Difference between revisions of "Sulfiknights"

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==Week 12/13 Milestones==
 
==Week 12/13 Milestones==
  
−
=== Milestone 1: Annotated Bibliography ===
+
===Project Manager===
  
−
* The Coder/Designer will work with their teams to develop an annotated bibliography of papers relating to their team's assigned paper.
+
Create a schedule by Tuesday, November 26 that has goals for each member of the Sulfiknights team. Though this may not be completely followed day-by-day it is still helpful to have a outline of checkpoints that should be met for completing this assignment.  
  
−
=== Milestone 2: Journal Club Presentation ===
+
Check in with the members of the team to assist in making sure the assignment is complete.
  
−
* The Coder/Designer will work with their teams to create and deliver a Journal Club presentation about to their team's assigned paper.
+
[[User:Ntesfaio|Ntesfaio]] ([[User talk:Ntesfaio|talk]]) 20:44, 21 November 2019 (PST)
  
−
=== Milestone 3: Working Environment Setup ===
+
===Quality Assurance===
  
−
Coder/Designer work will require the following software/accounts. The Seaver 120 lab computers are already set up for this; this list is provided for Coders/Designers who need to work on a different computer or outside of the lab.
+
As on Thursday, November 21st the Quality Assurance guilds were an intermediate for our designer (DeLisa) and our Data Analysts (Marcus and Ivy).  
−
* Microsoft Access
 
−
* Box account (provided by LMU)
 
−
** Databases created by the teams will be kept in a [https://lmu.box.com/s/gutpb5qm0a6b2pvjn1j6moqb6y47e903 "BIOL367_Fall2019 > Final Project Database" Box folder].
 
−
** Coder/Designer guild members have rights as editor to this folder; all others in the class can only view/download.
 
−
** This folder will serve as as the version control mechanism for the Coder/Designer guild.
 
  
−
=== Milestone 4: Design a Database to Store Time-course Microarray Data from four sources ===
+
Our goal before Tuesday, November 26 is to assist the Data Analysts in running an ANOVA and running stem. As for Quality Assurance we have completed Milestone 4 and are moving onto Milestone 5 as of Thursday, November 21st.
  
−
* Designer/Coders will work with the QA's to create a MS Access Database to store the yeast time-course microarray data for the dataset being analyzed by the Data Analysts.
+
[[User:Ntesfaio|Ntesfaio]] ([[User talk:Ntesfaio|talk]]) 18:40, 23 November 2019 (PST)
−
* The starting point will be the database already used for the [[Week 10]] assignment, which can be found [https://lmu.box.com/s/kn8l6r639af683ioojqoce5w1g3z7kd2 here] on Box.
 
−
** This database is already populated with tables for the Dahlquist Lab microarray data, degradation rates from Neymotin et al. (2014), and initial guesses for production rates.
 
−
*** You may need to change the table names of these existing tables so that they make sense with the overall database design.
 
−
** You will need to add one or more expression tables for the expression data from your team's article.
 
−
*** Work with your team's QA and Data Analysts to determine appropriate column headings for the expression table.
 
−
** You will also need to create one or more tables with metadata about the other tables because now the database will contain data from multiple sources, not just one.
 
−
*** A major part of the design work will be to figure out what information needs to be in the metadata table so that queries can be easily and uniquely performed on the data.
 
−
*** Think about what information would someone need to know to be able to understand how the dataset works.  Consult with the QA and Data Analysts to figure out the sample-data relationships and how that should be encoded.
 
  
−
=== Milestone 5: Build an individual database for your team ===
+
===Data Analysis===
  
−
* Once the design work has been completed, you need to actually import the data into the database.
 
−
* Initially, each team will have their own database so that the QA and Data analysts can validate and use the database.
 
  
−
=== Milestone 6: Validation and Quality Assurance on Database ===
+
===Coder/Designer===
  
−
* The QA will perform quality assurance to make sure that the database is correct and accurate.
 
−
** In particular, the QA needs to make sure that all of the rows of data were imported into the database for the expression table(s).
 
−
** The QA will make sure that both the ID (SGD systematic name) and Standard Names are included in each expression table and are correct.
 
−
* QA's will communicate to the Coder/Designers any changes needed to the database.
 
