For persons interested in an in-depth introduction to dynamic modeling and bioinformatics, with a focus on their use in the undergraduate biology classroom. Participants new to computational science or those who have attended an interdisciplinary workshop are encouraged to attend. Also, prior participants are encouraged to apply. Erin Hodgess  Jeff Krause jeffk@shodor.org Erin McNelis  Gloria Rendon  | | | Computational Biology for Biology Educators at Houston Community College
July 13 - July 19, 2008
| | | | 2 | Monday, July 14, 2008:
- Computational Resources for Biology Educators,
- System Dynamics Modeling with Vensim,
- Agent-Based Modeling with NetLogo,
- Systems of Ordinary Differential Equations in Octave
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2) System Dynamics Modeling with Vensim PLE
In the biological sciences and in the pre-college classroom students may not be comfortable dealing directly with the systems of equations used to represent and simulate the behaviors of dynamic systems. Fortunately, a number of software packages referred to as graphical interface differential equation solvers (GIDES) are available, enabling students to study and understand the behavior of dynamic systems without having to be fluent in calculus with differential equations.
These GIDES packages represent the system graphically as a flow chart consisting of state variables whose values can change over time. Change in the model is enabled by connections between states called rates, flows or fluxes. The rates and behaviors of the system may also be influenced by other parameters that are included in the model.
Vensim PLE is a free software package that allows you to build system dynamics models diagrammatically, add parameter values and formulas, and then run simulations of the behavior of the system. Vensim also assembles the system of equations for the model as it is built graphically, allowing the connection to the underlying mathematics to be made as students understanding progresses.
 Vensim PLE Download Site Vensim Tutorial - Modeling Sodium Channel Gating and Blockade by Tetrodotoxin- Vensim Documentation Page
 Vensim Models at Shodor-
3) Agent-Based Modeling with Netlogo
An alternative approach to modeling dynamic systems is to represent the components of the system as autonomous individuals which follow rules that govern their individual actions as well as their interactions with other system components. System behaviors in these agent-based models emerge from the simultaneous actions of the many individual autonomous agents. NetLogo is a free software tool that allows you to run, modify and build agent-based simulations using a full featured graphical user interface, and a programming language known as Logo.
- NetLogo Homepage
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- Follow the "Models" link to find a HUGE collection of user contributed models
- You can also view models found in the Models Library (which installs with the software)
- All of the models can be viewed in your browser as Java applets, or the NetLogo model files can be downloaded and run in NetLogo
 NetLogo Tutorial - An Agent-Based Predator Prey Model- NetLogo Documentation Page
- The Online Dictionary is Particularly Useful as a Language Reference
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4) Modeling Systems in Aggregate with Ordinary Differential Equations Using Octave or MATLAB.
Those with sufficient mathematical expertise find it easiest to deal directly with the mathematical, or numerical, representations of a dynamic system. Many software packages exist that enable this approach. The popular commercial packages include Mathematica, Maple and MATLAB. Octave is a free, open-source tool that is mostly compatible with code generated in MATLAB.
- GNU Octave Homepage
- Octave (and MATLAB) Tutorial - ODE Model of Predator Prey
- QtOctave Homepage - GUI front-end for Octave
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| | | 3 | Tuesday, July 15, 2008
- Image Analysis and Processing with ImageJ
- Modeling Cellular Systems with the Virtual Cell
- Bioinformatics with the Molecular Science Student Workbench
- Parallel and Cluster Computing with the BCCD and MPI
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1) Image Analysis and Processing with ImageJ
Basic research in the biological sciences has long depended on the analysis of images collected through the microscope. Contemporary biomedical science uses many more imaging techniques in both basic and clinical research as well as medical diagnosis. ImageJ is a free open source image analysis software tool implemented in Java. It includes a straightforward graphical user interface, with functionality that can be expanded by plug-in modules contributed by the user community. Some of the default functionality overlaps with image editing software, like PhotoShop, however it includes many measurement and analysis functions as well.
- ImageJ Homepage
- Tutorial - Image Analysis with ImageJ
- ImageJ for Microscopy Website
- Includes a collection of useful plugins and macros (which can be downloaded in a bundle with the ImageJ software for a single install, as was done for the workshop).
- Provides documentation for many of the plugins, and the actions they can be used for.
- Jim Ekstrom's Imaging Resources for Biology Educators
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2) Modeling Cellular Systems with the Virtual Cell
The genomic revolution has brought an explosion of data on the molecular components of living systems. The high-throughput measurement technologies that have become prevalent in recent years are able to capture information on the composition, abundance, functional state, and interactions among large numbers of components within the complex molecular networks that are the functional units of the cell. In order to effectively interpret and make inferences with these data it is necessary to understand both the properties of the individual molecular components, as well as the functional contexts in which they participate. Towards this end, a variety of efforts have been undertaken, under the very broad title of “systems biology”.
