LMU BioDB 2017 - User contributions [en]

Johnllopez616 Individual Statement

2017-12-16T00:33:03Z

Johnllopez616: /* Links */ Fixed the group paper link

==Statement of Work==
===Description===
I organized a majority of the Journal Club Presentation and made most of the slides, with the exceptions of "Software Development is More Than Just Building Products",
"Ford Shows Us How Modern Software Development Is Done", and "Software Development is an Ongoing Science". In the code, I created an XML parsing function and I wrote all the code pulling the data from NCBI and UniProt. For the presentation, I wrote and the "After the desired information was selected, it was pulled from the databases to be implemented on GRNsight." section. For the essay, I wrote most of the Materials and Methods section for the coders and the paragraph regarding the connection to the Paul Ford article in the conclusion. Finally, I wrote the entirety of the README file.
===Links===
*[[Media:JLopezEAzingeJournalClub.pptx | The Week 11 presentation.]]
*[https://github.com/bhamilton18/GRNsight/blob/master/web-client/public/js/api.js The getGeneInformation() Code]
*[[Media:Gene_hAPI_Group_Report.pdf | The group paper.]]
*[[Media:Gene_hAPI_Final_Presentation.pptx | The group presentation]]
*[[Media:GetGeneInformationREADME.txt | README]]

==Assessment of Project==
==Objective Assessment===
Given the timeline of the project and complications presented, I would say that within our group, we had effective teamwork and effective yet last minute workflow. I wish I had a better understanding of the process, since this was my first time working on a massive coding project like this. As the junior programmer, it felt difficult at times to keep up with Eddie and the JASPAR team until we reached the portion where we had to parse the data. I thought Eddie did a good job of helping me through the process. I wish I had communicated more with Dina and Corrine to update them as to what we were doing, but they did a good job at keeping us on track in terms of deliverables before the deadline. When it came to meeting to finish the deliverables, we did that well, but I wish we had submitted them earlier. However, given the fact this was during finals week, I was satisfied with what was accomplished.

===What worked and what didn't work?===
I felt that there was good collaboration between the coders of JASPAR and the API group. I felt that although it was hard to keep up with them at times, we helped each other out to finish our assignments. In addition, I felt that each member of our team submitted their portions of the assignment and did it well.
In terms of what didn't work, I felt that our group could have been more prepared for the presentation and had better rehearsal. In addition, I felt a sense of rush to get the materials submitted at the last minute from the code to the presentation, and this created a lot of pressure amidst final exams week. In terms of the code, because the APIs didn't contain all of the materials we needed to pull, it left several parts blank and created a sense of incompleteness.

===What would you do differently if you could do it all over again?===
Perhaps I would have devoted more time early in the project to get the materials organized. I felt like I didn't really do much to contribute until the final stages of the project, and I wish I could have been more useful at the start. In addition, I would have also liked to do things like the presentation or the essay ahead of time to avoid this last minute pressure.

==Team Evaluation==
===Content===
8/10. While the elements of the project meet the minimum standards and expectations, I believe our group had the potential to do better. In terms of code, although the parts omitted fell out of the scope of the project, I believe that if we had more time / worked ahead, we could have possibly located the parts of code we omitted. In terms of the presentation, if we had rehearsed earlier, we could have performed better and made adjustments to improve the powerpoint.

===Organization===
9/10. I felt Corrine did a good job keeping us on task and did a superior job organizing the group wiki. Unfortunately, I didn't contribute to the group wiki as much as I would have liked to and I don't believe the other members did as well. In terms of getting the code done, despite me not knowing what to do at first, I was able to get work done and code established after being caught up.

===Completeness===
10/10. As of this writing We finished every piece of the code within the scope of the project, we covered every aspect of the essay, and we submitted all the deliverables.

==Reflection on the Process==
===What did you learn?===
====With your head (biological or computer science principles)====
This project taught me several computer science principles, such as version control, XML parsing, a bit of jQuery, and a greater understanding of how different components of software come together to finish a final product.
====With your heart (personal qualities and teamwork qualities that make things work or not work)?====
I learned to not wait until the last minute to get deliverables uploaded. In addition, I learned that it's okay to ask for help when you're unsure about something.
====With your hands (technical skills)?====
As previously stated, I learned how source control works and how to work my way around Git.

===What lesson will you take away from this project that you will still use a year from now?===
Software development, especially for scientific purposes, requires much collaboration and several steps that might not always be intuitive but necessary.

[[User:Johnllopez616|Johnllopez616]] ([[User talk:Johnllopez616|talk]]) 15:47, 15 December 2017 (PST)
[[Template:johnllopez616]]

Johnllopez616 Individual Statement

2017-12-16T00:32:35Z

Johnllopez616: /* Statement of Work */ Added group paper

==Statement of Work==
===Description===
I organized a majority of the Journal Club Presentation and made most of the slides, with the exceptions of "Software Development is More Than Just Building Products",
"Ford Shows Us How Modern Software Development Is Done", and "Software Development is an Ongoing Science". In the code, I created an XML parsing function and I wrote all the code pulling the data from NCBI and UniProt. For the presentation, I wrote and the "After the desired information was selected, it was pulled from the databases to be implemented on GRNsight." section. For the essay, I wrote most of the Materials and Methods section for the coders and the paragraph regarding the connection to the Paul Ford article in the conclusion. Finally, I wrote the entirety of the README file.
===Links===
*[[Media:JLopezEAzingeJournalClub.pptx | The Week 11 presentation.]]
*[https://github.com/bhamilton18/GRNsight/blob/master/web-client/public/js/api.js The getGeneInformation() Code]
*[[Media::Gene_hAPI_Group_Report.pdf | The group paper.]]
*[[Media:Gene_hAPI_Final_Presentation.pptx | The group presentation]]
*[[Media:GetGeneInformationREADME.txt | README]]

==Assessment of Project==
==Objective Assessment===
Given the timeline of the project and complications presented, I would say that within our group, we had effective teamwork and effective yet last minute workflow. I wish I had a better understanding of the process, since this was my first time working on a massive coding project like this. As the junior programmer, it felt difficult at times to keep up with Eddie and the JASPAR team until we reached the portion where we had to parse the data. I thought Eddie did a good job of helping me through the process. I wish I had communicated more with Dina and Corrine to update them as to what we were doing, but they did a good job at keeping us on track in terms of deliverables before the deadline. When it came to meeting to finish the deliverables, we did that well, but I wish we had submitted them earlier. However, given the fact this was during finals week, I was satisfied with what was accomplished.

===What worked and what didn't work?===
I felt that there was good collaboration between the coders of JASPAR and the API group. I felt that although it was hard to keep up with them at times, we helped each other out to finish our assignments. In addition, I felt that each member of our team submitted their portions of the assignment and did it well.
In terms of what didn't work, I felt that our group could have been more prepared for the presentation and had better rehearsal. In addition, I felt a sense of rush to get the materials submitted at the last minute from the code to the presentation, and this created a lot of pressure amidst final exams week. In terms of the code, because the APIs didn't contain all of the materials we needed to pull, it left several parts blank and created a sense of incompleteness.

===What would you do differently if you could do it all over again?===
Perhaps I would have devoted more time early in the project to get the materials organized. I felt like I didn't really do much to contribute until the final stages of the project, and I wish I could have been more useful at the start. In addition, I would have also liked to do things like the presentation or the essay ahead of time to avoid this last minute pressure.

==Team Evaluation==
===Content===
8/10. While the elements of the project meet the minimum standards and expectations, I believe our group had the potential to do better. In terms of code, although the parts omitted fell out of the scope of the project, I believe that if we had more time / worked ahead, we could have possibly located the parts of code we omitted. In terms of the presentation, if we had rehearsed earlier, we could have performed better and made adjustments to improve the powerpoint.

===Organization===
9/10. I felt Corrine did a good job keeping us on task and did a superior job organizing the group wiki. Unfortunately, I didn't contribute to the group wiki as much as I would have liked to and I don't believe the other members did as well. In terms of getting the code done, despite me not knowing what to do at first, I was able to get work done and code established after being caught up.

===Completeness===
10/10. As of this writing We finished every piece of the code within the scope of the project, we covered every aspect of the essay, and we submitted all the deliverables.

==Reflection on the Process==
===What did you learn?===
====With your head (biological or computer science principles)====
This project taught me several computer science principles, such as version control, XML parsing, a bit of jQuery, and a greater understanding of how different components of software come together to finish a final product.
====With your heart (personal qualities and teamwork qualities that make things work or not work)?====
I learned to not wait until the last minute to get deliverables uploaded. In addition, I learned that it's okay to ask for help when you're unsure about something.
====With your hands (technical skills)?====
As previously stated, I learned how source control works and how to work my way around Git.

===What lesson will you take away from this project that you will still use a year from now?===
Software development, especially for scientific purposes, requires much collaboration and several steps that might not always be intuitive but necessary.

[[User:Johnllopez616|Johnllopez616]] ([[User talk:Johnllopez616|talk]]) 15:47, 15 December 2017 (PST)
[[Template:johnllopez616]]

Johnllopez Week 15

2017-12-16T00:28:07Z

Johnllopez616: /* Electronic Lab Notebook */ Added material

==Electronic Lab Notebook==
This week, I took the work completed in my XML function and put them into the main getGeneInformation() function.

I also created an XMLParser function using regular expressions to remove any sort of data within the tags.

var XMLParser = function (data) {
return serializer.serializeToString(data).replace(/\<.*?\>\s?/g, "");
};

You may see the work I completed on github [https://github.com/bhamilton18/GRNsight/blob/master/web-client/public/js/api.js here].

==Acknowledgements and References==
===Acknowledgements===
This week required collaboration between the coders [[User:cazinge | Eddie Azinge]], [[User:ebachour | Eddie Bachoura]], and [[User:simonwro120 | Simon Wroblewski]] to finalize the code to submit. In addition, I discussed the project's deliverables with [[User:cwong34 | Corrine Wong]] and [[User:dbashour | Dina Bashoura]] and worked on it with them.

While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.

[[User:Johnllopez616|Johnllopez616]] ([[User talk:Johnllopez616|talk]]) 16:24, 15 December 2017 (PST)

===References===
LMU BioDB 2017. (2017). Week 15. Retrieved December 11, 2017 from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15

{{Template:johnllopez616}}

Johnllopez Week 15

2017-12-16T00:24:24Z

Johnllopez616: Added acknowledgements

==Electronic Lab Notebook==
==Acknowledgements and References==
===Acknowledgements===
This week required collaboration between the coders [[User:cazinge | Eddie Azinge]], [[User:ebachour | Eddie Bachoura]], and [[User:simonwro120 | Simon Wroblewski]] to finalize the code to submit. In addition, I discussed the project's deliverables with [[User:cwong34 | Corrine Wong]] and [[User:dbashour | Dina Bashoura]] and worked on it with them.

While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.

[[User:Johnllopez616|Johnllopez616]] ([[User talk:Johnllopez616|talk]]) 16:24, 15 December 2017 (PST)

===References===
LMU BioDB 2017. (2017). Week 15. Retrieved December 11, 2017 from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15

{{Template:johnllopez616}}

Gene hAPI

2017-12-16T00:19:37Z

Johnllopez616: /* Executive Summaries */ Added john's week 15

==Gene hAPI==

===Links===
Our Deliverables: [[Gene hAPI Deliverables]]

Main Page: [[Main Page]]

Project Page: [[GRNsight Gene Page Project]]

[http://dondi.github.io/GRNsight/ GRNsight]

{{Template:GRNsight Gene Page Project Links}}

===General Information===
Eddie (Cazinge):
*Role: Coder
*User Page: [[User:cazinge|Eddie Azinge]]

Dina (Dbashour):
*Role: Data Analysis
*User Page: [[User:dbashour|Dina Bashoura]]

Corinne (Cwong34):
*Role: Project Manager/Quality Assurance
*User Page: [[User:Cwong34|Corinne Wong]]

John (johnllopez616):
*Role: Coder
*User Page: [[User:johnllopez616|John Lopez]]

===Executive Summaries===
'''Eddie''':
* [[Cazinge Week 11|Week 11]]:
** This week, I finished the bulk of the function logic for our final project; I also performed research on the items necessary for an effective journal club presentation this coming Thursday by completing the individual assignment that we were assigned for the week.
** Getting a large portion of our designated assignment completed early worked pretty successfully to alleviate our stress over the impending assignment and place us ahead of the pace of other groups so that we would be able to work on the more secondary parts of our final presentation across the next 4 weeks.
** Working on the project without having a proper development environment set up ended up detracting from the fluidity of our collaboration as a team; as the versions of the final function that John and I worked on weren't linked via git, and were somewhat unruly to collaborate on.
** Next time, I'll make sure to set up my development environment according to Dondi's instructions on the Coders Guild Page.
[[User:Cazinge|Cazinge]] ([[User talk:Cazinge|talk]]) 23:39, 20 November 2017 (PST)
* [[Cazinge Week 12|Week 12]]:
** This week my task was to set up my development environment for the coder milestones. As such, I've completed milestones 1-3, talked to the other coders, and established a plan to work on the assignment in the future along with the rest of my team.
** Setting up milestones 1-3 went pretty well; since they were all standard open source project tasks, I was able to complete them simply, efficiently, and without any real friction.
** The only thing that I found less than desirable from this week was our communication; As Thanksgiving weekend rolls around we only stand to fall behind if we continue without amending our communication situation.
** This next week, I'll focus on keeping an open line of communication with the rest of my team, as well as completing the majority of the coding milestones that we have left.
[[User:Cazinge|Cazinge]] ([[User talk:Cazinge|talk]]) 23:39, 20 November 2017 (PST)
*[[Cazinge Week 14|Week 14]]:
**This week's we reached a good spot in terms of the execution of Milestone 4. I was the main point of contact with regards to general coding questions, and we're approaching the completion of the final assignment.
**This week was fun as I was able to leisurely interact with my classmates in an environment more typically representing that of actual software development. As such, I was able to help out with typical software development problems and speed up the development of the final project.
**I don't feel as if I struggled with any specific part of this week's assignment, but we haven't exactly been proactive about writing our tests, so that eventually needs to be resolved.
**As far as what needs to get done for this next week, testing. Other than that, I'm feeling good about our progress going into the last week.
[[User:Cazinge|Cazinge]] ([[User talk:Cazinge|talk]]) 13:18, 8 December 2017 (PST)
*[[Cazinge Week 15|Week 15]]:
**This week we finished the final functionality of the API function, marking our progress with the final project complete.
[[User:Cazinge|Cazinge]] ([[User talk:Cazinge|talk]]) 13:18, 8 December 2017 (PST)

'''Dina''':
* [[Dbashour_Week_11 | Week 11]]
** For this week, I assisted with creating our group wiki page, adding the template and setting up the page in preparation for the later weeks to come. I also located two out of 4 research articles regarding cold shock, yeast, and microarray data that we might later use for our final project. I became familiar with how to narrow down search queries in order to yield the smallest amount of results that are related to your actual topic, as well as identify how many articles are cited and how many articles cite the articles I found.
** I liked being able to work on the assignment in class, this way I was able to ask questions or clarify certain things that I needed help with. I also like that we have a guild of people, this way there is more of a support system if I am ever lost or need assistance.
** Because my task for this week was simply following the directions on the wiki, there was nothing that went wrong or needed fixing.
** Next week, I will work with my guild to present on our found articles and collaborate with them all in order to make our presentation run smoothly. 
[[User:Dbashour|Dbashour]] ([[User talk:Dbashour|talk]]) 23:43, 13 November 2017 (PST)
*[[Dbashour_Week_12 | Week 12]]
** For this week, Corrine and I prepared for the journal club presentation by individually reading the article "Comprehensive expression analysis of time-dependent responses in yeast cells to low temperature" by Sahara, T., Goda, T., & Ohgiya, S. After reading this article, I developed an outline that highlighted the main points in each section of the article. With Corrine, I made a presentation on that outline, making sure to include each highlighted point. I also located and defined 10 words in the article that I was unfamiliar with and presented a flowchart of the overall experimental design.
** What worked well for this week was to collaborate with Corrine on who was going to present which parts of the article, this way there was no confusion on that matter and the overall flow of the presentation would be well executed.
** There was a lack of communication with all of us as a team, so I am unsure as to what John and Eddie have done for this week.
** Next week, we will all communicate via text either with the entire class or with just my group in order to clarify what the role of each person is and if we have been completing our tasks. 
[[User:Dbashour|Dbashour]] ([[User talk:Dbashour|talk]]) 12:10, 21 November 2017 (PST)
*[[Dbashour_Week_14 | Week 14]]
** This week, I corrected my week 8 and week 10 assignments on my [[Dbashour_Week_14 | Week 14]] individual page., fixing anything that Dr. Dahlquist and Dr. Dionisio had requested to fix on my talk page. I made my electronic notebook be written in the past tense, corrected my files, and added any information I needed to add. Also this week I completed the remainder of the week 10 assignment that we had not complete during that week. I made a network model of transcription factors based on my deletion strain dGLN3. I also met with the data analysts to see if we were all on the same page and made a group message in order to have a method of communication for any questions we had.
** Being on top of my assignments and my time management during class worked well this week. I was able to ask questions and accomplish a lot from working on my assignment in class in a timely manner.
** I would have liked to meet more with my group and touch base on where we all resided in the project. I wish that we updated each other more on what we were working on, specifically between the coders and the analysts/QA.
** Next week, I hope to continue my efforts of time management in class and communicate more with the coders to see how far we have all come. I will specifically ask the coders what they have done and what they plan on doing next in order to facilitate the communication barrier. 
[[User:Dbashour|Dbashour]] ([[User talk:Dbashour|talk]]) 13:00, 9 December 2017 (PST)
*[[Dbashour_Week_15 | Week 15]]
** This week, Dr. Dahlquist reviewed my files and made corrections to them so that they would work and be visualized in GRNsight. I organized my final deliverables in order to prepare for the final project. As a team we worked together to complete the final powerpoint and paper, meeting in class as well as outside of class to work on it. 
[[User:Dbashour|Dbashour]] ([[User talk:Dbashour|talk]]) 13:00, 9 December 2017 (PST)