  
−
=== Milestone 7: Merge completed databases into a single database for the class ===
+
==Team Journal Assignments==
 +
===Week 12/13===
 +
====Naomi Tesfaiohannes====
  
−
* As a guild, the Coder/Designers will merge their separate databases into a final product.
+
Each team member should reflect on the team's progress:
−
* With the QA's finalize the [https://www.quackit.com/microsoft_access/microsoft_access_2016/howto/how_to_create_a_database_diagram_in_access_2016.cfm database schema diagram]
+
 
 +
What worked?
 +
 
 +
Working together in class and taking advantage of asking questions while going through the assignment
 +
 
 +
What didn't work?
 +
 
 +
Not working on a shared document or excel workbook because progress could be made on one and not seen by the other partner. Also the metasheet was difficult to put together because of the inconsistent datapoints between the groups.
 +
 
 +
What will I do next to fix what didn't work?
 +
 
 +
Continue communicating with my team on how we want to progress through with the assignment
 +
 
 +
[[User:Ntesfaio|Ntesfaio]] ([[User talk:Ntesfaio|talk]]) 21:20, 25 November 2019 (PST)
 +
 
 +
====Ivy Macaraeg====
 +
#What worked?
 +
#*We figured out what we needed to be working on, and that helped get us going even more than before.
 +
#What didn't work?
 +
#*We had some trouble organizing the data in a way that would be clear but compatible with future programs.
 +
#What will I do next to fix what didn't work?
 +
#*I think sticking to the directions and making sure that we are thorough will help us.
 +
====John Nimmers-Minor====
 +
Each team member should reflect on the team's progress:
  
−
==Data/Files==
+
What worked?
−
'''[[Sulfiknights Deliverables]]'''
+
 
 +
A. Splitting up the work and knowing exactly what each role was in charge of helped tremendously this week.
 +
 
 +
What didn't work?
 +
 
 +
A. Having two people work on the exact same task didn't help because one of those two individuals could have potentially been working on a separate piece of the project.
 +
 
 +
What will I do next to fix what didn't work?
 +
 
 +
A. Communication throughout the project group will make sure that two people are not doing the same thing at the same time unnecessarily. This will allow us to complete more tasks in a shorter amount of time.
 +
 
 +
====DeLisa Madere====
 +
#What worked?
 +
#*It really helped that our team all were focused on the individual tasks at hand and we were able to finish the tasks efficiently.
 +
#What didn't work?
 +
#*For me, it was a little difficult to understand what was happening with my other group members' tasks since I had my own individual task.
 +
#What will I do next to fix what didn't work?
 +
#*To fix this, I will try harder to understand the purpose behind each step in order to completely give all my input if needed, or help is needed.
 +
#[[User:Dmadere|Dmadere]] ([[User talk:Dmadere|talk]]) 22:38, 25 November 2019 (PST)
  
−
[[Media:Biolpresentation_IM.pptx|Journal Club Presentation 11/14/19]]
+
====Marcus Avila====
 +
#What worked?
 +
#*We did a good job dividing the work and ensuring that everything was done.
 +
#What didn't work?
 +
#*We struggled with communication because it seemed each person had a lot going on as the break was approaching.
 +
#What will I do next time to fix what didn't work?
 +
#* Next time I will try to do a better job with communicating with my team members.
 +
[[User:Mavila9|Mavila9]] ([[User talk:Mavila9|talk]]) 23:59, 25 November 2019 (PST)
  
−
==Team Feedback==
+
===Week 11===
−
===Naomi Tesfaiohannes===
+
====Naomi Tesfaiohannes====
 
Each team member should reflect on the team's progress:
 
Each team member should reflect on the team's progress:
  
Line 68: Line 99:
  
 
[[User:Ntesfaio|Ntesfaio]] ([[User talk:Ntesfaio|talk]]) 00:08, 14 November 2019 (PST)
 
[[User:Ntesfaio|Ntesfaio]] ([[User talk:Ntesfaio|talk]]) 00:08, 14 November 2019 (PST)
−
 
+
====Joey Nimmers-Minor====
−
===Joey Nimmers-Minor===
 
 
*What worked?
 
*What worked?
 
