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Fall 2015 Newsletter

Each Fall the CCCE hosts online discussions of recent work of relevance to the use of computers in chemical education. The authors of each paper are available to discuss their work with the community on the days assigned to their papers, and both the papers and discussion are archived on our site. You do not need to be a member of ACS, CHED or the CCCE to participate in these discussion, but need to set up a free account by contacting the site moderator, Bob Belford at rebelford@ualr.edu.  

 

 Discussion Schedule

Oct.  29-31        21st Century Chemical Education, Harry Pence, SUNY Oneonta.

Nov.  02-04        Using Google Forms to Receive and Grade Online Lab Reports, Mark Ott, Jackson College
Nov.  05-07        PubChem Laboratory Chemical Safety Summary, Sughwan Kim, NCBI

Nov.  09-11        Chemistry and Diplomacy: Science Education and Science Communication in Disarmament, Jonathan Forman, OPCW
Nov.  12-14        A New Application for Discussing Chemical Ideas, Andras Stracz & Ivan Solt, 
ChemAxon

Nov.  16-18        CAMEO: A Place for Art and Science to Meet, Michele Derrick, Boston Museum of Fine Arts
Nov.  19-21        Why the ChemWiki?, Josh Halpern, Hope College

Nov. 30-Dec. 2   Henry Stewart Talks, Neil Bradman and Iris Margalit
Dec. 03-05         MolView: An attempt to get the cloud into chemistry classrooms, Herman Bergwerf 

Dec. 07-09         Looking Back at 20 Years of the MOLECULE OF THE MONTH Website, Paul May and Simon Cotton

Editor: 

Robert E. Belford
Rick Spinney

Newsletter Articles

Abstracts of Papers

Harry E. Pence, Dept. of Chemistry and Biochemistry, SUNY Oneonta. Oneonta, NY

Chemical education is facing a number of significant challenges in the 21st Century. There are demands to include more online learning, new learning techniques, such as flipped classrooms and POGIL, to implement personal and institutional learning analytics, and, of course, to respond to problems with enrollment and funding. This paper focuses only one of those challenges, how technology is changing industrial chemistry and chemical education.

Mark Ott,

A method is described whereby students submit their entire lab report electronically, the instructor still has ease of grading pen-on-paper, and all students can review everyone else’s submission (names are removed) such that they can learn from the other examples, albeit good or bad. The only software needed are freely available and simple to use.

Sunghwan Kim*†, Leah McEwen‡, Ralph Stuart§, Paul Thiessen†, Asta Gindulyte†, Jian Zhang†, Evan E. Bolton†, Stephen H. Bryant†
† National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, 20894.
‡ Clark Physical Sciences Library, Cornell University, Ithaca, NY, 14853.
§ Office of Environmental Health & Safety, Keene State College, Keene, NH, 03435.

A series of high profile laboratory accidents over the last 7 years has increased the academic community’s awareness of the importance of risk assessment in laboratories, both teaching and research. Because of the many different chemicals used in laboratory work, these risk assessments require ready access to safety information for a large number of chemicals. In order to provide researchers, educators and students with electronic access to chemical health and safety information, PubChem provides a “Laboratory Chemical Safety Summary” (LCSS) data view for more than three thousand chemicals commonly encountered in laboratories (https://pubchem.ncbi.nlm.nih.gov/lcss/).

        The LCSS contains pertinent chemical health and safety data for a given PubChem Compound record, based on the format described by the National Research Council in “Prudent Practices in the Laboratory: Handling and Management of Chemical Hazards”.  Information contained in the LCSS is a subset of the PubChem Compound Summary page content, and includes information on flammability, toxicity, exposure limits, exposure symptoms, first aid, handling, clean up and more.  These data are provided by various data contributors, including authoritative agencies such as the U.S. National Institute for Occupational Safety and Health (NIOSH), the Occupational Safety and Health Administration (OSHA), and the International Labor Organization (ILO). Of special interest in this collection is specific “Stability and Reactivity” information, which lists known chemical reactions between the chemical of interest and other chemicals and chemical classes. This information often extends beyond that found on Safety Data Sheets for the chemical of interest.