'''Corinne''':
* [[Cwong34_Week_11|Week 11]]:
** This week I helped to create the template and group page. I found two sources to contribute to our annotated bibliography, which we can use to research information for our final project. I researched the accessibility and publishing details of the sources.
** It was nice that we had some time in class to work, so we could easily check in with each other about what we were working on. It was also nice that Dina and I were working on the same project, so we could easily understand our work and help each other.
** It was a bit difficult to be fully aware of the progress of everyone because we had separate projects for this week and next week too. Both halves of our group are working on separate presentations, so we have different focuses, which makes it harder to keep up with each other.
** Next week, since it will be a similar situation, I will try to keep up with the other half of my group by fully understanding their objectives/assignments for the week and checking in some more.
*[[Cwong34_Week_12|Week 12]]:
**This week, I read the "Comprehensive expression analysis of time-dependent responses in yeast cells to low temperature" by Sahara, T., Goda, T., & Ohgiya, S. I came up with a flow chart of their methods for the experiment and made an outline for my individual assignment. I also found ten terms I didn't know and wrote down their definitions in my individual journal. I worked with Dina on our presentation of the article over the weekend.
**Having a collaborative assignment worked for me and Dina because we knew exactly what we needed to do for the project this week, and we worked together to get it done. Moreover, we had more time to meet up with each other this weekend, so it was easier to collaborate.
**It was still difficult to keep in touch with all of the members of the group since we all had different things to work on.
**However, now that we are done with our separate presentations, it will be more of a focus to know what each person is working on. Moreover, I will work to create more communication between group members to keep track of our progress, whether it's on our gene page or over text.
[[User:Cwong34|Cwong34]] ([[User talk:Cwong34|talk]]) 23:26, 20 November 2017 (PST)

*[[Cwong34_Week_14|Week 14]]:
**This week, I met with the group members to check in on where we were in the project. I met with the other QAs, and we worked together to come up with a list of information to pull from databases, and specifically which information to pull from where.
**Having time to work on the project in class was very helpful to be able to meet with everyone. I could easily communicate to my team members and check in with them, but I could also check in with other teams to work together. There was a lot more communication this week, and I feel I have a good idea of our progression for the rest of the semester.
**Having to split the class time between working with our team members and working with our guilds was a bit of a challenge because there was a lot to cover between both groups. We made it work, but hopefully we'll be able to find a time to meet outside of class as well this coming week to work on our project.
[[User:Cwong34|Cwong34]] ([[User talk:Cwong34|talk]]) 00:25, 5 December 2017 (PST)

*[[Cwong34_Week_15|Week 15]]
**

'''John''':
* [[Johnllopez Week 11|Week 11]]:
** This week my task was mostly focused around organizing the Journal Club Presentation. I created the initial outline for the powerpoint, created the style, and added over half the content to it. In addition, I spent some time with [[User:cazinge | Eddie Azinge]] who finished most of the deliverable portion of the assignment as he explained to me his process.
** I felt the assembling of the group was done so with ease because I worked with each of the people in the past on different assignments/projects. I felt like each of my members are dedicated and willing to work, so I'm glad that we have a good group. Eddie's experience in coding was an advantage for me because I shouldn't have any sort of confusion, however as I explain below, it is also a disadvantage.
** Despite the fact that Eddie provided an explanation for how he was able to develop the primary deliverable for the project, I felt a little disappointed that I couldn't go through the same discovery process he did. It essentially makes me feel like my role in the project isn't as important. In addition, I was also irritated that we didn't have many opportunities to work on the Journal Club Presentations in advance, for I felt like we weren't as prepared to create/give them as we could have been.
**Next week, I know that I have to get a head start on my individual portion of the assignment so that I'm not crunched for time like I was for the presentation. In addition, it's imperative that I review the code Eddie set up in detail so I can understand each line and how it works. Furthermore, I have to follow along with the other coders in setting up development rigs.
[[User:Johnllopez616|Johnllopez616]] ([[User talk:Johnllopez616|talk]]) 23:41, 13 November 2017 (PST)

* [[Johnllopez Week 12|Week 12]]:
** This week my task involved setting up my development environment for the later milestones. It included the establishment of milestones 1-3, talking to the other coders, and establishing a plan to work on the assignment in the future.
** I felt like the setting up of the environment went well. Once I understood what I had to do, it was not difficult to set up the environment. In addition, I had no problems setting it up on GitHub and my computer once it happened.
** Unfortunately I felt like this week wasn't a very productive week. Despite setting up the environment, I did not collaborate well with my teammates. We have yet to arrange a proper work schedule and plan, especially to ensure that over the thanksgiving break we are able to do some stuff. This has led to the group's progress existing in a state of limbo.
** On Thursday, I asked the class to obtain a WhatsApp to allow for communication. This will be essential to communicate between the coders to accomplish the project. On Tuesday I will connect with as many people in the class. More importantly, I will get my group together to work on a set plan to work on the assignment and establish deadlines. Although this week wasn't the most productive for me, I will ensure that we don't fall behind next week.
[[User:Johnllopez616|Johnllopez616]] ([[User talk:Johnllopez616|talk]]) 23:27, 20 November 2017 (PST)

*[[johnllopez Week 14|Week 14]]:
**This week's primary objective was to get as much of Milestone 4 as finished as possible. My portion of the assignment was to learn how to extract data from XML files and translate it so that the page developers could use it.
**Perhaps the best part about this portion of the assignment was being able to discover a bit of jQuery and DOM functions. Knowledge and exposure to both of these is fundamental in obtaining a potential job.
**One area where I struggled was figuring out how to extract JSON using javascript. This is something that both of the Eddies, however, were proficient in doing, so it's important that I seek their help in understanding this concept. In addition, I wish I communicated more with the coders during the development of the project.
**This week will be crucial in finishing Milestone 4 for the project. It's absolutely necessary that the coders and I not only integrate everything, but that I am following along with what they do. I will ask a lot of questions to truly understand what's happening.
[[User:Johnllopez616|Johnllopez616]] ([[User talk:Johnllopez616|talk]]) 23:16, 4 December 2017 (PST)

*[[johnllopez Week 15|Week 15]]:
**This week involved finalizing the XML extraction functions and examining the JSON to see what could be pulled. With this completed, we were able to finish the code and work on the rest of the project deliverables.
[[User:Johnllopez616|Johnllopez616]] ([[User talk:Johnllopez616|talk]]) 16:19, 15 December 2017 (PST)

==Journal Club Deliverable==
[[Media:JLopezEAzingeJournalClub.pptx | The presentation - Coder/Designer]] 
[[Media:Cold_Shock_Yeast_Genome_Response.pdf | Journal Club Week 12 Presentation - QA/Data Analyst]]

== Journal Club Article ==
Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.
 
{{template:Gene_hAPI}}

=Acknowledgments=
#We received help and guidance from Dr. Dondi and Dr. Dahlquist.

=References=
#Becerra M., Lombardía L.J., González-Siso M.I., Rodríguez-Belmonte E., Hauser N.C., & Cerdán M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301
#Paul Ford, 2015, Bloomberg, Retrieved from: https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#the-time-you-attended-the-e-mail-address-validation-meeting
#Homma T., Iwahashi H., & Komatsu Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237. https://doi.org/10.1016/S0011-2240(03)00028-2
#LMU BioDB 2017. (2017). GRNsight Gene Page Project. Retrieved from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/GRNsight_Gene_Page_Project
#Murata et. al.(2006). Genome-wide expression analysis of yeast response during exposure to 4 C. Extremophiles, 10(2), 117-128.
#Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.

Johnllopez616 Individual Statement

2017-12-16T00:10:36Z

Johnllopez616: Added links

==Statement of Work==
===Description===
I organized a majority of the Journal Club Presentation and made most of the slides, with the exceptions of "Software Development is More Than Just Building Products",
"Ford Shows Us How Modern Software Development Is Done", and "Software Development is an Ongoing Science". In the code, I created an XML parsing function and I wrote all the code pulling the data from NCBI and UniProt. For the presentation, I wrote and the "After the desired information was selected, it was pulled from the databases to be implemented on GRNsight." section. For the essay, I wrote most of the Materials and Methods section for the coders and the paragraph regarding the connection to the Paul Ford article in the conclusion. Finally, I wrote the entirety of the README file.
===Links===
*[[Media:JLopezEAzingeJournalClub.pptx | The Week 11 presentation.]]
*[https://github.com/bhamilton18/GRNsight/blob/master/web-client/public/js/api.js The getGeneInformation() Code]
*Group essay
*[[Media:Gene_hAPI_Final_Presentation.pptx | The group presentation]]
*[[Media:GetGeneInformationREADME.txt | README]]

==Assessment of Project==
==Objective Assessment===
Given the timeline of the project and complications presented, I would say that within our group, we had effective teamwork and effective yet last minute workflow. I wish I had a better understanding of the process, since this was my first time working on a massive coding project like this. As the junior programmer, it felt difficult at times to keep up with Eddie and the JASPAR team until we reached the portion where we had to parse the data. I thought Eddie did a good job of helping me through the process. I wish I had communicated more with Dina and Corrine to update them as to what we were doing, but they did a good job at keeping us on track in terms of deliverables before the deadline. When it came to meeting to finish the deliverables, we did that well, but I wish we had submitted them earlier. However, given the fact this was during finals week, I was satisfied with what was accomplished.

===What worked and what didn't work?===
I felt that there was good collaboration between the coders of JASPAR and the API group. I felt that although it was hard to keep up with them at times, we helped each other out to finish our assignments. In addition, I felt that each member of our team submitted their portions of the assignment and did it well.
In terms of what didn't work, I felt that our group could have been more prepared for the presentation and had better rehearsal. In addition, I felt a sense of rush to get the materials submitted at the last minute from the code to the presentation, and this created a lot of pressure amidst final exams week. In terms of the code, because the APIs didn't contain all of the materials we needed to pull, it left several parts blank and created a sense of incompleteness.

===What would you do differently if you could do it all over again?===
Perhaps I would have devoted more time early in the project to get the materials organized. I felt like I didn't really do much to contribute until the final stages of the project, and I wish I could have been more useful at the start. In addition, I would have also liked to do things like the presentation or the essay ahead of time to avoid this last minute pressure.

==Team Evaluation==
===Content===
8/10. While the elements of the project meet the minimum standards and expectations, I believe our group had the potential to do better. In terms of code, although the parts omitted fell out of the scope of the project, I believe that if we had more time / worked ahead, we could have possibly located the parts of code we omitted. In terms of the presentation, if we had rehearsed earlier, we could have performed better and made adjustments to improve the powerpoint.

===Organization===
9/10. I felt Corrine did a good job keeping us on task and did a superior job organizing the group wiki. Unfortunately, I didn't contribute to the group wiki as much as I would have liked to and I don't believe the other members did as well. In terms of getting the code done, despite me not knowing what to do at first, I was able to get work done and code established after being caught up.

===Completeness===
10/10. As of this writing We finished every piece of the code within the scope of the project, we covered every aspect of the essay, and we submitted all the deliverables.

==Reflection on the Process==
===What did you learn?===
====With your head (biological or computer science principles)====
This project taught me several computer science principles, such as version control, XML parsing, a bit of jQuery, and a greater understanding of how different components of software come together to finish a final product.
====With your heart (personal qualities and teamwork qualities that make things work or not work)?====
I learned to not wait until the last minute to get deliverables uploaded. In addition, I learned that it's okay to ask for help when you're unsure about something.
====With your hands (technical skills)?====
As previously stated, I learned how source control works and how to work my way around Git.

===What lesson will you take away from this project that you will still use a year from now?===
Software development, especially for scientific purposes, requires much collaboration and several steps that might not always be intuitive but necessary.

[[User:Johnllopez616|Johnllopez616]] ([[User talk:Johnllopez616|talk]]) 15:47, 15 December 2017 (PST)
[[Template:johnllopez616]]

Johnllopez616 Individual Statement

2017-12-16T00:01:21Z

Johnllopez616: Added my reflection

==Statement of Work==
===Description===
I organized a majority of the Journal Club Presentation and made most of the slides, with the exceptions of "Software Development is More Than Just Building Products",
"Ford Shows Us How Modern Software Development Is Done", and "Software Development is an Ongoing Science". In the code, I created an XML parsing function and I wrote all the code pulling the data from NCBI and UniProt. For the presentation, I wrote and the "After the desired information was selected, it was pulled from the databases to be implemented on GRNsight." section. For the essay, I wrote most of the Materials and Methods section for the coders and the paragraph regarding the connection to the Paul Ford article in the conclusion. Finally, I wrote the entirety of the README file.
===Links===

==Assessment of Project==
==Objective Assessment===
Given the timeline of the project and complications presented, I would say that within our group, we had effective teamwork and effective yet last minute workflow. I wish I had a better understanding of the process, since this was my first time working on a massive coding project like this. As the junior programmer, it felt difficult at times to keep up with Eddie and the JASPAR team until we reached the portion where we had to parse the data. I thought Eddie did a good job of helping me through the process. I wish I had communicated more with Dina and Corrine to update them as to what we were doing, but they did a good job at keeping us on track in terms of deliverables before the deadline. When it came to meeting to finish the deliverables, we did that well, but I wish we had submitted them earlier. However, given the fact this was during finals week, I was satisfied with what was accomplished.

===What worked and what didn't work?===
I felt that there was good collaboration between the coders of JASPAR and the API group. I felt that although it was hard to keep up with them at times, we helped each other out to finish our assignments. In addition, I felt that each member of our team submitted their portions of the assignment and did it well.
In terms of what didn't work, I felt that our group could have been more prepared for the presentation and had better rehearsal. In addition, I felt a sense of rush to get the materials submitted at the last minute from the code to the presentation, and this created a lot of pressure amidst final exams week. In terms of the code, because the APIs didn't contain all of the materials we needed to pull, it left several parts blank and created a sense of incompleteness.

===What would you do differently if you could do it all over again?===
Perhaps I would have devoted more time early in the project to get the materials organized. I felt like I didn't really do much to contribute until the final stages of the project, and I wish I could have been more useful at the start. In addition, I would have also liked to do things like the presentation or the essay ahead of time to avoid this last minute pressure.

==Team Evaluation==
===Content===
8/10. While the elements of the project meet the minimum standards and expectations, I believe our group had the potential to do better. In terms of code, although the parts omitted fell out of the scope of the project, I believe that if we had more time / worked ahead, we could have possibly located the parts of code we omitted. In terms of the presentation, if we had rehearsed earlier, we could have performed better and made adjustments to improve the powerpoint.

===Organization=== Comment on the organization of the project and of your group's wiki pages.
9/10. I felt Corrine did a good job keeping us on task and did a superior job organizing the group wiki. Unfortunately, I didn't contribute to the group wiki as much as I would have liked to and I don't believe the other members did as well. In terms of getting the code done, despite me not knowing what to do at first, I was able to get work done and code established after being caught up.

===Completeness===
10/10. As of this writing We finished every piece of the code within the scope of the project, we covered every aspect of the essay, and we submitted all the deliverables.

==Reflection on the Process==
===What did you learn?===
====With your head (biological or computer science principles)====
This project taught me several computer science principles, such as version control, XML parsing, a bit of jQuery, and a greater understanding of how different components of software come together to finish a final product.
====With your heart (personal qualities and teamwork qualities that make things work or not work)?====
I learned to not wait until the last minute to get deliverables uploaded. In addition, I learned that it's okay to ask for help when you're unsure about something.
====With your hands (technical skills)?====
As previously stated, I learned how source control works and how to work my way around Git.

===What lesson will you take away from this project that you will still use a year from now?===
Software development, especially for scientific purposes, requires much collaboration and several steps that might not always be intuitive but necessary.

