Bhamilton18 Week 15
Coding Updates
- This week Zach and I focused on major integration of the JASPAR, Gene Database APIs and Page Design teams.
- Due to some communication issues of Week 14, Zach and I were backtracked on certain integrations with other groups, but quickly made up for lost time.
- These backtracks include: gene id syntax and api referencing, as well as page-design collaboration on where classes should go.
- Our task for this week was to add IDs from: NCBI, SGD, Ensembl, Uniprot and JASPAR to the top of the gene page, as well as input the data onto the info.html page.
- This was completed with by taking the Gene Database APIs and JASPAR API calls and creating a link id on the info.js file.
- Currently there are IDs for all the databases and data that was requested by the biologists.
- By communicating with Dr. Dionisio we found the correct ID format to reference the info.html file as well as the api.js file.
- This looks as follows:
var sgdHrefTemplate = "https://www.yeastgenome.org/locus/";- When the template is then used as the URL foundation for other data entries.
var sgdId = gene.sgd.sgdID;- When the ID is used it is referencing the API calls from the Gene Database API code, located in api.js.
$(".sgd-link").text(sgdId).attr({ href: sgdHrefTemplate + sgdId });- This references jquery in which is grabs the info.html file class and puts in text as well as the data from the databases.
- Each ID was created and required a few git pull commands as the other teams needed to fix api calls and retrieve the correct data.
- As of today, December 13 2017, the information is pulling all correct data and is waiting on a few data points form the API team.
- This is how it is displayed for HMO1:
- After the IDs had been created Zach and I focused on using the similar format for all other p-tagged classes that required data.
- The reason we clarify p-tag was because for the gene frequency matrix and sequence logo the syntax was difference as they required an image and additional code to produce a table.
- While trying to create a table for the frequency matrix our team ran into a few bumps in the code and required Dr. Dionisio's help, and Eddie B's help to format a table.
- The table now uses multiple for-loops to integrate through the matrix elements as the sizing per gene changes for every gene. Anywhere from 0-15 elements.
- This is the code for the for loop, specifically the A matrix portion:
var frequencyMatrix = gene.jaspar.frequencyMatrix;var a = "";for (var i = 0; i < frequencyMatrix.A.length; i++) {a += "<td>" + frequencyMatrix.A[i] + "</td>";}$(".frequencyOfA").append($(a));
- An additional hurtle that needed jumping over was the sequence logo image. Through Dr.Dionisio's help, we created a link between the image src file and the JASPAR API call. Talking with Eddie B. about how his call retrieves the image URL was very helpful in retrieving this information.
- This can be seen here:
var sequenceLogo = gene.jaspar.sequenceLogo;$(".sequenceLogo").attr({ src : sequenceLogo });- The biggest difference from above is the src instead of href portion of the attributes.
- Here is how the data is displayed on the page for ASH1:
- After all the data had place holders, actual data or images, the final step was to create an appealing layout of the information. Through collaboration with the Page-Design team our ideas and the biologists hopes were implemented and hope to be complete by December 14.
- Below is the current look of the page, using HOT1 gene as the example:
Team Deliverable Progress
This week Katie, Zach and I were able to meet up twice in order to finalize our project presentation details. We practiced our respective parts and discussed our progress within our team tasks. As noted above the Coders had quite a few tasks to complete, and the Data Analyst and Project Manager were able to collaborate and help each other of the data progress and outputs. Our presentation was completed on Monday night. We communicated through text message, in person and created a google slide deck in order to collaborate off site. Zach and I inputed images, titles and text into the coding portion of the assignment as well as give flow chart details to Katie to update the presentation.
As for the final deliverables, the Coders will be doing a final pull and push request December 14 and potentially the 15th if any major changes need to be made. Our team will be communicating via text message and google docs in order to complete the paper portion of the assignment. Zach and I will be discussing our respective parts of the project and will divide the work load for the paper.
Our deliverables can be seen here: LCI! Deliverables
Acknowledgments
- I worked with Zachary Van Ysseldyk to collaborate on the integration portion of our assignment. We met in person as well as messaged each other with questions.
- We collaborated with Dr. Dionisio on the id syntax and class referencing portions.
- Interaction and Integration team worked with JASPAR team to check in about the frequency matrix and sequence logo syntax.
- Collaborated with Eddie Bachoura on creating a table/for-loop for the frequency matrix portion of the info.html page.
- Collaborated with Eddie Azinge on the gene name referencing between pages. For example, to get the gene name to appear at the top of the info.html page, Eddie A. helped by showing me how to attach an id to the name I wanted and then reference it in the info.js file.
- While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.
Bhamilton18 (talk) 12:58, 11 December 2017 (PST)
References
LMU BioDB 2017. (2017). Deliverables. Retrieved November 14, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/GRNsight_Gene_Page_Project_Deliverables
LMU BioDB 2017. (2017). Week 15. Retrieved December 5, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15
