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Not counting calculators, my first exposure to computers was making a Christmas reef in the fourth grade with computer punch cards.  We curled them over in a circular asymmetric fashion, put some pine cones in the center and spray painted the whole thing in gold.  My second experience was in the summer of my sixth or seventh grade watching my brother type in commands at a terminal at his college.  The mainframe would insult him on paper if he made an error in his entries.  "Try it again dummy."

My senior year was the first time my high school had computers.  Before, students punched out cards to send to a district processing center.  After two weeks the teacher admitted that she had just taken her first computer science course in the summer and that she had no more to teach us about the BASIC computer language syntax.  Thereafter, each week she gave us a new mathematics problem to solve on the computer.  Her challenge to us was to write better algorithms than she could devise or she would not give us an "A" for the course.

In the next and last semester of high school I could not take computer science with the other students because someone decided to schedule senior English, French and calculus at the same time.  I opted for calculus.  The teacher left me alone in the computer lab (about four to six TRS-80s for 30 students) under the pretext of taking an independent studies course in probability.  I spent my first weeks generating prime numbers just so that I could have all the computers running at the same time.  I then thought it would be nice to program my calculus homework on the computer.  Remember that we had the computers but absolutely no games or other programs to run.  During this time I discovered a method of numerically finding the roots of any polynomial function.  Unfortunately my calculus teacher recognized that Newton had discovered it more than three hundred years ago. My calculus teacher also asked me to prove to his algebra students that Gauss-Jordan elimination was more efficient than Cram's rule for solving systems of linear equations on the computer.  I enjoyed getting out of my other classes to demonstrate my computer programs to other students and teachers.   I now realize that I taught myself numerical analysis instead of probability in high school.

I came across a student of the official computer science course making a drawing on the computer by defining each screen pixel by a BASIC POKE command.  I was convinced that the computer science teacher had run out of things to teach and I told the student that they were wasting their time because mathematical functions could be used to draw the wheels of his train and so forth.  To prove the point (no pun intended) I programmed a pinball machine and an animation of the word calculus being swiped onto the screen, falling out like teeth, and being swept away with a dust pan, all in monochrome.  Towards the end of the year I enjoyed showing the calculus class my animation after showing them how a computer could be used to do calculus including adding up all those slices.

Around the same time the pocket TRS-80 and Commodore 64 came out.  I don't remember how much the pocket TRS-80 cost but I enlisted the help of my computer science teacher to convince my mother that I had to have it.  I also remember going to the local X-mart about 4 to 5 times before being assertive in telling the clerks not to give me another broken returned Commodore 64.  It was $199.  The Commodore 64 was great hooked on to a black and white television though I had no way of saving my programs until I bought a cassette tape drive for it.  There went all my paper route and birthday money.  I still enjoy listening to the shrieks of the Commodore 64 tapes I find around the house.

Having so much fun with computers in high school I first majored in electrical engineering to learn to build computers.  After a few weeks of taking FORTRAN in college I understand why Bill Gates and Steve Jobs are college dropouts.  Every week the instructor would assign a problem that by midweek he would say was too difficult for us to solve.  After class I would go tell him that I had solved the problem.  It also was a nightmare to program on terminals as all students would scream as the mainframe went down and everyone lost their work.  This was my last computer science course.  I switched to chemistry.

In college and graduate school I tried to keep up my computer skills by helping instructors figure out their programming problems, programming a word processing and music program, and trying to submit an article to Compute 64.  The program was a tutorial of how to multiply large numbers in your head.  It had blinking color lights and sound, and after hacking it for months it fit nicely on one sheet of paper.  The magazine responded that they had changed their emphasis to games.  The magazine did not last six months after its change of emphasis.

For my doctoral research on the mechanism and scope of the aza-Baeyer-Villiger reaction, I synthesized and identified known compounds by looking up their physical properties by compound name.  It was then that I realized that a most unscientific thing about chemistry is nomenclature.  Thus began my quest to teach computers to recognize chemical structures without names.  Besides synthesizing, enzymatically resolving and testing chiral auxiliaries; I spent my postdoctoral years devising and testing computer algorithms in Mathematica that could differentiate chemical graphs (pictures).  It was like being in high school again keeping a $40 k department computer running all weekend.

