CBBE Task List

Description: The Sunday evening activity is to serve as both an ice breaker as well as an introduction to modeling epidemiology. The "human" model suggested involves either dice or phenylalanine. As workshop participants mingle with each other, they must "share germs" by mixing the solution in his/her own cup with the person he/she is talking to. One of the cups contains a contaminated solution. Once done mingling, each person will use an indicator to determine whether or not he/she has been contaminated by the "sick" person. Then, the presenter should discuss how epidemiologists would then trace the origin of the disease.

The Sunday evening talk should serve to "wow" the workshop participants. The presenter should present "what are computational biologists doing today." No one topic is in-depth, but rather the participants should be exposed to a myriad of models including some on the research level as well as some aimed for educational purposes.

Description: This is the "what is computational science, and why do we care?" presentation. Both parts of that question should be adequately addressed. For the frist part, pattern recognition and characterization should be stressed. This is the time to show other cool models, some of which may have nothing to do with biology, but serve to exhibit the importance of computational science as a new approach to both learning and researching. The "why do we care" part of the presentation should emphasize current biological trends and the future curriculum changes and modifications which will be needed to match these trends. Such discussion could be motivated by the content in research documents such as "Biology 2010."

Description: This Monday afternoon session will serve as a preview of coming attractions. A myriad of modeling tools should be used to present various aspects of an epidemiological problem. For example, a nucleic acid sequence from hemoglobin from a person with sickle cell anemia can be compared to a wild type nucleic acid sequence using bioinformatics tools such as Biology Workbench. Protein Explorer can then be used to view the different shapes of the two different proteins (with and without the point mutation which causes sickle cell anemia). AgentSheets and Berkeley Madonna can be used to model the spread of contagious disease within a community. The focus in this section is not the content of the epidemiology material itself, but instead the idea that for one topic, many tools could be used to convey the important aspects of a field.

Description: An introduction to this dynamic modeling tool should include examples of the various ways the tool can be used in the classroom. Keep in mind that most participants will have never seen the tool before, and some time will need to be spent on "how" to build the model. With this in mind, the presenter may want to build a model with the participants in this session so the participants have "hands on" experience with the tool before lab. At the end of the session, similar tools such as Stella and Simile should be mentioned.

Description: An Introduction to this interface built as a portal to powerful bioinformatics tools should include a "how to" section as well as a "why" section of the presentation. The presenter should discuss what areas of the curriculum can be reinforced by the tool and show a variety of examples of the tool's use in various areas of the undergraduate introductory biology curriculum. Similar tools to the Workbench should be quickly addressed at the end of the session.

Description: An introduction to this agent-based dynamic modeling tool should include a presenter-led demonstration of how to build a simple model as well as an exhibition of the variety of models which can be built with the tool. Several examples which use this modeling tool and reinforce or address areas in the biological curriculum should be included in the presentation. At the end of the session, similar tools such as NetLogo and EcoBeaker should be mentioned.

Description: Imaging and visualization are not only important technical tools for researchers, but interesting and informative tools which can be used in the classroom to facilitate inquiry-based learning. As in the other large blocks of time dedicated to presenting a modeling tool, the presenter should lead the participants in doing their own mini project with the tool in order to give them hands on experience. Participants should also get a good idea of how the tool could be used to enrich their current curriculum.

Description: These "higher order" tools should be presented in order to show what a student with more advanced programming experience could do. The presenter should demonstrate the important functions in these programs which a biologist would typically use to build a useful model. Some examples might include plotting a function and/or data, fitting a line, sorting a list of data, displaying graphical output, and others. Certainly the presenter could pick one of the three tools to concentrate on, but should be familiar with all three.

Description: This simple, but powerful, tool is often overlooked in how it can help students model. An introduction of how to use Excel to program and create useful models should include walking through the building of a model together as well as the presenter showing how models which are already built can be integrated into the curriculum.

Description: Statistics is an important discipline to biologists, especially to researchers who need a means to analyze their data. These tools can be helpful in determining if an observed difference or behavior is statistically significant. The presenter should realize that some biologists lack the math background to tackle such tools on their own, and therefore need to be convinced that the field is not that intimidating.

