Page Desiigner

From LMU BioDB 2017
Jump to: navigation, search



Page Design Team Members

Coder: Arash Lari
Project Manager/ Quality Assurance: Hayden Hinsch
Data Analyst: Mary Balducci
Designer: Nicole Kalcic

Page Desiigner Deliverables Page

Page Desiigner Deliverables Page

Team Schedule

Page Desiigner Schedule

Page Desiigner Uploaded Files

Media:MaryHaydenWeek12JournalClubPresentation.pptx ‎
File:Data Driven Design.zip
File:Pagedesignprototype.zip
File:BiodbPageDesignFinalPresentation .pptx

Page Layout

  • Below are a series of rough ideas we will use to create the layout of the page

ACT1screenshot.png

  • We will be using a layout similar to the ACT1 gene page.

Sketchofpagedesign.png

  • This is a rough sketch of what the page will look like.
  • The section labeled description on the sketch will include the following:
    • Gene ID from each database
    • Description/Function (ensembl)
  • Within the dropdown menus we will be incorporating the following:
    • DNA Sequence (ensembl)
    • Protein Sequence (UniProt)
    • Locus tag (NCBI)
    • Also Known As (NCBI)
    • Consensus Sequence (JASPAR)
    • Regulation (SGD)
    • Interaction (SGD)
    • Similar Proteins (UniProt)
    • Gene Ontology (SGD)
    • JASPAR
      • Matrix ID
      • Class Heat shock factors
      • Family HSF factors
      • Sequence Logo
      • Frequency Matrix
  • A zip file containing the html file of prototype page can be downloaded by clicking the pagedesignprototype.zip link below.

File:Pagedesignprototype.zip


Annotated Bibliography

Mary's contribution:

Pizzaro, Jewett, Nielson, Agosin. (2008) Growth Temperature Exerts Differential Physiological and Transcriptional Responses in Laboratory and Wine Strains of Saccharomyces Cerevisiae. "Applied and Environmental Microbiology", 74, 6358-6368, doi:10.1128/AEM.00602-08


Homma, Iwahashi, Komatsu. (2003) Yeast Gene Expression During Growth at Low Temperature. Cryobiology, 46, doi: 10.1016/S0011-2240(03)00028-2

Hayden's Contribution

Dahlquist, K. D., Fitzpatrick, B. G., Camacho, E. T., Entzminger, S. D., & Wanner, N. C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. http://doi.org/10.1007/s11538-015-0092-6


Ando, A., Nakamura, T., Murata, Y., Takagi, H. and Shima, J. (2007), Identification and classification of genes required for tolerance to freeze–thaw stress revealed by genome-wide screening of Saccharomyces cerevisiae deletion strains. FEMS Yeast Research, 7: 244–253. doi:10.1111/j.1567-1364.2006.00162.x



Journal Club Presentations

Powerpoint Slides and Respective Articles

File:Data Driven Design.zip


Media:MaryHaydenWeek12JournalClubPresentation.pptx ‎

  • Pizzaro, Jewett, Nielson, Agosin. (2008) Growth Temperature Exerts Differential Physiological and Transcriptional Responses in Laboratory and Wine Strains of Saccharomyces Cerevisiae. "Applied and Environmental Microbiology", 74, 6358-6368, doi:10.1128/AEM.00602-08

Executive Summaries

Week 11 Executive Summaries

Arash

This week, I worked on researching the given article and the development terms within it as well as prepare a presentation on the article. I also began thinking of some page layout ideas with Nicole to prepare to implement in the coming weeks. All of this information could be found on my Week 11 page: ArashLari Week 11. ArashLari (talk) 02:09, 14 November 2017 (PST)

Mary

This week, I worked on creating an annotated bibliography. The articles I found were primary sources about experiments done involving cold shock on yeast, and the use of microarrays to show results. I used multiple databases to find these articles, and while doing so I learned what key words got me the results closest to what I wanted. While writing the annotated bibliography, I also learned more about the articles, such as when they were written, who published them, what kind of publisher they are, and other information. All of this is recorded in my Week 11 page.

