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Use of Wikis and Macromedia Breeze in Chemical Information and Cheminformatics Instruction

at Indiana UniversityGary Wiggins

Indiana UniversitySchool of Informaticswiggins@indiana.edu

June 6, 2007

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Abstract In 1991, McGraw-Hill published the book Chemical Information

Sources, an innovative textbook that included a disk with a database covering some 2500 reference materials and the software to search it. The database was later converted to a Web-searchable format, the Chemical Reference Sources Database (http://www.oscar.chem.indiana.edu/cfdocs/libchem/crsd/crsdintro.html), and the lecture notes for the Chemical Information Sources class were placed on the Web. In 2006, all instructional modules associated with the course were converted to the Wiki format, thus allowing others to contribute to the material. (http://cheminfo.informatics.indiana.edu/cicc/cis/index.php/Main_Page).

(continued on next slide)

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Abstract (cont’d) Wikis are also used for courses in the IU School of Informatics

graduate cheminformatics degree and certificate programs, e.g.:– Chemical Information Technology

http://cheminfo.informatics.indiana.edu/djwild/I571_2006_wiki/index.php/Main_Page

– Programming for Chemical and Life Science Informatics http://cheminfo.informatics.indiana.edu/djwild/I573_2007_wiki/index.php/Main_Page

These are two of the four required courses for the Graduate Certificate in Cheminformatics, as well as for the MS in Chemical Informatics and the cheminformatics track of the PhD in Informatics degree programs.

Distance Education at IU is facilitated through the use of Macromedia Breeze. The technology in use allows the lectures and slides to be recorded for later playback by DE students. The poster will cover the main features of the underlying techniques and some of the problems associated with their use.

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ACS Committee on Professional Training Statements on Chemical

Information Retrieval• “A student who intends to become a practicing chemist, or who will

use chemistry in allied fields of science and medicine, should know how to use the chemical literature effectively and efficiently.” (2003)

• “Students should be able to use the peer-reviewed scientific literature effectively and evaluate technical articles critically. They should learn how to retrieve specific information from the chemical literature, including the use of Chemical Abstracts and other compilations, with online, interactive database-searching tools.” (2007 draft)

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ACS CPT Recommendations on How to Gain Proficiency

• Proficiency in chemical information retrieval should be acquired through formal instruction.– Through a course dedicated to the subject of

chemical information retrieval• 37% used this option in 2005.

– Through integration into other chemistry courses• 73% used this option in 2005. (Garritano and Culp)

– Through coordination and monitoring of each student's satisfactory achievement, preferably by one faculty member or librarian.

• Not an option in the 2007 draft.

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Indiana University’s C471 Chemical Information Sources Class

• Taught by Gary Wiggins from 1976-2003• One semester-hour required course for

undergraduate chemistry majors• Usually taken in the junior or senior year• http://www.indiana.edu/~cheminfo/C471/471home.html

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Little Red Book

A good idea with the wrong info technology: mixedmedia textbook published in 1991.

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A Better Idea: Chemical Information Sources Wiki• http://cheminfo.informatics.indiana.edu/cic

c/cis/index.php/Main_Page

• Purposes: – To provide a free guide to the many sources of

reference materials available to those who have questions related to chemistry

– To provide a convenient, updatable text to supplement instruction in chemical information retrieval

• Converted from Web to Wiki format in Fall 2006

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CIS Wiki: Overall Organization

• How and Where to Start – Guides, reviews, background reading, etc.

• How and Where to Search: General– Searching by author, subject, chemical name or formula,

structure• How and Where to Search: Specialized Sources

– Synthesis, analysis, physical properties, patents, safety• Communication in Chemistry

– Blogs, discussion lists, aids to writing, molecular visualization• Miscellaneous

– History, biography, directories, industry standards, teaching and study, careers

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Books

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Interesting Features of Wiki• Built-in search engine

– Search of “Houben” yields four pages on the topic• Images can be uploaded by anyone who edits

– Images and text in the section on Houben–Weyl Methods of Organic Chemistry were contributed by Thieme.

• Can add RSS feeds to text– Book reviews in the previous slide are updated from the RSS

feed at ETH (using SimplePie on MediaWiki).• Always a possibility of inappropriate additions

– “Dual Disorders” and “Drug Treatment Program” contributed on May 21, 2007 (now deleted).

• RSS feed for “Recent Changes” can help keep track of edits.

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Beilstein 1

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Usage of the CIS Wiki

• Visitors since January 1, 2007 (as of 5/17/07)– Range from 1235 (Background Reading) to

10,700 (Chemical Name and Formula Searching)

– Average number of visits per page: 3263

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Other CIS Wiki Features

• SIRCh: Selected Internet Resources for Chemistry (converted from Web to Wiki)– http://cheminfo.informatics.indiana.edu/cicc/cis/

index.php/SIRCh:_Selected_Internet_Resources_for_Chemistry

• CRSD: Chemical Reference Sources Database (still a Web database)– http://www.oscar.chem.indiana.edu/cfdocs/

libchem/crsd/crsdintro.html

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Graduate Cheminformatics Courses Taught at IU with a Wiki

• I571 Chemical Information Technology– http://cheminfo.informatics.indiana.edu/djwild/I571_20

06_wiki/index.php/Main_Page

– Also required for the SLIS Chemical Information Specialist MIS or MLS degrees

• I573 Programming for Science Informatics– http://cheminfo.informatics.indiana.edu/djwild/I573_20

07_wiki/index.php/Main_Page

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Informatics MS Degree Programs

• http://www.informatics.indiana.edu • MS degree: 36 semester hours

– Includes a 6-hour capstone/research project – IUB: Bioinformatics, Cheminformatics, Human-

Computer Interaction Design– IUPUI: also, New Media, Health Informatics,

Laboratory Informatics

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MS in Cheminformatics

• http://cheminfo.informatics.indiana.edu • Sound knowledge of chemistry and

excellent facility in computer science– Students with CS background should have the

chemistry knowledge covered in an undergraduate minor in chemistry.

