Introduction to Bioinformatics

Term Project
Milestones - Part I

In this assignment, we wish to:

• research and consider alternative problems in the field of bioinformatics
• begin to develop an understanding of the "input" to a particular problem and what algorithms/code might be applicable to addressing that problem

There are two products associated with your term project in bioinformatics: a written report in the form of a WWW page describing your project and the oral defense of this WWW page in class. Your written report will evolve in essentially three drafts, one for each of the Project Milestone deadlines. I will review the first two drafts and grade the final version when you present it in class.

To begin the term project, you need to spend a bit of time reading your course text, visiting the library, and searching the WWW. Your goal is to define an interesting problem in the field of bioinformatics and to design and develop a non-trivial programming-based solution. Here are some of the questions you need to be thinking about to reach your first term project milestones:

1. What is a clearly defined description of your problem?
2. What is your motivation for investigating this particular problem?
3. What devices, tools, techniques, etc. are currently state-of-the-art for addressing this problem?
4. What specific "information" is processed when tackling this problem with current devices, tools, or techniques?
5. What does input to this problem "look like"? How would this input be represented in data files that a program might read and process?
6. Given the algorithms and code discussed in your labs and in class, which pieces might be applicable to your problem, and why?
7. Which of the algorithms and code discussed so far are definitely not suitable for your problem, and why?

• As a guideline, keep track of any references and images for your project and make copies of anything that seems particularly useful to you. The WWW is a great place for information, and I encourage you to show links to useful WWW sites on your project WWW page. However, within the text of your term project report, you must also cite official, published articles. In addition, all images used should have captions and citations giving credit to their source.
• When citing any references for your term project, follow a professional standard, such as the published APA style. Examples of this format include:
  • examples of APA style electronic references
  • examples of APA style hardcopy references
  Graduate students should note that use of such a professional standard will be required in their thesis writing.
• You should start thinking about data format issues early. As part of your first progress report, you will need to post a draft of a sample input file on your project WWW page.
• Think ahead. Your final project will be graded according to the stated criteria in the Part III Milestones. Review those criteria periodically as you work on your project. Your second set of milestones are also available here.

For the first draft of your term project report, please complete the following steps:

1. Create a WWW page which includes text, a link to at least one sample input file, a link to at least one sample output file, and includes at least one relevant image (with caption).
2. Create the page as a link on your course Webpage, under the heading "Term Project."
3. On your new term project page, make sure you have text that answers the questions listed above. Separate "chunks" of your problem discussion with professional section headings, such as:
   • Title
     Pick a title for your project that suggests the scope of the work to be undertaken.
   • Abstract
     This paragraph should provide a brief introduction to the overall topic of your research project and conclude with specific statements regarding the input data you propose to study and the specific analysis you propose to undertake. There are no citations within abstracts.
   • Introduction
     This section includes the bulk of your citations and meaningful images that help the reader to understand the "big picture" of your research project. It explains the devices, tools, and techniques that are currently state-of-the-art for addressing the research area. It summarizes the types of "information" researchers collect, and the analyses they perform on this "information" to obtain meaningful results.
   • Motivation/Rationale and Objectives
     This section explains both the larger motivations for doing research in the area, and any specific motivations you may have. You should use 3rd person when referring to your own motivations. You should then state specific objectives for your research. This forms the rationale for undertaking the research.
   • Materials and Methods
     This section provides details of the exact information to be collected (or simulated), and the exact methods used to collect (or create) the information. It includes a link to at least one sample text file called input.dat (or some other name) that provides clear examples of the information. After the link, you explain to the user exactly what the lines and columns in the input file mean. You can create the input file in Notepad, or save out as a text file from Word. Either way, this text file will become the input data file to your program. For ideas of what these files look like, search Previous Bioinformatics Student Researchers at UWF.
   • Results/Discussion
     You won't have any computed results to discuss for this portion of the assignment. However, you should have an idea of what questions you want to ask of the data and how you want to present the answer. Consequently, for the results section you should include a link to a file called results.out that shows the type of output you expect your program to produce. Prior to the link for this file, you should explain to the reader what question you asked of the data to produce the suggested output. You should also note any code developed in class that may be useful for producing the desired output.
   • Summary and Future Directions
     This section can probably be left blank for now, unless you already have ideas.
   • References
     This section must NOT be blank. You must fill in this section with APA-style references indicating the reading you have done to settle on your term project idea. You should have a minimum of 3-5 references at this point. Each reference should be cited somewhere in the sections above. In addition, all figures derived from other sources should include citations giving credit to the source.
   All of these sections may not be relevant now, but keep them in mind for your final products. You may also use your own set of professional section headings, using headings from published journal articles as a guide, for example. Where appropriate in any of these sections (with the exception of Abstract and References), include any images you find (or create) that help the reader to understand the problem, input data, expected results, etc.
4. You will not turn anything in for this milestone. At the concluding date of this module, I will look for the link to your project on your course Webpage. I will review your WWW site and provide comments to you in class or via email. I will follow all the links and review any images at your WWW site.