Mbalducc (talk) 23:03, 13 November 2017 (PST)

Nicole

This past week, I read the article The Data-Driven Design Era in Professional Web Design by L.A. Liikkanen. This allowed me to complete my individual journal: an informative outline of the article and list of ten definitions. Arash and I worked together to complete a 15 minute presentation that we are going to give on Tuesday. The presentation gives an overview of our individual journals and what we each learned. You can access more information on what I did this week here: Nicolekalcic Week 11. Nicolekalcic (talk) 01:27, 14 November 2017 (PST)

Hayden

This week I created part of the annotated bibliography we will be using for our final project. I conducted searched for "yeast cold shock microarray" articles and found which two articles I was going to use for the bibliography. The majority of the time this week was spent on finding the information needed for the annotated bibliography which can be found below on this page. More detailed information can be found on my hhinsch Week 11 page. This week I became proficient in finding reliable article to use for our final project. This week we also created the group's template and wiki page. Hhinsch (talk) 22:43, 13 November 2017 (PST)

Week 12 Executive Summaries

Arash

This week was rather light compared to the previous week. We mostly set up the files on our personal computers, which was convenient because as a computer science major I already had most of the necessary files. Nicole and I talked about some preliminary designs and set up a rough schedule that we'll make concrete after the break. This can be found on my week 12 page [[ArashLari Week 12] | Arash Lari Week 12]. ArashLari (talk) 20:43, 20 November 2017 (PST)

Mary

This week I read an article about an experiment done on wine and lab strains of yeast in different temperatures. The experimenters used DNA microarrays to determine which genes were affected by the change in temperatures and which were different based on the different strains of yeast. While reading the article, I can across words I had never seen before, so I also found and recorded the definitions of these words. I then made an outline of the article, to use as a basis for my presentation with our project manager, Hayden. All of this is on my Week 12 page.

Mbalducc (talk) 19:51, 19 November 2017 (PST)

Nicole

Because Arash and I presented last week, we didn't have a heavy work load this week. Arash explained a lot of technical things to me, and we completed the first coding milestones and talked about design possibilities. I officially have a GitHub (nicolekal). I also downloaded the software I needed but didn't have onto my laptop. A full update can be found on: [[Nicolekalcic Week 12] | Nicole Kalcic Week 12]. Nicolekalcic (talk) 23:45, 20 November 2017 (PST)

Hayden

This week I worked with Mary specifically in order to complete our journal club presentation. As a group we worked together to make corrections to the Page Desiigner group page in order to complete the deliverables for this week. Mary and I created a schedule for our group along with helpful links. As a class we decided we will be using WhatsApp to communicate. I spent most of this week outlining the article (it was a pretty difficult read) and defining terms on my hhinsch Week 12 page. Hhinsch (talk) 17:42, 20 November 2017 (PST)

Week 14 Executive Summaries

Arash

This week I worked on implementing our designs for the web page. Nicole and Hayden helped come up with some design ideas. We ended up deciding that ACT1 was a very well designed page and that it would be best to follow the format of that page. There's only a few things left to do but our portion of the project is nearly complete, the generic version of every gene's page needs just a few finishing touches. ArashLari (talk) 18:19, 4 December 2017 (PST)

Mary

This week I finished the Week 10 assignment, using YEASTRACT and GRNsight. I specifically chose one profile from the STEM results to use in YEASTRACT to find transcription factors that regulate a cluster of genes. First I uploaded the genes from profile #22 into YEASTRACT to find 20 significant transcription factors that regulate them. Then, I used Excel to get rid of the transcription factors that were not related to other transcription factors. Once I had those, I imported them into GRNsight to create a map of the transcription factors and their relations to each other. I took a screenshot of this map and uploaded it to my Week 14 page.

