March 22

3.18.19 Editing Poster Layout

Rationale:

To fix any layout issues that exist on the poster.

Procedures:

  1. I opened the google slide and proceeded to fix any alignment, layout, and sizing errors on the poster.
  2. I saved the poster and checked for any other errors.

Conclusions/Next-Steps:

The posters orientation and layout errors are fixed, the next step will be to conduct a final check of the poster in order for it to be eventually printed and presented at Scholars Week. We will also begin our independent research projects.

Category: Nathan Newton | LEAVE A COMMENT
March 21

Final Poster Touches and Starting Individual Project (3/20/19)

Rationale:

Finish figures for the poster so it can be sent off to print. Start researching a possible research question relating to the in-silico aspects of the lab that can be investigate for individual project.

Procedure:

  1. Changed colors on Phamerator.
  2. Modified supportive function graph.
  3. Re-created predicted function pie.
  4. Started researching topics.

Results:

The image below shows the Phamerator.

The image below shows the modified supportive function graph.

The image below shows the predicted function pie.

Conclusion:

It is hard to create a visual when people cannot communicate what they want.

Future Work:

Go to open lab to confirm that the figures created are acceptable. On Monday, decide and brainstorm with group what topics should be considered for the projects.

Category: Kathryn Adkins | LEAVE A COMMENT
March 21

Final posters and start of independent research 3/20

Rationale: In groups, finish the final posters In-Silico results and become familiar with the new databases that would help with the independent research project.

Procedure: Groups from 3/18 worked to finish the In-Silico results, and the results were finished. In groups, each member looked at each module to help form some start to a testable research project. Group explored the bacteriophages genomics databases, and the databases helped narrow potential research question.

Results: Two topics were taken into consideration for a testable question that the group could further expand on.

Conclusions: Further analyzations need to be made in order to form two testable research questions for Monday’s lab. Other outside sources need to be brought in to help target the question. Potential independent research topic could compare the start site preferences of NapoleonB with other phages in AM cluster and the preferred ribosome binding sites could help bring other questions as well.

Future work: Poster will be updated to ensure the poster is ready for URSA. Form two testable questions that would help kick start independent research.

Category: Michael Lum | LEAVE A COMMENT
March 21

In-Silico Results Figure Making (3/18/19)

Rationale:

Work on the research poster for scholar’s week.

Procedure:

  1. Divided class into teamsto work on different sections.
  2. Brainstormed possible figures to be used for the “In-Silico Results” section.
  3. Collected and organization data from PhageNotes on which databases supported the predicted functions.
  4. Collected cluster data and formed graph.

Results:

The graph below shows brainstormed figures to show the Phamerator number and cluster that were created using not PhagesDB and Phamerator data.

 

The table below shows the supported predicted function data collected where 1 represents that the predicted function was supporting and 0 represents that the predicted function was not supported.

Gene # NCBI Hhpred PhagesDB CDD
3 1 1 1 0
4 1 1 1 1
7 1 1 1 1
9 1 0 1 1
10 0 1 0 0
11 1 0 0 0
14 1 1 1 0
16 1 1 1 1
17 1 0 1 0
18 1 0 1 1
19 1 0 1 1
20 1 1 1 1
21 1 1 1 1
22 1 1 1 1
25 1 1 1 1
39 1 1 1 1
45 1 1 1 0
62 1 1 1 1
77 1 1 1 1
81 1 1 1 0
85 1 1 1 0
87 1 1 1 1
93 0 1 0 0
96 1 0 1 0
98 1 0 1 1

Conclusion:

Since PhagesDB and Phamerator have not received the annotations for NapoleonB, the data used to create the figures to display phamerator numbers and cluster graph was not accurate.

Future Work:

Ram has offered to create his own Phamerator program to have access to the most accurate data for NapoleonB. He will focus on the cluster graph when the rest of the group will continue on the other figures such as the supportive function graph and the predicted function pie.

Category: Kathryn Adkins | LEAVE A COMMENT
March 21

03/20/19 Independent Projects

Rationale: 

The purpose of today’s lab was to address any last changes needed on the class poster as well as begin the process of independent projects.

Tools:

  • Laptop
  • Google Slides
  • ExPASy

Procedure:

  • Last minute concerns were addressed regarding the poster.
  • Once this was complete, independent projects were introduced as well as groups and mentors.
  • Independent projects topics were then researches to decide if anything drew up any interest in the group.

Results:

  • The group for the independent project is Me, Kathryn, and Emily, with our coach being Lathan.
  • Several topics were looked over, but none have been decided yet to research.

