OrganicPad: a tablet PC based chemistry tool

This paper describes a software tool that provides a natural user interface through the use of a Tablet PC for organic chemistry. The use of Tablet PCs is spreading throughout the computer world. Proof of this is from increased submission count at ACM SIGCSE and IEEE FIE and new conferences such as WIPTE 2007 (Workshop on the Impact of Pen Technology in Education) and PLT 2007 (International Workshop on Pen-based Learning Technologies). The teacher and all students are equipped with wireless internet access and either a Tablet PC or a WACOM [3] slate device. This tool is aimed at students who are learning introductory organic chemistry. Our tool, called OrganicPad, enables students to complete stand alone exercises as well as engage with the teacher and other students in interactive quiz exercises. All communication is through the web, using the HTTP communication protocol. At any time, the instructor can automatically evaluate student submissions and can quickly understand where students are having difficulty. Furthermore, the instructor can hide the identities of the students and anonymously use the submissions pedagogically. Finally, the instructor can develop tutorial exercises that students can work on outside of class. We present how we have used OrganicPad and our plans to extend its functionality in the future.

Organic chemistry is a very technical and advanced field of study. Students who fail to understand the introductory material will never be able to succeed in later courses. Furthermore, the majority of introductory chemistry classes contain several hundred students and teachers cannot take the time to work with each student individually. Organic chemistry teachers have no real way of knowing how well students are grasping concepts until the test results come back and by then it is too late. A chemistry program is needed that is able to evaluate student's understanding of the material quickly. Furthermore, current chemistry programs are far too complex for introductory students to use effectively. In addition, commercial programs force students into specific formats and do not let them have the freedom that pen and paper provide.

OrganicPad aims to solve these problems. OrganicPad utilizes Tablet PC functionality to allow students to freely create molecular drawings without imposing predefined formats like so many other chemistry programs. Furthermore, OrganicPad allows a chemistry instructor to interact with their students during lecture, exercise their student's understanding of the course material by sending out word problems, collect student-developed answers to a problem, evaluate student submissions, and conduct lecture after the exercise using the students' own submissions as examples. The instructor can also develop tutorials which students can follow on their own time.

By breaking the user's strokes on a Tablet PC down into segments, OrganicPad can recognize a growing number of handwritten atoms such as Hydrogen, Carbon, Oxygen, Nitrogen, and the Halogens. For example, users who write an "H" on the screen will have that letter converted to an interactive atom which can be further built upon. Simply drawing a line between two atoms will transform the stroke into a bond. Following these simple steps, users can build a molecule for further analysis.

Some areas of chemistry challenge students to see molecules in three dimensions. In order to represent the third dimension on paper, special bonds are drawn to indicate atoms going into the paper or back out towards the student. OrganicPad has the ability to recognize these special bonds structures and display the molecule correctly. OrganicPad can then take the two dimensional drawings one step farther and actually display the molecule in three dimensions.

Once the molecule has been drawn, OrganicPad has the ability to analyze molecules drawn. By clicking the "Check" button, OrganicPad will check for common errors in drawn molecules that do not agree with specific chemical properties such as Octet rules. This is one of the most common errors students make.

Teachers and students can also interact in real time inside the classroom through quiz sessions. OrganicPad allows teachers to set up a server on their computer so that all the students may connect to it. At this step, OrganicPad has created an ad hoc network for the students to connect. OrganicPad will display the instructor's IP address for the students to use as way of connecting to the instructor's machine. The instructor will then display this IP address and the students will enter it into an OrganicPad prompt window along with their name. Next, OrganicPad will connect to the instructor's machine so that data may be sent back and forth between the instructor and students. It is important to note that all of this is done through HTTP. This allows for these sessions to be created anywhere there is internet access. This allows for interaction between students and instructors that are not physically together. Once students have connected they are able to receive questions from the instructor as well as respond with answers. While the students have been working on their solutions, the instructor would create the correct answer and add it to the solution bank. Teachers may add multiple solutions if more than one solution fits the criteria. Teachers may also select student submission and add them as solutions. Once all of the solutions have been gathered, OrganicPad will then use graph isomorphism algorithms to determine if the molecules are equal to that of the instructor. Following this comparison, OrganicPad will give feedback to the students indicating to them whether their solution was found to be correct or incorrect.

Another way or teachers to interact with students is through tutorial lessons. OrganicPad provides teachers with an authoring tool to create tutorial lessons which can step students through the process of creating specific molecules. Teachers then have the ability to upload these lessons online. Students then may download any of these lessons and proceed through them at their own pace. Tutorials are essentially a series of steps that are used to lead the student to a final molecular creation. Students must complete each step before proceeding to the next. OrganicPad will automatically determine this through graph comparisons. Once the student's current drawing structurally matches the one the teacher provided as the solution, the tutorial will automatically proceed on to the next step. Figure 6 shows what a student could expect from a tutorial.