Mbalducc (talk) 19:14, 4 December 2017 (PST)

Nicole

Hayden

This week I served as a "floater". I worked with Nicole and Arash in order to come up with how the page design prototype would look. We decided to use the ACT1 design along with Nicole's sketch in order to find a balance between aesthetic and function. The design we used is downloadable from this page and my hhinsch Week 14 page. My hhinsch Week 14 page has some more information regarding why we chose our current prototype design. I also spoke with Mary to make sure she knew I was there to help with her deliverables if needed. I also spent time with the other QA's this week in order to familiarize myself with the deliverables of the other groups. This was necessary for me to make sure we added everything to the page that is required. I uploaded images to my [hhinsch Week 14]] page as well as this page in order to further clarify our thought process behind the page prototype. Hhinsch (talk) 20:16, 4 December 2017 (PST)

Team Progress Reflections

Week 11 Team Progress Reflections

Nicole

  1. What worked?
    • We all work well in our positions. Arash and I worked together recently, so it was easy to coordinate what we are going to do as coder and designer. Everyone was open to opinions on the page and team name. Also, everyone communicated what they were having trouble finishing.
  2. What didn't work?
    • Like Mary said, we weren't able to meet in person. We planned out our meetup during class, but Friday ended up being a busy day for everyone.
  3. What will I do next to fix what didn't work?
    • Next week I will make sure to check in more with my partners. Even if we don't meet up, it is important to make sure everyone is caught up on the assignment and their individual parts.

Mary

  1. What worked?
    • I think as a team, we did a good job communicating and figuring out what needed to be done, and who would do each part.
  2. What didn't work?
    • We did not meet up outside of class. We had planned to, but we all ended up having conflicts so we couldn't meet.
  3. What will I do next to fix what didn't work?
    • I think this can be fixed just by making sure we all communicate in other ways, which is what we did. Through text messages we were able to talk about the assignment and help each other.

Hayden

  1. What worked?
    • We are all doing well communicating and completing our deliverables as individuals and as a group.
  2. What didn't work?
    • Everything worked well in regards to the group, but I did have some trouble finding all the information needed to create an annotated bibliography for the articles I used. Google Scholar gave me way too many results, and PubMed did not have a lot of articles that were either free or LMU had paid for.
  3. What will I do next to fix what didn't work?
    • I will continue to ask questions in class. I also feel more confident about finding useful articles after the completion of this assignment, so it shouldn't be a problem.

Hhinsch (talk) 22:44, 13 November 2017 (PST)

Arash

  1. What worked?
    • We were good at maintaining our own individual tasks and keeping each other updated via text message.
  1. What didn't work?
    • We were unable to schedule time to meet and work effectively.
  1. What will I do next to fix what didn't work?
    • Hopefully we will have lighter course loads and more free time for the next assignment, but besides that we will begin working sooner and try to work in person more than digitally.


Week 12 Team Progress Reflections

Arash

  1. What worked?
    • I think we all got a better grasp of the assignment and time management for the assignment. We have a clear idea where we're headed.
  2. What didn't work?
    • I wish we had more time to dedicate to this class, as often our schedules don't line up.
  3. What will I do next to fix what didn't work?
    • We'll try to be more proactive about all our tasks so they don't pile up. I'm planning on starting some work during the thanksgiving break to lighten the load afterwards.

Mary

  1. What worked?
    • I think that this week I felt more comfortable with the project as a whole. I also liked presenting after the other guilds because I got to see their presentations to get a better idea of what we should include in ours.
  2. What didn't work?
    • I wish that I had more time to read the article and make the presentation. I felt that I didn't understand the article completely, and had to read it a few times to be happy with the way that I understood it and formed my outline of it. Because of this, I couldn't spend as much time as I would've wanted on making the presentation.
  3. What will I do next to fix what didn't work?
    • I will try to spend more time on the entire project, instead of just one part.

Nicole

  1. What Worked?
    • Arash and I communicated via text and had a better idea of what we needed to do earlier on in the week, which made it easier to progress and do quality, time efficient work.
  2. What didn't work?
    • We weren't all able to meet in person. I don't know if this was a huge issue this week, but scheduling conflicts might become more of a problem in December.
  3. What will I do next week to fix what didn't work?
    • Next week I will try to make plans with the group on Tuesday. I am assuming everyone is going out of town for Thanksgiving, but perhaps we can make certain dates within the week to have things done by so the rest of the group can look over the work.

