March 20

DNA Day 16

20 March 2019 ✷ Final Poster Making + Research Projects

Rationale:  The combined poster for URSA Scholar’s day was edited and groups were designated to start independent research projects.

Procedure

  • The group poster was edited because a new gene was added (96b)
    • The discussion was edited to reflect this
  • Groups were assigned and potential topics were discussed
    • comparing the %CG between functional genes and nkf genes is a potential idea discussed within the group

Results

 

updated discussion

current poster (m&m is being edited to have better phrasing of each step)

Conclusion

The results section is incomplete, but should be fine by Friday. The materials and methods needs some refining so it will be inserted before Friday as well.

Future plans

This poster will be updated and edited until it reflects what is to be presented at Scholar’s Day. Research for independent projects will begin.

March 20

DNA Day 15

18 March 2019 ✷ Final Poster Making

Rationale:  The combined poster for URSA Scholar’s day was created and edited to make a functional poster that is informative and easy to look at.

Procedure

  • The 4 posters were combined into one and students were broken into groups for delegated tasks.
    • The discussion section was turned into a similar image as the materials and methods section
    • symbols were added to the headers of each section
    • The materials and methods section was expanded and edited several times to include more information on the in silico portion of the lab

Results

materials and methods new edit

discussion

image of our poster

Conclusion

Some groups still need to add in their portions, but other groups had a lot more work to do than others in order to complete this. The final poster will be created in the following class periods.

Future plans

This poster will be updated and edited until it reflects what is to be presented at Scholar’s Day.

March 20

March 20 2019 Posters and Final Projects

Purpose: The purpose of this lab is to make final edits to the poster, as well as begin learning about the final project and ways to conduct the research.

Tools/Procedures:

Tools:

  • Poster
  • Canvas Resources

Procedures:

  1. The parts of the poster that need to be fixed were outlined.
  2. Groups learned about the final project and the different tools that could be used for different research topics.
  3. The QTM was completed.
  4. Groups worked on fixing the elements of the poster.
  5. Work was saved.

Results:
The poster finalizations were analyzed. Work was begun on the final project.

Conclusions:
The poster was not finished, but a plan was made for its completion. Ideas were generated for the group final project, but a final question was not created.

Future Work:
Future work will include finalizing all figures for the poster and adding them, as well as finalizing the poster. Also, a question will need to be made for the final project, and then work on the final project will be started.

March 20

Final Poster and Individual Projects 3/20/19

Final Poster and Individual Projects 3/20/19

Rationale

The rationale behind these procedures is to ensure that poster creations for Scholar’s day follow the correct format and that basic poster requirements are understood. The procedures were also done to finish the poster for Scholar’s Day. In addition, the rubric and groups for the individual projects were introduced so that work can begin on the projects.

Tools/Procedure

  1. Final edits were made to the poster in order to have it ready by Friday
    • 2 edits were made to the discussion section of the poster to reflect changes in the genome annotations
  2. Groups for individual projects were introduced and rubric was discussed
  3. Groups brainstormed about what individual questions to pursue and consulted with the coaches

Results

The image above shows the 2 small changes made to the discussion section to reflect new annotations. There are no other results to report as group brainstorming is currently a work in progress.

Conclusion

There is not much that can be said as a conclusion as this was a poster making and brainstorming day. I can say that Rachel and I may pursue research into comparing NapoleonB to the Arthobacter host that it came from to see if it acquired any bacterial DNA.

Future Plans

In the future, we will continue working as a class to create a poster for Scholar’s day and Rachel and I will begin research for our individual projects.

March 20

3.18.19 Finalizing Poster

3.18.19 Finalizing Poster

Rationale: Since the poster had a solid beginning and an understanding of what needed to be done, it was necessary to all play roles in wrapping up the loose ends of the poster. Therefore, I worked on ensuring the formatting and shapes were all consistent and optimal for displaying the ideas of our project.

Tools and Procedure:

Google Slides was used to collaborate on the final version of the poster to ensure that everyone could access the project in real-time.

Results:

The shapes were reconfigured twice because there was a small error in the scaling that required all of the work to be redone. Also, the shape for the in silico results section was changed to a more optimal L-shape to ensure that all of the figures and data could be incorporated.

