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Bringing Cheminformatics into the College Chemistry Classroom
This report is on selected presentations from a symposium organized by Robert Belford (Universty of Arkansas at Little Rock (UALR)) and Sunghwan Kim (PubChem), which sought papers related to the teaching of cheminformatics to chemistry majors. Papers were sought related to both teaching cheminformatics classes and the use of cheminformatics in other classes across the chemistry curriculum. The objective of the symposium was to give cheminformaticians and chemical educators a chance to share resources and experiences. The symposium was attended by both faculty and students, and afterwards we went to lunch at JOY TSIN LAU to further our discussions on bringing cheminformatics into the college chemistry classroom.
Participants of the symposium who continued the discussions over a lunch of dim sum
Thibault Géoui of Elsevier started the symposium with “Learning to find the right information: A survey of chemistry information literacy in the undergraduate classroom”, which was based on a survey of 138 educators. The survey identified that students expect information immediacy, expect information to be easy to find, want direct answers, and assume search engines understand them, all of which identified a mismatch between the structure of scientific information and student behavioral expectations. These behaviors could be the result of usage of Internet search engines like Google and indicate a need to introduce search engines like Reaxys into the classroom in order to improve student learning outcomes.
The second paper was presented by Ralph Stuart (Keene State) and coauthored by Leah McEwen (Cornell) on “Co-developing chemical information management and laboratory safety skills”. “Chemical Information” and “Laboratory Safety” are two skill sets identified by the ACS Committee on Professional Training (CPT) that undergraduate programs should impart to their students. Stuart and McEwen identified that these two skills support each other when taught as connected topics, and this could be done through the RAMP hazard assessment method described in the CPT guidelines as a chemical information research challenge. This approach enables determining the relevant question to search, identification of information sources, assessment of source quality, developing decisions based on the information collected, and documenting the basis for those decisions. This approach is described in an open access Journal of Chemical Education article that the authors coauthored last fall (https://dx.doi.org/10.1021/acs.jchemed.5b00511)
Douglas A. Vander Griend of Calvin College followed this with a presentation on “Introducing SIVVU.org, a Web-based program for modeling spectrophotometric titration data”. SIVVU (UVVIS spelled backwards) can analyze spectrophotometric titration data used to thermodynamically characterize multicomponent systems. Designed from a chemist’s perspective, it can use factor analysis to analyze the mathematical structure of pertinent datasets, and model the data according to user-provided chemical reactions to determine spectroscopic signatures and binding constants for the system. The site SIVVU.org is free to use, making it ideal for implementation in undergraduate chemistry laboratories.
Following a short break, Bob Belford (UALR) presented a paper coauthored with Delmar Larsen (UC-Davis) and Andrew Cornell (UALR) on “Integration of cheminformatics material in the STEMWiki hyperlibrary”. One of the objectives of the Cheminformatics OLCC, a multi-campus course taught in the fall of 2015, was to make educational material that could be used in the traditional courses of the undergraduate curriculum. By moving material created in the OLCC to the Libretext Hyperlibrary (formerly STEMWiki, of which the chemwiki alone had 55 million page views last year), the cheminformatics material became available to other classes across the curriculum. Currently 37 schools have libretexts within the Chemistry LibreText hyperlibrary, covering the spectrum of core courses taught in the undergraduate curriculum. So now, if a student in organic chemistry or any other class at one of those schools searches for InChI or SMILES in his textbook, the student is directly connected to educational material, including videos, that were used in the Fall Cheminformatics OLCC.
Hao Zhu of Rutgers-Camden then presented on “Cheminformatics education and research at home: the best way to teach graduate chemistry in the professional community”. Fifty percent of Rutgers-Camden graduate students are part-time students, most with full time jobs, and Hao presented a cheminformatics program that leveraged the flexibility of cheminformatics in the sense that “lab work” could be done off-site and at home. He show-cased several students who participated in this program, and whose interest became so great that they went on to earn PhDs. One of these students was an elementary school teacher. The take-home message of his presentation was threefold. First, as a relatively new field, cheminformatics is open for innovation; second, it is a topic of great interest to today’s youth; and third, cheminformatics research provides an option for students with full-time jobs to continue their education if their work obligations would prevent them from working in a traditional academic chemistry laboratory.
Following a second break, Bob Belford stood in for Brian Murphy, a student of the Fall 2015 Cheminformatics OLCC and presented on Brian’s paper “Fall 2015 Cheminformatics OLCC project based learning: Validation of Wikipedia Chembox hazard information,” while morphing the talk to cover multiple student projects. The presentation discussed aspects of the Drupal-based Cheminformatics OLCC course management system that was designed to facilitate multi-campus collaborative projects, and how students generated screen-capture videos showing the process of how they solved their projects. Specific projects presented included use of Google sheets to webscrape from Wikipedia Chemboxes and connecting academic laboratory inventories to PubChem Laboratory Chemical Safety Summaries (LCSS). The presentation ended with an overview of the upcoming spring 2017 Cheminformatics OLCC.
The final presentation was by Chase Smith (Massachusetts College of Pharmacy and Health Sciences (MCPHS) University) and Tamsin Mansley (Optibrium) on “Modern cheminformatics tools in the teaching laboratory: A practical exercise simulating a drug discovery project”. This presentation reported on a five-week long laboratory exercise that was incorporated into the Pharmaceutical Sciences graduate program at MCPHS University to simulate early-stage hit-to-lead and lead optimization in a drug discovery program. Students use the StarDrop cheminformatics software package from Optibrium Ltd. to guide the selection and design of compounds with an optimal balance of properties, together with publicly available datasets downloaded from the European Molecular Biology Laboratory (EMBL) Neglected Tropical Disease website. The laboratory simulation exercise provided a much-needed hands-on experience related to complex topics normally discussed only in theory, including mining primary screening data, predictive modeling, and drug metabolism, and provided the students with practical experience utilizing modern cheminformatics software.
Dr. Robert E. Belford, UALR Department of Chemistry