[[User:Johnllopez616|Johnllopez616]] ([[User talk:Johnllopez616|talk]]) 15:47, 15 December 2017 (PST)
[[Template:johnllopez616]]

Johnllopez616 Individual Statement

2017-12-15T23:47:50Z

Johnllopez616: Added basic page

==Statement of Work==
===Description===
I organized a majority of the Journal Club Presentation and made most of the slides, with the exceptions of "Software Development is More Than Just Building Products",
"Ford Shows Us How Modern Software Development Is Done", and "Software Development is an Ongoing Science". In the code, I created an XML parsing function and I wrote all the code pulling the data from NCBI and UniProt. For the presentation, I wrote and the "After the desired information was selected, it was pulled from the databases to be implemented on GRNsight." section. For the essay, I wrote most of the Materials and Methods section for the coders and the paragraph regarding the connection to the Paul Ford article in the conclusion. Finally, I wrote the entirety of the README file.
===Links===

==Assessment of Project==
==Objective Assessment===
Given the timeline of the project and complications presented, I would say that within our group, we had effective teamwork and effective yet last minute workflow. I wish I had a better understanding of the process, since this was my first time working on a massive coding project like this. As the junior programmer, it felt difficult at times to keep up with Eddie and the JASPAR team until we reached the portion where we had to parse the data. I thought Eddie did a good job of helping me through the process. I wish I had communicated more with Dina and Corrine to update them as to what we were doing, but they did a good job at keeping us on track in terms of deliverables before the deadline. When it came to meeting to finish the deliverables, we did that well, but I wish we had submitted them earlier. However, given the fact this was during finals week, I was satisfied with what was accomplished.

==What worked and what didn't work?==
I felt that there was good collaboration between the coders of JASPAR and the API group. I felt that although it was hard to keep up with them at times, we helped each other out to finish our assignments. In addition, I felt that each member of our team submitted their portions of the assignment and did it well.
In terms of what didn't work, I felt that our group could have been more prepared for the presentation and had better rehearsal. In addition, I felt a sense of rush to get the materials submitted at the last minute from the code to the presentation, and this created a lot of pressure amidst final exams week. In terms of the code, because the APIs didn't contain all of the materials we needed to pull, it left several parts blank and created a sense of incompleteness.

==What would you do differently if you could do it all over again?==
Perhaps I would have devoted more time early in the project to get the materials organized. I felt like I didn't really do much to contribute until the final stages of the project, and I wish I could have been more useful at the start. In addition, I would have also liked to do things like the presentation or the essay ahead of time to avoid this last minute pressure.

==Team Evaluation==
===Content===
8/10. While the elements of the project meet the minimum standards and expectations, I believe our group had the potential to do better. In terms of code, although the parts omitted fell out of the scope of the project, I believe that if we had more time / worked ahead, we could have possibly located the parts of code we omitted. In terms of the presentation, if we had rehearsed earlier, we could have performed better and made adjustments to improve the powerpoint.

===Organization=== Comment on the organization of the project and of your group's wiki pages.
9/10. I felt Corrine did a good job keeping us on task and did a superior job organizing the group wiki. Unfortunately, I didn't contribute to the group wiki as much as I would have liked to and I don't believe the other members did as well. In terms of getting the code done, despite me not knowing what to do at first, I was able to get work done and code established after being caught up.

===Completeness===
10/10. As of this writing We finished every piece of the code within the scope of the project, we covered every aspect of the essay, and we submitted all the deliverables.

==Reflection on the Process==

[[User:Johnllopez616|Johnllopez616]] ([[User talk:Johnllopez616|talk]]) 15:47, 15 December 2017 (PST)
[[Template:johnllopez616]]

Gene hAPI Deliverables

2017-12-15T23:21:45Z

Johnllopez616: /* Gene hAPI Deliverables */ Added a link for my (John's) Personal Statement

[[Gene hAPI]]

Members:
*[[User:Cazinge|Eddie Azinge]]
*[[User:Dbashour|Dina Bashoura]]
*[[User:Johnllopez616|John Lopez]]
*[[User:Cwong34|Corinne Wong]]

= Gene hAPI Deliverables =
# Organized team deliverables wiki page
#* [[Gene_hAPI_Deliverables|Gene hAPI Deliverables page (this current page)]]
# Group report
#*
# Individual statements
#* Eddie A.:
#* Dina:
#* John: [[Johnllopez616_Individual_Statement|John's Individual Statement]]
#* Corinne: [[Cwong34_Individual_Statement|Corinne's individual statement]]
# Group PowerPoint presentation
#* [[Media:Gene_hAPI_Final_Presentation.pptx | Gene hAPI final presentation]]
#* [[Media:JLopezEAzingeJournalClub.pptx | Coders' Journal Club Presentation]] 
#* [[Media:Cold_Shock_Yeast_Genome_Response.pdf | QA/Data Analyst Journal Club Presentation]]
# Code (GitHub pull request)
#*
# README
#* [[Media:GetGeneInformationREADME.txt | getGeneInformation() Readme]]
# Excel spreadsheet with ANOVA results/stem formatting
#*[[Media:DGLN3_ANOVA_DB.xlsx | DGLN3 ANOVA/Stem]]
# PowerPoint of screenshots of stem results
#*[[Media:DGLN3_ppt_Dina.pptx | DGLN3 ppt Dina]]
# Gene List and GO List files from each significant profile
#*[[Media:Gene_List_GO_List_DB.zip | DGLN3 Gene List and GO list]]
# YEASTRACT "rank by TF" results
#*[[Media:Yeastract_results_TF_DB_Gene_hAPI.xlsx | Yeastract TF List]]
# GRNmap input workbook (with network adjency matrix)
#*[[Media:GRNmap_dGLN3_input.xlsx | GRNmap dGLN3 input]]
# GRNmap output workbook
#*[[Media:15-genes_32-edges_team-hAPI_Sigmoid_estimation_output.xlsx | GRNmap dGLN3 output]]
# Electronic notebooks
#* [[Dbashour_Week_8|Dina's Week 8]]
#* [[Dbashour_Week_10|Dina's Week 10]]
#* [[Dbashour_Week_11|Dina's Week 11]]
#* [[Dbashour_Week_12|Dina's Week 12]]
#* [[Dbashour_Week_14|Dina's Week 14]]
#* [[Dbashour_Week_15|Dina's Week 15]]

= Deliverables Checklist =

# Organized Team deliverables wiki page (or other media (CD or flash drive) with table of contents)
# Group Report (''.doc'', ''.docx'' or ''.pdf'' file)
# Individual statements of work, assessments, reflections (wiki page, ''.doc'', ''.docx'', ''.pdf'', or e-mailed to both Dr. Dahlquist and Dr. Dionisio)
# Group PowerPoint presentation (given on Tuesday, December 12, ''.ppt'', ''.pptx'' or ''.pdf'' file)
# Code (GitHub pull request)
#* Each team should coordinate in performing a final integration and integration testing iteration (see [[Coder]] milestone for details) which the Interaction and Integration team then submits to the ''original'' GRNsight GitHub repository as a single, unified pull request from the class project’s fork
# Supply a README that summarizes the functionality of your team's new feature (''.txt'' or ''.md'', ''one README per team'')
# Excel spreadsheet with ANOVA results/stem formatting (''.xlsx'')
# PowerPoint of screenshots of stem results (''.pptx'')
# Gene List and GO List files from each significant profile (''.txt'' compressed together in a ''.zip'' file)
# YEASTRACT "rank by TF" results (''.xlsx'')
# GRNmap input workbook (with network adjacency matrix, ''.xlsx'')
# GRNmap output workbook (''.xlsx'')
# Electronic notebook corresponding to these the microarray results files ([[Week 8]], [[Week 10]], and Weeks 11-15) support ''reproducible research'' so that all manipulations of the data and files are documented so that someone else could begin with your starting file, follow the protocol, and obtain your results.

=Group Report Update=
*1-2 page introduction
*Methods
**Data analyst
**QA
**Coders
*Combine results/discussion - add few sentences about significance after each result
**DA
**QA
**Coders
*Conclusion 1-2 pages
**Connect to JC papers
**Future direction
**Summary

[[Category: Gene hAPI]]

[[Category: Group Project]]

[[Category: Deliverables]]

Gene hAPI Deliverables

2017-12-15T23:11:05Z

Johnllopez616: /* Gene hAPI Deliverables */ Added readme

[[Gene hAPI]]

Members:
*[[User:Cazinge|Eddie Azinge]]
*[[User:Dbashour|Dina Bashoura]]
*[[User:Johnllopez616|John Lopez]]
*[[User:Cwong34|Corinne Wong]]

= Gene hAPI Deliverables =
# Organized team deliverables wiki page
#* [[Gene_hAPI_Deliverables|Gene hAPI Deliverables page (this current page)]]
# Group report
#*
# Individual statements
#* Eddie A.:
#* Dina:
#* John:
#* Corinne: [[Cwong34_Individual_Statement|Corinne's individual statement]]
# Group PowerPoint presentation
#* [[Media:Gene_hAPI_Final_Presentation.pptx | Gene hAPI final presentation]]
#* [[Media:JLopezEAzingeJournalClub.pptx | Coders' Journal Club Presentation]] 
#* [[Media:Cold_Shock_Yeast_Genome_Response.pdf | QA/Data Analyst Journal Club Presentation]]
# Code (GitHub pull request)
#*
# README
#* [[Media:GetGeneInformationREADME.txt | getGeneInformation() Readme]]
# Excel spreadsheet with ANOVA results/stem formatting
#*
# PowerPoint of screenshots of stem results
#*
# Gene List and GO List files from each significant profile
#*
# YEASTRACT "rank by TF" results
#*
# GRNmap input workbook (with network adjency matrix)
#*
# GRNmap output workbook
#*
# Electronic notebooks
#* [[Dbashour_Week_8|Dina's Week 8]]
#* [[Dbashour_Week_10|Dina's Week 10]]
#* [[Dbashour_Week_11|Dina's Week 11]]
#* [[Dbashour_Week_12|Dina's Week 12]]
#* [[Dbashour_Week_14|Dina's Week 14]]
#* [[Dbashour_Week_15|Dina's Week 15]]

= Deliverables Checklist =

# Organized Team deliverables wiki page (or other media (CD or flash drive) with table of contents)
# Group Report (''.doc'', ''.docx'' or ''.pdf'' file)
# Individual statements of work, assessments, reflections (wiki page, ''.doc'', ''.docx'', ''.pdf'', or e-mailed to both Dr. Dahlquist and Dr. Dionisio)
# Group PowerPoint presentation (given on Tuesday, December 12, ''.ppt'', ''.pptx'' or ''.pdf'' file)
# Code (GitHub pull request)
#* Each team should coordinate in performing a final integration and integration testing iteration (see [[Coder]] milestone for details) which the Interaction and Integration team then submits to the ''original'' GRNsight GitHub repository as a single, unified pull request from the class project’s fork
# Supply a README that summarizes the functionality of your team's new feature (''.txt'' or ''.md'', ''one README per team'')
# Excel spreadsheet with ANOVA results/stem formatting (''.xlsx'')
# PowerPoint of screenshots of stem results (''.pptx'')
# Gene List and GO List files from each significant profile (''.txt'' compressed together in a ''.zip'' file)
# YEASTRACT "rank by TF" results (''.xlsx'')
# GRNmap input workbook (with network adjacency matrix, ''.xlsx'')
# GRNmap output workbook (''.xlsx'')
# Electronic notebook corresponding to these the microarray results files ([[Week 8]], [[Week 10]], and Weeks 11-15) support ''reproducible research'' so that all manipulations of the data and files are documented so that someone else could begin with your starting file, follow the protocol, and obtain your results.

=Group Report Update=
*1-2 page introduction
*Methods
**Data analyst
**QA
**Coders
*Combine results/discussion - add few sentences about significance after each result
**DA
**QA
**Coders
*Conclusion 1-2 pages
**Connect to JC papers
**Future direction
**Summary

[[Category: Gene hAPI]]

[[Category: Group Project]]

[[Category: Deliverables]]

File:GetGeneInformationREADME.txt

2017-12-15T23:07:21Z

Johnllopez616: The README for getGeneInformation()

The README for getGeneInformation()

Johnllopez Week 15

2017-12-12T03:26:31Z

Johnllopez616: Added references

==Electronic Lab Notebook==
==Acknowledgements and References==
===Acknowledgements===
===References===
LMU BioDB 2017. (2017). Week 15. Retrieved December 11, 2017 from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15

{{Template:johnllopez616}}

Johnllopez Week 15

2017-12-12T03:25:13Z

Johnllopez616: Added my template

==Electronic Lab Notebook==
==Acknowledgements and References==
===Acknowledgements===
===References===
{{Template:johnllopez616}}

Johnllopez Week 15

2017-12-12T03:24:40Z

Johnllopez616: Set up the page outline

==Electronic Lab Notebook==
==Acknowledgements and References
===Acknowledgements===
===References===

Gene hAPI

2017-12-05T07:16:27Z

Johnllopez616: /* Gene hAPI */ Added my week 14 entry (John Lopez)

==Gene hAPI==

===General Information===
Eddie (Cazinge):
*Role: Coder
*User Page: [[User:cazinge|Eddie Azinge]]

Dina (Dbashour):
*Role: Data Analysis
*User Page: [[User:dbashour|Dina Bashoura]]

Corinne (Cwong34):
*Role: Project Manager/Quality Assurance
*User Page: [[User:Cwong34|Corinne Wong]]

John (johnllopez616):
*Role: Coder
*User Page: [[User:johnllopez616|John Lopez]]

===Executive Summaries===
'''Eddie''':
* [[Cazinge Week 11|Week 11]]:
** This week, I finished the bulk of the function logic for our final project; I also performed research on the items necessary for an effective journal club presentation this coming Thursday by completing the individual assignment that we were assigned for the week.
** Getting a large portion of our designated assignment completed early worked pretty successfully to alleviate our stress over the impending assignment and place us ahead of the pace of other groups so that we would be able to work on the more secondary parts of our final presentation across the next 4 weeks.
** Working on the project without having a proper development environment set up ended up detracting from the fluidity of our collaboration as a team; as the versions of the final function that John and I worked on weren't linked via git, and were somewhat unruly to collaborate on.
** Next time, I'll make sure to set up my development environment according to Dondi's instructions on the Coders Guild Page.
[[User:Cazinge|Cazinge]] ([[User talk:Cazinge|talk]]) 23:39, 20 November 2017 (PST)
* [[Cazinge Week 12|Week 12]]:
** This week my task was to set up my development environment for the coder milestones. As such, I've completed milestones 1-3, talked to the other coders, and established a plan to work on the assignment in the future along with the rest of my team.
** Setting up milestones 1-3 went pretty well; since they were all standard open source project tasks, I was able to complete them simply, efficiently, and without any real friction.
** The only thing that I found less than desirable from this week was our communication; As Thanksgiving weekend rolls around we only stand to fall behind if we continue without amending our communication situation.
** This next week, I'll focus on keeping an open line of communication with the rest of my team, as well as completing the majority of the coding milestones that we have left.
[[User:Cazinge|Cazinge]] ([[User talk:Cazinge|talk]]) 23:39, 20 November 2017 (PST)

'''Dina''':
* [[Dbashour_Week_11 | Week 11]]
** For this week, I assisted with creating our group wiki page, adding the template and setting up the page in preparation for the later weeks to come. I also located two out of 4 research articles regarding cold shock, yeast, and microarray data that we might later use for our final project. I became familiar with how to narrow down search queries in order to yield the smallest amount of results that are related to your actual topic, as well as identify how many articles are cited and how many articles cite the articles I found.
** I liked being able to work on the assignment in class, this way I was able to ask questions or clarify certain things that I needed help with. I also like that we have a guild of people, this way there is more of a support system if I am ever lost or need assistance.
** Because my task for this week was simply following the directions on the wiki, there was nothing that went wrong or needed fixing.
** Next week, I will work with my guild to present on our found articles and collaborate with them all in order to make our presentation run smoothly. 
[[User:Dbashour|Dbashour]] ([[User talk:Dbashour|talk]]) 23:43, 13 November 2017 (PST)
*[[Dbashour_Week_12 | Week 12]]
** For this week, Corrine and I prepared for the journal club presentation by individually reading the article "Comprehensive expression analysis of time-dependent responses in yeast cells to low temperature" by Sahara, T., Goda, T., & Ohgiya, S. After reading this article, I developed an outline that highlighted the main points in each section of the article. With Corrine, I made a presentation on that outline, making sure to include each highlighted point. I also located and defined 10 words in the article that I was unfamiliar with and presented a flowchart of the overall experimental design.
** What worked well for this week was to collaborate with Corrine on who was going to present which parts of the article, this way there was no confusion on that matter and the overall flow of the presentation would be well executed.
** There was a lack of communication with all of us as a team, so I am unsure as to what John and Eddie have done for this week.
** Next week, we will all communicate via text either with the entire class or with just my group in order to clarify what the role of each person is and if we have been completing our tasks. 
[[User:Dbashour|Dbashour]] ([[User talk:Dbashour|talk]]) 12:10, 21 November 2017 (PST)

'''Corinne''':
* [[Cwong34_Week_11|Week 11]]:
** This week I helped to create the template and group page. I found two sources to contribute to our annotated bibliography, which we can use to research information for our final project. I researched the accessibility and publishing details of the sources.
** It was nice that we had some time in class to work, so we could easily check in with each other about what we were working on. It was also nice that Dina and I were working on the same project, so we could easily understand our work and help each other.
** It was a bit difficult to be fully aware of the progress of everyone because we had separate projects for this week and next week too. Both halves of our group are working on separate presentations, so we have different focuses, which makes it harder to keep up with each other.
** Next week, since it will be a similar situation, I will try to keep up with the other half of my group by fully understanding their objectives/assignments for the week and checking in some more.
*[[Cwong34_Week_12|Week_12]]:
**This week, I read the "Comprehensive expression analysis of time-dependent responses in yeast cells to low temperature" by Sahara, T., Goda, T., & Ohgiya, S. I came up with a flow chart of their methods for the experiment and made an outline for my individual assignment. I also found ten terms I didn't know and wrote down their definitions in my individual journal. I worked with Dina on our presentation of the article over the weekend.
**Having a collaborative assignment worked for me and Dina because we knew exactly what we needed to do for the project this week, and we worked together to get it done. Moreover, we had more time to meet up with each other this weekend, so it was easier to collaborate.
**It was still difficult to keep in touch with all of the members of the group since we all had different things to work on.
**However, now that we are done with our separate presentations, it will be more of a focus to know what each person is working on. Moreover, I will work to create more communication between group members to keep track of our progress, whether it's on our gene page or over text.

