------------------------------------------------------------------------------ ------------------------------------------------------------------------------ Winter 1999 CONFCHEM - ARCHIVE OF LISTSERV DISCUSSION, Nov. 14 - Nov. 19, 1999. Paper 3: "Development and Student Use of Web-Based Prelabs in Analytical Chemistry Courses" by Mark Anderson and Brian Tissue. Paper 4: "Interactive Visualization of Infrared Spectral Data: Synergy of Computation, Visualization and Experiment for Learning Spectroscopy" by Robert Lancashire and Paul Lahti. Papers available at: http://www.ched-ccce.org/confchem/1999/d/index.html. ------------------------------------------------------------------------------ ------------------------------------------------------------------------------ Date: Sun, 14 Nov 1999 07:01:00 -0400 From: Scott Van Bramer Subject: SVB: Paper 3, questions Questions about paper 3 "Development and Student Use of Web-Based Prelabs in Analytical Chemistry Courses" First, I have a question to ask everyone. There are lots of great resources on the web for teaching spectroscopy. Please share the web sites that you have developed or that you have found that helps your students come to lab more prepared. Mark and Brian, I am very excited about the potential you demonstrated with SMIL to produce interactive video clips. This seems like an ideal compliment to video, which is great for showing things but lacks interactively. By making the video interactive I would expect that the viewer is much more involved. Does this fit with your experience? The other question that I have about the use of SMIL, is about the authoring tools available at this time. How hard is it to put this together? How much time did you spend learning to do this? Now that you know how to put this together, how long does it take to produce a prelab? And finally, after considering the amount of time and effort that it takes to produce material like this, how do we make it available? To be effective does the material need to be done locally to match the content and instrumentation at each school? Could it be shared, and if so how? Respectfully, Scott Van Bramer Department of Chemistry Widener University, Chester, PA 19013 svanbram@science.widener.edu http://science.widener.edu/~svanbram ------------------------------------------------------------------------------ Date: Sun, 14 Nov 1999 07:00:00 -0400 From: Scott Van Bramer Subject: SVB: Begin Paper 3 discussion Good Morning, Today is Sunday November 14 and it is time to open discussion for Paper #3. "Development and Student Use of Web-Based Prelabs in Analytical Chemistry Courses" by Mark R. Anderson (manderson@chemserver.chem.vt.edu) and Brian M. Tissue (tissue@vt.edu), Virginia Polytechnic Institute and State University. The paper is available on the ConfChem website at: http://www.ched-ccce.org/confchem/1999/d/ Respectfully, Scott Van Bramer Department of Chemistry Widener University, Chester, PA 19013 svanbram@science.widener.edu http://science.widener.edu/~svanbram ------------------------------------------------------------------------------ Date: Sun, 14 Nov 1999 19:11:38 -0500 From: "Mark R. Anderson" Subject: Re: Paper 3, questions Scott, SMIL (Synchronized Multimedia Integration Language) is simply a markup language, much like HTML. Learning the language is relatively simple as there are not that many tags. The code for the spec-20 calibration in the paper is:

The first portion of the code provides the layout information. Between the body tags, the SMIL code tells the player to play two files in parallel, what region of the layout to play the different files in, and what files to play. This is a relatively simple example of what can be done with SMIL but illustrates how straightforward the tags are (esp. if you are familiar with HTML). In our applications, the interactivity and timing are contained within the streaming video and streaming text files (spec20.rm and spec20text.rt) that the SMIL file calls. SMIL is a relatively new markup language and its capabilities are expanding. There are tools available for generating SMIL files, but I haven't been using them so I can't really comment on how useful they are. The RealNetworks site (www.real.com) has a lot of information that I used as I was learning about producing streaming audio, video, and SMIL files. I find the Production guides particularly helpful. RealText, SMIL, and RealPix files can be generated using a text editor. RealAudio and RealVideo need software tools for generating the files. I use RealProducer G2 (a commercial product, I don't believe that there is a freeware version of this audio/video encoder). RealProducer