In 1992, the first grant I received at the University of Texas at El Paso was a Teaching Effectiveness Grant to develop my graph theory ideas into a teaching tool.  In 1993, with the help of Tony MacTutis (who insisted that I indent my code and use word instead of letter variables) and Richard Duran , we programmed and I began using GRADE (Graph Recognition Algorithm Developed for Education) in CHEM 1408, a survey of organic and biochemistry for non-science majors.  The program took flatland drawings that students made in a commercial drawing program and recognized them.  Students could thus do homework on naming and drawing organic compounds in our department computer laboratory.  This automated homework made a big difference in the attitude of students towards my board scribbles and in the level of the course since I didn't have to spend all the lecture on nomenclature, and I could explain a little more about physical properties and reactions.

The original GRADE without a commercial drawing program.

With funding from the National Science Foundation (1994-97); James Moody tested algorithms to recognize 3D chemical structures built in commercial software, Adriana Beltran and Adrian Hernandez tested faster algorithms, and I began learning to program molecular models in object oriented Visual Basic.  After a 1996 summer research experience at JPL, Adrian returned to tell me that we were programming neural-network artificial-intelligence algorithms.  Adrian also suggested that I take a look at a new fangled computer programming language called Java.  When James, Adriana, and Adrian left, since code inheritance and overriding makes reading C++ code impossible, I started from scratch and wrote NetGRADE (a line drawing program with 3D chemical recognition) in Java with Perl connectivity to record grades.   The internet, and automated and ubiquitous NetGRADE feedback made it possible for science majors to learn 3D organic chemistry in school laboratories and their homes up to the spring of 2003.  My favorite of the twelve lessons of this program was the stereochemistry of carbohydrates lesson that drove students to my office for help.  No more pretending to teach, no more pretending to learn!

In 1997, I also discovered that upgrading the software of our SGI workstation automatically turned it into a web server.  Hence we have greatly benefited from open source software such as the Apache Web server, Perl, Tomcat, PHP, MySQL, Wikimedia, etc.

Upon adding anaglyph viewing (3D with red-blue glasses) to NetGRADE, I was disappointed to find by informal polling that over 10 % of my students and the general population do not have static 3D perception either because of a dominant eye or function of only one eye, e.g., lazy eye.  Further, after testing student responses and response times (Isn't improving your teaching human subject research?) I found that students were more confused with the anaglyph viewing when images are projected in front of the computer screen.

You need a Java enabled browser!

The program used to test which molecular model format students can see better with red blue glasses.

The results of our visual test, blue with the blue atom projected to the front, red with the blue atom projected to the back.

I spent 1999-2000 as the interim director of the Center for Effective Teaching and Learning, CETaL.  Besides getting to work with some fine people to share good teaching practice, I came to the realization that I had to continue collecting and analyzing data on how my students are learning beyond an anecdotal level.

The mascot of the January 2000 Active Learning Conference.

To overcome 3D perception problems I began developing an open source molecular model kit with funding from the Camille & Henry Dreyfus Foundation in 2000-01.  The kit was the basis for teaching a special topics course on programming molecular model sets to chemistry and bioinformatics students in 2002.  As practice for this kit I wrote OOLe, an online 3D parametric plotter program with anaglyph and stereoscopic viewing, and Algebriser and WiMath, programs that check that students can convert word problems to algebraic equations and that they can manipulate the equations to isolate a variable.

Stereoscopic viewing works nicely with the "Make Your Own Polarizers from Gel-Glue" module that I developed for entering students.  In this module students see all kinds of applications of polarizers including making 3D movies and images, and then make polarizers from ordinary household materials.  I have shown this module to just about everyone.

In 2001 with funding from NASA-MuSPIN-NRTS, I developed a version of NetGRADE that could be used on pocket PCs.  Unfortunately there can never be enough of these expensive computers for the courses I teach. Thus I developed the CyGRADE Socratic course management system for the inexpensive wireless Cybiko toy in C with SQL recording student responses.  After a false start in the fall of 2001 (since students don't all share well, show up on time, take care of school equipment), I tested the system in a 2002 summer course.  I liked the fact that it broke up the fatigue of a 2 hour course by keeping students actively participating by drawing answers to my questions every fifteen minutes.  I also learned that I don't want to be a hardware manager.  In addition I experimented with writing code for the intermediately expensive Palm device but the J2ME emulator runs slower than Cybiko C programs.  I have also built prototypes for Java cell phones, the Pocket PC using the Mysaifu Java Virtual Machine, and the Nintendo DS using Devkitpro.

A working MidGRADE prototype on a Java cell phone.