[[User:Cwong34|Cwong34]] ([[User talk:Cwong34|talk]]) 23:26, 20 November 2017 (PST)

'''John''':
* [[Johnllopez Week 11|Week 11]]:
** This week my task was mostly focused around organizing the Journal Club Presentation. I created the initial outline for the powerpoint, created the style, and added over half the content to it. In addition, I spent some time with [[User:cazinge | Eddie Azinge]] who finished most of the deliverable portion of the assignment as he explained to me his process.
** I felt the assembling of the group was done so with ease because I worked with each of the people in the past on different assignments/projects. I felt like each of my members are dedicated and willing to work, so I'm glad that we have a good group. Eddie's experience in coding was an advantage for me because I shouldn't have any sort of confusion, however as I explain below, it is also a disadvantage.
** Despite the fact that Eddie provided an explanation for how he was able to develop the primary deliverable for the project, I felt a little disappointed that I couldn't go through the same discovery process he did. It essentially makes me feel like my role in the project isn't as important. In addition, I was also irritated that we didn't have many opportunities to work on the Journal Club Presentations in advance, for I felt like we weren't as prepared to create/give them as we could have been.
**Next week, I know that I have to get a head start on my individual portion of the assignment so that I'm not crunched for time like I was for the presentation. In addition, it's imperative that I review the code Eddie set up in detail so I can understand each line and how it works. Furthermore, I have to follow along with the other coders in setting up development rigs.
[[User:Johnllopez616|Johnllopez616]] ([[User talk:Johnllopez616|talk]]) 23:41, 13 November 2017 (PST)

* [[Johnllopez Week 12|Week 12]]:
** This week my task involved setting up my development environment for the later milestones. It included the establishment of milestones 1-3, talking to the other coders, and establishing a plan to work on the assignment in the future.
** I felt like the setting up of the environment went well. Once I understood what I had to do, it was not difficult to set up the environment. In addition, I had no problems setting it up on GitHub and my computer once it happened.
** Unfortunately I felt like this week wasn't a very productive week. Despite setting up the environment, I did not collaborate well with my teammates. We have yet to arrange a proper work schedule and plan, especially to ensure that over the thanksgiving break we are able to do some stuff. This has led to the group's progress existing in a state of limbo.
** On Thursday, I asked the class to obtain a WhatsApp to allow for communication. This will be essential to communicate between the coders to accomplish the project. On Tuesday I will connect with as many people in the class. More importantly, I will get my group together to work on a set plan to work on the assignment and establish deadlines. Although this week wasn't the most productive for me, I will ensure that we don't fall behind next week.
[[User:Johnllopez616|Johnllopez616]] ([[User talk:Johnllopez616|talk]]) 23:27, 20 November 2017 (PST)

*[[johnllopez Week 14|Week 14]]:
**This week's primary objective was to get as much of Milestone 4 as finished as possible. My portion of the assignment was to learn how to extract data from XML files and translate it so that the page developers could use it.
**Perhaps the best part about this portion of the assignment was being able to discover a bit of jQuery and DOM functions. Knowledge and exposure to both of these is fundamental in obtaining a potential job.
**One area where I struggled was figuring out how to extract JSON using javascript. This is something that both of the Eddies, however, were proficient in doing, so it's important that I seek their help in understanding this concept. In addition, I wish I communicated more with the coders during the development of the project.
**This week will be crucial in finishing Milestone 4 for the project. It's absolutely necessary that the coders and I not only integrate everything, but that I am following along with what they do. I will ask a lot of questions to truly understand what's happening.
[[User:Johnllopez616|Johnllopez616]] ([[User talk:Johnllopez616|talk]]) 23:16, 4 December 2017 (PST)

==Journal Club Deliverable==
[[Media:JLopezEAzingeJournalClub.pptx | The presentation - Coder/Designer]] 
[[Media:Cold_Shock_Yeast_Genome_Response.pdf | Journal Club Week 12 Presentation - QA/Data Analyst]]

== Journal Club Article ==
Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.
 
{{template:Gene_hAPI}}

Template:Johnllopez616

2017-12-05T07:10:24Z

Johnllopez616: Added project journal links

Johnllopez Week 14

2017-12-05T07:08:59Z

Johnllopez616: Added link to github

==Electronic Lab Notebook==
===Pulling Data===
Thanks to [[User:cwong34 | Corrine Wong]], I was able to use the following table to figure out what processes had to be made in order to pull certain data from the functions:

'''NCBI'''
*Locus tag < Parse from page https://www.ncbi.nlm.nih.gov/gene/854068
*Gene ID < Parse from conversion algorithm

'''UniProt'''
*Protein type/name <Parse XML?
*Protein sequence <Parse XML
*Gene ID <Parse XML
*Similar proteins <Could not find on XML, found on Page

'''Ensembl'''
*DNA sequence < Pull from http://www.ensembl.org/Saccharomyces_cerevisiae/Transcript/Sequence_cDNA?db=core;g=YJL128C;r=X:178097-180103;t=YJL128C
*Gene description < Pulled from JSON
*Gene ID < Pulled from JSON / Conversion Necessary

'''SGD'''
*Gene ID < Pulled from JSON/ Possible conversion necessary
*Gene expression < NO IDEA HOW WE CAN PULL THIS
*Gene regulation <Pull from page https://www.yeastgenome.org/locus/S000005446
*Gene ontology <SUummary in JSON

'''JASPAR'''
*Sequence logo
*Frequency matrixon her

===Learning XML DOM===
I was first tasked to figure out how to extract data from XML files. This was necessary to pull the pieces above marked "XML". I did so by using aspects from the jQuery library and XML Document Object Model.

The functions I used from jQuery were $get and $append, and I learned how to use these thanks to the [[Week 7]] assignment. They allowed me to directly pull XML files from a query and append to a webpage. The next challenge was figuring out how to parse the data given to me and extract what I need.

I then figured out since XML was a markup language like HTML, I could use the same Document Object Model functions that I would to parse HTML. Of course, I had no idea how to do either, so I used [https://developer.mozilla.org/en-US/docs/Web/API/Document_Object_Model | MDN] to explain certain aspects of it.

I figured that the serializeToString() and getElementsByTagName() were useful, so that allowed me to pull lines of XML.

One problem was, such in the case of extracting the LOTUS tag and Other Names data from NCBI, the string that returned contained both pieces of data! The way I got around this was by taking the data as a string, using the split() function to make each word a node of an array, then further manipulating this array using the splice() function to remove the LOTUS tag once it was called.

Another problem I encountered was that some elements shared names, so I had to modify getElementsByTagName() by specifying that I wanted to view nodes and children of larger, more accessible XML tags. An example of this was getting the "Protein Type/Name" from UniProt. This was done through getting the child node of a child node of the "protein" tag.

There was one piece of data that I could unfortunately not figure out how to extract because I could not find the API call for it. This is something I will discuss with my partners on Tuesday.

You may see the work I completed on github [https://github.com/bhamilton18/GRNsight/blob/gene-database-apis/XML/XMLfunction.js here].
==Acknowledgements and References==
===Acknowledgements===
This week required collaboration between the coders [[User:cazinge | Eddie Azinge]], [[User:ebachour | Eddie Bachoura]], and [[User:simonwro120 | Simon Wroblewski]]. While they developed the necessary components for JSON, I developed the XML portion. In addition, I discussed with [[User:cwong34 | Corrine Wong]] which functions were necessary to pull from the data provided.

While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.
[[User:Johnllopez616|Johnllopez616]] ([[User talk:Johnllopez616|talk]]) 23:06, 4 December 2017 (PST)

===References===
MDN. ''Document Object Model''. Retrieved December 1, 2017, from https://developer.mozilla.org/en-US/docs/Web/API/Document_Object_Model
LMU BioDB 2017. (2017). Week 14. Retrieved December 4, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_14
LMU BioDB 2017. (2017). Week 7. Retrieved December 1, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_7

{{Template:johnllopez616}}

Johnllopez Week 14

2017-12-05T07:07:00Z

Johnllopez616: /* Acknowledgements and References */ Added acknowledgements

==Electronic Lab Notebook==
===Pulling Data===
Thanks to [[User:cwong34 | Corrine Wong]], I was able to use the following table to figure out what processes had to be made in order to pull certain data from the functions:

'''NCBI'''
*Locus tag < Parse from page https://www.ncbi.nlm.nih.gov/gene/854068
*Gene ID < Parse from conversion algorithm

'''UniProt'''
*Protein type/name <Parse XML?
*Protein sequence <Parse XML
*Gene ID <Parse XML
*Similar proteins <Could not find on XML, found on Page

'''Ensembl'''
*DNA sequence < Pull from http://www.ensembl.org/Saccharomyces_cerevisiae/Transcript/Sequence_cDNA?db=core;g=YJL128C;r=X:178097-180103;t=YJL128C
*Gene description < Pulled from JSON
*Gene ID < Pulled from JSON / Conversion Necessary

'''SGD'''
*Gene ID < Pulled from JSON/ Possible conversion necessary
*Gene expression < NO IDEA HOW WE CAN PULL THIS
*Gene regulation <Pull from page https://www.yeastgenome.org/locus/S000005446
*Gene ontology <SUummary in JSON

'''JASPAR'''
*Sequence logo
*Frequency matrixon her

===Learning XML DOM===
I was first tasked to figure out how to extract data from XML files. This was necessary to pull the pieces above marked "XML". I did so by using aspects from the jQuery library and XML Document Object Model.

The functions I used from jQuery were $get and $append, and I learned how to use these thanks to the [[Week 7]] assignment. They allowed me to directly pull XML files from a query and append to a webpage. The next challenge was figuring out how to parse the data given to me and extract what I need.

I then figured out since XML was a markup language like HTML, I could use the same Document Object Model functions that I would to parse HTML. Of course, I had no idea how to do either, so I used [https://developer.mozilla.org/en-US/docs/Web/API/Document_Object_Model | MDN] to explain certain aspects of it.

I figured that the serializeToString() and getElementsByTagName() were useful, so that allowed me to pull lines of XML.

One problem was, such in the case of extracting the LOTUS tag and Other Names data from NCBI, the string that returned contained both pieces of data! The way I got around this was by taking the data as a string, using the split() function to make each word a node of an array, then further manipulating this array using the splice() function to remove the LOTUS tag once it was called.

Another problem I encountered was that some elements shared names, so I had to modify getElementsByTagName() by specifying that I wanted to view nodes and children of larger, more accessible XML tags. An example of this was getting the "Protein Type/Name" from UniProt. This was done through getting the child node of a child node of the "protein" tag.

There was one piece of data that I could unfortunately not figure out how to extract because I could not find the API call for it. This is something I will discuss with my partners on Tuesday.

===Working with JSON===
==Acknowledgements and References==
===Acknowledgements===
This week required collaboration between the coders [[User:cazinge | Eddie Azinge]], [[User:ebachour | Eddie Bachoura]], and [[User:simonwro120 | Simon Wroblewski]]. While they developed the necessary components for JSON, I developed the XML portion. In addition, I discussed with [[User:cwong34 | Corrine Wong]] which functions were necessary to pull from the data provided.

While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.
[[User:Johnllopez616|Johnllopez616]] ([[User talk:Johnllopez616|talk]]) 23:06, 4 December 2017 (PST)

===References===
MDN. ''Document Object Model''. Retrieved December 1, 2017, from https://developer.mozilla.org/en-US/docs/Web/API/Document_Object_Model
LMU BioDB 2017. (2017). Week 14. Retrieved December 4, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_14
LMU BioDB 2017. (2017). Week 7. Retrieved December 1, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_7

{{Template:johnllopez616}}

Johnllopez Week 14

2017-12-05T07:02:57Z

Johnllopez616: Added references

==Electronic Lab Notebook==
===Pulling Data===
Thanks to [[User:cwong34 | Corrine Wong]], I was able to use the following table to figure out what processes had to be made in order to pull certain data from the functions:

'''NCBI'''
*Locus tag < Parse from page https://www.ncbi.nlm.nih.gov/gene/854068
*Gene ID < Parse from conversion algorithm

'''UniProt'''
*Protein type/name <Parse XML?
*Protein sequence <Parse XML
*Gene ID <Parse XML
*Similar proteins <Could not find on XML, found on Page

'''Ensembl'''
*DNA sequence < Pull from http://www.ensembl.org/Saccharomyces_cerevisiae/Transcript/Sequence_cDNA?db=core;g=YJL128C;r=X:178097-180103;t=YJL128C
*Gene description < Pulled from JSON
*Gene ID < Pulled from JSON / Conversion Necessary

'''SGD'''
*Gene ID < Pulled from JSON/ Possible conversion necessary
*Gene expression < NO IDEA HOW WE CAN PULL THIS
*Gene regulation <Pull from page https://www.yeastgenome.org/locus/S000005446
*Gene ontology <SUummary in JSON

'''JASPAR'''
*Sequence logo
*Frequency matrixon her

===Learning XML DOM===
I was first tasked to figure out how to extract data from XML files. This was necessary to pull the pieces above marked "XML". I did so by using aspects from the jQuery library and XML Document Object Model.

The functions I used from jQuery were $get and $append, and I learned how to use these thanks to the [[Week 7]] assignment. They allowed me to directly pull XML files from a query and append to a webpage. The next challenge was figuring out how to parse the data given to me and extract what I need.

I then figured out since XML was a markup language like HTML, I could use the same Document Object Model functions that I would to parse HTML. Of course, I had no idea how to do either, so I used [https://developer.mozilla.org/en-US/docs/Web/API/Document_Object_Model | MDN] to explain certain aspects of it.

I figured that the serializeToString() and getElementsByTagName() were useful, so that allowed me to pull lines of XML.

One problem was, such in the case of extracting the LOTUS tag and Other Names data from NCBI, the string that returned contained both pieces of data! The way I got around this was by taking the data as a string, using the split() function to make each word a node of an array, then further manipulating this array using the splice() function to remove the LOTUS tag once it was called.

Another problem I encountered was that some elements shared names, so I had to modify getElementsByTagName() by specifying that I wanted to view nodes and children of larger, more accessible XML tags. An example of this was getting the "Protein Type/Name" from UniProt. This was done through getting the child node of a child node of the "protein" tag.

There was one piece of data that I could unfortunately not figure out how to extract because I could not find the API call for it. This is something I will discuss with my partners on Tuesday.

===Working with JSON===
==Acknowledgements and References==
===Acknowledgements===
===References===
MDN. '''Document Object Model'''. Retrieved December 1, 2017, from https://developer.mozilla.org/en-US/docs/Web/API/Document_Object_Model
LMU BioDB 2017. (2017). Week 14. Retrieved December 4, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_14
LMU BioDB 2017. (2017). Week 7. Retrieved December 1, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_7

{{Template:johnllopez616}}

Johnllopez Week 14

2017-12-05T03:30:54Z

Johnllopez616: Finished the XML section

==Electronic Lab Notebook==
===Pulling Data===
Thanks to [[User:cwong34 | Corrine Wong]], I was able to use the following table to figure out what processes had to be made in order to pull certain data from the functions:

'''NCBI'''
*Locus tag < Parse from page https://www.ncbi.nlm.nih.gov/gene/854068
*Gene ID < Parse from conversion algorithm

'''UniProt'''
*Protein type/name <Parse XML?
*Protein sequence <Parse XML
*Gene ID <Parse XML
*Similar proteins <Could not find on XML, found on Page

'''Ensembl'''
*DNA sequence < Pull from http://www.ensembl.org/Saccharomyces_cerevisiae/Transcript/Sequence_cDNA?db=core;g=YJL128C;r=X:178097-180103;t=YJL128C
*Gene description < Pulled from JSON
*Gene ID < Pulled from JSON / Conversion Necessary

'''SGD'''
*Gene ID < Pulled from JSON/ Possible conversion necessary
*Gene expression < NO IDEA HOW WE CAN PULL THIS
*Gene regulation <Pull from page https://www.yeastgenome.org/locus/S000005446
*Gene ontology <SUummary in JSON

'''JASPAR'''
*Sequence logo
*Frequency matrixon her

===Learning XML DOM===
I was first tasked to figure out how to extract data from XML files. This was necessary to pull the pieces above marked "XML". I did so by using aspects from the jQuery library and XML Document Object Model.