       LCSSs are available for PubChem Compound records which have GHS (Globally Harmonized System of Classification and Labeling of Chemicals) hazard classification information from PubChem’s data contributors.  PubChem is actively recruiting this GHS information from additional contributors in order to expand its LCSS coverage. If a PubChem Compound record has an LCSS, the link to view it is provided at the top of the Compound Summary page of that compound under the heading “Safety Summary”.  In addition, one can get the complete list of chemicals with an LCSS by visiting the PubChem LCSS project webpage (https://pubchem.ncbi.nlm.nih.gov/lcss/) or by using the PubChem Classification Browser (https://pubchem.ncbi.nlm.nih.gov/classification/). If desired, LCSS data can be downloaded from the LCSS page for each compound, or in bulk from the PubChem LCSS project webpage.

Jonathan Forman,
Science Policy Adviser, Office of Strategy and Policy,
Organisation for the Prohibition of Chemical Weapons

Science plays a critical role in international disarmament policy and diplomacy; it informs negotiation of international agreements and underpins the key provisions that define the mechanisms of treaty implementation.   From an outside view, the world of international disarmament appears to be driven by diplomats and policy makers, not scientific experts; yet, to be effective, disarmament treaties require a sound science and policymaker partnership.   Such a partnership must overcome challenges to communication and trust (much like the partnerships between States Parties to international treaties), begging the question, how can this work?   It requires clear science communication and engagement between the two perspectives – scientists providing analytical thinking and technical assessments to policy makers, who in turn provide global perspectives on the role and need for science in their work.

Exemplifying the need for scientific (and specifically chemistry) expertise in diplomacy is the Chemical Weapons Convention (CWC), an international disarmament treaty that completely prohibits an entire class of weapons of mass destruction.   The implementing body for the CWC, the Organisation for the Prohibition of Chemical Weapons (OPCW), bridges the gap between policy makers and scientific experts through its scientific advisory board and a variety of science communication initiatives.   Initiatives that include “Science for Diplomats” briefings and informal science and technology newsletters that are both accessible to non-technical audiences and provide useful links to informative technical publications.   We describe here the role of science in disarmament and look at materials and resources made available to scientific and diplomatic communities alike through the OPCW website (Figure 1).

Figure 1:  Online resources available from www.opcw.org and OPCW social media accounts; this figure is interactive with hyperlinks to the indicated materials and information.

Andras Stracz, Ivan Solt, ChemAxon

In this article, we look at a new application called Marvin Live, developed by ChemAxon for online collaboration. Marvin Live offers a novel approach to designing molecules and leading chemical discussions among remote participants.

We will describe the pharmaceutical industry and academic needs that led to these developments and the workflows made possible, all the way from simple chemical reaction drawing tasks, to connecting globally distributed research teams for project design meetings. We look at use cases that enable their use for tutoring and mentoring, and their capabilities to automate the otherwise time-consuming aspects of meeting preparations and note-taking.

Michele Derrick

CAMEO (Conservation and Art Materials Encyclopedia Online at cameo.mfa.org), is a set of Internet databases that serve art-related professionals as well as the general public.  Started in 1999, the original material database contains technical, historical, chemical, and visual information on historic and contemporary materials used in the preservation and production of artistic, architectural, and archaeological artifacts. Continually growing, CAMEO established a collaborative agreement with an EU working group of museum scientists to enhance the content, breadth, and transnational accessibility of the database. This resulted in Google statistics of more than 300,000 page hits in over 200 countries in just the past year.  The CAMEO database is now based on a MediWiki platform and resides on a cloud server, placing it in the unique position to offer homes to small collaborative databases that benefit many art conservation and museum communities. All sections of the database are freetoby users on the World Wide Web and could provide educators with some very interesting resources and contexts for the teaching of chemistry that they could use in their classes and lesson plans.