Conclusions:

Editing the formatting of posters is a very tedious, yet satisfying job that requires a lot of attention to detail. While formatting rarely makes a poster more influential or memorable (the results or procedure tend to do that), it can detract from the information being presented which can damage the overall presentation. Therefore, it was important to make sure everything was done correctly to give the poster the best possible chance to succeed.

Next Steps:

After the formatting was fixed, there are still some final tweaks that need to be added on the rest of the poster. Once these tweaks are added and inputted, the poster will be complete and ready for a final check before printing and presenting.

March 20

Begin Individual Projects

Purpose: Finish Final Poster and begin narrowing down a testable research question for us to look at next month

Procedure:

  • Got into assigned groups
  • Read through module and different genomic tools
  • Decided to research Repeats in NapoleonB and compare to other phages in the AM cluster
  • Completed QTM and reviewed final poster

Future Research: Search for repeats using instructions from the module. Identify the most common/interesting repeat, and investigate further.

March 20

Lab Day 16-17: Final Poster

Rationale

Create a final poster to present at URSA. Correct any format issues and add any missing information into the poster.

Procedure

  1. Got assigned into groups based on sections of the poster
  2. Fixed any mistakes in regards to which section
  3. Updated poster with final edits

Conclusion/Next Steps

The discussion was fixed with other group member. We had to change the format and had small issues along the way in terms of how to insert it into the poster. We had another classmate to help take the discussion and transfer it to another program. Formating is fixed. In the future, we will continue to work and try to find any other small mistakes and perfect it as much as possible.

March 20

Continuing Graph Making 3/20/19

Rationale: I currently only have half the data I need to make the graph so I’m going to be searching for the database call and making the graph today.

Tools: Excel, DNAMaster, phagesDB, Phamerator, Javascript, Meteor, MySQL, CLion, Purdue Robotics Operating System(PROS)

Procedure:

1. Sifted through phamerator code to locate call to Meteor script. Followed meteor script call to 236th line of code in Phamerator. Copied the 236th line of code into PROS to do further analysis.

2. Broke single line of code into a more readable format using PROS which resulted in 467 pages of code.

3. Read through the code to find database call which led me to the Hatfull database which is written in MySQL.

4. Used the Hatfull database to collect data on which AM phages are in each pham that the genes for NapoleonB were called to.

5. Graphed results in Excel.

Results:

Conclusions and Future Work: The Hatfull database is extremely useful and could be used for a lot more bioinformatic endeavors. The coming weeks we will be conducting our individual research in a group under the guidance of Aadil.

March 20

Class Poster Creation 3/18/19

Class Poster Creation 3/18/19

Rationale

The rationale behind these procedures is to ensure that poster creations for Scholar’s day follow the correct format and that basic poster requirements are understood. The procedures were also done to finish the poster for Scholar’s Day.

Tools/Procedure

  1. The previously chosen design was critiqued and groups were assigned to fix each problem
  2. The discussion section was rewritten and graphics were created for it
  3. The layout of the poster was modified until it was deemed acceptable
  4. Other small groups collaborated to address other aspects of the poster

Results

The results of both the total class collaboration and my small group collaboration on the discussion are shown in the images above. As can be seen, the class poster is almost complete with the exception of the In Silico results section that was not completed enough to be added to the final poster by the end of the lab. The discussion section is broken up into the wet lab and In Silico sections that wrap up the presentation.

Conclusion

There is not much that can be said as a conclusion as this was a poster making day; however, based on the class poster that is underway I fee that I and the class demonstrate an understanding of poster making that will lead to an effective Scholar’s Day poster.

Future Plans

In the future, we will continue working as a class to create a poster for Scholar’s day.

March 20

Final Poster

03/18/19

Rationale:

To make a final draft of the poster board, which will later be combined with other poster boards in the group for a final poster for scholars day

Procedure:

  1. The changes to be made to the first draft of the posters were discussed
  2. responsibilities were assigned to groups for making certain edits
  3. edits were to be made according to the prescription of the TA
  4. the group made graphics for the poster and made edits to methods and materials.

Results:

current version of the edited poster is above.

Conclusion

the progress so far is great but some more content needs to be added to this poster. the poster will be easy to present when completed according to plan.

Future steps

More graphics will be added to the poster. more data will also be presented about the Napoleon B and its relation to other phages and clusters.