The functions I used from jQuery were $get and $append, and I learned how to use these thanks to the [[Week 7]] assignment. They allowed me to directly pull XML files from a query and append to a webpage. The next challenge was figuring out how to parse the data given to me and extract what I need.

I then figured out since XML was a markup language like HTML, I could use the same Document Object Model functions that I would to parse HTML. Of course, I had no idea how to do either, so I used [https://developer.mozilla.org/en-US/docs/Web/API/Document_Object_Model | MDN] to explain certain aspects of it.

I figured that the serializeToString() and getElementsByTagName() were useful, so that allowed me to pull lines of XML.

One problem was, such in the case of extracting the LOTUS tag and Other Names data from NCBI, the string that returned contained both pieces of data! The way I got around this was by taking the data as a string, using the split() function to make each word a node of an array, then further manipulating this array using the splice() function to remove the LOTUS tag once it was called.

Another problem I encountered was that some elements shared names, so I had to modify getElementsByTagName() by specifying that I wanted to view nodes and children of larger, more accessible XML tags. An example of this was getting the "Protein Type/Name" from UniProt. This was done through getting the child node of a child node of the "protein" tag.

There was one piece of data that I could unfortunately not figure out how to extract because I could not find the API call for it. This is something I will discuss with my partners on Tuesday.

===Working with JSON===
==Acknowledgements and References==
===Acknowledgements===
===References===
https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_7
https://developer.mozilla.org/en-US/docs/Web/API/Document_Object_Model
{{Template:johnllopez616}}

Johnllopez Week 14

2017-12-05T03:25:28Z

Johnllopez616: Explained how I got NCBI

Johnllopez Week 14

2017-12-05T03:19:10Z

Johnllopez616: Explained how I used jquery

Johnllopez Week 14

2017-12-05T01:46:51Z

Johnllopez616: Added my template

Johnllopez Week 14

2017-12-05T01:46:12Z

Johnllopez616: Added a template for the page structure

Johnllopez Week 14

2017-11-30T08:50:18Z

Johnllopez616: /* Pulling Data */ Added how to get the data

==Pulling Data==
Thanks to [[User:cwong34 | Corrine Wong]], I was able to use the following table to figure out what processes had to be made in order to pull certain data from the functions:

'''NCBI'''
*Locus tag < Parse from page https://www.ncbi.nlm.nih.gov/gene/854068
*Gene ID < Parse from conversion algorithm

'''UniProt'''
*Protein type/name <Parse XML?
*Protein sequence <Parse XML
*Gene ID <Parse XML
*Similar proteins <Could not find on XML, found on Page

'''Ensembl'''
*DNA sequence < Pull from http://www.ensembl.org/Saccharomyces_cerevisiae/Transcript/Sequence_cDNA?db=core;g=YJL128C;r=X:178097-180103;t=YJL128C
*Gene description < Pulled from JSON
*Gene ID < Pulled from JSON / Conversion Necessary

'''SGD'''
*Gene ID < Pulled from JSON/ Possible conversion necessary
*Gene expression < NO IDEA HOW WE CAN PULL THIS
*Gene regulation <Pull from page https://www.yeastgenome.org/locus/S000005446
*Gene ontology <SUummary in JSON

'''JASPAR'''
*Sequence logo
*Frequency matrixon her

Johnllopez Week 14

2017-11-30T08:02:03Z

Johnllopez616: Added table for what information needs to be pulled from where

==Pulling Data==
Thanks to [[User:cwong34 | Corrine Wong]], I was able to use the following table to figure out what processes had to be made in order to pull certain data from the functions:

'''NCBI'''
*Locus tag
*Gene ID

'''UniProt'''
*Protein type/name
*Protein sequence
*Gene ID
*Similar proteins

'''Ensembl'''
*DNA sequence
*Gene description
*Gene ID

'''SGD'''
*Gene ID
*Gene expression
*Gene regulation
*Gene ontology

'''JASPAR'''
*Sequence logo
*Frequency matrixon her

Johnllopez Week 12

2017-11-21T07:44:05Z

Johnllopez616: Wrote milestone 4

==Milestone 0==
As performed on Thursday, [[Media:JLopezEAzingeJournalClub.pptx | this file]] contains the deliverable for my presentation.
==Milestone 1==
To achieve this milestone, I had to ensure that my PC had the following programs installed:

#Node.js 8.4.0 or newer
#Code-savvy editor such as Atom or Microsoft Visual Studio Code
#Web browser with developer tools (Seaver 120 uses Google Chrome)
#git version control software
#curl command
Fortunately, each of the programs were! I had Node.JS from the [[Week 7 | Week 7]] assignment, atom from my Programming Lab class, and Chrome + Git were already installed on my pc! I also ran the following test on git:

curl https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Main_Page

This returned the HTML for the page, so curl was definitely working!

==Milestone 2==
This was the first milestone that required collaboration with my teammates. It also required some interaction on GitHub.

You can access my GitHub with the following link:
https://github.com/johnllopez616

Then, on Thursday in class, I talked to [[User:Bhamilton18 | Blair Hamilton]] who created a fork of GRNSight. In addition, she added each of the coders to said fork. You can find the fork here:

https://github.com/bhamilton18/GRNsight

Then, I created a branch called gene-database-apis. You can find it here:

https://github.com/bhamilton18/GRNsight/tree/gene-database-apis
==Milestone 3==
These steps were necessary to ensure I had a working development environment. Prior to this, however, I did not use git, so I had to follow each step carefully to ensure that my environment worked.

# I had to git clone Blair's fork onto my computer. To do this, I had [[User:cazinge | Eddie Azinge]] show me how. I was able to do each step on my own from that moment.
# I had to cd into the folder on my pc (C:\Users\John\GRNSight)
# I performed the following command: git checkout gene-database-apis. From here, whenever I would CD into GRNSight, it would automatically go into that branch.
# Finally, I performed npm install in that branch as suggested by the following link: https://github.com/dondi/GRNsight/wiki/Running-the-Applications. Then, I went to
http://localhost:5001/, and saw that GRNSight was here!

==Milestone 4==
For this milestone, I consulted my partner [[User:cazinge | Eddie Azinge]]. He has written most of what we believe to be the code needed for our portion of the assignment. However, we have yet to write any sort of unit tests to see if it works. In addition, he has explained to me how his code works and what I need to do to write my function.

==Acknowledgements and References==
===Acknowledgements===
In class, I consulted [[User:Bhamilton18 | Blair Hamilton]] and [[User:cazinge | Eddie Azinge]] to ensure Milestones 1-3 were completed for this task. We discussed how GitHub would be set up, and Eddie helped me with the first step of Milestone 3. While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.

[[User:Johnllopez616|Johnllopez616]] ([[User talk:Johnllopez616|talk]]) 23:42, 20 November 2017 (PST)

===References===
LMU BioDB 2017. (2017). ''Week 12''. Retrieved November 15, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
GRNSight. ''Running the Applications''. Retrieved November 20, 2017, from https://github.com/dondi/GRNsight/wiki/Running-the-Applications.

{{Template:johnllopez616}}

Johnllopez Week 12

2017-11-21T07:42:18Z

Johnllopez616: Added signature

==Milestone 0==
As performed on Thursday, [[Media:JLopezEAzingeJournalClub.pptx | this file]] contains the deliverable for my presentation.
==Milestone 1==
To achieve this milestone, I had to ensure that my PC had the following programs installed:

#Node.js 8.4.0 or newer
#Code-savvy editor such as Atom or Microsoft Visual Studio Code
#Web browser with developer tools (Seaver 120 uses Google Chrome)
#git version control software
#curl command
Fortunately, each of the programs were! I had Node.JS from the [[Week 7 | Week 7]] assignment, atom from my Programming Lab class, and Chrome + Git were already installed on my pc! I also ran the following test on git:

curl https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Main_Page

This returned the HTML for the page, so curl was definitely working!

==Milestone 2==
This was the first milestone that required collaboration with my teammates. It also required some interaction on GitHub.

You can access my GitHub with the following link:
https://github.com/johnllopez616

Then, on Thursday in class, I talked to [[User:Bhamilton18 | Blair Hamilton]] who created a fork of GRNSight. In addition, she added each of the coders to said fork. You can find the fork here:

https://github.com/bhamilton18/GRNsight

Then, I created a branch called gene-database-apis. You can find it here:

https://github.com/bhamilton18/GRNsight/tree/gene-database-apis
==Milestone 3==
These steps were necessary to ensure I had a working development environment. Prior to this, however, I did not use git, so I had to follow each step carefully to ensure that my environment worked.

# I had to git clone Blair's fork onto my computer. To do this, I had [[User:cazinge | Eddie Azinge]] show me how. I was able to do each step on my own from that moment.
# I had to cd into the folder on my pc (C:\Users\John\GRNSight)
# I performed the following command: git checkout gene-database-apis. From here, whenever I would CD into GRNSight, it would automatically go into that branch.
# Finally, I performed npm install in that branch as suggested by the following link: https://github.com/dondi/GRNsight/wiki/Running-the-Applications. Then, I went to
http://localhost:5001/, and saw that GRNSight was here!

==Milestone 4==
==Acknowledgements and References==
===Acknowledgements===
In class, I consulted [[User:Bhamilton18 | Blair Hamilton]] and [[User:cazinge | Eddie Azinge]] to ensure Milestones 1-3 were completed for this task. We discussed how GitHub would be set up, and Eddie helped me with the first step of Milestone 3. While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.

[[User:Johnllopez616|Johnllopez616]] ([[User talk:Johnllopez616|talk]]) 23:42, 20 November 2017 (PST)

===References===
LMU BioDB 2017. (2017). ''Week 12''. Retrieved November 15, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
GRNSight. ''Running the Applications''. Retrieved November 20, 2017, from https://github.com/dondi/GRNsight/wiki/Running-the-Applications.

{{Template:johnllopez616}}

Johnllopez Week 12

2017-11-21T07:41:34Z

Johnllopez616: Added milestone 4

==Milestone 0==
As performed on Thursday, [[Media:JLopezEAzingeJournalClub.pptx | this file]] contains the deliverable for my presentation.
==Milestone 1==
To achieve this milestone, I had to ensure that my PC had the following programs installed:

#Node.js 8.4.0 or newer
#Code-savvy editor such as Atom or Microsoft Visual Studio Code
#Web browser with developer tools (Seaver 120 uses Google Chrome)
#git version control software
#curl command
Fortunately, each of the programs were! I had Node.JS from the [[Week 7 | Week 7]] assignment, atom from my Programming Lab class, and Chrome + Git were already installed on my pc! I also ran the following test on git:

curl https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Main_Page

This returned the HTML for the page, so curl was definitely working!

==Milestone 2==
This was the first milestone that required collaboration with my teammates. It also required some interaction on GitHub.

You can access my GitHub with the following link:
https://github.com/johnllopez616

Then, on Thursday in class, I talked to [[User:Bhamilton18 | Blair Hamilton]] who created a fork of GRNSight. In addition, she added each of the coders to said fork. You can find the fork here:

https://github.com/bhamilton18/GRNsight

Then, I created a branch called gene-database-apis. You can find it here:

https://github.com/bhamilton18/GRNsight/tree/gene-database-apis
==Milestone 3==
These steps were necessary to ensure I had a working development environment. Prior to this, however, I did not use git, so I had to follow each step carefully to ensure that my environment worked.

# I had to git clone Blair's fork onto my computer. To do this, I had [[User:cazinge | Eddie Azinge]] show me how. I was able to do each step on my own from that moment.
# I had to cd into the folder on my pc (C:\Users\John\GRNSight)
# I performed the following command: git checkout gene-database-apis. From here, whenever I would CD into GRNSight, it would automatically go into that branch.
# Finally, I performed npm install in that branch as suggested by the following link: https://github.com/dondi/GRNsight/wiki/Running-the-Applications. Then, I went to
http://localhost:5001/, and saw that GRNSight was here!

==Milestone 4==
==Acknowledgements and References==
===Acknowledgements===
In class, I consulted [[User:Bhamilton18 | Blair Hamilton]] and [[User:cazinge | Eddie Azinge]] to ensure Milestones 1-3 were completed for this task. We discussed how GitHub would be set up, and Eddie helped me with the first step of Milestone 3. While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.

===References===
LMU BioDB 2017. (2017). ''Week 12''. Retrieved November 15, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
GRNSight. ''Running the Applications''. Retrieved November 20, 2017, from https://github.com/dondi/GRNsight/wiki/Running-the-Applications.

{{Template:johnllopez616}}

Johnllopez Week 12

2017-11-21T07:40:57Z

Johnllopez616: Added milestone 4

==Milestone 0==
As performed on Thursday, [[Media:JLopezEAzingeJournalClub.pptx | this file]] contains the deliverable for my presentation.
==Milestone 1==
To achieve this milestone, I had to ensure that my PC had the following programs installed:

#Node.js 8.4.0 or newer
#Code-savvy editor such as Atom or Microsoft Visual Studio Code
#Web browser with developer tools (Seaver 120 uses Google Chrome)
#git version control software
#curl command
Fortunately, each of the programs were! I had Node.JS from the [[Week 7 | Week 7]] assignment, atom from my Programming Lab class, and Chrome + Git were already installed on my pc! I also ran the following test on git:

curl https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Main_Page

This returned the HTML for the page, so curl was definitely working!

==Milestone 2==
This was the first milestone that required collaboration with my teammates. It also required some interaction on GitHub.

You can access my GitHub with the following link:
https://github.com/johnllopez616

Then, on Thursday in class, I talked to [[User:Bhamilton18 | Blair Hamilton]] who created a fork of GRNSight. In addition, she added each of the coders to said fork. You can find the fork here:

https://github.com/bhamilton18/GRNsight

Then, I created a branch called gene-database-apis. You can find it here:

https://github.com/bhamilton18/GRNsight/tree/gene-database-apis
==Milestone 3==
These steps were necessary to ensure I had a working development environment. Prior to this, however, I did not use git, so I had to follow each step carefully to ensure that my environment worked.

# I had to git clone Blair's fork onto my computer. To do this, I had [[User:cazinge | Eddie Azinge]] show me how. I was able to do each step on my own from that moment.
# I had to cd into the folder on my pc (C:\Users\John\GRNSight)
# I performed the following command: git checkout gene-database-apis. From here, whenever I would CD into GRNSight, it would automatically go into that branch.
# Finally, I performed npm install in that branch as suggested by the following link: https://github.com/dondi/GRNsight/wiki/Running-the-Applications. Then, I went to
http://localhost:5001/, and saw that GRNSight was here!

==Milestone 4==
For this portion, my partner [[User:cazinge | Eddie Azinge]] finished up most of the code. However, we have yet to write unit tests so we are unsure if the code produced works. So far, he discussed what was produced with me and what are the steps I need to do to finish said code.

==Acknowledgements and References==
===Acknowledgements===
In class, I consulted [[User:Bhamilton18 | Blair Hamilton]] and [[User:cazinge | Eddie Azinge]] to ensure Milestones 1-3 were completed for this task. We discussed how GitHub would be set up, and Eddie helped me with the first step of Milestone 3. While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.

===References===
LMU BioDB 2017. (2017). ''Week 12''. Retrieved November 15, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
GRNSight. ''Running the Applications''. Retrieved November 20, 2017, from https://github.com/dondi/GRNsight/wiki/Running-the-Applications.

{{Template:johnllopez616}}

Johnllopez Week 12

2017-11-21T07:39:40Z

Johnllopez616: Fixed up acknowledgements and references

==Milestone 0==
As performed on Thursday, [[Media:JLopezEAzingeJournalClub.pptx | this file]] contains the deliverable for my presentation.
==Milestone 1==
To achieve this milestone, I had to ensure that my PC had the following programs installed:

#Node.js 8.4.0 or newer
#Code-savvy editor such as Atom or Microsoft Visual Studio Code
#Web browser with developer tools (Seaver 120 uses Google Chrome)
#git version control software
#curl command
Fortunately, each of the programs were! I had Node.JS from the [[Week 7 | Week 7]] assignment, atom from my Programming Lab class, and Chrome + Git were already installed on my pc! I also ran the following test on git:

curl https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Main_Page

This returned the HTML for the page, so curl was definitely working!

