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Table of contents:

Introduction to Scientific Visualization
Authors: Shawn Liner, Gerald Knapp, and Chris Hynes*

It has been my experience that there has always been some kind of visualization aspect to scientific data e.g. 2D plots, pie charts or bar graphs. Even in the Humanities, data or models are rendered into visualizations such as geopolitical maps, personality charts, or timelines (e.g. Charles Minard's Napolean's March).
This iBook is a compilation of different learning exercises that have or will be used in a course called "Introduction to Scientific Visualization". It is a unique collection of topics and exercises that brings together skills from Arts, Computer Science, Math, and Sciences. The topics are generally brief and will demonstrate skill levels from basic to low-moderate.
Various freeware (and O/S-ware) will be examined to demonstrate styles of image renderings from data, terminology, and the basic math manipulations required to generate the images. This iBook is a work in progress with Version 1 discussing Excel and ImageJ software in some detail as applicable to the Introduction to Scientific Visualization course. Later versions of the iBook will add more exercises with Excel and ImageJ as well as add newer software demonstrations with VisIt, VMD and ParaView software. It is hoped that KiwiViewer, 123D, and augmented reality can be included sometime in the near future.
Links are provided in the text to direct the reader to a few websites where files, software, and documentation can be downloaded. A PDF version of the iBook will be made available for those readers that don't have an iPad. The interactive widgets won’t be active, but in the case of the Gallery widgets, short Powerpoint presentations will be available to show step by step instructions on how to perform the described task. Although the word "Scientific" is used in the course title, by no means is that a restriction as to the origins of the data, but rather the method in which it was collected, i.e. applying the Scientific Method. For example, in the Excel Chapter, a "4D" graph will be created using a song playlist.
After browsing the iBook, it is hoped that the reader will at least have an appreciation for Scientific Visualization, the math and art that goes along with it, and perhaps inspire them to pursue it as part of their profession.
The mathematician/scientist will exercise their artistic skill. A humanities researcher can convert qualitative information into quantitative information and thus communicate their discoveries via a visualization. The artist can discover the art hidden within data and how basic math can significantly alter the art.
Virtual reality and reality can be combined, for example I have seen an awesome animation that combined a virtual image of a sun with real coronal data from our sun and thus a virtual/real hybrid image was created.

Book (PDF format), README
Gallery 1.1 Symbols, icons, color, communication
Gallery 2.1 Overlay,Trim axis,Marker color
Gallery 2.2 Smooth Lined Scatter, Trim, Reverse
Gallery 2.3 Bubble Graph
Gallery 3.1 X, Y coordinates and RGB in ImageJ
Gallery 3.2 Histograms in ImageJ
Gallery 3.3 Self-paced step by step image subtraction
Gallery 3.4 Reproducibility and Real change
Gallery 3.5 Adjusting the Threshold
Gallery 3.6 Dilate and Outline
Gallery 3.7 Adding Outlines to Resultant
Gallery 3.8 Changing Outlines to green
Gallery 3.9 Drawing different line styles
Gallery 3.10 Obtaining a Plot Profile
Gallery 3.11 Measuring Length in images
Gallery 3.12 Measuring Areas
Gallery 3.13 Paint brush with Areas
Gallery 3.14 Angle measure

* For more information, please contact Chris Hynes at chynes -AT- lsmsa DOT edu

Quick Chemistry Demonstrations for the High School Classroom
Author: Jessica Shelton

Course: Chemistry. Grade Level: 10 and 11
This PDF Document has a set of quick chemistry demos, each less than 10 minutes. Demos include purpose, objectives, pre-demonstration questions, procedures, and post-demonstration questions.
Demos are "Burning Money", "Zinc Covered Penny", "Dry Ice Sublimation in Balloon", "Density of Liquids", "Air takes up space!", "Density of different gases in balloons", "Rutherford's Gold Foil", "What's in a name...nomenclature demo", "Reactivity of Alkali Metals", "Elephant toothpaste, a look at a decomposition reaction", "Visualizing the Mole", "Limiting Reactants", and "Physical Change vs. Chemical Change". It also includes "Paper Chromatography" demo (15-20 min).

For more information, please contact Jessica Shelton at jessica.shelton -AT- parkviewbaptist DOT com

Wetting and Contact Angle
Author: Genia Roper

Course: Physical Science Honors.
This PDF Document aims to answer the following questions: What makes water stick to itself and form bubbles and droplets? Why do water droplets stick to things? What causes water to be absorbed by a paper towel or move up a capillary tube?
It has a set of one lesson,
"Wetting and Contact Angle: Lesson": What makes water stick to itself and form bubbles and droplets? Why do water droplets stick to things? What causes water to be absorbed by a paper towel or move up a capillary tube?
and three demos,
"Magic Sand vs. Regular Sand": Explore the properties of molecular bonding. Demonstrate the concepts of hydrophobic and hydrophilic behavior.
"Wetting and Contact Angle: Lab": Describe and predict the behavior of water and hydrophilic and hydrophobic surfaces and explain in general terms what causes the difference in behavior. Discuss situations in which applying a hydrophobic or hydrophilic surface would be advantageous.
"Hydrophobic and Hydrophilic Reactions in Milk": Recognize and understand the general composition of elements and their organization into a chemical structure including bonding, ring structures, functional groups and dispersion properties and relate these to the chemical compounds of foods.