In the fall of 2003, I independently deployed  At this site students can automatically register, login, and take over 50 lessons on organic chemistry in a variety of visual formats.  The site uses totally new graph recognition algorithms.  I am continuously adding functionality, lessons and instructions so that students don't always have to depend on in class instructions.  My goal is to add sufficient instructions so that students don't have to buy a different text.  I already am dreaming of a distance education organic chemistry course.  For a summer 2004 Masters of Art in Teaching course, I instructed high school teachers how to instruct using this site.  A few teachers are still using it with their students.

Also in the fall of 2003, growing tired of student plagiarism and excused for not turning them in on time, I decided to require that my students turn in their lab reports as web pages.  The idea is that students would not plagiarize if they knew that everyone could see their work and it would be a form of electronic delivery.  The first semester was difficult because it took the university a long time to give each student a space to post his or her webpages.  Many students went out a got "free" internet sites which only had the problem of too much advertisement or metered bandwidth easily exceeded by too large of pictures.  Being able to post pictures made the reports ever more interesting to students.  In 2004, to avoid the infrastructure problems,  I decided to provide students with ftp access to this computer and promoted the use of FrontPage.  Many students went overboard making designer websites.  In 2006 I switched over to free Wiki software.  This software allows students to focus more on the content rather than the form.

In the fall of 2005, I deployed Surveyor and Cyrveyor (for the Cybiko) in PHP/MySQL to allow students to answer free response questions in lecture.  Students used their laptop, cell phone, PDA, PSP or Cybiko to view and respond on a tiny web page.  The program groups and sorts student responses so that I can grade them in front of the class.  It is painful to see how little gets across in a lecture but it is better for students to make their mistakes before the exam.  From the raw participation rate, at first I believed that one third of students were always missing class but upon further analysis it turns out that one third of students always go to class and two thirds a floating in and out one day and not the other.

In the spring of 2006, I started capturing my lectures using Microsoft's Media Encoder.  This free utility allows me to capture my computer screen along with audio in a most compressed format. After each lecture I upload its video to the school website to allow students to review it at their own leisure, finally a good use for Internet 2.  Although initially I feared that students could use my words and mistakes against me, it turns out that now I can always reference the video to tell students "I told you so!".  I also worry that less students will come to lecture with this resource but most students tell me they really like it as a supplement since they can concentrate more on listening in lecture and then go home and transcribe the video by pausing or jumping around in it.  Depending on the resolution of your screen (800 x 600 pixels and medium resolution for good play back speed), a whole semester of lectures and more can easily be preserved in a DVD.  For graduate courses, video recording also allows all students to see how other students workout organic mechanisms outside of lecture.  I have also tested the streaming properties of this program (along with messenger programs) in case some day we want students to participate in lecture from their homes.

Although a few students have complained that I do not give them beautiful PowerPoint presentations in my lectures, I am apprehensive of presenting material so quickly (like the transparencies of my youth) that I look for ways to slow me down.  One way is to draw structures in lecture in a commercial drawing program, build molecular models in front of the students or to electronically capture my hand drawing as they are created and I talk.  Initially I used the relatively inexpensive Nexconcepts Mobile Notetaker to capture my handwriting on screen (a poor man's whites screen) but now the College of Science has provided me with a tablet computer to draw on the computer directly.

In the summer of 2007, I deployed a new version of  This version incorporates lessons, with video of explanations of each lesson, and a course response system that allows students to answer questions through text or drawing.  Since I grade the answers in front of the students, the system is more spontaneous that commercial infrared voting systems.  With at least one third of students having a laptop, sharing allows all students to participate.  A lower student to computer ratio will be a real test of the wireless infrastructure.  It is ironic that all these wireless devices are still not cordless.

In the spring of 2008, I developed software to allow peer-leaders to turn in their grades to students and me directly.  The software was great for getting peer-leaders to turn in their grades on time without prodding and to give students faster workshop feedback.  In the fall of 2008, I generalized the software to allow other instructors the chance to use it as well as to allow cut and paste grade input from a spreadsheet.  Going along with this software was a wiki site, which is a wiki for allowing peer-leaders and instructors to add peer-lead team learning content.

Ester to Tertiary Alcohol
brought to you by Livescribe

A Livescribe "Lecture"/Acyclic Alkanes on the Livescribe Pulse Smartpen

In the spring of 2009 I began experimenting with recording lectures using the Livescirbe Pulse Smartpen.  Click full screen and rotate the image right to see an example, above left.  The main use of this pen is linking recording to note taking so that you can listen to your notes by just clicking on them on paper or searching key words on a computer.  Being unemployed for the first time since 1980, in the summer of 2009, I wrote programs for this pen.  These programs name Acyclic Alkanes and Amino Acids that the user writes on special dot paper.  Amazingly this pen has a 200 MHz ARM processor.  The program I am most proud of is MusicComposer which learns to recognize your hand written musical notes.  This basically demonstrates that some day we will be able to recognize the molecules that students draw on paper.  Unfortunately, the Livescribe Developer Program was terminated before I could also submit programs such as Functional Groups.