takes an AVI file (or WAV for just audio) and converts it to the streaming format. I generate the AVI files using Adobe Premier. Streaming technology is improving literally continuously, and the quality of the produced files and the stream over the net is dramatically better than it was when I first started doing this about 2 years ago. I have been producing SMIL files for only about 6 months. There are some really neat things that can be done to enhance the educational value of the streams that we are just beginning to explore. For example, you can map the video (like an image map in HTML) and use the video map as a link to other material. My experience with using streaming Video's in Quantitative Analysis is that the students use them and come to the laboratory better prepared than in past years. We have not used the SMIL files in a class yet - that is planned for the spring. I suspect that the interactivity of the SMIL, along with the ability to make connections between the experiment and the background will prove valuable. Brian and I intend for all the Internet material that we generate to be as widely available as possible, and the videos are no exception. The current problem with the video's is the server - you need to have separate serving software for streaming the files. I currently run the Basic Server G2. The license for this server only allows 25 simultaneous accesses. This has not been a problem so far, but we have limited the use to just the Analytical Chemistry classes at Virginia Tech. We would like to expand the availability locally to include more classes, but we will need a new server license that provides more simultaneous accesses. Ultimately, Server load dictates how available the files become. Currently, some of our files are specific for equipment and experiments that we run, but others discuss general topics. I imagine that we will eventually develop a library of audio/video files that will cover a range of topics in Analytical Chemistry. We would be happy to share what we have, please send either Brian or myself an email if you have interest using the material. Sharing could simply be done by providing the url to the files that you would like to use, or by providing the files if you have a RealServer. Likewise, if you have video's (AVI or QuickTime) and would like to convert them to streaming format - please let me know if I can be of help. Mark - -- ************************************************ Mark R. Anderson Associate Professor of Chemistry Virginia Tech phone: (540)231-3869 FAX: (540)231-3255 email: mark.anderson@vt.edu ******************************************************* >-----Original Message----- >From: Scott Van Bramer [SMTP:svanbram@SCIENCE.WIDENER.EDU] >Sent: Sunday, November 14, 1999 6:01 AM >To: confchem@mail.clarkson.edu >Subject: SVB: Paper 3, questions > >Questions about paper 3 "Development and Student Use of Web-Based Prelabs in >Analytical Chemistry Courses" > >First, I have a question to ask everyone. There are lots of great resources on >the web for teaching spectroscopy. Please share the web sites that you have >developed or that you have found that helps your students come to lab more >prepared. > >Mark and Brian, >I am very excited about the potential you demonstrated with SMIL to produce >interactive video clips. This seems like an ideal compliment to video, which >is great for showing things but lacks interactively. By making the video >interactive I would expect that the viewer is much more involved. Does this >fit with your experience? > >The other question that I have about the use of SMIL, is about the authoring >tools available at this time. How hard is it to put this together? How much >time did you spend learning to do this? Now that you know how to put this >together, how long does it take to produce a prelab? > >And finally, after considering the amount of time and effort that it takes to >produce material like this, how do we make it available? To be effective does >the material need to be done locally to match the content and instrumentation >at each school? Could it be shared, and if so how? > >Respectfully, > >Scott Van Bramer >Department of Chemistry >Widener University, Chester, PA 19013 >svanbram@science.widener.edu >http://science.widener.edu/~svanbram ------------------------------------------------------------------------------ Date: Mon, 15 Nov 1999 15:49:59 -0500 From: Scott Van Bramer Subject: Re: Paper 3, questions At 07:11 PM 11/14/99 , Mark Anderson wrote: >SMIL (Synchronized Multimedia Integration Language) is simply a markup >language, much like HTML. Learning the language is relatively simple as >there are not that