1 Use of Wikis and Macromedia Breeze in Chemical Information and Cheminformatics Instruction at Indiana University Gary Wiggins Indiana University School of Informatics June 6, 2007

2 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 ( ), 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. ( ). (continued on next slide)

3 Abstract (contd) Wikis are also used for courses in the IU School of Informatics graduate cheminformatics degree and certificate programs, e.g.: –Chemical Information Technology ge ge –Programming for Chemical and Life Science Informatics ge ge 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.

4 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)

5 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 –Through integration into other chemistry courses 73% used this option in (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.

6 Indiana Universitys C471 Chemical Information Sources Class Taught by Gary Wiggins from One semester-hour required course for undergraduate chemistry majors Usually taken in the junior or senior year

7 Little Red Book A good idea with the wrong info technology: mixed media textbook published in 1991.

8 A Better Idea: Chemical Information Sources Wiki c/cis/index.php/Main_Pagehttp://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

9 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

10 Books

11 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.

12 Beilstein 1

13 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

14 Other CIS Wiki Features SIRCh: Selected Internet Resources for Chemistry (converted from Web to Wiki) – s/index.php/SIRCh:_Selected_Internet_Resou rces_for_Chemistryhttp://cheminfo.informatics.indiana.edu/cicc/ci s/index.php/SIRCh:_Selected_Internet_Resou rces_for_Chemistry CRSD: Chemical Reference Sources Database (still a Web database) – chem/crsd/crsdintro.htmlhttp:// chem/crsd/crsdintro.html

15 Graduate Cheminformatics Courses Taught at IU with a Wiki I571 Chemical Information Technology – 06_wiki/index.php/Main_Pagehttp://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 – 07_wiki/index.php/Main_Pagehttp://cheminfo.informatics.indiana.edu/djwild/I573_20 07_wiki/index.php/Main_Page

16 Informatics MS Degree Programs 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

17 MS in Cheminformatics 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.

18 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!

19 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 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

20 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.

21 Acrobat Connect Professional Classes can be recorded. –Were moving toward recording lectures beforehand and using the class time for discussion and interaction with remote students. Can give control to a remote presenter

22 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.

23 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.

24 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

25 Breeze Workarounds Used an auxiliary microphone on the PC to record lectures –Stopping the screen share every 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

26 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.

27 Bibliography Adobe Acrobat Connect Professional demo American Chemical Society Committee on Professional Training. Chemical Information Retrieval. (Prepared with the assistance of the ACS Division of Chemical Information). C=education\cpt\ts_cheminfo.html C=education\cpt\ts_cheminfo.html ACS Committee on Professional Training. Undergraduate Professional Education in Chemistry: Guidelines and Evaluation Procedures. Draft, 2/27/ Garritano, Jeremy R.; Culp, F. Bartow. Chemical information instruction, : Who is leading the charge? Abstracts of Papers, 229th ACS National Meeting, San Diego, CA, March 13-17, 2005, CINF-107. Also found at:

28 Bibliography (contd) Macromedia Breeze. Breeze Meeting User Guide for Meeting Hosts and Presenters. – 5/meeting_ug_presenters.pdfhttp://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), 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),