)
Chemical information literacy
(for critical assessment of data)
Computer & informatics skills
(for dealing with big data)

4. Lack of faculty members with cheminformatics expertise.
No textbook suitable for undergraduate chemistry majors.
Not considered as a core chemistry skill set.
The Cheminformatics OLCC addresses
some of these issues!
Unique Challenges to Teaching Cheminformatics

5. Cheminformatics OLCC
Collaborative Teaching
Instructors at
multiple schools
Open Education
Resource (OER)
Development
Cheminformatics
experts from
outside

6. Course website
Cheminformatics
experts
Prepare online reading materials &
homework problem sets
Course
Instructor
Students
Run the course
using the course materials
at multiple schools
Face-to-face
meeting
Online discussion among
experts, instructors & students
Instructional Approach

7. Enrollment Statistics
Semester # Schools# Students Participating schools
a
Fall 2015 4 36
UALR (6), Centre (4), WVU (5), UNF
(21)
Spring 2017 9 47
UALR (12), Centre (0
b
), UHSP (3),
IQS (6
c
), SDSU (4), Potsdam (3),
UIS (6), Campbell (12), Rutgers (1)
Fall 2019 5 23
UALR (2), Centre (3), UHSP (4),
IQS (9
c
), Otterbein (5),
a
Numbers in parentheses are the numbers of enrolled students at individual schools.
b
The course was taken by three faculty and staff members who participated in a faculty learning circle.
No students enrolled.
c
Not formally enrolled as the course was offered as a non-credit seminar.

8. OLCC Course websites
2015•http://olcc.ccce.divched.org/Fall2015OLCC
•https://chem.libretexts.org/link?50598
2017•http://olcc.ccce.divched.org/Spring2017OLCC
•https://chem.libretexts.org/link?83678
2019•https://chem.libretexts.org/link?143689
Course Websites
All course materials are freely available for reuse at:
Committee on Computers in Chemical Education (CCCE) website
(http://olcc.ccce.divched.org)
LibreTexts (https://libretexts.org)

9. Topics Covered in Cheminformatics OLCC

10. Critical assessment of chemical information
Chemical representations (e.g., InChI and SMILES)
Search by chemical name
Search by chemical structure
oIdentity search
o2-D/3-D similarity search
oSubstructure/superstructure search
Structure clustering
structure-activity relationship analysis
Automation of chemical data retrieval
PubChem-Related Topics

11. Python Jupyter Notebooks
(with sample codes and assignments)
oProgrammatic access to PubChem data
oCheminformatics tasks using open- source
software packages
(e.g., RDKit, scikit-learn, and Mordred).
oBioactivity prediction using machine learning
and PubChem data.
Similar materials for the R language
(using JupyterLab and R-Studio)
Python/R Programming (Fall 2019)

12. Students had two options to run the notebooks:
oDownload and run them on their own computers.
oRun the notebooks on JupyterHubavailable through LibreTexts.
Python/R Programming (Fall 2019)
After the 2019 OLCC, the Jupyter notebooks were converted
into Mathematicascripts.
(thanks to Joshua Schrier, Fordham University)

13. Small projects for the last 2- 4 weeks of the semester
(in 2015 & 2017 OLCCs).
Various projects weredone, ranging from the development of
an Android app to the creation of educational video tutorials.
oSelect students had opportunities to give oral presentations about their
projects at a special symposium at the Spring 2016 ACS National
Meeting in San Diego.
oSome student projects were evolved into more formal, long- term projects
oOne student's project eventually became the basis of a master's thesis.
Student Projects

14. NIST Reference Data Challenge (during the 2015 OLCC)
oMobile App development competition using NIST Standard Reference
Data (SRD).
oSome students participated in this competition and
one of them students won the second place.
(
https://nistdata.devpost.com/project-gallery)
Student Projects

15. Setting aside four weeks out of one semester for student
projects made it difficult to cover a broad area of
cheminformatics with the remaining time.
→Inclusion of student projects in the 2019 OLCC was up to the discretion
of the instructor at each participating school.
Student Projects

16. Cheminformatics OLCC (Fall 2021)
Internet of Things OLCC (Spring 2022)
If you are interested, please contact:
oDr. Sunghwan Kim ([email protected])
NIH/NLM/NCBI
oProf. Ehren Bucholtz (
[email protected])
University of Health Sciences & Pharmacy in St. Louis
oProf. Robert Belford (
[email protected])
University of Arkansas, Little Rock
Future OLCC Offerings (Tentative)

17. Summary
The Cheminformaics OLCC is a collaborative teaching project that involves
instructors in participating schools and external cheminformatics experts.
Please reach out to us for collaboration if you are interested.
It has two goals:
Offer a cheminformatics course for undergraduate chemistry majors
Develop free online cheminformatics textbook.
It has been offered three times (2015, 2017 & 2019).
All course materials are freely available for reuse
(CC BY-NC-SA 3.0 US, unless otherwise noted).

18. Acknowledgements
The PubChem Team
ACS DivCHED CCCE
LibreTexts / UC Davis
Cheminformatics OLCC participants
Funding
NLM/NIH (PubChem)
NSF (Cheminformatics OLCC)
NSF & Dept. of Ed (LibreTexts)
ACS CINF/CHED Innovative Project Grant(Travel support for students)

19. Thank you!
Questions?
Sunghwan Kim, Ph.D., M.Sc.
Email:
[email protected]
SlideShare: https://www.slideshare.net/SunghwanKim95/presentations