Joshua Halpern, Dept. of Chemistry, Howard University, Washington, DC 2002
jhalpern@howard.edu

Discussion about textbook price is anchored to cost.  Here I argue that cost is a relatively minor issue in the choice of books by instructors but rather ancillary services offered by the publishers dominates.  Thus, any attempt to replace published textbooks with open on line educational resources must pay careful attention to providing these.  This drives the current transformation of the ChemWIKI into a Stem Hyperlibrary

Neil Bradman
Iris Margalit

The Biomedical and Life Sciences Collection is a commercially produced online resource of specially prepared, seminar style, animated, audio-visual lectures accessed on subscription by academic institutions, research centres and pharmaceutical/biotech companies. The content of the collection and how it is used is described, and examples of the talks presented. The business model followed enables relatively high set-up and operational costs to be spread across multiple subscribers at a low charge per institution for unlimited use. 

Herman Bergwerf
hermanbergwerf@gmail.com

MolView is a web application which helps students and teachers to visualize molecular structures and view their properties. There are numerous databases publicly available to provide the required data such as PubChem, ChemSpider, ChEMBL, DrugBank, the Crystallography Open Database[1], and many more.[2][3] Currently, MolView uses PubChem, RCSB, the Crystallography Open Database, the Chemical Identifier Resolver[4], and the NIST WebBook[5] to retrieve data. MolView offers a simple search interface to find small molecules, proteins and crystal structures in these databases. MolView uses JavaScript libraries, that use modern web technologies such as WebGL, to visualize these structures. In the past year I have designed a new version of this application from the ground up to facilitate the implementation of new databases and tools. Along with a new architecture and user interface, this version will include internationalization, interactive instructions, advanced search tools, more import/export tools, and more presentation tools. I also intend to include more computational chemistry tools to make the analysis and processing of complex data easier and more fun.

Paul May (University of Bristol, UK)
Simon Cotton (University of Birmingham, UK)

The Molecule of the Month website administered from the University of Bristol, UK, is one of the longest running websites on the web (started Jan 1996).  As its name implies, each month a new article is posted describing a particular molecule, along with its history, science and numerous interesting anecdotes.  The aim of the site is to make chemistry accessible to non-scientific readers, and so the articles are written in an easy-to-read question-and-answer format, and illustrated with photographs, cartoons and structure diagrams, along with quotations from movie stars, rock songs and other snippets from popular culture.  The website has been of the pioneers for web innovations such as Chime, Chemsymphony and JMol.  As it comes up to its 20th anniversary, we shall look back at two decades of contributions from authors from all over the world, comment about the way the site has evolved over this time due to changing technology, and discuss what the future may hold for sites like these.

Comments

Greetings,

This is both a test of the ConfChem site and a post for new members on how we run ConfChem/Newsletter discussions.

We post papers and discuss them with their authors for three days.  We do this by subscribing the confchem list (ConfChem@ualr.edu) to each paper while it is discussed.  In this test I subscribed the list to the Newsletter homepage and made a comment on the homepage.

PLEASE DO NOT REPLY TO THIS EMAIL, but if this was a real question or comment that you want to reply to, click the link in this email, which takes you to the comment, and reply to the comment.  That will trigger another email to the list. Please note, you need to log into the site, and only people who have accounts can comment, but anyone can read the comments. Contact me if you have problems.

This allows us to archive the discussions with the paper and allows people to follow the discussion threads.

If you are getting too many emails you can unsubscribe anytime and there are instructions at the bottom of each email on how to do this.

Please feel free to contact me in private if you have any questions or problems  (rebelford@ualr.edu – do not reply to this email).

Let me repeat, PLEASE DO NOT REPLY TO EMAILS, but use the link in the email and reply to the comments that are under each of the papers.

Cheers,
Bob

Dec. 5 test, it appears some comments are not triggering email.

William Roby's picture

Got it when I logged in.