BISC209/S12: Lab10: Difference between revisions

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==LAB 10: Data Analysis & Science Writing Workshop==
==LAB 10: Data Analysis & Final Paper & Presentation Workshop I==
We will learn how to use the RDB (ribosomal data base, a public data base provided by Michigan State University) to analyze your sequencing results. Lab to be held in a computer classroom (TBA). Make sure you have signed up for an account on the RDB and received a username and password before you come to lab. Link to the RDB:<BR>
This lab (and the next will) be devoted to instructor designed workshop activities to help prepare you to write your final paper and to give you time to work with your group on a presentation that you will give in Lab 12.
[ https://rdp.cme.msu.edu/index.jsp]


Click on myRDP (orange sidebar on the left of the screen).
==Assignment==
In LAB 11 we will have another Data Analysis/Science Writing & Presentation Workshop to continue preparing you to write your semester long investigation as an original research report and to help you and your teammates (soil sampling groups) prepare an oral group presentation in Lab 12. Some suggestions and things to think about in choosing the topic for your group presentation are found in [[BISC209/S12: Lab12 | Lab12 ]].<br>


Click on "Not a user? Sign up!" and this will take you to a registration screen. Fill out the information required and then check your email. You will be sent a password. Go back to the myRDP site and login with your email and this password. It will then prompt you to change that password to something you can remember.
(If your group's gene sequencing didn't work well, omit the exercise described in this paragraph.)If your soil sample's 16s rRNA gene sequencing yielded enough data, prepare draft table/figure(s) on the information gleaned from your RDP data base analysis of the DNA sequence information on the cultured isolates from your soil sample. This analysis should identify them as much as possible (from the 16s rRNA gene sequence comparisons done using the RDP data base or from an NCBI BLAST. Do your isolated bacteria belong to the genus or family you expected from the morphologic and metabolic information you have saw in your test results? You can use Wellesley's electronic version of ''The Procaryotes'' found at [http://0-www.springerlink.com.luna.wellesley.edu/content/?k=title%3a%28the+prokaryotes%29&sortorder=asc&Content+Type=Reference+Works] and/or ''Bergey's Manual'' found at [http://0-www.springerlink.com.luna.wellesley.edu/content/?k=Bergey%27s+Manuals] to look up more information on the isolates identified by 16s rDNA sequencing. It would be interesting to compare the characteristics described in these reference books to the characteristics you noted in your analyses. Do you have evidence for phylogenetic diversity in your soil sample? (This is a different form of richness in the community.) Create a phylogenetic tree of your soil sample's community members (using a variety of non-members as reference points to try to determine evolutionary relatedness among your soil sample's cultured isolates. Keep in mind that if you find broad phylogenetic diversity it is significant and can be used as evidence for another kind of richness in your microbial soil community. However, if all your cultured isolates belong to closely related clads, it does NOT mean that your soil community is ''not'' phylogenetically diverse. Why? Bring these table/figures, including a phylogenetic tree to Lab 11. We will workshop your figures and talk about our findings and discuss how they might be used in your final paper.<BR>


WRITE THIS DOWN!  Don't lose your password!<BR><BR>
Your research report on your semester project is due in your lab instructor's office by 4pm on your lab day April 24 or April 25. Please make sure there is an electronic copy of your paper uploaded to your folder in your Lab's Drop Box in Sakai by that time. The electronic copy is required ''in addition'' to a required hard copy that must be submitted to your instructor per her instructions. <BR><BR>
More information about the final paper can be found at:
Assignment: [[BISC209/S12: Assignment_209_Lab10 | Assignment: Final Paper]]. A grading rubric is posted to the Rubrics folder in the Resources section of your lab Sakai site. <br>


In Lab 10 you will have a lab practical exam. See the Assignment section below for tips for how to prepare for this assessment.
'''Discard and clean up any remaining tests and cultures on your isolates. Note that there are 5 bonus points awarded for perfect clean-up. Your instructor will explain the "rules" for obtaining these bonus points. '''
 
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In LAB 11 we will not have a formal lab. Instead, We will have another Science Writing & Presentation Workshop to prepare you for writing up your semester long investigation as an original research report (NOT AS A TRADITIONAL LAB REPORT!!) and to help you and your teammates (soil sampling groups) prepare to present a "virtual poster" in Lab 12.  At the end of the Data Analysis lab today, we will brainstorm some potential topics for you to choose for this oral presentation. Some suggestions and things to think about in choosing your topic are found in [[BISC209/S12: Lab12 | Lab12 ]]<br>