many tags. The code for the spec-20 calibration in the >paper is: Thanks for the details. It looks a lot like image maps and javascript. Not trivial, but workable given enough time. Respectfully, Scott Van Bramer Department of Chemistry Widener University, Chester, PA 19013 svanbram@science.widener.edu http://science.widener.edu/~svanbram ------------------------------------------------------------------------------ Date: Wed, 17 Nov 1999 07:01:00 -0400 From: Scott Van Bramer Subject: SVB: Paper 4, questions WOW, I have been excited about the potential of this interactive multimedia visualization tool since I first saw it. The result is a very elegant connection between spectral data and the molecular structure. This could never be done in a textbook, and earlier attempts with video animations lack the interactive part that makes this so attractive for teaching. And finally, by using the web and a free plugin it can be widely distributed. I have two main questions for the authors. First, how do we use this for our teaching? What classes do you use these animations with and how are they received by your students. Second, how to we do this? With the tools provided in the paper a computer savvy faculty member can assemble the pieces needed to make a web page. But it will take a significant effort. The examples given here are great, but how can they be assembled in a useful way for students to learn from? Seems like it would be a great supplement for an organic textbook or a spectroscopy text. Respectfully, Scott Van Bramer Department of Chemistry Widener University, Chester, PA 19013 svanbram@science.widener.edu http://science.widener.edu/~svanbram ------------------------------------------------------------------------------ Date: Wed, 17 Nov 1999 07:00:00 -0400 From: Scott Van Bramer Subject: SVB: Begin Paper 4 discussion Good Morning, Today is Wednesday November 17 and it is time to open discussion for Paper #4. "Interactive Visualization of Infrared Spectral Data: Synergy of Computation, Visualization and Experiment for Learning Spectroscopy" by Robert J. Lancashire (rjlanc@uwimona.edu.jm), University of the West Indies and Paul M. Lahti (lahti@chem.umass.edu), University of Massachusetts. The paper is available on the ConfChem website at: http://www.ched-ccce.org/confchem/1999/d/ Respectfully, Scott Van Bramer Department of Chemistry Widener University, Chester, PA 19013 svanbram@science.widener.edu http://science.widener.edu/~svanbram ------------------------------------------------------------------------------ Date: Wed, 17 Nov 1999 09:50:25 -0500 From: george long Subject: GRL Re: Paper 4, questions > WOW, I agree with Scott, I have a few questions, First you noted that Spartan for UNIX can be used as the MM package. Is there a reason why SpartanPC cannot be used ? What would you estimate the time required to produce an interactive spectrum as you describe here ? Do you think the time factor will hinder the use of the technique? I suspect time required to produce these interactive spectra may be a problem, are there any plans to address this, perhaps a CD with a compendium of spectra, and molecules ? ************************************************** Dr. George R. Long Department of Chemistry Indiana Univ. of PA Indiana, PA http://wey238ab.ch.iup.edu/grlong/ grlong@grove.iup.edu ************************************************** ------------------------------------------------------------------------------ Date: Wed, 17 Nov 1999 10:40:11 -0500 From: "Huggins msimanga" Subject: Re: SVB: Begin Paper 4 discussion ** Reply Requested by 11/21/1999 (Sunday) ** I see the Abstract for Paper #4, where is the rest of the paper? Huggins Z. Msimanga, Ph.D. Associate Professor, Chemistry 1000 Chastain Road Kennesaw, GA 30144 Phone: 770-423-6088 email: hmsimang@ksumail.kennesaw.edu ------------------------------------------------------------------------------ Date: Wed, 17 Nov 1999 10:54:45 -0500 From: Scott Van Bramer Subject: Re: SVB: Begin Paper 4 discussion At 10:40 AM 11/17/99 , Huggins Z. Msimanga wrote: >I see the Abstract for Paper #4, where is the rest of the paper? The rest of the paper is in the links at the bottom showing how to produce the interactive spectra and showing examples. You need the CHIME plug in to see what the authors are showing. Respectfully, Scott Van Bramer Department of Chemistry Widener University, Chester, PA 19013 svanbram@science.widener.edu http://science.widener.edu/~svanbram ------------------------------------------------------------------------------ Date: Wed, 17 Nov 1999 09:51:41 -0700 From: Patty Subject: Re: SVB: Paper 4, questions One comment: I tried a few things