==Milestone 2==
This was the first milestone that required collaboration with my teammates. It also required some interaction on GitHub.

You can access my GitHub with the following link:
https://github.com/johnllopez616

Then, on Thursday in class, I talked to [[User:Bhamilton18 | Blair Hamilton]] who created a fork of GRNSight. In addition, she added each of the coders to said fork. You can find the fork here:

https://github.com/bhamilton18/GRNsight

Then, I created a branch called gene-database-apis. You can find it here:

https://github.com/bhamilton18/GRNsight/tree/gene-database-apis
==Milestone 3==
These steps were necessary to ensure I had a working development environment. Prior to this, however, I did not use git, so I had to follow each step carefully to ensure that my environment worked.

# I had to git clone Blair's fork onto my computer. To do this, I had [[User:cazinge | Eddie Azinge]] show me how. I was able to do each step on my own from that moment.
# I had to cd into the folder on my pc (C:\Users\John\GRNSight)
# I performed the following command: git checkout gene-database-apis. From here, whenever I would CD into GRNSight, it would automatically go into that branch.
# Finally, I performed npm install in that branch as suggested by the following link: https://github.com/dondi/GRNsight/wiki/Running-the-Applications. Then, I went to
http://localhost:5001/, and saw that GRNSight was here!

==Milestone 4==
==Acknowledgements and References==
===Acknowledgements===
In class, I consulted [[User:Bhamilton18 | Blair Hamilton]] and [[User:cazinge | Eddie Azinge]] to ensure Milestones 1-3 were completed for this task. We discussed how GitHub would be set up, and Eddie helped me with the first step of Milestone 3. While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.

===References===
LMU BioDB 2017. (2017). ''Week 12''. Retrieved November 15, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
GRNSight. ''Running the Applications''. Retrieved November 20, 2017, from https://github.com/dondi/GRNsight/wiki/Running-the-Applications.

{{Template:johnllopez616}}

Gene hAPI

2017-11-21T07:27:08Z

Johnllopez616: Added my responses for week 12 (John Lopez)

Johnllopez Week 12

2017-11-21T07:05:28Z

Johnllopez616: Added acknowledgements

==Milestone 0==
As performed on Thursday, [[Media:JLopezEAzingeJournalClub.pptx | this file]] contains the deliverable for my presentation.
==Milestone 1==
To achieve this milestone, I had to ensure that my PC had the following programs installed:

#Node.js 8.4.0 or newer
#Code-savvy editor such as Atom or Microsoft Visual Studio Code
#Web browser with developer tools (Seaver 120 uses Google Chrome)
#git version control software
#curl command
Fortunately, each of the programs were! I had Node.JS from the [[Week 7 | Week 7]] assignment, atom from my Programming Lab class, and Chrome + Git were already installed on my pc! I also ran the following test on git:

curl https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Main_Page

This returned the HTML for the page, so curl was definitely working!

==Milestone 2==
This was the first milestone that required collaboration with my teammates. It also required some interaction on GitHub.

You can access my GitHub with the following link:
https://github.com/johnllopez616

Then, on Thursday in class, I talked to [[User:Bhamilton18 | Blair Hamilton]] who created a fork of GRNSight. In addition, she added each of the coders to said fork. You can find the fork here:

https://github.com/bhamilton18/GRNsight

Then, I created a branch called gene-database-apis. You can find it here:

https://github.com/bhamilton18/GRNsight/tree/gene-database-apis
==Milestone 3==
These steps were necessary to ensure I had a working development environment. Prior to this, however, I did not use git, so I had to follow each step carefully to ensure that my environment worked.

# I had to git clone Blair's fork onto my computer. To do this, I had [[User:cazinge | Eddie Azinge]] show me how. I was able to do each step on my own from that moment.
# I had to cd into the folder on my pc (C:\Users\John\GRNSight)
# I performed the following command: git checkout gene-database-apis. From here, whenever I would CD into GRNSight, it would automatically go into that branch.
# Finally, I performed npm install in that branch as suggested by the following link: https://github.com/dondi/GRNsight/wiki/Running-the-Applications. Then, I went to
http://localhost:5001/, and saw that GRNSight was here!

==Milestone 4==
==Acknowledgements and References==
In class, I consulted [[User:Bhamilton18 | Blair Hamilton]] and [[User:cazinge | Eddie Azinge]] to ensure Milestones 1-3 were completed for this task. We discussed how GitHub would be set up, and Eddie helped me with the first step of Milestone 3. While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.

===Acknowledgements===
===References===
LMU BioDB 2017. (2017). ''Week 12''. Retrieved November 15, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
GRNSight. ''Running the Applications''. Retrieved November 20, 2017, from https://github.com/dondi/GRNsight/wiki/Running-the-Applications.

{{Template:johnllopez616}}

Johnllopez Week 12

2017-11-21T07:02:10Z

Johnllopez616: Added milestone 3

==Milestone 0==
As performed on Thursday, [[Media:JLopezEAzingeJournalClub.pptx | this file]] contains the deliverable for my presentation.
==Milestone 1==
To achieve this milestone, I had to ensure that my PC had the following programs installed:

#Node.js 8.4.0 or newer
#Code-savvy editor such as Atom or Microsoft Visual Studio Code
#Web browser with developer tools (Seaver 120 uses Google Chrome)
#git version control software
#curl command
Fortunately, each of the programs were! I had Node.JS from the [[Week 7 | Week 7]] assignment, atom from my Programming Lab class, and Chrome + Git were already installed on my pc! I also ran the following test on git:

curl https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Main_Page

This returned the HTML for the page, so curl was definitely working!

==Milestone 2==
This was the first milestone that required collaboration with my teammates. It also required some interaction on GitHub.

You can access my GitHub with the following link:
https://github.com/johnllopez616

Then, on Thursday in class, I talked to [[User:Bhamilton18 | Blair Hamilton]] who created a fork of GRNSight. In addition, she added each of the coders to said fork. You can find the fork here:

https://github.com/bhamilton18/GRNsight

Then, I created a branch called gene-database-apis. You can find it here:

https://github.com/bhamilton18/GRNsight/tree/gene-database-apis
==Milestone 3==
These steps were necessary to ensure I had a working development environment. Prior to this, however, I did not use git, so I had to follow each step carefully to ensure that my environment worked.

# I had to git clone Blair's fork onto my computer. To do this, I had [[User:cazinge | Eddie Azinge]] show me how. I was able to do each step on my own from that moment.
# I had to cd into the folder on my pc (C:\Users\John\GRNSight)
# I performed the following command: git checkout gene-database-apis. From here, whenever I would CD into GRNSight, it would automatically go into that branch.
# Finally, I performed npm install in that branch as suggested by the following link: https://github.com/dondi/GRNsight/wiki/Running-the-Applications. Then, I went to
http://localhost:5001/, and saw that GRNSight was here!

==Milestone 4==
==Acknowledgements and References==
===Acknowledgements===
===References===
LMU BioDB 2017. (2017). ''Week 12''. Retrieved November 15, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
GRNSight. ''Running the Applications''. Retrieved November 20, 2017, from https://github.com/dondi/GRNsight/wiki/Running-the-Applications.

{{Template:johnllopez616}}

Johnllopez Week 12

2017-11-21T06:48:20Z

Johnllopez616: Added references

Johnllopez Week 12

2017-11-21T06:37:00Z

Johnllopez616: Added milestone 2

Johnllopez Week 12

2017-11-21T06:28:05Z

Johnllopez616: Added milestone 1

Johnllopez Week 12

2017-11-21T06:22:51Z

Johnllopez616: Added my template and milestone 0

==Milestone 0==
As performed on Thursday, [[Media:JLopezEAzingeJournalClub.pptx | this file]] contains the deliverable for my presentation.
==Milestone 1==
==Milestone 2==
==Milestone 3==
==Milestone 4==
==Acknowledgements and References==
===Acknowledgements===
===References===
{{Template:johnllopez616}}

Johnllopez Week 12

2017-11-21T06:20:56Z

Johnllopez616: Added the skeleton for the page

==Milestone 0==
==Milestone 1==
==Milestone 2==
==Milestone 3==
==Milestone 4==
==Acknowledgements and References==
===Acknowledgements===
===References===

Gene hAPI

2017-11-14T07:58:08Z

Johnllopez616: /* Journal Club Deliverable */ added break

Gene hAPI

2017-11-14T07:57:31Z

Johnllopez616: added link to presentation

Johnllopez Week 11

2017-11-14T07:56:22Z

Johnllopez616: added link to presentation

==Development Vocabulary==
*'''RFC 5321:''' RFC 5321 is a document that defines Simple Mail Transfer Protocol for the community to discuss, suggest, and make improvements upon. SMTP is intended to be the basic protocol for e-mail transport and is intended to be the standards of designing the way emails are sent (Klensin, 2008).
*'''RFC 5322:''' Like RFC 5321, RFC 5322 is designed to be a basic protocol for a form of internet communication and is created for the community to discuss, suggest, and make improvements upon. However, RFC 5322 defines the Internet Message Format, a syntax for text messages that are sent between computer users, within the framework of "electronic mail" messages (Resnick, 2008).
*'''Java Applet:''' An applet is Java program that a browser enabled with Java technology can download from the internet and run. An applet is typically embedded inside a web page and runs in the context of a browser ("Lesson: Java Applets").
*'''SQLite:''' An embedded SQL database engine with multiple tables, indices, triggers, and views contained in a single disk file. In addition, it does not need a server. It is free to use for anybody ("About SQLite").
*'''Enterprise Programming:''' Enterprise programming is when a programmer develops software for a large company/organization whose main objective is not to develop software. The software is typically meant to have a great number of users (Ilardi, 2017).
*'''Bytecode:''' The machine language of the Java virtual machine. This means any instructions written by the programmer are translated into this from the original syntax, and the results are interpreted by the JVM. (Venners, 1996).
*'''Clojure:''' Clojure is a programming language that runs off the Java Virtual Machine and uses Java's structure while maintaining the syntax of the Lisp programming language. ("Rationale").
*'''NPM:''' Short for Node Package Manager, NPM contains thousands of reusable, free JavaScript packages for software developers to use. NPM is installed alongside Node.js. New packages can be installed from the command line and packages can be used within typical JavaScript syntax. ("Node.js NPM").
*'''V8:''' V8 is a JavaScript engine that compiles and executes JavaScript source code, handles memory allocation for objects, and garbage collects objects it no longer needs. V8 enables any C++ application to expose its own objects and functions to JavaScript code. (Thompson, 2015).
*'''Netscape:''' Just as Paul Ford's article says, Netscape was one of the first commercial browsers. Netscape was released in 1994 and did not offer support for Java and JavaScript until version 2.0. (Heisler, 2014).

==Article Outline==
#Paul Ford's main message is that what appear to be simple programming tasks require the most contemporary tools and resources, yet these resources have similarities with those already established.
##Ford provides 3 of the most common languages/practices in most modern programming operations.
###Relational Databases.
###Java.
###JavaScript.
##Ford explains that the modern environment for programming is constantly changing and complex, yet similar to practices in the past.
###Programming languages are always changing for the better.
###Despite the differences in task, modern programmers use some arrangement of the most common practices.
###Programming tasks are more complex than anticipated.
#Paul Ford describes the cause and effect relationship between modern programming practices and informs the reader that adapting to the industry changes the industry.
##Explicates the origins of several contemporary programming languages and why they were developed.
##Provides insight to the ever changing environment of software development and how developers adjust to meet the demands of the industry.
##Explains how the needs over time change for software use, yet developers have the ability to adapt.
#Ford discusses the most important/popular languages and development environments, like relational databases, Java, and JavaScript.
##Implementing Relational Databases is the Best Approach to Handle Big Data.
###Relational Databases use the Structured Query Language.
###Represent the world using tables containing rows and columns.
###"Data management is the problem that programming is supposed to solve" (Ford).
###Allows us to have web services that store large quantities of different types of data (Amazon, Netflix, Spotify).
##Also lets data be retrieved on small devices (SQLite).
##A Majority of "Big Corporate Programmers" use Java Because of Its Class Library, Available Documentation/Manuals, and Virtual Machine.
###Class Library contained classes and methods needed for several commonly used purposes such as math, databases, document management, and network services.
###Documentation automatically generated using javadoc.
###Several manuals, workshops, lessons, and training opportunities.
###Virtual machine enabled Java to run on most common computers, allowing implementation for many large companies for several purposes.
##Over Time, the Functionality of JavaScript Grew from Simply Making Pages Interactive, to Using Web Pages as Software, to Being Used Outside of Web Pages.
###Initially used within pages for animations and page style.
###With the rise of Ajax, JavaScript became the main language for web programming web applications.
###V8 engine in Chrome allowed JavaScript to run faster.
###Modifications on the V8 engine allowed JavaScript to run outside of the browser.
###Creation of packages like Node.js.
###"If you knew how JavaScript worked on a Web page, then you could make it work on a server" (Ford).
###NPM helps install packages for JavaScript.
##Improvements in Software Engineering Allow New and Greater Things to be Made
###Relational databases allows us to have web services that store large quantities of different types of data.
####Amazon - "Books"
####Netflix - Video Files
####Spotify - MP3 Files
###Also lets data be retrieved on small devices (SQLite).
###Java is a versatile language with implementations everywhere!
####Used in “enterprise programming” for companies like GE.
####Used by software companies like Google.
###JavaScript allows people to make real software using web pages.
####Google Documents
####Amazon Web Services
#Ford strongly argues that programming languages change for the better, there are similar trends in modern development, and development is more complex than it first appears to be.
##Programming languages are constantly changing to increase usability and proficiency.
###Some languages have different syntax yet run using the JVM.
####Clojure
####Jython
####JRuby
###Formerly common languages such as PHP are becoming obsolete in favor of newer, more efficient languages
###Java applets, once used widely are considered impractical now
##Although each programming project serves a different purpose, there are similar trends in development despite differences in the objective.
###Enterprise programming uses Java despite the fact they don't specifically sell software.
###Academic research develops with Java despite generally lacking user interfaces.
###Software development companies use Java for a multitude of tasks and project sizes.
###Several groups of programmers can use JavaScript despite its original intended use to create page interactivity:
####Web Application Developers
####Database Managers
####Web Page Designers
##The Process of Software Development is More Complex than Writing Code.
###Different protocols and methods for making a similar product.
####Simple Mail Transfer Protocol vs. Internet Message Format.
####Installing a package from NPM and configuring it to your individual server.
###Requires dozens of tasks to be distributed to people at the company.
###Despite hundreds of packages/libraries existing, picking out the right one for your purpose and your company.
#This article taught me why it's important to stay up to date to current programming practices, and it gave me a greater idea of how my group can use JavaScript.
##If I don't stay up to date with the ever-changing JavaScript, I can not unlock its true capabilities
##Using resources like NPM, it's quite possible to make JavaScript do anything I need it do.
###JavaScript libraries and methods will have to be used to complete my task.

==Project Deliverable==
[[Media:JLopezEAzingeJournalClub.pptx | The presentation.]]