Hayden

  1. What Worked?
    • This week we were a little more prepared to work together and complete the deliverables. As time goes by the end goal is becoming more apparent.
  2. What didn't work?
    • I spent a lot of time reading the article multiple times and it is still a bit confusing to me. A lot of the vocabulary wasn't even found in the dictionaries we provided and a lot of the information needed a lot of background knowledge to comprehend.
  3. What will I do next week to fix what didn't work?
    • Next week I will try and do the bulk of the assignment earlier in the week rather than on the weekend, so I may have more time to understand the material.Hhinsch (talk) 21:09, 20 November 2017 (PST)

Week 14 Team Progress Reflections

Arash

  1. What worked?
    • Our design idea turned out pretty nicely, and was not that difficult to implement.
  2. What didn't work?
    • Coming up with what the final aesthetics will look like.
  3. What will I do next to fix what didn't work?
    • We will discuss the matter in class with the professors and our fellow students to see what works best for everyone.

Mary

  1. What worked?
    • Using YEASTRACT, Excel, and GRNsight to create a map of significant transcription factors in the profile I chose.
  2. What didn't work?
    • I have not fixed Weeks 8 and 10 as much as I would have wanted to.
  3. What will I do next to fix what didn't work?
    • Take more time, make sure I do things right the first time so I don't have to back and fix them later.

Hayden

  1. What worked?
    • We did a pretty good job getting everything done we needed to get done this week in a timely fashion while dealing with adversity.
  2. What didn't work?
    • We still need to complete the prototype and add the other groups' deliverables to our page.
  3. What will I do next to fix what didn't work?
    • We just simply need to take a final assessment of the deliverables as well as gather feedback from the entire class regarding the final layout of the page.

Nicole

  1. What worked?
    • We completed the basic structure of the page, and everyone was able to finish their work in time despite my absence on Thursday.
  2. What didn't work?
    • We haven't finalized anything yet, or implemented any information into the page.
  3. What will I do next to fix what didn't work?
    • We will talk with everyone in class, including the Dahlquist and Dionisio in order to make final decisions moving into Week 15.


Week 15 Team Progress Reflections

Arash

This week I worked on adding the finishing touches to our info.html file in order to make the information easier to digest and nicer to look at. I also worked on my parts of the group presentation and report, which basically entailed me writing out, in detail, everything I did for the GRNsight project. I also wrote an individual statement of work that I emailed to the professors. ArashLari (talk) 22:44, 14 December 2017 (PST) ArashLari Week 15

Hayden

This week I helped complete the final presentation for our team as well as the final paper. I made sure all of the deliverables were accurately produced as well as formulates the final presentation and final paper layout. In regards to what worked and what didn't work, everything was completed on time and we all communicated fairly effectively so I don't have anything to note on. Our deliverables can be found on my Page Desiigner Deliverables Page page. A More detailed summary of work can be found on my hhinsch Week 15 page. Hhinsch (talk) 06:21, 15 December 2017 (PST)

Mary

This week I finished analyzing the data from Dr. Dahlquist's lab. I used YEASTRACT and GRNSight to create a gene regulation matrix of the significant transcription factors and then made them into a visual map which showed the interactions between the genes. I also help create a powerpoint for our team so that we could present on the work that we've done in the last few weeks. My Week 15 page outlines this as well.

Mbalducc (talk) 11:36, 15 December 2017 (PST)

Nicole

This week, I helped format the presentation. I also completed my part of the group paper. In addition, I created a logo for GRNSight on Adobe Illustrator. Arash wanted a bar for the top of the page that had a small logo on it. This was done as a scalable vector graphic and then emailed to Arash. Nicolekalcic (talk) 10:32, 15 December 2017 (PST)

GRNsight Gene Page Project Links
Overview Deliverables Reference Format Guilds Project Manager Quality Assurance Data Analysis Coder
Teams Page Desiigner Lights, Camera, InterACTION! Gene hAPI JASPAR the Friendly Ghost

Page Desiigner Deliverables Page

Page Desiigner Deliverables Page

Page Desiigner Schedule

Page Desiigner Schedule

Uploaded Files

File:Data Driven Design.zip
File:MaryHaydenWeek12JournalClubPresentation.pptx
File:BiodbPageDesignFinalPresentation .pptx
File:PageDesignREADME.txt

Individual Contributer Pages

Arash Lari
Hayden Hinsch
Mary Balducci
Nicole Kalcic

Retrieved from "https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php?title=Page_Desiigner&oldid=5815"