==Conference With Your Lab Instructor==
This week or early next week, schedule a time for your team to have a 30 minute conference with your instructor to clear up any questionable aspects of your data analysis and to get any questions answered as you prepare for your presentation. Please come in your poster presentation groups of 3 or 4 students to your lab instructor's office. '''Have a draft of all of the figures your plan to show in your poster and have a written summary of your discussion points and conclusions.''' There will be time for you to ask questions but, primarily, think of this conference as articulating a preview of your poster.<BR><BR>
==Assignment==
Prepare for your group "virtual" poster presentation. In LAB 11, teams of 3-4 students will prepare and present a powerpoint slide in the style of a poster that would be presented informally and talked about at a scientific research conference. You and your partners will not print the poster and stand by it at a conference but, instead, you will show it to the class "virtually" on a projection screen and use it in a 20-30 minute group oral presentation that is worth 25 points, based on the assessment of the class and your instructor of the poster and the presentation's quality. However, you will also be assessing the quality and level of participation of your peers for a potential loss of no more than 10 individual points from the 25 point total.  This individual grade is determined by the consensus of your group members on each member's contribution. The contribution grade includes the data collection, data analysis, and the preparation of the poster and presentation. Grading rubrics will be provided. You will also be provided with links and handouts of helpful information about making a poster. There is a folder in SAKAI: RESOURCES: Virtual Poster Presentation with useful information including examples of effective posters to look at from the following web site: [http://www.ncsu.edu/project/posters/examples | http://www.ncsu.edu/project/posters/examples/]. The Resources section of the wiki contains a tip sheet prepared by the PLTC oral presentation peer-tutors about how to give an effective oral presentation. We will not do these presentations in the lab but in a room TBA. Please make sure that you email your powerpoint to yourself in First Class as an attachment before lab time so we can access it on the computer in the presentation room. Email a copy to your instructor, too.
<BR><BR>
'''Discard and clean up any remaining tests and cultures. Note that there are 5 bonus points awarded for perfect clean-up. Your instructor will explain the "rules" for obtaining these bonus points. '''
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==Links to Labs==
==Links to Labs==
[[BISC209/S12: Lab1 | Lab 1 ]]<br>
[[BISC209/S12: Lab1 | Lab 1 ]]<br>

Latest revision as of 11:37, 15 March 2012

Wellesley College-BISC 209 Microbiology -Spring 2012

LAB 10: Data Analysis & Final Paper & Presentation Workshop I

This lab (and the next will) be devoted to instructor designed workshop activities to help prepare you to write your final paper and to give you time to work with your group on a presentation that you will give in Lab 12.

Assignment

In LAB 11 we will have another Data Analysis/Science Writing & Presentation Workshop to continue preparing you to write your semester long investigation as an original research report and to help you and your teammates (soil sampling groups) prepare an oral group presentation in Lab 12. Some suggestions and things to think about in choosing the topic for your group presentation are found in Lab12 .

(If your group's gene sequencing didn't work well, omit the exercise described in this paragraph.)If your soil sample's 16s rRNA gene sequencing yielded enough data, prepare draft table/figure(s) on the information gleaned from your RDP data base analysis of the DNA sequence information on the cultured isolates from your soil sample. This analysis should identify them as much as possible (from the 16s rRNA gene sequence comparisons done using the RDP data base or from an NCBI BLAST. Do your isolated bacteria belong to the genus or family you expected from the morphologic and metabolic information you have saw in your test results? You can use Wellesley's electronic version of The Procaryotes found at [1] and/or Bergey's Manual found at [2] to look up more information on the isolates identified by 16s rDNA sequencing. It would be interesting to compare the characteristics described in these reference books to the characteristics you noted in your analyses. Do you have evidence for phylogenetic diversity in your soil sample? (This is a different form of richness in the community.) Create a phylogenetic tree of your soil sample's community members (using a variety of non-members as reference points to try to determine evolutionary relatedness among your soil sample's cultured isolates. Keep in mind that if you find broad phylogenetic diversity it is significant and can be used as evidence for another kind of richness in your microbial soil community. However, if all your cultured isolates belong to closely related clads, it does NOT mean that your soil community is not phylogenetically diverse. Why? Bring these table/figures, including a phylogenetic tree to Lab 11. We will workshop your figures and talk about our findings and discuss how they might be used in your final paper.

Your research report on your semester project is due in your lab instructor's office by 4pm on your lab day April 24 or April 25. Please make sure there is an electronic copy of your paper uploaded to your folder in your Lab's Drop Box in Sakai by that time. The electronic copy is required in addition to a required hard copy that must be submitted to your instructor per her instructions.

More information about the final paper can be found at: Assignment: Assignment: Final Paper. A grading rubric is posted to the Rubrics folder in the Resources section of your lab Sakai site.

Discard and clean up any remaining tests and cultures on your isolates. Note that there are 5 bonus points awarded for perfect clean-up. Your instructor will explain the "rules" for obtaining these bonus points.

Links to Labs

Lab 1
Lab 2
Lab 3
Lab 4
Lab 5
Lab 6
Lab 7
Lab 8
Lab 9
Lab 10
Lab11
Lab 12

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