==Acknowledgements and References==

===Acknowledgements===
I worked with my partner [[User:cazinge | Eddie Azinge]] on this assignment. We met outside of class on Monday, November 13 to discuss the presentation and worked on it in person and over Google Documents shortly after. In addition, we will meet on Tuesday, November 14, to rehearse the presentation.
While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.
[[User:Johnllopez616|Johnllopez616]] ([[User talk:Johnllopez616|talk]]) 23:22, 13 November 2017 (PST)

===References===
Cojure. ''Rationale''. Retrieved November 12, 2017, from https://clojure.org/about/rationale
Ford, Paul. (2015, June 11). ''What is Code?''. Retrieved November 12, 2017, from https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#the-time-you-attended-the-e-mail-address-validation-meeting
Heisler, Naomi. (2014, October 14) ''A Visual History of Netscape Navigator''. Retrieved November 12, 2017,from https://www.networkworld.com/article/2833526/software/a-
visual-history-of-netscape-navigator.html
Ilardi, Robert. (2017, November).''About Enterprise Programming''. Retrieved November 12, 2017, from https://enterpriseprogrammer.com/about-enterprise-programming/
Java. ''Lesson: Java Applets'''. Retrieved November 12, 2017, from https://docs.oracle.com/javase/tutorial/deployment/applet/index.html
Klensin, J. (2008, October). ''RFC 5321''. Retrieved November 12, 2017, from https://tools.ietf.org/html/rfc5321
LMU BioDB 2017. (2017). Week 11. Retrieved November 12, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_10
Resnick, Ed. (2008, October). ''RFC 5322''. Retrieved November 12, 2017, from https://tools.ietf.org/html/rfc5322
SQLite.''About SQLite''. Retrieved November 12, 2017, from https://www.sqlite.org/about.html
Thompson, Seth. (2015, November 25). ''Introduction''. Retrieved November 12, 2017, from https://github.com/v8/v8/wiki/Introduction
Venners, Bill. (1996, September 1). '''Bytecode Basics'''. Retrieved November 12, 2017, from https://www.javaworld.com/article/2077233/core-java/bytecode-basics.html
W3Schools. '''Node.js NPM'''. Retrieved November 12, 2017, from https://www.w3schools.com/nodejs/nodejs_npm.asp

{{Template:johnllopez616}}

File:JLopezEAzingeJournalClub.pptx

2017-11-14T07:54:06Z

Johnllopez616: John Lopez Eddie Azinge PPT

John Lopez Eddie Azinge PPT

Template:Johnllopez616

2017-11-14T07:44:13Z

Johnllopez616: Added my project link

Gene hAPI

2017-11-14T07:42:04Z

Johnllopez616: changed the format of the outline

Gene hAPI

2017-11-14T07:41:15Z

Johnllopez616: Added my portion to the journal club assignment (John Lopez)

Johnllopez Week 11

2017-11-14T07:22:46Z

Johnllopez616: Added acknowlesgements and link to powerpoint presentation

==Development Vocabulary==
*'''RFC 5321:''' RFC 5321 is a document that defines Simple Mail Transfer Protocol for the community to discuss, suggest, and make improvements upon. SMTP is intended to be the basic protocol for e-mail transport and is intended to be the standards of designing the way emails are sent (Klensin, 2008).
*'''RFC 5322:''' Like RFC 5321, RFC 5322 is designed to be a basic protocol for a form of internet communication and is created for the community to discuss, suggest, and make improvements upon. However, RFC 5322 defines the Internet Message Format, a syntax for text messages that are sent between computer users, within the framework of "electronic mail" messages (Resnick, 2008).
*'''Java Applet:''' An applet is Java program that a browser enabled with Java technology can download from the internet and run. An applet is typically embedded inside a web page and runs in the context of a browser ("Lesson: Java Applets").
*'''SQLite:''' An embedded SQL database engine with multiple tables, indices, triggers, and views contained in a single disk file. In addition, it does not need a server. It is free to use for anybody ("About SQLite").
*'''Enterprise Programming:''' Enterprise programming is when a programmer develops software for a large company/organization whose main objective is not to develop software. The software is typically meant to have a great number of users (Ilardi, 2017).
*'''Bytecode:''' The machine language of the Java virtual machine. This means any instructions written by the programmer are translated into this from the original syntax, and the results are interpreted by the JVM. (Venners, 1996).
*'''Clojure:''' Clojure is a programming language that runs off the Java Virtual Machine and uses Java's structure while maintaining the syntax of the Lisp programming language. ("Rationale").
*'''NPM:''' Short for Node Package Manager, NPM contains thousands of reusable, free JavaScript packages for software developers to use. NPM is installed alongside Node.js. New packages can be installed from the command line and packages can be used within typical JavaScript syntax. ("Node.js NPM").
*'''V8:''' V8 is a JavaScript engine that compiles and executes JavaScript source code, handles memory allocation for objects, and garbage collects objects it no longer needs. V8 enables any C++ application to expose its own objects and functions to JavaScript code. (Thompson, 2015).
*'''Netscape:''' Just as Paul Ford's article says, Netscape was one of the first commercial browsers. Netscape was released in 1994 and did not offer support for Java and JavaScript until version 2.0. (Heisler, 2014).

==Article Outline==
#Paul Ford's main message is that what appear to be simple programming tasks require the most contemporary tools and resources, yet these resources have similarities with those already established.
##Ford provides 3 of the most common languages/practices in most modern programming operations.
###Relational Databases.
###Java.
###JavaScript.
##Ford explains that the modern environment for programming is constantly changing and complex, yet similar to practices in the past.
###Programming languages are always changing for the better.
###Despite the differences in task, modern programmers use some arrangement of the most common practices.
###Programming tasks are more complex than anticipated.
#Paul Ford describes the cause and effect relationship between modern programming practices and informs the reader that adapting to the industry changes the industry.
##Explicates the origins of several contemporary programming languages and why they were developed.
##Provides insight to the ever changing environment of software development and how developers adjust to meet the demands of the industry.
##Explains how the needs over time change for software use, yet developers have the ability to adapt.
#Ford discusses the most important/popular languages and development environments, like relational databases, Java, and JavaScript.
##Implementing Relational Databases is the Best Approach to Handle Big Data.
###Relational Databases use the Structured Query Language.
###Represent the world using tables containing rows and columns.
###"Data management is the problem that programming is supposed to solve" (Ford).
###Allows us to have web services that store large quantities of different types of data (Amazon, Netflix, Spotify).
##Also lets data be retrieved on small devices (SQLite).
##A Majority of "Big Corporate Programmers" use Java Because of Its Class Library, Available Documentation/Manuals, and Virtual Machine.
###Class Library contained classes and methods needed for several commonly used purposes such as math, databases, document management, and network services.
###Documentation automatically generated using javadoc.
###Several manuals, workshops, lessons, and training opportunities.
###Virtual machine enabled Java to run on most common computers, allowing implementation for many large companies for several purposes.
##Over Time, the Functionality of JavaScript Grew from Simply Making Pages Interactive, to Using Web Pages as Software, to Being Used Outside of Web Pages.
###Initially used within pages for animations and page style.
###With the rise of Ajax, JavaScript became the main language for web programming web applications.
###V8 engine in Chrome allowed JavaScript to run faster.
###Modifications on the V8 engine allowed JavaScript to run outside of the browser.
###Creation of packages like Node.js.
###"If you knew how JavaScript worked on a Web page, then you could make it work on a server" (Ford).
###NPM helps install packages for JavaScript.
##Improvements in Software Engineering Allow New and Greater Things to be Made
###Relational databases allows us to have web services that store large quantities of different types of data.
####Amazon - "Books"
####Netflix - Video Files
####Spotify - MP3 Files
###Also lets data be retrieved on small devices (SQLite).
###Java is a versatile language with implementations everywhere!
####Used in “enterprise programming” for companies like GE.
####Used by software companies like Google.
###JavaScript allows people to make real software using web pages.
####Google Documents
####Amazon Web Services
#Ford strongly argues that programming languages change for the better, there are similar trends in modern development, and development is more complex than it first appears to be.
##Programming languages are constantly changing to increase usability and proficiency.
###Some languages have different syntax yet run using the JVM.
####Clojure
####Jython
####JRuby
###Formerly common languages such as PHP are becoming obsolete in favor of newer, more efficient languages
###Java applets, once used widely are considered impractical now
##Although each programming project serves a different purpose, there are similar trends in development despite differences in the objective.
###Enterprise programming uses Java despite the fact they don't specifically sell software.
###Academic research develops with Java despite generally lacking user interfaces.
###Software development companies use Java for a multitude of tasks and project sizes.
###Several groups of programmers can use JavaScript despite its original intended use to create page interactivity:
####Web Application Developers
####Database Managers
####Web Page Designers
##The Process of Software Development is More Complex than Writing Code.
###Different protocols and methods for making a similar product.
####Simple Mail Transfer Protocol vs. Internet Message Format.
####Installing a package from NPM and configuring it to your individual server.
###Requires dozens of tasks to be distributed to people at the company.
###Despite hundreds of packages/libraries existing, picking out the right one for your purpose and your company.
#This article taught me why it's important to stay up to date to current programming practices, and it gave me a greater idea of how my group can use JavaScript.
##If I don't stay up to date with the ever-changing JavaScript, I can not unlock its true capabilities
##Using resources like NPM, it's quite possible to make JavaScript do anything I need it do.
###JavaScript libraries and methods will have to be used to complete my task.

==Project Deliverable==

==Acknowledgements and References==

===Acknowledgements===
I worked with my partner [[User:cazinge | Eddie Azinge]] on this assignment. We met outside of class on Monday, November 13 to discuss the presentation and worked on it in person and over Google Documents shortly after. In addition, we will meet on Tuesday, November 14, to rehearse the presentation.
While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.
[[User:Johnllopez616|Johnllopez616]] ([[User talk:Johnllopez616|talk]]) 23:22, 13 November 2017 (PST)

===References===
Cojure. ''Rationale''. Retrieved November 12, 2017, from https://clojure.org/about/rationale
Ford, Paul. (2015, June 11). ''What is Code?''. Retrieved November 12, 2017, from https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#the-time-you-attended-the-e-mail-address-validation-meeting
Heisler, Naomi. (2014, October 14) ''A Visual History of Netscape Navigator''. Retrieved November 12, 2017,from https://www.networkworld.com/article/2833526/software/a-
visual-history-of-netscape-navigator.html
Ilardi, Robert. (2017, November).''About Enterprise Programming''. Retrieved November 12, 2017, from https://enterpriseprogrammer.com/about-enterprise-programming/
Java. ''Lesson: Java Applets'''. Retrieved November 12, 2017, from https://docs.oracle.com/javase/tutorial/deployment/applet/index.html
Klensin, J. (2008, October). ''RFC 5321''. Retrieved November 12, 2017, from https://tools.ietf.org/html/rfc5321
LMU BioDB 2017. (2017). Week 11. Retrieved November 12, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_10
Resnick, Ed. (2008, October). ''RFC 5322''. Retrieved November 12, 2017, from https://tools.ietf.org/html/rfc5322
SQLite.''About SQLite''. Retrieved November 12, 2017, from https://www.sqlite.org/about.html
Thompson, Seth. (2015, November 25). ''Introduction''. Retrieved November 12, 2017, from https://github.com/v8/v8/wiki/Introduction
Venners, Bill. (1996, September 1). '''Bytecode Basics'''. Retrieved November 12, 2017, from https://www.javaworld.com/article/2077233/core-java/bytecode-basics.html
W3Schools. '''Node.js NPM'''. Retrieved November 12, 2017, from https://www.w3schools.com/nodejs/nodejs_npm.asp

{{Template:johnllopez616}}

Johnllopez Week 11

2017-11-14T07:18:43Z

Johnllopez616: /* Article Outline */ Added main message and periods

==Development Vocabulary==
*'''RFC 5321:''' RFC 5321 is a document that defines Simple Mail Transfer Protocol for the community to discuss, suggest, and make improvements upon. SMTP is intended to be the basic protocol for e-mail transport and is intended to be the standards of designing the way emails are sent (Klensin, 2008).
*'''RFC 5322:''' Like RFC 5321, RFC 5322 is designed to be a basic protocol for a form of internet communication and is created for the community to discuss, suggest, and make improvements upon. However, RFC 5322 defines the Internet Message Format, a syntax for text messages that are sent between computer users, within the framework of "electronic mail" messages (Resnick, 2008).
*'''Java Applet:''' An applet is Java program that a browser enabled with Java technology can download from the internet and run. An applet is typically embedded inside a web page and runs in the context of a browser ("Lesson: Java Applets").
*'''SQLite:''' An embedded SQL database engine with multiple tables, indices, triggers, and views contained in a single disk file. In addition, it does not need a server. It is free to use for anybody ("About SQLite").
*'''Enterprise Programming:''' Enterprise programming is when a programmer develops software for a large company/organization whose main objective is not to develop software. The software is typically meant to have a great number of users (Ilardi, 2017).
*'''Bytecode:''' The machine language of the Java virtual machine. This means any instructions written by the programmer are translated into this from the original syntax, and the results are interpreted by the JVM. (Venners, 1996).
*'''Clojure:''' Clojure is a programming language that runs off the Java Virtual Machine and uses Java's structure while maintaining the syntax of the Lisp programming language. ("Rationale").
*'''NPM:''' Short for Node Package Manager, NPM contains thousands of reusable, free JavaScript packages for software developers to use. NPM is installed alongside Node.js. New packages can be installed from the command line and packages can be used within typical JavaScript syntax. ("Node.js NPM").
*'''V8:''' V8 is a JavaScript engine that compiles and executes JavaScript source code, handles memory allocation for objects, and garbage collects objects it no longer needs. V8 enables any C++ application to expose its own objects and functions to JavaScript code. (Thompson, 2015).
*'''Netscape:''' Just as Paul Ford's article says, Netscape was one of the first commercial browsers. Netscape was released in 1994 and did not offer support for Java and JavaScript until version 2.0. (Heisler, 2014).

==Article Outline==
#Paul Ford's main message is that what appear to be simple programming tasks require the most contemporary tools and resources, yet these resources have similarities with those already established.
##Ford provides 3 of the most common languages/practices in most modern programming operations.
###Relational Databases.
###Java.
###JavaScript.
##Ford explains that the modern environment for programming is constantly changing and complex, yet similar to practices in the past.
###Programming languages are always changing for the better.
###Despite the differences in task, modern programmers use some arrangement of the most common practices.
###Programming tasks are more complex than anticipated.
#Paul Ford describes the cause and effect relationship between modern programming practices and informs the reader that adapting to the industry changes the industry.
##Explicates the origins of several contemporary programming languages and why they were developed.
##Provides insight to the ever changing environment of software development and how developers adjust to meet the demands of the industry.
##Explains how the needs over time change for software use, yet developers have the ability to adapt.
#Ford discusses the most important/popular languages and development environments, like relational databases, Java, and JavaScript.
##Implementing Relational Databases is the Best Approach to Handle Big Data.
###Relational Databases use the Structured Query Language.
###Represent the world using tables containing rows and columns.
###"Data management is the problem that programming is supposed to solve" (Ford).
###Allows us to have web services that store large quantities of different types of data (Amazon, Netflix, Spotify).
##Also lets data be retrieved on small devices (SQLite).
##A Majority of "Big Corporate Programmers" use Java Because of Its Class Library, Available Documentation/Manuals, and Virtual Machine.
###Class Library contained classes and methods needed for several commonly used purposes such as math, databases, document management, and network services.
###Documentation automatically generated using javadoc.
###Several manuals, workshops, lessons, and training opportunities.
###Virtual machine enabled Java to run on most common computers, allowing implementation for many large companies for several purposes.
##Over Time, the Functionality of JavaScript Grew from Simply Making Pages Interactive, to Using Web Pages as Software, to Being Used Outside of Web Pages.
###Initially used within pages for animations and page style.
###With the rise of Ajax, JavaScript became the main language for web programming web applications.
###V8 engine in Chrome allowed JavaScript to run faster.
###Modifications on the V8 engine allowed JavaScript to run outside of the browser.
###Creation of packages like Node.js.
###"If you knew how JavaScript worked on a Web page, then you could make it work on a server" (Ford).
###NPM helps install packages for JavaScript.
##Improvements in Software Engineering Allow New and Greater Things to be Made
###Relational databases allows us to have web services that store large quantities of different types of data.
####Amazon - "Books"
####Netflix - Video Files
####Spotify - MP3 Files
###Also lets data be retrieved on small devices (SQLite).
###Java is a versatile language with implementations everywhere!
####Used in “enterprise programming” for companies like GE.
####Used by software companies like Google.
###JavaScript allows people to make real software using web pages.
####Google Documents
####Amazon Web Services
#Ford strongly argues that programming languages change for the better, there are similar trends in modern development, and development is more complex than it first appears to be.
##Programming languages are constantly changing to increase usability and proficiency.
###Some languages have different syntax yet run using the JVM.
####Clojure
####Jython
####JRuby
###Formerly common languages such as PHP are becoming obsolete in favor of newer, more efficient languages
###Java applets, once used widely are considered impractical now
##Although each programming project serves a different purpose, there are similar trends in development despite differences in the objective.
###Enterprise programming uses Java despite the fact they don't specifically sell software.
###Academic research develops with Java despite generally lacking user interfaces.
###Software development companies use Java for a multitude of tasks and project sizes.
###Several groups of programmers can use JavaScript despite its original intended use to create page interactivity:
####Web Application Developers
####Database Managers
####Web Page Designers
##The Process of Software Development is More Complex than Writing Code.
###Different protocols and methods for making a similar product.
####Simple Mail Transfer Protocol vs. Internet Message Format.
####Installing a package from NPM and configuring it to your individual server.
###Requires dozens of tasks to be distributed to people at the company.
###Despite hundreds of packages/libraries existing, picking out the right one for your purpose and your company.
#This article taught me why it's important to stay up to date to current programming practices, and it gave me a greater idea of how my group can use JavaScript.
##If I don't stay up to date with the ever-changing JavaScript, I can not unlock its true capabilities
##Using resources like NPM, it's quite possible to make JavaScript do anything I need it do.
###JavaScript libraries and methods will have to be used to complete my task.