Conclusions:

There are several things regarding NapoleonB, but the group is still trying to find something that is unique regarding NapoleonB to research. It is possible there is something regarding NapoleonB’s relationship to other phages in its cluster as it does contain an orfam, but no clear decision has been made yet.

Next Steps:

The next steps for this are to continue with the research of these different topics so the group can begin its independent research project.

Category: Gabriel Andino | LEAVE A COMMENT
March 21

03/18/19 Class Poster Edits

Rationale: 

The purpose of today’s lab was to split up the responsibilities of poster editing among the class to get it ready for Scholar’s Week.

Tools:

  • Laptop
  • Google Slides
  • AdobeSpark

Procedure:

  • The class looked over the edits needed on the poster that Lathan gave us.
  • Then, groups were divided tasks, our group being in charge of graphics on the poster and methods revising.
  • Methods and materials were extended to include more information regarding the in silico portion of the lab, while also creating new graphics for the added sections through AdobeSpark.
  • Figures for each heading were made as well to help make it a reoccurring theme throughout the poster.
  • The discussion was also edited and formatted in AdobeSpark, with corresponding figures as well.

Results:

  • The methods and materials were updates and corrected.
  • The final poster result with figures in each heading

Conclusions:

Though missing figures for the in silico results, the majority of the poster is complete. Centering errors, wording, and colors were altered and changed to best fit the poster, and the poster now has a unique theme and aspect with all the self-created images scattered throughout.

Next Steps:

The next steps for this are to finish the finishing touches on the class poster, begin creating a presentation to showcase at Scholar’s Week, and begin thinking about independent projects.

Category: Gabriel Andino | LEAVE A COMMENT
March 21

3.20.19 Reflecting on Poster and Introducing Individual Products

3.20.19 Reflecting on Poster and Introducing Individual Products

Rationale: After reaching a consensus on the main points of the final poster and reaching a stage where only minor personal changes were necessary, it was found to be beneficial to reflect on the process to help learning for future posters. Also, since an independent research project is required, the project was introduced and brainstorming began.

Tools/Procedure: Google slides for presentation and Microsoft Word for QTM. As an independent project group, we finished our QTMs independently, then began discussions about the topic for our independent project and determined what should be researched to develop a proper question.

Results: The QTM was successfully completed and a topic to research was chosen.

Conclusion: Since a topic to research has been determined, it will be possible to spend more time honing a broader topic to get a developed and polished research question. Therefore, this strategy will help to ensure the results of the experiment end up being useful and interesting.

Next Steps: The next steps of the project will be to investigate the literature about this topic and later finalize the question before lab on Monday.

Category: Henry Burns | LEAVE A COMMENT
March 21

Final Posters and Individual Projects 3/20/19

Rationale

Final touches were worked on in the poster today and independent research projects were introduced to the class.

Procedure

  • Remaining edits to the poster were discussed and made
  • Groups were assigned to work under a “Coach”
  • Tools and topics were explored for use in individual research projects

Results

The group of Lily, Lucy and I found the difference of %GC between no known function genes and genes with a function to be a potential research topic.

Conclusion/Next Steps

Next, we will dive more into the topic of %GC and the tools used to research it. It will be determined if %GC is a good research topic for the group.

Category: Emily Gaw | LEAVE A COMMENT
March 21

Class Poster Revisions 3/18/19

Rationale

Today we will discuss what needs to be worked on in our poster and fix any issues before printing for Scholars Day.

Procedure

  • Discuss what changes need to be made to the poster as a class.
  • Different parts of the poster that needed to be revised were assigned to different groups in class.
  • Each section was edited to an acceptable standard.

Results

The updated poster is shown below.

Conclusion/Next Steps

Next, the remaining section of the poster will be added and the poster will be looked over for final revisions. After approval by the others, the poster will be presented for Scholars Day.

 

Category: Emily Gaw | LEAVE A COMMENT
March 21

Individual Research Discussion

03/20/19

Rationale:

To learn how to conduct research , from forming a question to forming and performing a your own experiment.

Procedure:

  1. The edits to be made for the final poster were discussed and are due on Friday
  2. Assigned groups were then allowed to explore the various tools and topics to explore for questions for individual research.
  3. All the tools available were explored.
  4. all proposed topics to discover were also discussed.
  5. Two topics that seemed interesting were stoperators and start site preferences.

Results:

these were the tools that were proposed. we were encouraged to find and use more.

Conclusion:

Individual research is going to be very difficult but also very interesting. it will require a great deal of productivity to finish it on time.

Future steps:

come up with a research question and begin planning the experiment.

Category: Uncategorized | LEAVE A COMMENT