Presentations
Posters
Teaching

Presentations

Selected Slide Sets, Posters, etc:

Posters:

 

William C. Ray, Abhilash Mohan, and Jeffrey Bartlett. “Using Flow-Visualization for Studying Sub-Molecular Motions”, Association for Computing Machinery SIGGRAPH, 33rd International Conference on Computer Graphics and Interactive Techniques, Boston, MA. July/August 2006.

William C. Ray and Joseph A. Jurcisek. “Modeling the fluffy lens: Construction of the Virtual Chinchilla”, Association for Computing Machinery SIGGRAPH, 32nd International Conference on Computer Graphics and Interactive Techniques, Los Angeles, CA. July/August 2005.

William C. Ray and Hatice Gulcin Ozer. “Discovering Biostructure Constraints using VRML Visualization”, Association for Computing Machinery SIGGRAPH, 32nd International Conference on Computer Graphics and Interactive Techniques, Los Angeles, CA. July/August 2005.

William C. Ray and Robert S. Munson Jr. “Comparative Analysis of the organization of the Haemophilus ducreyi and Haemophilus influenzae genomes”, TIGR/ASM conference on Microbial Genomes, Monterey, CA. January 2001.
Self-Running/PDF Presentations:

 

Invited Speaker, SuperComputing ‘06, representing the Ohio Supercomputer Center and Ohio Bioinformatics topics to the SuperComputing conference, Tampa, Florida. “Acidification of the adeno-associated virus capsid confers a persistent conformational change”, Nov 2006.

PDF Tutorial for Caffeinated (Java) StickWRLD server

MPEG-4 Quicktime Tutorial for VRML StickWRLD server

Quicktime version of original StickWRLD algorithm presentation

Teaching:

Biophysics 702 : Advanced Experimental Methods - Bioinformatics and Computational Biology Module

Week 1:
The Science and Philosophy of Bioinformatics
  • Monday: Introduction to Bioinformatics
    Slides
  • Wednesday: Transforming Biological Problem Domains into Bioinformatics Research Topics
    Slides
  • Friday: A Bioinformatics Case Study : StickWRLD
  • Homework:
    Generate a Scientific Hypothesis regarding a Bioinformatics topic
    Remember that your hypothesis must:
    • Make Testable Predictions
    • Be Falsifiable by Experiments based on those Predictions

    This assignment is due at the beginning of the period on the last day of class. Please be prepared to present:
    • Your Hypothesis
    • Two or more testable predictions based on the hypothesis
    • One or more experiments, per prediction, that would disprove the hypothesis, if it were incorrect
Week 2:
Computational Biology - Simulating and Modeling Reality
  • Monday: Computational Biology Domains
    Slides
  • Wednesday: Computational Biology Methods - Discretization
    Slides
  • Friday: Guest Lecturer Carlos Alvarez : TBA
    Please read:
    TBA
  • Homework:
    Please read: Modeling Population Growth
    Answer the questions listed in the PDF.
    This assignment requires either a small amount of programming in Perl, or re-coding the expressions from the PDF into the programming environment of your choice. There is a Perl script that implements the math required here.
    This assignment is due on Wednesday March 5th at the beginning of class. Please do not wait until the last minute to try to test the equations, or answer the questions.
Week 3:
Scientific Visualization
  • Monday: Sci-Vis Concepts
    Slides
  • Wednesday: Visualization Techniques
    Slides
  • Friday: Visualization Art-Crit, Bioinformatics Discussion
  • Three homework options:

    1. flow visualization : Homework 5 Slides
    2. Microarray dataset visualization : Nontypeable H. influenzae OxyR regulon data (save and open in excel, etc)
      The data details the behavior of a wild-type (designated '86') bacterial population, and gene-knockout mutant (designated 'OxyR') population, under experimental (designated '+') and control (designated '-') conditions. The OxyR mutant has had its oxidative-stress response regulator gene knocked out. The experimental condition is the addition of Hydrogen Peroxide (a strong inducer of oxidative stress). A simplistic analysis would suggest that under control conditions (86-:OxyR-) conditions, both populations should behave similarly, ad neither are experiencing oxidative stress, while under experimental conditions (86+:OxyR+), the regulon controlled by the oxyR gene product should be differentially regulated in 86, but should be unchanged from control conditions in the OxyR mutant. The same simplistic analysis would suggest that the 86+:86- comparison would reveal all genes modulated by oxidative stress (regardless of whether they are controlled by OxyR), and that the OxyR+:OxyR- comparison would reveal the subset of these that are modulated independently of OxyR - implying that 86+:86- minus OxyR+:OxyR- should approximate 86+:OxyR+. Present the data such that the actual behaviors are as immediately apparent as possible.
    3. Gene Order and Relationship visualization : Develop a Textual scheme for conveying gene organization (starts, stops, direction and overlap) for any neighboring subset of genes on a chromosome. The scheme should encapsulate the information on a single line so that it can be searchable with database/text-searching routines, and be human-readable so that a reader can easily disambiguate the positional relationships of the genes.

    Choose one. Your assignment in each case is to effectively present the data - that is, convey the information that's contained in the data to the viewer, in as rapid, intuitive, and complete a fashion as possible.

    This assignment is due at the beginning of class on Friday. Be prepared to very briefly present your results, and discuss key points of what features you have chosen to accent, what techniques you have used, and why they are contextually appropriate for the data and the viewing audience.
    REMEMBER: The goal of visualization is to make the information accessible and understandable to the viewer. It is very likely that information regarding some features will need to be sacrificed, to make other features understandable. Be prepared to discuss which features you have chosen to omit (or de-emphasize) and why, as part of your presentation on Friday.
    NOTE: It is nearly impossible to invent a completely new, totally untried way to visualize the flow and present the information. Don't be concerned if the things you try have aspects that overlap previous work, or other student's efforts.
    ALSO NOTE: I shouldn't have to say this, but previous experience with this assignment suggests that I must anyway. I expect, regardless of whether your submission parallels others that have already been done, that it will be your work. Be aware that I have probably looked at almost every 2D fluid-flow image and animation that you can find published, or on the web, and if you turn in a literal copy of something you find online or in a paper, even if you re-illustrate it, you will not enjoy the result.
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