Dividing up responsibilities and meeting in person in order to avoid missed texts and simply make communication simpler and smoother.
 
Dividing up responsibilities and meeting in person in order to avoid missed texts and simply make communication simpler and smoother.
Line 78: Line 108:
  
 
[[User:Jnimmers|Jnimmers]] ([[User talk:Jnimmers|talk]]) 00:08, 14 November 2019 (PST)
 
[[User:Jnimmers|Jnimmers]] ([[User talk:Jnimmers|talk]]) 00:08, 14 November 2019 (PST)
−
 
+
====Marcus Avila====
−
===Marcus Avila===
 
 
# What worked?
 
# What worked?
 
#* The team dynamic and communication worked out very well. I feel that we each did our part and were even able to help each other out in some places.
 
#* The team dynamic and communication worked out very well. I feel that we each did our part and were even able to help each other out in some places.
Line 87: Line 116:
 
#* Next time I will allocate more time to the assignment.
 
#* Next time I will allocate more time to the assignment.
 
[[User:Mavila9|Mavila9]] ([[User talk:Mavila9|talk]]) 17:24, 15 November 2019 (PST)
 
[[User:Mavila9|Mavila9]] ([[User talk:Mavila9|talk]]) 17:24, 15 November 2019 (PST)
−
 
+
====DeLisa Madere====
−
===DeLisa Madere===
 
  
 
'''What Worked?'''
 
'''What Worked?'''
Line 98: Line 126:
 
'''What will I do next to fix what didn't work?'''
 
'''What will I do next to fix what didn't work?'''
 
*Next time, there will not be any other tests, therefore, more time can be delegated to this assignment.
 
*Next time, there will not be any other tests, therefore, more time can be delegated to this assignment.
−
 
+
====Ivy Macaraeg====
−
===Ivy Macaraeg===
 
 
*What worked?
 
*What worked?
 
*:-I think we worked together well, even under pressure. We were able to coordinate with each other and help each other out.  
 
*:-I think we worked together well, even under pressure. We were able to coordinate with each other and help each other out.  
Line 109: Line 136:
  
 
==Annotated Bibliography Sources==
 
==Annotated Bibliography Sources==
−
 
 
===DeLisa Madere===
 
===DeLisa Madere===
  
Line 115: Line 141:
  
 
2. Sanchez, Y., Taulien, J., Borkovich, K. A., & Lindquist, S. (1992). Hsp104 is required for tolerance to many forms of stress. The EMBO journal, 11(6), 2357-2364. doi: https://doi.org/10.1002/j.1460-2075.1992.tb05295.x
 
2. Sanchez, Y., Taulien, J., Borkovich, K. A., & Lindquist, S. (1992). Hsp104 is required for tolerance to many forms of stress. The EMBO journal, 11(6), 2357-2364. doi: https://doi.org/10.1002/j.1460-2075.1992.tb05295.x
−
 
 
===Naomi Tesfaiohannes===
 
===Naomi Tesfaiohannes===
  
Line 121: Line 146:
  
 
2. Zhou, X., Arita, A., Ellen, T. P., Liu, X., Bai, J., Rooney, J. P., ... & Costa, M. (2009). A genome-wide screen in Saccharomyces cerevisiae reveals pathways affected by arsenic toxicity. Genomics, 94(5), 294-307. https://doi.org/10.1016/j.ygeno.2009.07.003
 
2. Zhou, X., Arita, A., Ellen, T. P., Liu, X., Bai, J., Rooney, J. P., ... & Costa, M. (2009). A genome-wide screen in Saccharomyces cerevisiae reveals pathways affected by arsenic toxicity. Genomics, 94(5), 294-307. https://doi.org/10.1016/j.ygeno.2009.07.003
−
 
 
===Ivy Macaraeg===
 
===Ivy Macaraeg===
  
Line 127: Line 151:
  
 
2. Das, S., Majumder, B., & Biswas, A. K. (2018). Modulation of growth, ascorbate-glutathione cycle and thiol metabolism in rice (Oryza sativa L. cv. MTU-1010) seedlings by arsenic and silicon. Ecotoxicology, 27(10), 1387-1403. 10.1007/s10646-018-1994-5
 
