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Navigating an Internet of Chemistry via ChemSpider by Antony Williams

On October 14, 2011 Dr. Antony Williams presented the second online talk to students and faculty at the University of Arkansas at Little Rock dealing with cheminformatics.  This presentation was on the use of ChemSpider to acquire information on chemical compounds over the web and included material like the use of InChI and InChI keys for structure and substructure searches. 

This was presented with the open source BigBlueButton conference management system and Dr. Williams has shared his presentation with us which you may watch through the one hour video below, or access Dr. William's slides through the slideshare presentation below.

Dr. Williams Video:

http://www.youtube.com/watch?v=wYfjpSkau2c Dr. Williams Slides:


Essential Cheminformatics by David J. Wild

On October 7, 2011 Dr. David J. Wild, Director of the Cheminformatic Program at Indiana University-Bloomington gave the first hybrid online presentation to the UALR department of Chemistry seminar series using BigBlueButton conference management system and Skype.  Although this was a lecture to departmental faculty and students, Dr. Wild was presenting on core cheminformatic material which we feel graduating students should be cognizant of, and components of this lecture would be incorporated into the Cheminformatics OLCC.  That is, how do you represent molecules in a way that computers understand, and what are the issues with such representations.  This is actually the first of two presentations and Dr. Tony Williams will give a followup on Oct. 14 which will build upon the material presented here.  Dr. Wild was kind enough to allow us to record this and share his slides through slideshare.

Here is a YouTube video of Dr. Wild's presentation.

Here is a slideshow from slideshare.

Oct 2011 ualr

Cheminformatics OLCC

This Blog was originally made 2011-04-13 and has been moved to this new "home" as it was created as an orphaned "post"

This Blog is being started to jot down ideas concerning a new CCCE On-Line College Course (OLCC) in Chemical Information Sciences and Cheminformatics. The driving force behind the organization of this course lies in the recognition that the digital revolution has resulted in recent advances in information sciences and cheminformatics which need to be addressed in the chemistry curriculum. There are several aspects to this which I would like to see addressed. But first I think I need to address some semantic/terminology issues associated with an OLCC.

This is an intercollegiate course involving faculty from multiple institutions in multiple roles. The idea is to allow a school to offer a course which there are no resident faculty qualified to teach by bringing in outside experts, and in so doing, not only teach the students, but also train/update the faculty. So in essence there is a strong element of faculty development. Recent advance in chemical informatics and information sciences make this an ideal topic for such a course. So there are several types of faculty and schools in this class.

Defintions: (please suggest revisions on the last two)  

  • Lecturer - Professional who gives online presentation and provides course content. May or may not be an academic professional.
  • Facilitator - Faculty member at a school which offers the course to students for credit.  
  • Presenting school/organization School or professional organization which is providing curriculum content  
  • Host school school where the course is offered to students for credit. OK, Now lets tackle some of the issues this class needs to address

There are 4 things I would like this course to approach

1. New and emerging learning styles of digitally native students
2. Information Sciences
3. Cheminformatics
4. Disparate Teaching


1. New and emerging learning styles of digitally native students. Recent research indicates that "digitally native" students and "free-agent learner" are using technology in new and novel ways which few instructors are prepared to deal with. I suggest a review of Project Tomorrow if you are in question of the research associated with this. project tomorrowand especially the April 2011 Speakup report. I am not talking about using the social networking tools like Facebook and Twitter which they use in their lives, but finding ways to utilize their nativity with these types of technologies to integrate social media tools into their scholastic workflow. Thus I would like to start of with an introduction to social research tools like Zotero, Diigo and the Google Docs suite, and search/share functionalities like social tagging instead of hierarchical information structures for information retreival.  

2. Information Sciences The library has changed since I went to school. Elite schools have access to resources which smaller schools do not. The digital revolution has done a lot to share these resources, and an up-to-date evaluation/exposure to library resources would assist many students (and faculty members). We need to recognize the strengths and weaknesses of the current information architecture in the chemical sciences and failure to do so results in a dis-service to our students. One strong idea I have which is based on educational research, would be to involve some librarians of large universities (presenting organizations) not just as lectures, but to laisie with resident librarians of host schools. This interaction could be facilitated by a student survey project, where the students go to their library, work with their librarian, and get a feel for what resources they have, and what resources they don't. Then they can tackle how to rectify any identified deficiencies. But fundamental to this would be for the host school librarian to function as a local in-person expert.  

3. Cheminformatics This is the big one, and why I realized this OLCC needs to be done. Chemistry is behind biology and there are bioinformatics programs all over the world which are changing the way biology is performed. I think part of this deals with the role the pharmaceutical industry has had in the evolution of cheminformatics with the consequence of proprietary database systems. But it needs to be done in a way which acknowledges the role of proprietary systems and provides a students an understanding of them, but promotes open science. That is, I believe the quantity of open access/open source cheminformatics resources has reached the critical mass where it can influence the way science is performed. For example, how many students understand the significance of predictive properties or the validation issues associated with empirical data?  

4. Disparate Teaching OK, I know I need to come up with a better name, but the structure of this course amplifies the challenges of teaching with guest lecturers. Simple speaking, in the eyes of the student, who is the teacher? The lecturer who presents the information? Or the facilitator who writes the tests and awards the grade? And it is worse than that. If you have m lecturers and n facilitators you have an m by n matrix of combinatorial interactions between different lecturers and facilitators, each with their own styles, competencies, standards etc.. So how do you provide a unified presentation to the student with consistent learning, especially if different host schools have different standards? And add on to this a third dimension, that associated with repurposing the material into other future classes once the course is over.

We could have the presenters and facilitators submit questions indicative of the learning outcomes they would like for each module. This would span a variety of competency expectations. Some could be appropriate for a freshmen level course, others junior or even graduate. We could then make screen capture videos of on-line interviews of each presenter using the BigBluebutton conference management software. The presenter would have the questions ahead of time and prepared presentations to answer them. Each question/Answer (Q&A) would be a separate file (video). If this was done by all facilitators for all presenters you would have every cell of the presenter/facilitator interaction matrix filled. This would then enable curriculum alignment at multiple levels for the same content by the cells of the matrix used. (Each column represent the questions representing the expectations of an individual facilitator while each row represents content presented by a specific presenter). Although this is not the "content" of the course, it is one of the most important aspects of the project.

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