getting these to work on my Mac to no avail. Guess I'll have to go to an IBM. Still, a lot of people have Macs. Hopefully I'll be able to comment later if and when I find time to get it working on an IBM. Patty CU Boulder Organic Chem Lab Coordinator ------------------------------------------------------------------------------ Date: Wed, 17 Nov 1999 10:03:15 -0700 (MST) From: "Barbara A. Gaddis" Subject: prerequisite for biochemistry To meet ACS standards, we are going to be offering a one-semester biochemistry course, different from the two-semester biochemistry course taught in the biology department. We have been advised that first semester general biology class and lab and an upper division cell course should be prerequisites for this class. This would add an additional 7 hours for our BS chem majors, even before they take the biochemistry course. Could you please tell me what you are doing at your school? That is, if you offer a BS degree that requires biochemistry, what prerequisites do you attach to the course? Also, I would also like to know what textbook you are using for the course. Thank you very much. You may reply directly to me and I will summarize for the whole group. Thanks for your help. Barbara Gaddis, Director Science Learning Center Univ. of Colorado at Colorado Springs P. O. Box 7150 Colorado Springs, CO 80933-7150 phone: (719) 262-3688 email: bagaddis@mail.uccs.edu FAX: (719) 262-3047 ------------------------------------------------------------------------------ Date: Wed, 17 Nov 1999 12:04:16 -0500 From: Jack Martin Miller Subject: Re: SVB: Begin Paper 4 discussion >Good Morning, > >Today is Wednesday November 17 and it is time to open discussion for Paper >#4. > >"Interactive Visualization of Infrared Spectral Data: Synergy of Computation, >Visualization and Experiment for Learning Spectroscopy" by Robert J. >Lancashire >(rjlanc@uwimona.edu.jm), University of the West Indies and Paul M. Lahti >(lahti@chem.umass.edu), University of Massachusetts. > >The paper is available on the ConfChem website at: > http://www.ched-ccce.org/confchem/1999/d/ not much use to u MAC people with the requirement for Windows only version of CHIME!!!!!!! Prof. Jack M. Miller, Associate Vice-President, Research and Dean of Graduate Studies, Professor of Chemistry, Brock University, St. Catharines, Ont., Canada, L2S 3A1. Phone (905) 688 5550, ext 3789 FAX (905) 682 2277 e-mail jmiller@brocku.ca http://chemiris.labs.brocku.ca/~chemweb/faculty/miller/ ------------------------------------------------------------------------------ Date: Wed, 17 Nov 1999 13:48:43 -0500 From: Albert Fry Subject: Re: SVB: Paper 4, questions >One comment: > >I tried a few things getting these to work on my Mac to no avail. >Guess I'll have to go to an IBM. Still, a lot of people have Macs. > >Hopefully I'll be able to comment later if and when I find time to >get it working on an IBM. > >Patty >CU Boulder >Organic Chem Lab Coordinator You might want to consider the PC emulator VirtualPC, from Connectix. It runs quite quickly on a Power Mac. Our experience over the last year is that it runs PC software without a hitch. I think I paid ca. $185 recently; that includes a copy of Windows 98 which is included in the Installer. Albert J. Fry Chemistry Department Phone: (860)685-2622 Wesleyan University FAX: (860)685-2211 Middletown, CT 06459 email: afry@wesleyan.edu ------------------------------------------------------------------------------ Date: Wed, 17 Nov 1999 21:01:22 -0500 (EST) From: Dr Robert Lancashire Subject: Re: SVB: Begin Paper 4 discussion Greetings, I have been in a "non-virtual" conference all day so just getting email. 2 people mention that they were MAC users. As you quickly discovered the present version of CHIME for MAC does not support the spectral viewer. This issue is being addressed and the new release CHIME 3 will be a JAVA version that should allow MAC users to see the spectra OK. In the meantime, do try to borrow some time on a PC. Thanks I dot not have SPARTAN for UNIX or PC and so have got these files from Paul Lahti at UMass. I do have Gaussian 90 on our Convex and the calculations take about 30 minutes. I think the PC version of the various software packages run significantly faster than that so setting up a data set and doing a run can be done in under 30 minutes. Trying to work out which IR peak bin a spectrum elongs to which frequency can take a while considering the level of accuracy of the predictions! A CD with interpreted spectra is a good possibility. Robert ______________________________________________________________________ Dr. Robert J. Lancashire E-mail mailto:rjlanc@uwimona.edu.jm