2. Das, S., Majumder, B., & Biswas, A. K. (2018). Modulation of growth, ascorbate-glutathione cycle and thiol metabolism in rice (Oryza sativa L. cv. MTU-1010) seedlings by arsenic and silicon. Ecotoxicology, 27(10), 1387-1403. 10.1007/s10646-018-1994-5
−
 
 
===Marcus Avila===
 
===Marcus Avila===
  
Line 133: Line 156:
  
 
2. Tang, L., Wang, W., Zhou, W., Cheng, K., Yang, Y., Liu, M., ... & Wang, W. (2015). Three-pathway combination for glutathione biosynthesis in Saccharomyces cerevisiae. Microbial cell factories, 14(1), 139. https://doi.org/139. 10.1186/s12934-015-0327-0
 
2. Tang, L., Wang, W., Zhou, W., Cheng, K., Yang, Y., Liu, M., ... & Wang, W. (2015). Three-pathway combination for glutathione biosynthesis in Saccharomyces cerevisiae. Microbial cell factories, 14(1), 139. https://doi.org/139. 10.1186/s12934-015-0327-0
−
 
 
===John Nimmers-Minor===
 
===John Nimmers-Minor===
  
Line 139: Line 161:
  
 
2.Hayakawa, T., Kobayashi, Y., Cui, X. et al. Arch Toxicol (2005) 79: 183. https://doi.org/10.1007/s00204-004-0620-x
 
2.Hayakawa, T., Kobayashi, Y., Cui, X. et al. Arch Toxicol (2005) 79: 183. https://doi.org/10.1007/s00204-004-0620-x
 +
 +
==Data/Files==
 +
[[Media:Biolpresentation_IM.pptx|Journal Club Presentation 11/14/19]]
 +
*Other files can be found on our [[Sulfiknights Deliverables|deliverables page]]
 +
 +
[[Media:DM_Metadata_Sheet.xlsx|Sulfiknights Meta Data Sheet]]
 +
 +
[[Media:SK_Expression-and-Degradation-rate-database_2019.zip | Expression and Degradation Sheet of Thorsen & Dahlquist Data]]
  
 
==References==
 
==References==
−
*Thorsen, M., Lagniel, G., Kristiansson, E., Junot, C., Nerman, O., Labarre, J., & Tamás, M. J. (2007). Quantitative transcriptome, proteome, and sulfur metabolite profiling of the Saccharomyces cerevisiae response to arsenite. Physiological genomics, 30(1), 35-43. DOI: 10.1152/physiolgenomics.00236.2006
+
*Thorsen, M., Lagniel, G., Kristiansson, E., Junot, C., Nerman, O., Labarre, J., & Tamás, M. J. (2007). Quantitative transcriptome, proteome, and sulfur metabolite profiling of the Saccharomyces cerevisiae response to arsenite. Physiological genomics, 30(1), 35-43. DOI: https://doi.org/10.1152/physiolgenomics.00236.2006
  
  

Latest revision as of 15:40, 3 December 2019

Sulfiknight Links
BIOL Databases Main Page Sulfiknights: Project Overview Page Final Project Deliverables Requirements Sulfiknights: Final Project Deliverables Members Project Manager & Quality Assurance: Naomi Tesfaiohannes Quality Assurance: Joey Nimmers-Minor Data Analysis: Ivy-Quynh Macaraeg & Marcus Avila Designer: DeLisa Madere
Assignment Pages Week 11 Week 12/13 Week 15

Template:Sulfiknights

Week 12/13 Milestones

Project Manager

Create a schedule by Tuesday, November 26 that has goals for each member of the Sulfiknights team. Though this may not be completely followed day-by-day it is still helpful to have a outline of checkpoints that should be met for completing this assignment.

Check in with the members of the team to assist in making sure the assignment is complete.

Ntesfaio (talk) 20:44, 21 November 2019 (PST)

Quality Assurance

As on Thursday, November 21st the Quality Assurance guilds were an intermediate for our designer (DeLisa) and our Data Analysts (Marcus and Ivy).

Our goal before Tuesday, November 26 is to assist the Data Analysts in running an ANOVA and running stem. As for Quality Assurance we have completed Milestone 4 and are moving onto Milestone 5 as of Thursday, November 21st.