– Students with a Chemistry background should have the knowledge covered in an undergraduate minor in computer science.

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Graduate Certificate in Chemical Informatics

• Requirements: 4 courses; each 3 cr. hours– I571 Chemical Information Technology– I572 Computational Chemistry and Molecular

Modeling – I573 Programming for Science Informatics – I553 Independent Study in Chemical Informatics

• For on-site IUB and Distance Education students• DE Students pay in-state fees, regardless of where they

live!

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Cheminformatics Enrollment Data, 2005/2007 (NIH Grant)

• Currently have 4 PhD, 6 MS students • 99 graduate students have taken at least one

cheminformatics course since Aug 2005.• 39 of the grads (40 percent) accessed the

courses through distance education (DE).– CIC CourseShare with University of Michigan– Use Macromedia Breeze and phone for DE

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Macromedia Breeze (now Adobe Acrobat Connect)

• Virtual meeting/classroom environment for sharing presentations, images, and desktop applications with remote participants

• Features a digital whiteboard, text chat, polling, and audio/video broadcasting

• Participants need only a Web browser with Flash plugin and a broadband Internet connection.– We used phone line for audio and no video due to

problems with VOIP and bandwidth.

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Acrobat Connect Professional

• Classes can be recorded.– We’re moving toward recording lectures

beforehand and using the class time for discussion and interaction with remote students.

• Can give control to a remote presenter

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Experiences with Breeze, I572

• Audio: Poor. We often deferred to phone.• Video: Good. Once connected we had very few

instances of connectivity loss.• For most PowerPoint presentations maybe 1-2

second delay.• A short movie did not display on the Breeze

interface– Could see it on the local projector and computer

screen• Able to perform Spartan as well as PC Model

simulations, but usually a 5-7 second delay.

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Experiences with Breeze, I573: Good Points

• Interface is more polished than previous version.

• Reliable for screen sharing and slide sharing

• Recording available (but some reliability problems: see next slide)

• Playback of recordings don't require special software.

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Experiences with Breeze, I573: Bad Points

• Using webcam video caused all kinds of problems (slowdowns, crashes, etc.).

• VOIP audio is not reliable nor of good enough quality.

• Recording requires VOIP audio (difficult to record from teleconference).

• Not sufficient mechanism for eliciting student feedback

• Latency builds up over time: gets audio out of synch with video

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Breeze “Workarounds”

• Used an auxiliary microphone on the PC to record lectures– Stopping the screen share every 10-15 minutes

should keep latency to a minimum. • Used Flashpaper for converting PowerPoints to

SWF files (Breeze presentation format)– Can load PPT, SWF, JPEG, or FLV files from your

computer into a Share pod– .doc and .pdf files not supported

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Recent Feedback on Breeze

• I571, I573 Instructor at Indiana University– We used it for giving live lectures, as well as recording for students who

missed the lectures.  In our current set up, we found VOIP audio too unreliable, so we only use it for recording (and run an audio teleconference alongside Breeze for the live participants), and don't use video. I haven't tested the video any further so I wouldn't know if things had improved.

• I 572 Instructor at Indiana University– Generally pleased with the quality of the video coupled with the

PolyCom audio. By video we do not include video-conferencing (via WebCam etc.).  For our purposes this component was unnecessary and not feasible given bandwidth considerations.

• Instructor at the University of Manchester– Generally satisfied with performance; student response was positive.

On recordings the slides and voice go out of synch after a while. No problem with VOIP at Manchester.

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Bibliography• Adobe Acrobat Connect Professional demo

http://www.adobe.us/products/acrobatconnectpro/demo/ • American Chemical Society Committee on Professional Training.

Chemical Information Retrieval. (Prepared with the assistance of the ACS Division of Chemical Information). http://www.chemistry.org/portal/Chemistry?PID=acsdisplay.html&DOC=education\cpt\ts_cheminfo.html

• ACS Committee on Professional Training. Undergraduate Professional Education in Chemistry: Guidelines and Evaluation Procedures. Draft, 2/27/2007. http://acswebcontent.acs.org/education/cpt/acs_draftguidelines.pdf

• Garritano, Jeremy R.; Culp, F. Bartow.   ”Chemical information instruction, 1984-2004: Who is leading the charge?” Abstracts of Papers, 229th ACS National Meeting, San Diego, CA, March 13-17, 2005,  CINF-107. Also found at: http://units.sla.org/division/dche/2005/garritano.pdf

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Bibliography (cont’d)• Macromedia Breeze. Breeze Meeting User Guide for

Meeting Hosts and Presenters. – http://download.macromedia.com/pub/documentation/en/

breeze/5/meeting_ug_presenters.pdf • Wiggins, Gary. “Teaching chemical literature, databases,

and chemical informatics.” CPT; Committee on Professional Training [newsletter] Spring 2004, 4(1), 1-2. http://acswebcontent.acs.org/PDF/cpt/nl_cpt_spring2004.pdf

• Wild, David J.; Wiggins, Gary D. “Videoconferencing and Other Distance Education Techniques in Chemoinformatics Teaching and Research at Indiana University.” Journal of Chemical Information and Modeling 2006, 46(2), 495-502.