Investigating Water Behavior
Author: Brandon Edwards

Audience: Middle School Science (6-8)
Water has many unique and important properties and can be used to demonstrate other key chemical and physical processes. By understanding these properties, we can better understand our natural and living environment. Students will learn key parts of the scientific method by investigating water behavior.
This PDF Document aims to answer the following questions: How do we conduct scientific investigations? How do we conduct a fair test? How do we design effective experiments? How do we gather, analyze, and communicate data from an experiment?
Learning Objectives: Describe science as being a process of proposing and testing hypotheses. Distinguish between statements that are testable by science and those that are not. Describe the meaning and purpose of experimental variables: control, independent and dependent. Write a testable hypothesis. Gather data from an experiment and analyze the data. Complete a conclusion or summary. Design an experiment to test a hypothesis.

* For more information, please contact Brandon Edwards at brandon.edwards AT

Perl Puzzles. Introducting PERL through the NPR Sunday Puzzle
Author: Brad Burkman

The NPR Sunday Puzzles are often questions about permuting letters in words, and analogous to questions in computational biology about permuting genome bases. The lingustic questions are more intuitively accessible to students, and everybody loves puzzles. Most people play the puzzle with pen and paper, perhaps a Scrabble board.
This set of exercises introduces students to one of the main tools in computational biology, the computer language PERL.
The file Perl gives a link to the NPR website for a particular puzzle, explains the puzzle, and gives code that finds multiple solutions. Comments in the code explain what the code is doing. In the comments are links to other NPR puzzles that the student can solve by adapting the code.
The file wordsEn.txt, from the website of SIL (formerly the Summer Institute of Linguistics), has over one hundred thousand common English words that the PERL code reads over and over to find words or sets of words that solve the puzzle.
To use the code, you need to install PERL For the version you have installed, find the manual and read the section on getting started.

For more information, please contact Brad Burkman at bburkman -AT- lsmsa DOT edu

Where's Nucleosome A now?
Author: Anna Drago

This PDF presentation talks about DNA basics and why nucleosome A is important. After looking at the presentation, you can complete the activity "DNA Detectives: What is Your DNA Alias?".

For more information, please contact Anna Drago at Anna.Drago -AT- BossierSchools DOT org

Spinning Compass
Author: Harry Henderson

Grade level content standard(s)/Standard(s) for mathematical practice:
N-Q.2 Define appropriate quantities for the purpose of descriptive modeling.
G-MG Modeling with Geometry, apply geometric concepts in modeling situations

DOK levels and learning targets 1, 2, 3:
Applying geometry law of sines and law of cosines equations to real world problem. Modifying agent based model into a serial code [C++] then paralellize. Another object is optimizing the code. Using technology to explore mathematical relations.

Essential questions:
How do we convert between agent based and serial?
How do we optimize the code?
How do we paralellize the code?

Phase 1: Develop differential equations to represent the physical object
Phase 2: Convert agent based code to serial code and use those equations to build the serial code in C++
Phase 3: Optimize code using gradient
Phase 4: Introduce and apply OpenMP to the serial code

Resources/Materials needed:
Computer with access to a multi-core supercomputer with OpenMP.

Spinning Compass Lesson Plan Part 1, Spinning Compass Lesson Plan Part 2

For more information, please contact Harry Henderson at electricmotorcycles -AT- yahoo DOT com

Introduction to Computers: Programming Logic and Design
Author: Debra Borskey, BRCC CS Associate Professor

Purpose: To help inexperienced students become familiar with programming in C++ using Visual Studio
This PDF Document has a user friendly introductory C++ curriculum module for students who have no previous programming experience. Students learn that a computer program is designed to solve problems. Additionally, students grasp C++ is an object oriented program that provides a user friendly approach to solving any problem. Novice learn simple steps to find a solution to problems are the same basic steps used to write a program and principally can be defined as follows:

When creating a program in C++:

File: PDF

For more information, please contact Ms. Debra Borskey, borskeyd -AT-

Superconductivity: An Introduction for High School Students
Author: Shawn Liner, Parkview Baptist School

This Book was written as an introduction to individuals curious about superconductivity. It was born from a frustration in getting a clear idea about superconductivity without getting frustrated on currently available webpages. The target audience is high school students with some science background. However, the casual adult might find it interesting as well. It does not attempt to teach detailed, merely to introduce the topic and hopefully pique curiosity.

Files: PDF version, ePub version

For more information, please contact Mr. Shawn Liner, -AT-

Introduction to Regression Analysis – Grade 11 and 12
Author: Roland Dante, Baton Rouge Charter Academy

Working together, students determine a regression line and a coefficient of correlation for bivariate data. Students determine relationships between the regression line and the coefficient of correlation in a group learning activity. Students examine scatter plots with similar lines of regression and different correlation coefficients to explore the value of correlation coefficients.