Ntesfaio (talk) 18:40, 23 November 2019 (PST)

Data Analysis

Coder/Designer

Team Journal Assignments

Week 12/13

Naomi Tesfaiohannes

Each team member should reflect on the team's progress:

What worked?

Working together in class and taking advantage of asking questions while going through the assignment

What didn't work?

Not working on a shared document or excel workbook because progress could be made on one and not seen by the other partner. Also the metasheet was difficult to put together because of the inconsistent datapoints between the groups.

What will I do next to fix what didn't work?

Continue communicating with my team on how we want to progress through with the assignment

Ntesfaio (talk) 21:20, 25 November 2019 (PST)

Ivy Macaraeg

  1. What worked?
    • We figured out what we needed to be working on, and that helped get us going even more than before.
  2. What didn't work?
    • We had some trouble organizing the data in a way that would be clear but compatible with future programs.
  3. What will I do next to fix what didn't work?
    • I think sticking to the directions and making sure that we are thorough will help us.

John Nimmers-Minor

Each team member should reflect on the team's progress:

What worked?

A. Splitting up the work and knowing exactly what each role was in charge of helped tremendously this week.

What didn't work?

A. Having two people work on the exact same task didn't help because one of those two individuals could have potentially been working on a separate piece of the project.

What will I do next to fix what didn't work?

A. Communication throughout the project group will make sure that two people are not doing the same thing at the same time unnecessarily. This will allow us to complete more tasks in a shorter amount of time.

DeLisa Madere

  1. What worked?
    • It really helped that our team all were focused on the individual tasks at hand and we were able to finish the tasks efficiently.
  2. What didn't work?
    • For me, it was a little difficult to understand what was happening with my other group members' tasks since I had my own individual task.
  3. What will I do next to fix what didn't work?
    • To fix this, I will try harder to understand the purpose behind each step in order to completely give all my input if needed, or help is needed.
  4. Dmadere (talk) 22:38, 25 November 2019 (PST)

Marcus Avila

  1. What worked?
    • We did a good job dividing the work and ensuring that everything was done.
  2. What didn't work?
    • We struggled with communication because it seemed each person had a lot going on as the break was approaching.
  3. What will I do next time to fix what didn't work?
    • Next time I will try to do a better job with communicating with my team members.

Mavila9 (talk) 23:59, 25 November 2019 (PST)

Week 11

Naomi Tesfaiohannes

Each team member should reflect on the team's progress:

  • What worked?

Breaking up the sections of the paper to understand the transcription factors and cells affected by the arsenite exposure.

  • What didn't work?

My time management due to other coursework

  • What will I do next to fix what didn't work?

Have a better control of what work I put in each day for this assignment

Ntesfaio (talk) 00:08, 14 November 2019 (PST)

Joey Nimmers-Minor

  • What worked?

Dividing up responsibilities and meeting in person in order to avoid missed texts and simply make communication simpler and smoother.

  • What didn't work?

Waiting until the last minute to do the assignment because every member of the team had tests to get through this week

  • What will I do next to fix what didn't work?

I'll make sure to begin the assignments much sooner and communicate responsibilities with the rest of my team pomtply so we don't have to worry about rushing/procrastinating regardless of what assignments or tests we have the next week.

Jnimmers (talk) 00:08, 14 November 2019 (PST)

Marcus Avila

  1. What worked?
    • The team dynamic and communication worked out very well. I feel that we each did our part and were even able to help each other out in some places.
  2. What didn't work?
    • I believe the amount of time given to complete the individual outline and group presentation was insufficient.
  3. What will I do next to fix what didn't work?
    • Next time I will allocate more time to the assignment.

Mavila9 (talk) 17:24, 15 November 2019 (PST)

DeLisa Madere

What Worked?

  • Being able to come together as a group and collaborate our ideas of the paper really allowed us to efficiently break up the work. We all assisted each other if we needed help.

What didn't work?

  • This week there was a lot of work going into this assignment along with the tests we have had from our other class, so we did not have a great amount of delegated time due to the workload.

What will I do next to fix what didn't work?

  • Next time, there will not be any other tests, therefore, more time can be delegated to this assignment.