Sub-Dean, Technology Management and Development Department of Chemistry Tel (876) 9271910 University of the West Indies, Kingston 7 Fax (876) 9771835 Mona Campus, JAMAICA. http://wwwchem.uwimona.edu.jm:1104/chrl.html ------------------------------------------------------------------------------ Date: Thu, 18 Nov 1999 08:00:22 -0500 (EST) From: Dr Robert Lancashire Subject: Re: SVB: Paper 4, questions Scott this only arrived Thurs morning (lost in ether?) At UWI, little use has been made so far in classes since our infrastructure is just coming together. I have suggested that Paul Lahti add a few comments from his experiences at U Mass. We run 6 hour laboratory classes for both 2nd and 3rd year courses in Organic Chem and an exercise around this would fit in within those time constraints OK given sufficient guidance from a supervisor. For our students with access to Gaussian 90 on mainframe. Step 1 run FTIR and save file in JCAMP-DX format (30 minutes) Step 2 draw molecule in ChemSketch or ISIS (we have site licences for both and free versions are available) - 15 minutes) Step 3 use BABEL to obtain Gaussian input file (free software - 5 minutes) Step 4 run Gaussian (purchased in 1994 - 30 minutes) Step 5 run VIBREAD (free from UMass - 5 minutes) Step 6 view individual animations with CHIME (free from MDL - 30 minutes if you have a lot, just load .XYZ file directly) Step 7 assign predicted frequencies to experimental peaks (depends how detailed you want it- first 5 peaks about 10 minutes?) Step 8 edit JCAMP-DX file to create links (10 minutes - cut and paste from an existing file as a template) Step 9 edit HTML files for final display (10 minutes - cut and paste from an existing file as a template) Total time under 3 hours.... It gets easier the more you do! Robert ps for classes with access to SPARTAN or HYPERCHEM steps 2, 3 and 4 are replaced by one step. ______________________________________________________________________ Dr. Robert J. Lancashire E-mail mailto:rjlanc@uwimona.edu.jm Sub-Dean, Technology Management and Development Department of Chemistry Tel (876) 9271910 University of the West Indies, Kingston 7 Fax (876) 9771835 Mona Campus, JAMAICA. http://wwwchem.uwimona.edu.jm:1104/chrl.html ------------------------------------------------------------------------------ Date: Thu, 18 Nov 1999 07:15:05 -0600 From: "Lara Trinkler" Subject: [none] This has nothing to do with the conference articles but it is interesting information that I came across in this weeks Chemical and Engineering News magazine. The NIH has education courses for students at the high school level. The three courses they are offering now (Cell Biology and Cancer, Emerging and Reemerging Infectious Diseases, and Human Genetic Variation) are probably geared toward biology class, but other courses could be more chemistry oriented. I know that many chemistry high school teachers are also their school's biology teacher so I thought it might be helpful. The course information can be viewed at http://science-education.nih.gov/supplements ------------------------------------------------------------------------------ Date: Thu, 18 Nov 1999 10:18:50 -0600 From: "Kay Davis" Subject: RE: prerequisite for biochemistry Mary Campbell's text Prerequisites: a semester of freshman biology which is mostly cell biology, organic 1, and quantitatitive analysis - -----Original Message----- From: confchem-owner@clarkson.edu [mailto:confchem-owner@clarkson.edu]On Behalf Of Barbara A. Gaddis Sent: Wednesday, November 17, 1999 11:03 AM To: confchem@mail.clarkson.edu Cc: Allen M. Schoffstall Subject: prerequisite for biochemistry To meet ACS standards, we are going to be offering a one-semester biochemistry course, different from the two-semester biochemistry course taught in the biology department. We have been advised that first semester general biology class and lab and an upper division cell course should be prerequisites for this class. This would add an additional 7 hours for our BS chem majors, even before they take the biochemistry course. Could you please tell me what you are doing at your school? That is, if you offer a BS degree that requires biochemistry, what prerequisites do you attach to the course? Also, I would also like to know what textbook you are using for the course. Thank you very much. You may reply directly to me and I will summarize for the whole group. Thanks for your help. Barbara Gaddis, Director Science Learning Center Univ. of Colorado at Colorado Springs P. O. Box 7150 Colorado Springs, CO 80933-7150 phone: (719) 262-3688 email: bagaddis@mail.uccs.edu FAX: (719) 262-3047 ------------------------------------------------------------------------------ Date: Thu, 18 Nov 99 15:14:39 EST From: Donald Rosenthal Subject: P4 PML: Response to Short Question FORWARDED TO CONFCHEM by Majordomo Manager - ----------------------------Original message---------------------------- From: "Paul M. Lahti" Subject: Response to your query Dear Prof. van Bramer: Thanks for your kind words. (1) We are just starting to implement use of these IR animations in courses around here. I think that people at smaller schools have gotten of the mark faster. A J. Chem. Ed. paper by Dr. Lancashire, myself, and an undergrad will come out soon that gives some references with sites that do similar things. I am not aware of heavy usage of these techniques in "point-and- click" spectroscopic analysis in courses, but I am not exhaustively informed. (2) Actually, there is a moderately steep learning curve to figure out how to do the structure plus spectrum animata, but once the curve is mastered, turning the crank is relatively straightforward, depended on how obsessive one is. One must master the following: (i) use of compuational chemistry to optimize a geometry and get a vibrational analysis with Spartan, GAMESS, Gaussian, or Hyperchem (GAMESS is free) (ii) obtaining or generating JCAMP-DX format files (can be done using a variety of spectrometers using software such as GRAMS/32, or can get from databases -- not aware of many of the latter that are freely available, other than NIST) (iii) generate animation file of vibrations from computations in (i), using my VIBREAD program for Intel based computers (iv) editing JCAMP-DX file to reference to a specific animation file (v) editing HTML template files to input specific structure, spectrum files. I would say it would take a pretty committed month to do this. Then, one can do a pretty full workup of a display as fast as one can run the computation in (i), and obtain/edit the spectrum in (ii). Hope this is useful. Paul M. Lahti - -- Paul M. Lahti, Department of Chemistry University of Massachusetts Amherst, MA 01003-4510 Phone (413)-545-2318 or -4890 Fax (413)-545-4490 E-mail lahti@chem.umass.edu WWW http://www.chem.umass.edu/~lahti "Fortidine vincimus" ------------------------------------------------------------------------------ Date: Thu, 18 Nov 1999 16:36:56 -0500 From: Bill Bordeaux Subject: RE: prerequisite for biochemistry We require freshman chemistry, organic chemistry and cell biology for our 1-semester biochemistry course, which is taken by most biology majors and virtually all chemistry majors. We also use Mary Cambell's Biochemistry text (now in its third edition). Bill Bordeaux Professor of Chemistry Huntington College 2303 College Avenue Huntington, IN 46750 219-359-4204 He has shown you, O man, what is good; and what the LORD requires of you, but to do justly, to love mercy, and to walk humbly with your God. Micah 6:8 > ---------- > From: Kay Davis > Reply To: confchem@mail.clarkson.edu > Sent: Thursday, November 18, 1999 11:18 AM > To: confchem@mail.clarkson.edu > Subject: RE: prerequisite for biochemistry > > Mary Campbell's text > Prerequisites: a semester of freshman biology which is mostly cell > biology, organic 1, and quantitatitive analysis > > -----Original Message----- > From: confchem-owner@clarkson.edu [mailto:confchem-owner@clarkson.edu]On > Behalf Of Barbara A. Gaddis > Sent: Wednesday, November 17, 1999 11:03 AM > To: confchem@mail.clarkson.edu > Cc: Allen M. Schoffstall > Subject: prerequisite for biochemistry > > To meet ACS standards, we are going to be offering a one-semester > biochemistry course, different from the two-semester biochemistry course > taught in the biology department. We have been advised that first > semester general biology class and lab and an upper division cell course > should be prerequisites for this class. This would add an additional 7 > hours for our BS chem majors, even before they take the biochemistry > course. > > Could you please tell me what you are doing at your school? That is, if > you offer a BS degree that requires biochemistry, what prerequisites do > you attach to the course? Also, I would also like to know what textbook > you are using for the course. > > Thank you very much. You may reply directly to me and I will summarize > for the whole group. Thanks for your help. > > Barbara Gaddis, Director > Science Learning Center > Univ. of Colorado at Colorado Springs > P. O. Box 7150 > Colorado Springs, CO 80933-7150 > > phone: (719) 262-3688 > email: bagaddis@mail.uccs.edu > FAX: (719) 262-3047 --------------------------- END OF DOCUMENT ---------------------------------- -------- Prepared by B. Tissue 11/20/99. Edited to reduce file size. ---------