The main driving force behind the interactive features of OrganicPad is graph comparisons. OrganicPad handles these comparisons using an algorithm called graph isomorphism. This algorithm simply detects if two graphs are logically equivalent.

In OrganicPad, the molecule that has been drawn can be thought of as a graph. The number of nodes (atoms) and the degree (maximum bond) in any one graph (molecule) will rarely exceed 20 and 3, respectively. Hence, although the graph isomorphism algorithm for a general graph problem is potentially time-consuming for large graphs, the graphs in OrganicPad are small and bounded allowing for fast and efficient comparison of each student's molecule submission and the instructor's solution list. This small size also makes it possible for the graph to contain many cycles which is common in molecular drawings. Usually cycles are a time consuming problem in graph comparisons but because of the small size of the graph all of the comparisons can be handled without any slow down for the user.

This comparison algorithm is even simpler than the standard graph isomorphism algorithm because unlike the regular algorithm, no relabeling of the student's solution is necessary. The approach OrganicPad takes is to work with one of the teacher's solutions at a time. By holding the solution fixed, OrganicPad uses a backtracking algorithm to test for equality. If an atom match is found is found, mark it, and continue matching the solution key's subsequent atoms with the student's remaining atoms. The student's node names (atoms) must match those of the instructor exactly, so although some backtracking may be necessary to investigate alternative bijections, no renaming of student nodes is necessary. Once this backtracking discovers that a student's graph matches the solution, the student's submission is marked as correct.

OrganicPad is currently being tested in an organic chemistry class at Clemson University. Feedback from the students and instructor are helping strengthen its functionality and improve its usability.

In initial trials with student volunteers using a WACOM drawing tablet attached to a desktop computer (rather than a tablet PC), all the students were able to access the software and draw a given structure within five minutes of the beginning of the trial. Subsequently all students were able to connect to the instructor's PC, receive assignments, and send answers back to the instructor on each attempt. The instructor could access each student's structure -- evaluate and store comments for each student.

Students who participated in these trials were asked to complete a short survey on their experience. In this informal evaluation, all of the students strongly agreed (average 5.0 on a Likert scale where 5 is strongly agree and 1 is strongly disagree) that the software would be very useful in learning to draw Lewis structures, they thought the interface was intuitive and easy to use and get started.

Since the initial trial, we have had another one with updated software. This trial was a little more challenging than the first one. Students were generally asked to create more complex molecular structures than the first trial. In addition, the number of students increased from 22 students to 36 students. We again used a Likert scale in a survey to evaluate the students' impressions of the software. On average, students who participated in this trial felt that OrganicPad was easy to use, OrganicPad would be useful to help students learn to draw Lewis Structures, and OrganicPad allows you to draw structures in the same manner that you would draw structures with a paper and pencil.

Because of the flexibility of the core structures and algorithms, the principles of OrganicPad can be applied to other academic fields such as computer science and mathematics. The relationship to computer science is probably the more obvious expansion since the structure of a molecule could be stripped down to just represent a graph. The main features of OrganicPad would remain in place as well since they are all based on flexible graph isomorphism algorithms.

We have already started to create a computer science version of OrganicPad called GraphPad. The GraphPad software was used frequently last semester during a section of CpSc 212: Advanced Structures. Students responded very positively to the software. As a result of the positive response of GraphPad, we are experimenting with a similar concept in algebra.

OrganicPad has steadily been improving since it was initially created in the Fall of 2006. Several papers have been submitted already using OrganicPad as the premise. Notably a paper has been accepted at PLT 2007 and a poster was accepted at WIPTE 2007. In addition, a proposal for grant funding was submitted to NSF and was accepted. With this grant, we plan on purchasing a server to help improve OrganicPad's features. This server will enable us to store user information and chemical drawings into a database. Not only will analysis of the final structures be able to help a teacher identify problems, but since we store each step of the creation process we will be able to identify at which points the student got off course. Teachers could then go back and correct certain repeated errors by reinforcing them in classroom activities.

Most of our future work will surround using OrganicPad in the classroom. We are planning on using OrganicPad in a lab section to get a better feel for student ease of use and statistical evidence that OrganicPad can be used to improve learning. Furthermore unlike the first trial for the software, we now are equipped with enough Tablet PC's for a small class of students. By using a Tablet PC instead of WACOM slates, we believe students will respond even better. In subsequent evaluations, we will design studies to investigate whether the software improves a student's ability to draw accurate structures, and ultimately whether they can use this skill to predict physical and chemical properties.