Ivy Macaraeg

  • What worked?
    -I think we worked together well, even under pressure. We were able to coordinate with each other and help each other out.
  • What didn't work?
    -All of us were under a lot of pressure concerning other classes, so the amount of time we had to come together and work on this project was limited. Therefore, what didn't work was the timing we had to complete it.
  • What will I do next to fix what didn't work?
    -Next time, I will try to get ahead on my individual page more, so that I will be able to allocate more time to group areas.

Imacarae (talk) 00:12, 14 November 2019 (PST)

Annotated Bibliography Sources

DeLisa Madere

1. Ibstedt, S., Sideri, T. C., Grant, C. M., & Tamás, M. J. (2014). Global analysis of protein aggregation in yeast during physiological conditions and arsenite stress. Biology open, 3(10), 913-923. https://doi.org/10.1242/bio.20148938

2. Sanchez, Y., Taulien, J., Borkovich, K. A., & Lindquist, S. (1992). Hsp104 is required for tolerance to many forms of stress. The EMBO journal, 11(6), 2357-2364. doi: https://doi.org/10.1002/j.1460-2075.1992.tb05295.x

Naomi Tesfaiohannes

1. Tsai, S. L., Singh, S., & Chen, W. (2009). Arsenic metabolism by microbes in nature and the impact on arsenic remediation. Current Opinion in Biotechnology, 20(6), 659-667. https://doi.org/10.1016/j.copbio.2009.09.013

2. Zhou, X., Arita, A., Ellen, T. P., Liu, X., Bai, J., Rooney, J. P., ... & Costa, M. (2009). A genome-wide screen in Saccharomyces cerevisiae reveals pathways affected by arsenic toxicity. Genomics, 94(5), 294-307. https://doi.org/10.1016/j.ygeno.2009.07.003

Ivy Macaraeg

1. Khullar, S., & Sudhakara Reddy, M. (2019). Cadmium and arsenic responses in the ectomycorrhizal fungus Laccaria bicolor: glutathione metabolism and its role in metal (loid) homeostasis. Environmental microbiology reports, 11(2), 53-61. https://doi.org/10.1111/1758-2229.12712

2. Das, S., Majumder, B., & Biswas, A. K. (2018). Modulation of growth, ascorbate-glutathione cycle and thiol metabolism in rice (Oryza sativa L. cv. MTU-1010) seedlings by arsenic and silicon. Ecotoxicology, 27(10), 1387-1403. 10.1007/s10646-018-1994-5

Marcus Avila

1. Parrish, A. R., Zheng, X. H., Turney, K. D., Younis, H. S., & Gandolfi, A. J. (1999). Enhanced transcription factor DNA binding and gene expression induced by arsenite or arsenate in renal slices. Toxicological sciences: an official journal of the Society of Toxicology, 50(1), 98-105. https://doi.org/10.1093/toxsci/50.1.98

2. Tang, L., Wang, W., Zhou, W., Cheng, K., Yang, Y., Liu, M., ... & Wang, W. (2015). Three-pathway combination for glutathione biosynthesis in Saccharomyces cerevisiae. Microbial cell factories, 14(1), 139. https://doi.org/139. 10.1186/s12934-015-0327-0

John Nimmers-Minor

1.Silver, S., & Phung, L. T. (2005). Genes and enzymes involved in bacterial oxidation and reduction of inorganic arsenic. Appl. Environ. Microbiol., 71(2), 599-608. DOI: https://doi.org/10.1128/AEM.71.2.599-608.2005

2.Hayakawa, T., Kobayashi, Y., Cui, X. et al. Arch Toxicol (2005) 79: 183. https://doi.org/10.1007/s00204-004-0620-x

Data/Files

Journal Club Presentation 11/14/19

Sulfiknights Meta Data Sheet

Expression and Degradation Sheet of Thorsen & Dahlquist Data

References

  • Thorsen, M., Lagniel, G., Kristiansson, E., Junot, C., Nerman, O., Labarre, J., & Tamás, M. J. (2007). Quantitative transcriptome, proteome, and sulfur metabolite profiling of the Saccharomyces cerevisiae response to arsenite. Physiological genomics, 30(1), 35-43. DOI: https://doi.org/10.1152/physiolgenomics.00236.2006
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