In retrospect, I did not specify the assignment well enough. I take the blame for that!

So I will try to provide more specifics now. Some of you will want to throw out whole sections and rewrite them. Some teams did a fine job on some sections and need not redo those.

The final version is still due next Wednesday Nov 5th. I will provide feedback on new drafts if the team desires.

1. Feasibility Report - General

In a Feasibility Report, you propose WHAT you plan to do and discuss WHY it is feasible.

Feasible means ``what is capable of being done successfully.''

Also, you discuss why this is the best plan for the CONSTRAINTS on the team. Therefore, the Report need to discuss these constraints.

2. The Pieces of the Report

a). COVER SHEET - all did fine. :^)

b). EXECUTIVE SUMMARY - this is a separate page. It should be written after the rest of the Report is done. It should be written with the assumption that your boss is too busy to read anything but the cover page and Executive Summary. Therefore, you state carefully why you wrote the Report, what you propose to do and and any action required by her.

* Starred lines are comments on your recent Drafts of Report.

* Some teams spent the whole Executive Summary discussing why such
* and such a platform and computer language would be used and NOT
* mention the purpose of the Report and what you propose to do.

c. INTRODUCTION - The introduction should state the problem that is being solved. You define the scope of the problem that your proposal attempts to solve. Why is this problem important and its solution important?

* In your Reports this was weak or non existent. 

* Your Introduction should say something like this.

"We were asked to explore the computational aspects of gene sequencing as a potential software product." - the problem. Explain why this is important to solve.

``We propose to design a software product that .... [ state the refined problem].''

I have suggested three areas as potential refinements:

I would say a subset of any ONE of the above is more that adequate for a team project.

* In your Reports, the teams have not clearly stated what the problem
* is they proposed to do.  Some have indicated all three of the above
* (probably not understanding what is involved, e. g. in shot-gunning).
* Way too much!! 

* Others have hinted at some of #2 and some of #3 but very vague at
* what.  This is understandable given you limited knowledge.  But you
* still need to decide.

For example, you could propose a simple version of #2 (to have a GUI interface) that does transliteration and translation to form an amino acid sequence. This amino acid sequence is searched in a database for similar match (#3) where the major effort of the project is exploring different matching algorithms.

[I moved the phrase `` the computing environment in which the system is to be implemented and constraints that affect the project.'' to the the ALTERNATIVES section. Confusing where it was.]

d. BACKGROUND

This should start with a paragraph or two about DNA and explain terms like transcription, translation.

* One team had a very good start here.  Most had material which did
not belong in a Background.

Also, here is where any other gene sequencing software you found should be discussed.

e. ALTERNATIVES

Given the refined problem of the INTRODUCTION, discuss alternative solutions including the one that you are proposing. Provide convincing reasons for selecting the one alternative over the other.

* Most teams had some of this but in some it was scattered in other
* sections.

f. SYSTEM DESCRIPTION

For this assignment it is not clear what you put here without repeating information from previous section. Perhaps, delete it???

g. COST-BENEFIT ANALYSIS

What are cost for the project? Don't need new equipment or software. Is it worth to perform a software patent search ($200-$500/search)? What should be the product selling cost??

* What are cost for the project?  In the virtual world of Bison
* Scientific. In the Reports, some teams 
* shifted back and forth between the real world of a student and the
* virtual world of Bison Scientific.  Report should be consistent.  One
* report was clever in bridging this gap.  They said something like ``We
* have other projects which consume our time.''

* The teams that seriously attempted this section had good ideas.  

You can assume that for your analysis that a person hour cost the company $40. This is NOT her salary but how much it cost the company to have the person work an hour. Includes her salary, her benefits, office space, maintaining a library, equipment, electricity, etc. Typical to be a factor of individual salary, say 2.5 times.

h. EVALUATION OF TECHNICAL RISK

Or Technical feasibility, i . e., what is capable of being done successfully. You should say things like algorithms are in the literature, data is available on the web, etc. What are the risks? However, our team is inexperienced. Schedule is tight.

i. LEGAL RAMIFICATIONS

You say things like: We should protect our investment by copyright, carefully documented lab notebooks, etc. Should we worry about patent infringements? Should we try to license other company software or design ourselves?

j. A WRAPUP SECTION [new]

A quick restatement of your problem and proposed solution.

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Note this is a LIVING DOCUMENT. What changes would you suggest??? I might think of some more to add.

Also, a team asked why some gene sequencing software uses a ring to show the DNA molecular. It turns out that bacteria (a prokaryotic cell, i. e., lower life) has a DNA molecular which is circular, i. e., the two ends bound together. An example is E. coli, a bacteria that exist in all human lower colons at a high concentration like 10^7/ml. Since bacteria are easy to grow and to control many biologist study them. Also, they are important for medicine. Higher plants and animals (eukaryotic cells) usually are portrayed as linear DNA. See page 264 in current Biol 121 text "Biology: Life on Earth" by Teresa Audesirk and Gerald Audesirk for a picture of bacterial DNA diagram that is circular.

A team may decide to limit their programs to only a subset of DNA, e. g., only Human or only bacteria. This narrows the graphical representations required for program.