Introduction to Bioinformatics

Term Project
Milestones - Part II

Prep readings:

• On-line resources related to your term project
• Hardcopy references derived from library or other sources
• What to expect in Term Project Milestones - Part III

In this assignment, we wish to:

• continue to research materials related to your term project
• develop and test initial code developed for your term project goals

• Keep track of anything that seems particularly useful to you, both WWW pages and any hardcopy reference articles.
• Remember, that within the text of your term project report, you must cite official, published articles. You may also include a list of WWW resources, but these cannot be the only source of your reference materials.
• Update your term project report, using the major working chunks of your first progress report and incorporating any and all changes discussed with me. Please revisit the Part I Project Milestones and make sure to include anything you missed.
• Feel free to create new subheadings for your report and add to existing sections. For example:
  • Introduction
    The information for this section can likely be pulled from your initial project report, with appropriate corrections and additions from your newly found references.
  • Motivation/Rationale and Objectives
    Be sure this section is updated to include appropriate discussions of the significance of any emphasis you have placed on data mining, visualization, simulation, etc.
  • Materials and Methods
    Be sure to include links to any input files within your discussions of materials and methods. A description of the input data and data collection methods must also be included.
  • Hypotheses
    If your term project has a section on Hypotheses, you should list clearly defined hypotheses, and then provide clearly marked input data sets and any surveys used to gather subjective ratings.
  • Results
    In this section, include sample output results of processing the input files you have described. This section must include representative outputs for each type of input data and proposed "query" of the data.
  • Discussion
    In this section, discuss the strengths and limits of your current approaches. Think about how what you've done so far fits into the "big picture" of current research in your term project area.
  • Summary and Future Directions
    In this section, professionally summarize your progress and suggest changes and additional avenues for exploration.
  • Appendix
    In this section, include links to the current drafts of any Perl source code or HTML pages you have developed for your project so far with a brief description of any contents. (There may also be links to the HTML pages in other parts of your report as appropriate.)
• Make sure your project report is clear and thorough, and please confirm that I can easily locate the WWW page from your course homepage.
• Finally, please provide an updated process flowchart or set of flowcharts describing the process you are using to analyze your data. A hand-drawn flowchart is fine, or you can use your favorite drawing tool (I recommend Powerpoint). Indicate all processing you do in the relevant steps, including anything done by hand, or done automatically with Perl code or some other process. (Electronic versions of your flowcharts should eventually be linked in the appendix of your report.)

• I will review your WWW site and provide comments to you in class or via email. I will follow all the links and review your images at your WWW site
• Also resubmit the Worksheet for Project Milestones Part II discussion sheets completed in class. (Click here for the Word document.) Feel free to add any details which may be relevant, if you didn't completely finish these in class.
• Also submit the associated process flowchart(s) you've developed, with any new version(s) stapled on top of the class version. Remember, this will be a starting point for the process flowchart(s) for your oral presentation, so any time you spend making this information more clear and complete now will save you time later. In addition, you will get more feedback from me now regarding the progress you are making.