Among the projects underway in this field are efforts to create large repositories of information on biomolecular species and the functional networks that they form. An essential part of these efforts has been the development of standards to enable the exchange of information, tools, and models among researchers in the field. These efforts towards standardization will benefit the education community at least as much as the research community. Now educators can learn to use a small set of tools and have access to large quantities of information as well as repositories of models in standard formats.
The tools that have resulted from these efforts are more specialized than Vensim, Netlogo or Octave, they are designed to model biological systems, and therefore may require significant subject matter expertise for their effective use. However, the specificity of these tools also means that they include functionality that allows one to model situations occurring in biological settings much more easily than if one had to build them from scratch.
The Virtual Cell is one such modeling tool that is designed to model processes that occur within and between cellular compartments. It is compatible with the prevalent model format standards, provides access to a large model repository, and is run on a high-performance parallel computing environment that enables any researcher to run very sophisticated models in reasonable amounts of time.
- The Virtual Cell Homepage
- The VCell Documentation Page
- Includes the tutorials that were used in the workshop, and more
- systems-biology.org
- This is a portal site for researchers in the field of systems biology,
- It provides links to a number of useful resources for learning about the field
3) Bioinformatics with the Molecular Science Student Workbench
A large, and growing portion of computation in the life sciences is in the area of bioinformatics. Storing, maintaining, analyzing and characterizing the massive amounts of information being generated through a variety of high-throughput measurement technologies. Biological sequence data has been at the epicenter of bioinformatics since its inception, and new analytical approaches and tools are constantly being developed. Keeping up with new developments in the field can be a daunting task.
The Biology Workbench is a web-based tool developed by the San Diego Supercomputer Center (SDSC) that integrates database search capabilities with a variety of widely used analysis and modeling tools. The site is freely available and provides a cohesive environment within which most of the basic methods of biological sequence analysis can be explored. Behind the scenes, the jobs you run through the Biology Workbench are run on high-performance computing resources located at the SDSC and elsewhere on the TeraGrid, thus enabling research class tasks to be run from any educational institution.
The Molecular Science Student Workbench is another web-based environment, this one developed by the National Center for Supercomputing Applications (NCSA) and the University of Illinois at Urbana-Champaign (UIUC), which extends the Biology Workbench and is focused on the mission of bioinformatics education. IT adds access to other web-based resources as well as the ability to access online lessons within a session. Educators can also use tools provided by the site to build new lesson plans online.
- SDSC Biology Workbench
- Molecular Science Student Workbench
- Reading phylogenetic trees: A quick review
- Constructing phylogenetic trees with Biology Workbench
- MSSW lesson building tutorial
4) Parallel and Cluster Computing with the BCCD and MPI
All of the computational tools described in this workshop have been enabled by the ever-increasing availability of inexpensive computational power. This trend is increasing into the future and is currently being realized through parallelization. Even our desktop and laptop machines are becoming parallel computers using multi-core processors. This continued increase in computational power will enable us to carry out more and more sophisticated, detailed and accurate simulations and analyses. Having some understanding of what the man (or silicon wafers) behind the curtain is doing helps us to become, and teach students to become, more effective users and developers of the computational tools to of the future.
The Bootable Cluster CD (BCCD) is a completely non-destructive live CD, based on Linux. It can be used to turn any lab of Windows, Mac, or Linux computers into a temporary but fully functional clusters. It also contains several stand-alone utilities used for teaching parallelism and debugging. MPI stands for "Message Passing Interface". MPI is an application programmer interface that defines a set of functions. These functions allow for multi-process, distributed parallelism.
- BCCD Homepage
 BCCD presentation BCCD and MPI commands file
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| | | 4 | Wednesday, July 16, 2008
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| | | 5 | Thursday, July 17, 2008
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| | | 6 | Friday, July 18, 2008
- 3D Rendering and Analysis with VolView
While ImageJ enables powerful analysis and processing of 2D images, it is limited in its ability to handle and manipulate 3D reconstructions of volumetric data. VolView is a commercial product that enables this functionality on Windows based PCs. OsiriX is a free, open source tool with similar capabilities for Mac OSX.
- VolView website
- VolView tutorial
- VolView 2.0 Users Guide
- This file is 3.3 Mb!
- This file includes the tutorial that we handed out at the workshop
- OsiriX image analysis & 3D software for Mac
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