Description: This session would introduce and explain the mathematical theory and concepts behind dynamic modeling. It would answer the question, "What is Berkeley Madonna/AgentSheets doing behind the scenes?" In essence, this mini-session would introduce participants to the algorithm of dynamic modeling.

Description: This session would introduce and explain the mathematical theory and concepts behind bioinformatics. It would answer the question, "What is Biology Workbench doing behind the scenes?" In essence, this mini-session would introduce participants to the algorithm of sequence matching.

Description: The goal of Stella2Java is to make a built model web-accessible. The presenter should step through the process of transferring a Stella model to a Java applet using Shodor's form. The presenter should then discuss how the applet (in general) could be used in the classroom, and specifically how the Java applet is useful in the student being able to change parameters and see real-time changes in the graphical output.

Description: This tool's greatest virtue is perhaps its ability to convey the cell as a very dynamic system. The presenter should give a quick tutorial for how to use the tool as well as a variety of examples of the ways the tool could be used in a variety of biology classes (not just cell biology). Biochemistry, microbiology, pharmacy, and other fields could be used in the presentation.

Description: Similar to AgentSheets in that it is an agent-based modeling tool, the presenter during this mini-session should compare and contrast the two tools and show examples where EcoBeaker is a particularly useful tool to do the computational biology.

Description: This session is a discussion on how to "tweak" your model. A discussion of why changing integration methods can very drastically affect a model's output should be included in this session. Also, the presenter should also lead a discussion on the limitations of modeling, as well as other topics which seem to fit here.

Description: These two modeling tools are agent-based modeling tools. These two tools require a bit more programming experience from the students and teachers who use the tools to build models. The presentation should include information on the advantages of using NetLogo and StarLogo (although you can focus on just one, such as NetLogo, which is free), as well as some biological examples of models built with these tools.

Description: BioQUEST is a curriculum-building organization which concentrates on innovative ways of developing biology curriculum. The presenter of this mini-session should be very familiar with the resources available through BioQUEST. This mini-session should serve to provide the faculty with yet another resource for good computational biology tools.

Description: NCBI is an authoratative resource for today's researchers in the biological field. This session would serve to introduce the participants to this online resource and its features.

Description: Many biology undergraduate faculty are attempting to prepare their students for medical professions. Medical visualization and imaging plays a significant part in medicine today. The presenter of this session should present examples, perhaps from biomedical engineering, in which imaging and visualization are integrated into the medical profession. Several tools, including NIH Image and perhaps GIS Imaging software should be used in this session as the session is focued on a topic, not a specific tool.

Description: In this session, the presenter would present venues for publication and presentation, and perhaps even explain the importance of both.

Description: As faculty become more and more interested in implementing what they take away from the CBBE Workshop, they may need extra funds to carry out their ideas. This mini-session would serve to inform those interested in starting something on their own campus of the funding opportunities available.

Description: In changing, modifying, or creating new curriculum there seems to be issues. Some issues are interdepartmental and others concern the faculty/administrator relationship, among others. The leaders of this discussion should bring in someone or they themselves be someone who has overcome some of these issues. Strategies on overcoming these issues could be presented by those who have overcome such obstacles.

Resources:

Lead: Ethel Stanley Supporting Partners: John Jungck Sam Donovan

24. Leader for the Round Table Discussion of Pedagogical Issues
Approximate Duration: 1 hour

Description: Some pedagogical issues arise when a faculty member takes what he/she has learned from the workshop to their campus. The discussion here should include how to integrate modeling into a classroom with: one computer and a screen, multiple computers, or a 1:1 student to computer ratio.

Description: This speaker would tie together what has been discovered during the CBBE workshop that week. There is a lot of flexibility here, but motivating the faculty to implement what they have learned the past week is the deliverable in this 15-20 minute talk.

Description: An in-depth look at the tool, more in depth than the introduction at the beginning of the week.

Description: An in-depth look at the tool, more in depth than the introduction at the beginning of the week.

Description: An in-depth look at the tool, more in depth than the introduction at the beginning of the week.

Description: An in-depth look at the tool, more in depth than the introduction at the beginnning of the week.

Description: An in-depth look at the tool, more in depth than the introduction at the beginning of the week.

Description: An in-depth look at the tool, more in depth than the introduction at the beginning of the week.