Biol 346 Bioinformatics | Final project proposal

Bioinformatics .title

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Final "Not-the -Final" Project

Due 12/16/03 at 5 pm. 50 points.

Introduction:

Now is the time to start asking some relevant questions and generate an independent project relating bioinformatics to an area of your interest. By doing this, you can learn more about molecular biology, genetics, and evolution while at the same time learning something specific aboutsomething else. You may wish to focus on structural characteristics of a protein and use modeling tools; or to focus on sequence conservation of a domain or motif and use alignment and/or phylogenetic tools; or you may wish to focus on variable sequences of some group of proteins. Before deciding, you may want to explore your texts and browse on-line, such as at the Taxonomy site or through other useful web sites. You can also go to PubMed at NCBI, then search the journal literature for ideas and background.

Part 1: Generating a project idea

The normal process of coming up with an idea and executing a project goes something like the following: "I have no idea at all. I still don't know enough about any of this stuff yet." ... "There is so much to sort through- how am I going to choose?" ..."Well I had the perfect idea, but it would take months to do right." ... "I just spent hours downloading & learning how to use the software I found I needed. Then it crashed" ... "I'm dead. My hypothesis is bogus or maybe there just aren't enough sequences available yet to prove my point." ... "I'm saved! This new site is perfect- I just wish I knew about it at the beginning. Then I could have done this assignment in just a couple of hours."

Then there are the procrastinators: "It's due when? Tomorrow? Oh, gee... Hey, do you want to go out and help me brainstorm a good excuse?"

1. First, write down a few key ideas during a bit of browsing and brainstorming.

2. Next, pre-search these ideas to see if there is some data available which would be useful. The search strategies introduced in Unit 1 can serve as a basis for getting started. For a given target, you may find more nucleotide sequences than protein sequences, so you may want to work with the nucleotides rather than the proteins. On the other hand, you may be more interested in comparing structures, therefore you'll want to restrict your search to proteins for which there is structural data. If you are stuck, talk to me or to another student.

3. You may very well need to locate and use some applications and analysis tools, about which you are unfamiliar. In fact, you may not even know what to call them in order to search for them. Browse through some of the key sites listed below to learn about the variety of applications and tools available. These may help you sharpen your focus on what you want to do and how to do it.

4. Decide which of your ideas shows the most promise and write a brief draft proposal for yourself. Read about the goal below, to help scale the size of project you are proposing.

Part 2: Defining your goal

You have a choice of one of the following methods of presenting your proposal. In most cases, a project could last about one semester. In some cases, it may last longer.

1. For a project proposal, a finished hardcopy is to be limited to three pages of text and four pages of appended graphs, tables, images, etc. Although somewhat flexible, the basic format should include:

Title

Author

Abstract- brief

Hypothesis or purpose of project [besides earning points]

Introduction/Background- brief

Methods- include databases; websites & URLs; search and analysis tools, along with settings

Analysis- include reference to how you will evaluate your data and validity of your results

Timeline for completing project in one semester, or longer if ambitious

Discussion- make clear the significance of this proposal

References- literature, web sites- including support sites you used or will need for the project

2. Post a web pageproposal, which can then be linked to the class web site to share with the rest of the class. You should include clear explanations and any necessary images, tables, etc. You may include links to other pages or sites as appropriate. Logistics will be discussed if you are interested in this option.

Points = 50. Due 12/16. Grading will be on content, organization, spelling, & grammar.

Part 3: Reaching the goal

1. Once you receive feedback on your proposal, begin mapping and identifying the components of the project. Tag possible applications to components and/or questions in your map. Identify unknowns, difficulties, or sticking points.

2. Prepare a problems & questions list before 12/9 & 12/11 lab sessions. Bring your map and problems/questions list to lab. During the lab sessions, we will try to answer & discuss as many of these as possible.

3. Now that you are organized, you only have to complete your project. [For most, getting to this point is the hardest part. The rest should be come together nicely.]