This lesson provides a review discussion of correlation versus causation as part of the pre-assessment. The lesson also provides the opportunity for students to learn the material in different ways, including visually, and symbolically. The lesson gives options for flexible use of time and gives an excellent introduction on lines of regression.

File: PDF

For more information, please contact Mr. Roland Dante, -AT-

Coding and Geometry
Authors: Michelle Hills*, St. James Parish Science and Math Academy, Fernando Alegre, Baton Rouge Community College, and Juana Moreno, Louisiana State University

Coding and Geometry is a method of illustrating the use of coding in the context of high school geometry. The students will learn skills to manipulate programs step by step throughout the lessons. From basic skills such as drawing points on a display to more advanced functionality such as calculating the perimeter of an arbitrary triangle, these lessons encompass the goal of incorporating computer science skills into the high school mathematics classroom. The lessons are hands-on, and so they will require student computers and teacher facilitation.

Student Lesson (PDF)
Teacher Manual (PDF)
Haskell File - Student (ZIP)
Haskell File - Teacher (ZIP)

For more information, please contact Ms. Michelle Hills*, -AT-

Incorporating Scientific Research Methods into High School Programming Classes
Author: Shawn Liner, Parkview Baptist School

Perhaps the best start is to tell what this documents is not. It is not intended to teach programming. It is instead strictly a resource for teachers looking for that kick-start or for interesting projects for their programming classes that have scientific bases and logic.

Files: Booklet (PDF), Sample Code (ZIP)

For more information, please contact Mr. Shawn Liner, -AT-

Chemistry Education and Computing: A Computational Approach to Teaching Intro to Chemistry
Author: Karen N. Marshall, International School of Louisiana

Chemistry is best taught using visual cues, research supports use of animation in teaching chemistry. This lesson introduces software packages Gview and VMD as teaching tools. In this lesson plan, students should

Intro (PDF)
Unit 1: Atoms and Bonding (PDF)
GaussianView Intro for Students (PDF)
Sample Lab Report - Experimental (PDF)
Sample Lab Report - Computational (PDF)
Sample Lab Report: Comparison: Comp vs. Experimental (PDF)

For more information, please contact Ms. Karen Marshall, -AT-

Integrating LA-SiGMA Strategies into School Instruction
Author: Keith Smith, Forest Brook Middle

Introduction to simulation programming. Objective: Create a hands on engaging program my student can use that stimulates interest in programming basics. Students will use a VPL (Visual Programming Language) to drag and drop visual block to write code. These are the foundations of computer science. Students will be introduce to code by utilizing Anna and Elisa miniscule coding. (PDF)

Archimedes' Principle Lesson. In this lesson we want students to visualize all the forces that are acting on the object. There is the force acting on top from the weight of the fluid, the buoyant force from the bottom, and the force exerted on the sidewalls. (PDF)

Latent and Specific Heat Lesson. In this lesson the student is expected to identify the formation of a new substance by using the evidence of a possible chemical change such as production of a gas, change in temperature, production of a precipitate, or color change. (PDF)

Motion Lesson. The student is expected to identify and describe the changes in position, direction, and speed of an object when acted upon by unbalanced forces AND calculate average speed using distance and time measurements, AND measure and graph changes in motion. (PDF)

For more information, please contact Mr. Keith Smith, -AT-

Energy Connections
Author: Lacy Smith, St. Amant Middle

The concept of the project was to conduct research on a topic that affected the classroom and the one concept that spans the entire year in 6th grade Louisiana science is energy. In doing this project, lessons were created to help new and old teachers alike make connections to energy that may not be incredibly clear in the curriculum. These connections will help students have a better understanding of energy and how energy makes everything happen in our world!

Lesson plans, resources and survey results can be found at

One finding in the survey was the desire for resources so a website has been set up for that as well here:

For more information, please contact Ms. Lacy Smith, lacy.smith -AT- apsb DOT info

Inquiry-Based Experiments for High School Physics Students
Author: Jane R. Pablico, Walker High School

Research has shown that engaging students in generating, developing, and justifying explanations is an important element to helping students learn science. In a meta-analysis of experimental and quasi-experimental studies on inquiry-based instruction from 1996 to 2006, Furtak and his team (Furtak, Seidel, Iverson & Briggs, 2012) found an overall positive effect of inquiry-based instruction on student learning of science. This finding also agrees with the result of a research synthesis conducted by Minner, Levy & Century (2010). The authors found a statistically significant increase in student conceptual learning when there was more student responsibility in the instruction and higher inquiry saturation. They found a clear, positive trend in favor of inquiry-based learning (Furtak,, 2012).

This summer project was inspired by the above-mentioned research findings. The project aimed to develop a set of inquiry-based experiments that can be used in high school Physics classes. Furthermore, it aimed to modify experiments from College Physics level to fit into high school setting. It is hoped that when the developed material is improved and used, it will contribute in improving the conceptual understanding of high school students in physics. The material can be found at


For more information, please contact Ms. Jane R. Pablico, jane.pablico -AT- lpsb DOT org