RIT Protein Separations Simulation for Education

JBioFramework (JBF) is a set of two different chemical separations simulations (2D Electrophoresis and Mass Spectrometry) that are frequently used in chemistry, biochemistry, and proteomics research. It is written in the Java programming language and will run on any and all systems that have the JVM installed. What's New? JBF's next release will contain a 1D Electrophoresis simulation as well as a tab containing ChemAxon's MarvinSketch.

Hello Educators! We are happy that you decided to try JBF in your class. Our goal is to improve student learning with our simulation of protein separation and analysis tools. The simulation is easy to use, free, and fun and will help prepare students for lab experiments.

When we started to test JBF with students to assess their learning outcomes, we entered an iterative process of revising the problem sets that we have created to go along with JBF. We have also incorporated Bloom's taxonomy to clarify the learning goals for each aspect of JBF Biology in Bloom: Implementing Bloom's Taxonomy to Enhance Student Learning in Biology by Alison Crow, Clarissa Dirks, and Mary Pat Wenderoth.

We are still learning how to make JBF better by using student surveys after each trial, so don't hesitate to send us your suggestions to improve JBF. Finally, we would like to express our sincere gratitude for your interest in providing all the materials that you need to get started right away.

Fisher, Amanda, Emily Sekera, Jill Payne, and Paul Craig. 2012. "Simulation of Two Dimensional Electrophoresis and Tandem Mass Spectrometry for Teaching Proteomics." 

• A Wet Lab Simulation to Enhance the Learning Experience of Undergraduates
• A 2DE-Tandem MS Simulation with a Structural Interface
• A Mass Spectrometry Simulation for Biochemistry Education
• Developing and Sustaining Scientific Software Applications for Biochemistry Education

We wish to thank all those who contributed to the JBioFramework project:

• RIT College of Science
• RIT Golisano College of Computing and Information Sciences
• RIT Office of the Vice President for Research 
• Merck/AAAS Undergraduate Science Research Program
• Dr. Thomas Kim and Dr. Scott Franklin
• Sheneka Linton, Benjamin Russell, and Amanda Fisher
• ChemAxon for providing MarvinSketch Java API

• SourceForge JBioframeWork [Download Page]
• ChemAxon MarvinSketch [Download Page]