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Up dated 12/4/03 by thatcher@sonoma.edu

	*Bioinformatics* .title
	Home \| Site Index \| Syllabus \| Schedule \| Study aids \| Computing \| Links \| Course Materials Home
	Final "Not-the -Final" Project Due 12/16/03 at 5 pm. 50 points. Introduction: Now is the time to start asking some relevant questions and generate an independent project relating bioinformatics to an area of your interest. By doing this, you can learn more about molecular biology, genetics, and evolution while at the same time learning something specific aboutsomething else. You may wish to focus on structural characteristics of a protein and use modeling tools; or to focus on sequence conservation of a domain or motif and use alignment and/or phylogenetic tools; or you may wish to focus on variable sequences of some group of proteins. Before deciding, you may want to explore your texts and browse on-line, such as at the Taxonomy site or through other useful web sites. You can also go to PubMed at NCBI, then search the journal literature for ideas and background. Part 1: Generating a project idea The normal process of coming up with an idea and executing a project goes something like the following: "I have no idea at all. I still don't know enough about any of this stuff yet." ... "There is so much to sort through- how am I going to choose?" ..."Well I had the perfect idea, but it would take months to do right." ... "I just spent hours downloading & learning how to use the software I found I needed. Then it crashed" ... "I'm dead. My hypothesis is bogus or maybe there just aren't enough sequences available yet to prove my point." ... "I'm saved! This new site is perfect- I just wish I knew about it at the beginning. Then I could have done this assignment in just a couple of hours." Then there are the procrastinators: "It's due when? Tomorrow? Oh, gee... Hey, do you want to go out and help me brainstorm a good excuse?" 1. First, write down a few key ideas during a bit of browsing and brainstorming. 2. Next, pre-search these ideas to see if there is some data available which would be useful. The search strategies introduced in Unit 1 can serve as a basis for getting started. For a given target, you may find more nucleotide sequences than protein sequences, so you may want to work with the nucleotides rather than the proteins. On the other hand, you may be more interested in comparing structures, therefore you'll want to restrict your search to proteins for which there is structural data. If you are stuck, talk to me or to another student. 3. You may very well need to locate and use some applications and analysis tools, about which you are unfamiliar. In fact, you may not even know what to call them in order to search for them. Browse through some of the key sites listed below to learn about the variety of applications and tools available. These may help you sharpen your focus on what you want to do and how to do it. 4. Decide which of your ideas shows the most promise and write a brief draft proposal for yourself. Read about the goal below, to help scale the size of project you are proposing. Part 2: Defining your goal You have a choice of one of the following methods of presenting your proposal. In most cases, a project could last about one semester. In some cases, it may last longer. 1. For a project proposal, a finished hardcopy is to be limited to three pages of text and four pages of appended graphs, tables, images, etc. Although somewhat flexible, the basic format should include: Title Author Abstract- brief Hypothesis or purpose of project [besides earning points] Introduction/Background- brief Methods- include databases; websites & URLs; search and analysis tools, along with settings Analysis- include reference to how you will evaluate your data and validity of your results Timeline for completing project in one semester, or longer if ambitious Discussion- make clear the significance of this proposal References- literature, web sites- including support sites you used or will need for the project 2. Post a web pageproposal, which can then be linked to the class web site to share with the rest of the class. You should include clear explanations and any necessary images, tables, etc. You may include links to other pages or sites as appropriate. Logistics will be discussed if you are interested in this option. Points = 50. Due 12/16. Grading will be on content, organization, spelling, & grammar. Part 3: Reaching the goal 1. Once you receive feedback on your proposal, begin mapping and identifying the components of the project. Tag possible applications to components and/or questions in your map. Identify unknowns, difficulties, or sticking points. 2. Prepare a problems & questions list before 12/9 & 12/11 lab sessions. Bring your map and problems/questions list to lab. During the lab sessions, we will try to answer & discuss as many of these as possible. 3. Now that you are organized, you only have to complete your project. [For most, getting to this point is the hardest part. The rest should be come together nicely.]

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