In the spring of 2010, I began streaming a live feed of my lectures using and then  This service is intended to allow students that cannot attend lecture because of work, health, transportation, childcare, etc. problems to participate in answering lecture questions.  The resolution of my desktop capture is poor because the streaming software assumes that I am presenting fast moving video.  The software would work much better if it realized that I am only sending 5 frames per second.  In the event of another flu scare and the university has to close, we are ready to continue class remotely!

In the spring of 2011, I began working on a virtual organic laboratory using the Microsoft X-Box Kinect sensor.  Two REAP supported high school students created virtual 3D labware to include in a program that manipulates the objects by hand motions.  Inspired by the Johnny Lee's Wii Remote head-tracking work, the program also adjusts to the viewers perspective to hopefully allow people that do not have stereoscopic vision to perceive 3D.  Our goal is to more safely introduce students to the laboratory before they enter the room.

In the spring of 2012, with great instructions from and, I repurposed the PogoPlug Series 4 ($50) to a Moodle server. The PogoPlug is intended as a headless (no monitor, mouse or keyboard) cloud server that allows you to access your own personal files through the internet but our purpose is to allow teachers to have their own classroom management system for automatically graded class assignments and class response sessions.  I am even contemplating replacing the desktop that currently hosts this site with this inexpensive and low power server.

In 2013, I began working on creating an online course for learning how to program your own molecular modeling software.  The goal is to go beyond learning how to use commercial software to making your own molecular modeling software.

In the spring of 2014, 21 years after I first proposed it, I finally deployed a ubiquitous drawing class-response system at  Tying together HTML5, CSS, Javascript, PHP, and SQL; students can now use their phone, tablet or laptop to answer in class questions through drawing.  If I had to give a talk about the long road to writing this software I would entitle it "What Steve Jobs made me do!".  Basically I had to rewrite everything in Javascript because of the demise of Java in the browser (forced upgrade to Java 8, a required certificate and/or permissions set for individual websites, having to install a plug-in, security concerns, etc.) and the fact that many students only own a phone or tablet.  The class response system was also augmented to handle reactions and show students how they responded to previous questions.

During the 2014-25 academic year, I proposed and promoted the development of UTEP's own text-based class-response system.  Socrates was developed by Academic Technologies to allow all students to log on with their university credentials with no need to re-register with or pay an outside service from semester to semester.  Several instructors  tested the program but unfortunately support and development was not continued.  Fortunately, the university continues to support the use of class-response systems to the point of engaging with outside vendors to integrate the cost with student fees and providing instructor training.  Lost was the opportunity to learn from all the student data gathered just as all the large internet companies are learning from all the information that we provide them.

In the spring of 2015, 13 years after its initial launch, I spent my vacation converting to Javascript.  This again means that students can complete more than 50 lessons on drawing, naming, and moving arrows on whatever device they want.  The conversion entailed recalculating the identity of over 3,000 structures from the old to new database because the identity of chiral centers was greatly improved.  To do this, I wrote a program that drew each structure from the old database, displayed it, recalculated its identity, and wrote it to the new database.  It was a true nerd activity to see the program display all the structures in a matter of minutes.  This was done just in time, because during the 2015-16 academic year, over one thousand students used the homework and class-response system in the courses that I taught.

In the fall of 2015, I added more online lessons to the chemical information portion of the molecular modeling course.  This work was supported by a UTEP Library Literacy Enhancement Grant.

In the fall of 2016, after years of showing high school teachers how to setup, use, and create their own database of randomly generated numeric questions for Moodle, and using it for my own labs and lectures, all organic chemistry laboratories where run through this free open-source learning management system.  This means that close to 400 students from 22 labs with 7 different instructors of record all took their pre-lab quizzes and completed their post-lab reports online in a more thorough and consistent manner.   Second semester students in my organic lecture reported that they preferred the online instruction 4 to 1 to their first semester lab with paper quizzes and lab reports.  Although there was a two week delay to allow all students to take their quizzes, the consistent feedback provided to all students was a major reason for their opinion.  In addition, grading corrections are also instantaneous.




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Saturday, April 22, 2017

jsal at utep dot edu