==Acknowledgements and References==
===References===
Cojure. ''Rationale''. Retrieved November 12, 2017, from https://clojure.org/about/rationale
Ford, Paul. (2015, June 11). ''What is Code?''. Retrieved November 12, 2017, from https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#the-time-you-attended-the-e-mail-address-validation-meeting
Heisler, Naomi. (2014, October 14) ''A Visual History of Netscape Navigator''. Retrieved November 12, 2017,from https://www.networkworld.com/article/2833526/software/a-
visual-history-of-netscape-navigator.html
Ilardi, Robert. (2017, November).''About Enterprise Programming''. Retrieved November 12, 2017, from https://enterpriseprogrammer.com/about-enterprise-programming/
Java. ''Lesson: Java Applets'''. Retrieved November 12, 2017, from https://docs.oracle.com/javase/tutorial/deployment/applet/index.html
Klensin, J. (2008, October). ''RFC 5321''. Retrieved November 12, 2017, from https://tools.ietf.org/html/rfc5321
LMU BioDB 2017. (2017). Week 11. Retrieved November 12, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_10
Resnick, Ed. (2008, October). ''RFC 5322''. Retrieved November 12, 2017, from https://tools.ietf.org/html/rfc5322
SQLite.''About SQLite''. Retrieved November 12, 2017, from https://www.sqlite.org/about.html
Thompson, Seth. (2015, November 25). ''Introduction''. Retrieved November 12, 2017, from https://github.com/v8/v8/wiki/Introduction
Venners, Bill. (1996, September 1). '''Bytecode Basics'''. Retrieved November 12, 2017, from https://www.javaworld.com/article/2077233/core-java/bytecode-basics.html
W3Schools. '''Node.js NPM'''. Retrieved November 12, 2017, from https://www.w3schools.com/nodejs/nodejs_npm.asp

{{Template:johnllopez616}}

Johnllopez Week 11

2017-11-14T06:53:28Z

Johnllopez616: /* Article Outline */ Added sixth content slide

==Development Vocabulary==
*'''RFC 5321:''' RFC 5321 is a document that defines Simple Mail Transfer Protocol for the community to discuss, suggest, and make improvements upon. SMTP is intended to be the basic protocol for e-mail transport and is intended to be the standards of designing the way emails are sent (Klensin, 2008).
*'''RFC 5322:''' Like RFC 5321, RFC 5322 is designed to be a basic protocol for a form of internet communication and is created for the community to discuss, suggest, and make improvements upon. However, RFC 5322 defines the Internet Message Format, a syntax for text messages that are sent between computer users, within the framework of "electronic mail" messages (Resnick, 2008).
*'''Java Applet:''' An applet is Java program that a browser enabled with Java technology can download from the internet and run. An applet is typically embedded inside a web page and runs in the context of a browser ("Lesson: Java Applets").
*'''SQLite:''' An embedded SQL database engine with multiple tables, indices, triggers, and views contained in a single disk file. In addition, it does not need a server. It is free to use for anybody ("About SQLite").
*'''Enterprise Programming:''' Enterprise programming is when a programmer develops software for a large company/organization whose main objective is not to develop software. The software is typically meant to have a great number of users (Ilardi, 2017).
*'''Bytecode:''' The machine language of the Java virtual machine. This means any instructions written by the programmer are translated into this from the original syntax, and the results are interpreted by the JVM. (Venners, 1996).
*'''Clojure:''' Clojure is a programming language that runs off the Java Virtual Machine and uses Java's structure while maintaining the syntax of the Lisp programming language. ("Rationale").
*'''NPM:''' Short for Node Package Manager, NPM contains thousands of reusable, free JavaScript packages for software developers to use. NPM is installed alongside Node.js. New packages can be installed from the command line and packages can be used within typical JavaScript syntax. ("Node.js NPM").
*'''V8:''' V8 is a JavaScript engine that compiles and executes JavaScript source code, handles memory allocation for objects, and garbage collects objects it no longer needs. V8 enables any C++ application to expose its own objects and functions to JavaScript code. (Thompson, 2015).
*'''Netscape:''' Just as Paul Ford's article says, Netscape was one of the first commercial browsers. Netscape was released in 1994 and did not offer support for Java and JavaScript until version 2.0. (Heisler, 2014).

==Article Outline==
#Paul Ford's main message is that what appear to be simple programming tasks require...
#Paul Ford describes the cause and effect relationship between modern programming practices and informs the reader that adapting to the industry changes the industry.
##Explicates the origins of several contemporary programming languages and why they were developed.
##Provides insight to the ever changing environment of software development and how developers adjust to meet the demands of the industry.
##Explains how the needs over time change for software use, yet developers have the ability to adapt.
#Ford discusses the most important/popular languages and development environments, like relational databases, Java, and JavaScript.
##Implementing Relational Databases is the Best Approach to Handle Big Data.
###Relational Databases use the Structured Query Language
###Represent the world using tables containing rows and columns
###Commercial Enterprises (Oracle) and Free Software Databases (PostgreSQL, MySQL, SQLite)
###"Data management is the problem that programming is supposed to solve" (Ford).
###Allows us to have web services that store large quantities of different types of data (Amazon, Netflix, Spotify)
##Also lets data be retrieved on small devices (SQLite)
##A Majority of "Big Corporate Programmers" use Java Because of Its Class Library, Available Documentation/Manuals, and Virtual Machine.
###Class Library contained classes and methods needed for several commonly used purposes such as math, databases, document management, and network services.
###Documentation automatically generated using javadoc.
###Several manuals, workshops, lessons, and training opportunities.
###Virtual machine enabled Java to run on most common computers, allowing implementation for many large companies for several purposes.
##Over Time, the Functionality of JavaScript Grew from Simply Making Pages Interactive, to Using Web Pages as Software, to Being Used Outside of Web Pages
###Initially used within pages for animations and page style.
###With the rise of Ajax, JavaScript became the main language for web programming web applications
###V8 engine in Chrome allowed JavaScript to run faster
###Modifications on the V8 engine allowed JavaScript to run outside of the browser
###Creation of packages like Node.js
###"If you knew how JavaScript worked on a Web page, then you could make it work on a server" (Ford).
###NPM helps install packages for JavaScript
##Improvements in Software Engineering Allow New and Greater Things to be Made
###Relational databases allows us to have web services that store large quantities of different types of data
####Amazon - "Books"
####Netflix - Video Files
####Spotify - MP3 Files
###Also lets data be retrieved on small devices (SQLite)
###Java is a versatile language with implementations everywhere!
####Used in “enterprise programming” for companies like GE
####Used by software companies like Google
###JavaScript allows people to make real software using web pages
####Google Documents
####Amazon Web Services
#The main points of this work were:
##Programming languages are constantly changing to increase usability and proficiency.
###Some languages have different syntax yet run using the JVM.
####Clojure
####Jython
####JRuby
###Formerly common languages such as PHP are becoming obsolete in favor of newer, more efficient languages
###Java applets, once used widely are considered impractical now
##Although each programming project serves a different purpose, there are similar trends in development despite differences in the objective.
###Enterprise programming uses Java despite the fact they don't specifically sell software.
###Academic research develops with Java despite generally lacking user interfaces.
###Software development companies use Java for a multitude of tasks and project sizes.
###Several groups of programmers can use JavaScript despite its original intended use to create page interactivity:
####Web Application Developers
####Database Managers
####Web Page Designers
##The Process of Software Development is More Complex than Writing Code
###Different protocols and methods for making a similar product
####Simple Mail Transfer Protocol vs. Internet Message Format
####Installing a package from NPM and configuring it to your individual server
###Requires dozens of tasks to be distributed to people at the company
###Despite hundreds of packages/libraries existing, picking out the right one for your purpose and your company
#This article taught me why it's important to stay up to date to current programming practices, and it gave me a greater idea of how my group can use JavaScript.
##If I don't stay up to date with the ever-changing JavaScript, I can not unlock its true capabilities.
##Using resources like NPM, it's quite possible to make JavaScript do anything I need it do.
###JavaScript libraries and methods will have to be used to complete my task.

==Acknowledgements and References==
===References===
Cojure. ''Rationale''. Retrieved November 12, 2017, from https://clojure.org/about/rationale
Ford, Paul. (2015, June 11). ''What is Code?''. Retrieved November 12, 2017, from https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#the-time-you-attended-the-e-mail-address-validation-meeting
Heisler, Naomi. (2014, October 14) ''A Visual History of Netscape Navigator''. Retrieved November 12, 2017,from https://www.networkworld.com/article/2833526/software/a-
visual-history-of-netscape-navigator.html
Ilardi, Robert. (2017, November).''About Enterprise Programming''. Retrieved November 12, 2017, from https://enterpriseprogrammer.com/about-enterprise-programming/
Java. ''Lesson: Java Applets'''. Retrieved November 12, 2017, from https://docs.oracle.com/javase/tutorial/deployment/applet/index.html
Klensin, J. (2008, October). ''RFC 5321''. Retrieved November 12, 2017, from https://tools.ietf.org/html/rfc5321
LMU BioDB 2017. (2017). Week 11. Retrieved November 12, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_10
Resnick, Ed. (2008, October). ''RFC 5322''. Retrieved November 12, 2017, from https://tools.ietf.org/html/rfc5322
SQLite.''About SQLite''. Retrieved November 12, 2017, from https://www.sqlite.org/about.html
Thompson, Seth. (2015, November 25). ''Introduction''. Retrieved November 12, 2017, from https://github.com/v8/v8/wiki/Introduction
Venners, Bill. (1996, September 1). '''Bytecode Basics'''. Retrieved November 12, 2017, from https://www.javaworld.com/article/2077233/core-java/bytecode-basics.html
W3Schools. '''Node.js NPM'''. Retrieved November 12, 2017, from https://www.w3schools.com/nodejs/nodejs_npm.asp

{{Template:johnllopez616}}

Johnllopez Week 11

2017-11-14T06:42:53Z

Johnllopez616: /* Article Outline */ Broke the lists down even further

==Development Vocabulary==
*'''RFC 5321:''' RFC 5321 is a document that defines Simple Mail Transfer Protocol for the community to discuss, suggest, and make improvements upon. SMTP is intended to be the basic protocol for e-mail transport and is intended to be the standards of designing the way emails are sent (Klensin, 2008).
*'''RFC 5322:''' Like RFC 5321, RFC 5322 is designed to be a basic protocol for a form of internet communication and is created for the community to discuss, suggest, and make improvements upon. However, RFC 5322 defines the Internet Message Format, a syntax for text messages that are sent between computer users, within the framework of "electronic mail" messages (Resnick, 2008).
*'''Java Applet:''' An applet is Java program that a browser enabled with Java technology can download from the internet and run. An applet is typically embedded inside a web page and runs in the context of a browser ("Lesson: Java Applets").
*'''SQLite:''' An embedded SQL database engine with multiple tables, indices, triggers, and views contained in a single disk file. In addition, it does not need a server. It is free to use for anybody ("About SQLite").
*'''Enterprise Programming:''' Enterprise programming is when a programmer develops software for a large company/organization whose main objective is not to develop software. The software is typically meant to have a great number of users (Ilardi, 2017).
*'''Bytecode:''' The machine language of the Java virtual machine. This means any instructions written by the programmer are translated into this from the original syntax, and the results are interpreted by the JVM. (Venners, 1996).
*'''Clojure:''' Clojure is a programming language that runs off the Java Virtual Machine and uses Java's structure while maintaining the syntax of the Lisp programming language. ("Rationale").
*'''NPM:''' Short for Node Package Manager, NPM contains thousands of reusable, free JavaScript packages for software developers to use. NPM is installed alongside Node.js. New packages can be installed from the command line and packages can be used within typical JavaScript syntax. ("Node.js NPM").
*'''V8:''' V8 is a JavaScript engine that compiles and executes JavaScript source code, handles memory allocation for objects, and garbage collects objects it no longer needs. V8 enables any C++ application to expose its own objects and functions to JavaScript code. (Thompson, 2015).
*'''Netscape:''' Just as Paul Ford's article says, Netscape was one of the first commercial browsers. Netscape was released in 1994 and did not offer support for Java and JavaScript until version 2.0. (Heisler, 2014).

==Article Outline==
# What is the main message of this work? *Although people will program using techniques from a certain foundation, the methods will change over time //This is crap, reword it
#Paul Ford describes the cause and effect relationship between modern programming practices and informs the reader that adapting to the industry changes the industry.
##Explicates the origins of several contemporary programming languages and why they were developed.
##Provides insight to the ever changing environment of software development and how developers adjust to meet the demands of the industry.
##Explains how the needs over time change for software use, yet developers have the ability to adapt.
#Ford discusses the most important/popular languages and development environments, like relational databases, Java, and JavaScript.
##Implementing Relational Databases is the Best Approach to Handle Big Data.
###Relational Databases use the Structured Query Language
###Represent the world using tables containing rows and columns
###Commercial Enterprises (Oracle) and Free Software Databases (PostgreSQL, MySQL, SQLite)
###"Data management is the problem that programming is supposed to solve" (Ford).
###Allows us to have web services that store large quantities of different types of data (Amazon, Netflix, Spotify)
##Also lets data be retrieved on small devices (SQLite)
##A Majority of "Big Corporate Programmers" use Java Because of Its Class Library, Available Documentation/Manuals, and Virtual Machine.
###Class Library contained classes and methods needed for several commonly used purposes such as math, databases, document management, and network services.
###Documentation automatically generated using javadoc.
###Several manuals, workshops, lessons, and training opportunities.
###Virtual machine enabled Java to run on most common computers, allowing implementation for many large companies for several purposes.
##Over Time, the Functionality of JavaScript Grew from Simply Making Pages Interactive, to Using Web Pages as Software, to Being Used Outside of Web Pages
###Initially used within pages for animations and page style.
###With the rise of Ajax, JavaScript became the main language for web programming web applications
###V8 engine in Chrome allowed JavaScript to run faster
###Modifications on the V8 engine allowed JavaScript to run outside of the browser
###Creation of packages like Node.js
###"If you knew how JavaScript worked on a Web page, then you could make it work on a server" (Ford).
###NPM helps install packages for JavaScript
##Improvements in Software Engineering Allow New and Greater Things to be Made
###Relational databases allows us to have web services that store large quantities of different types of data
####Amazon - "Books"
####Netflix - Video Files
####Spotify - MP3 Files
###Also lets data be retrieved on small devices (SQLite)
###Java is a versatile language with implementations everywhere!
####Used in “enterprise programming” for companies like GE
####Used by software companies like Google
###JavaScript allows people to make real software using web pages
####Google Documents
####Amazon Web Services

#The main points of this work were:
##Programming languages are constantly changing to increase usability and proficiency.
###Some languages have different syntax yet run using the JVM.
####Clojure
####Jython
####JRuby
###Formerly common languages such as PHP are becoming obsolete in favor of newer, more efficient languages
###Java applets, once used widely are considered impractical now
##Although each programming project serves a different purpose, there are similar trends in development despite differences in the objective.
###Enterprise programming uses Java despite the fact they don't specifically sell software.
###Academic research develops with Java despite generally lacking user interfaces.
###Software development companies use Java for a multitude of tasks and project sizes.
###Several groups of programmers can use JavaScript despite its original intended use to create page interactivity:
####Web Application Developers
####Database Managers
####Web Page Designers
##The Process of Software Development is More Complex than Writing Code
###Different protocols and methods for making a similar product
####Simple Mail Transfer Protocol vs. Internet Message Format
####Installing a package from NPM and configuring it to your individual server
###Requires dozens of tasks to be distributed to people at the company
###Despite hundreds of packages/libraries existing, picking out the right one for your purpose and your company
#Keeping up to date with current JavaScript practices and possibly using the NPM
##Something about staying up to date
##Something about Node.JS

==Acknowledgements and References==
===References===
Cojure. ''Rationale''. Retrieved November 12, 2017, from https://clojure.org/about/rationale
Ford, Paul. (2015, June 11). ''What is Code?''. Retrieved November 12, 2017, from https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#the-time-you-attended-the-e-mail-address-validation-meeting
Heisler, Naomi. (2014, October 14) ''A Visual History of Netscape Navigator''. Retrieved November 12, 2017,from https://www.networkworld.com/article/2833526/software/a-
visual-history-of-netscape-navigator.html
Ilardi, Robert. (2017, November).''About Enterprise Programming''. Retrieved November 12, 2017, from https://enterpriseprogrammer.com/about-enterprise-programming/
Java. ''Lesson: Java Applets'''. Retrieved November 12, 2017, from https://docs.oracle.com/javase/tutorial/deployment/applet/index.html
Klensin, J. (2008, October). ''RFC 5321''. Retrieved November 12, 2017, from https://tools.ietf.org/html/rfc5321
LMU BioDB 2017. (2017). Week 11. Retrieved November 12, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_10
Resnick, Ed. (2008, October). ''RFC 5322''. Retrieved November 12, 2017, from https://tools.ietf.org/html/rfc5322
SQLite.''About SQLite''. Retrieved November 12, 2017, from https://www.sqlite.org/about.html
Thompson, Seth. (2015, November 25). ''Introduction''. Retrieved November 12, 2017, from https://github.com/v8/v8/wiki/Introduction
Venners, Bill. (1996, September 1). '''Bytecode Basics'''. Retrieved November 12, 2017, from https://www.javaworld.com/article/2077233/core-java/bytecode-basics.html
W3Schools. '''Node.js NPM'''. Retrieved November 12, 2017, from https://www.w3schools.com/nodejs/nodejs_npm.asp

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