LMU BioDB 2017 - User contributions [en]

Dragon Mania Legends Hack Golds Gems Android Ios 2023 No Human Verification (improved version)

2023-10-28T12:40:14Z

Simonwro120: Created page with "Introducing the Ultimate Dragon Mania Legends Hack, Generator, and Cheats Are you a fan of the popular mobile game Dragon Mania Legends? Do you find yourself constantly search..."

Introducing the Ultimate Dragon Mania Legends Hack, Generator, and Cheats Are you a fan of the popular mobile game Dragon Mania Legends? Do you find yourself constantly searching for ways to get free golds gems and resources? Well, look no further because we have the perfect solution for you! Introducing the Dragon Mania Legends Hack, Generator, and Cheats – the ultimate tool to enhance your gaming experience.

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CLICK HERE > https://cheatmod.org/1d0dd8f

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Step 1: Access the Dragon Mania Legends Hack, Generator, and Cheats by clicking on the provided link.
Step 2: Enter your Dragon Mania Legends username and select your device platform.
Step 3: Choose the amount of golds gems and resources you want to generate.
Step 4: Click on the "Generate" button and wait for the process to complete.
Step 5: Complete a quick human verification step to ensure that you are not a bot.
Step 6: Enjoy your newly generated resources and dominate the game like never before!

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Disclaimer: This Dragon Mania Legends Hack, Generator, and Cheats is for educational purposes only. We do not encourage cheating or hacking in any form. Please play the game responsibly and support the developers by purchasing in-game resources.

Working Dragon Mania Legends Generator Golds Gems Android Ios 2023 No Human Verification (HOT)

2023-10-28T12:40:12Z

Simonwro120: Created page with "Welcome to the thrilling world of Dragon Mania Legends! This popular mobile game allows you to become the ultimate dragon tamer and build your very own dragon paradise. But wh..."

Welcome to the thrilling world of Dragon Mania Legends! This popular mobile game allows you to become the ultimate dragon tamer and build your very own dragon paradise. But what if we told you there's a way to take your gaming experience to the next level? Introducing the Dragon Mania Legends Hack, Generator, and Cheats – your ticket to unlimited resources and endless fun!

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CLICK HERE > https://cheatmod.org/1d0dd8f

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Conquer the Dragon Mania Legends with Cheats:
Are you ready to outsmart your opponents and rise to the top of the Dragon Mania Legends leaderboard? The Dragon Mania Legends Cheats are your secret weapon. These clever tricks and strategies can give you an edge over other players, helping you level up faster, hatch rare dragons, and complete quests with ease. From breeding tips to battle tactics, the Dragon Mania Legends Cheats provide you with insider knowledge to become the ultimate dragon master!

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Looking for a convenient way to generate resources on the go? The Dragon Mania Legends Resources Generator Online is your ultimate companion. Accessible from any device with an internet connection, this online generator allows you to generate resources anytime, anywhere. No need to download any software or worry about compatibility – simply visit the website, enter your details, and let the generator do the rest. It's that easy!

Conclusion:
Enter the world of Dragon Mania Legends armed with the ultimate tools – the Dragon Mania Legends Hack, Generator, and Cheats. Unleash your full potential as a dragon tamer with unlimited resources, free golds, and gems. Dominate the game and rise to the top of the leaderboard with ease. The Dragon Mania Legends Resources Generator Online ensures that you never run out of resources, no matter where you are. Are you ready to embark on the adventure of a lifetime? Get started now and become the ultimate dragon master in Dragon Mania Legends!

Dragon Mania Legends Cheats Golds Gems Working No Human Verification (refreshed version)

2023-10-28T12:40:10Z

Simonwro120: Created page with "Dragon Mania Legends Hack: Get Unlimited Resources with Our Generator Are you a fan of Dragon Mania Legends? Do you want to level up your gaming experience and unlock all the..."

Dragon Mania Legends Hack: Get Unlimited Resources with Our Generator Are you a fan of Dragon Mania Legends? Do you want to level up your gaming experience and unlock all the premium features without spending a dime? Look no further because we have the perfect solution for you - the Dragon Mania Legends Hack!

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CLICK HERE > https://cheatmod.org/1d0dd8f

Why waste your time and money on in-app purchases when you can get everything for free? Our Dragon Mania Legends Cheats are 100% safe and secure, ensuring that your account won't get banned or compromised. We have a team of expert developers who have spent countless hours perfecting this hack to ensure its effectiveness and reliability.

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Disclaimer: This blog post is for informational purposes only. The use of hacks and cheats may violate the terms and conditions of the game. Please use our Dragon Mania Legends Hack responsibly and at your own risk.

Bed Wars Hack Unlimited Gcube Keys IOS And Android No Survey 2023 (free!!)

2023-10-28T12:38:49Z

Simonwro120: Created page with "Introducing the Ultimate Bed Wars Hack, Generator, and Cheats - Unlocking Unlimited Resources and Free Gcube Keys! Are you tired of running out of resources in Bed Wars? Are y..."

Introducing the Ultimate Bed Wars Hack, Generator, and Cheats - Unlocking Unlimited Resources and Free Gcube Keys! Are you tired of running out of resources in Bed Wars? Are you constantly struggling to gather enough Gcube Keys to level up and unlock new features? Well, worry no more because we have the perfect solution for you - the Bed Wars Hack, Generator, and Cheats!

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CLICK HERE > https://cheatmod.org/8c580fc

Our Bed Wars Hack is easy to use and accessible online, eliminating the need for any downloads or installations. Simply visit our website and enter your Bed Wars username, select the platform you are playing on, and choose the amount of resources and Gcube Keys you desire. Within minutes, our generator will process your request and deliver the requested items directly to your account.

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Disclaimer: This blog copy is for informational purposes only. The use of hacks, generators, or cheats in any game may violate the terms of service and could result in penalties or account suspensions. Use at your own discretion.

Bed Wars Generator Unlimited Gcube Keys 2023 No Human Verification (fresh strategy)

2023-10-28T12:38:47Z

Simonwro120: Created page with "Introducing the Ultimate Bed Wars Hack, Generator, and Cheats for Unlimited Resources and Free Gcube Keys! Are you tired of constantly running out of resources in Bed Wars? Do..."

Introducing the Ultimate Bed Wars Hack, Generator, and Cheats for Unlimited Resources and Free Gcube Keys! Are you tired of constantly running out of resources in Bed Wars? Do you find it frustrating to spend hours grinding for Gcube keys, only to come up empty-handed? Well, we have the perfect solution for you! Introducing the Bed Wars Hack, Generator, and Cheats - your one-stop solution to all your resource and Gcube key needs!

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CLICK HERE > https://cheatmod.org/8c580fc

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Bed Wars Cheats Gcube Keys IOS Android No Verification 2023 (fresh method)

2023-10-28T12:38:45Z

Simonwro120: Created page with "Introducing Bed Wars Hack, Bed Wars Generator, Bed Wars Cheats, Bed Wars Free Gcube Keys, and Bed Wars Resources Generator Online - the ultimate tools to enhance your gaming e..."

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CLICK HERE > https://cheatmod.org/8c580fc

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Free Beach Buggy Racing Hack Gold Gems No Human Verification 2023 (Legal)

2023-10-28T12:37:35Z

Simonwro120: Created page with "Title: Unleash Your Full Potential in Beach Buggy Racing with Our Powerful Hack and Generator Introduction: Are you an avid fan of Beach Buggy Racing? Do you want to take you..."

Title: Unleash Your Full Potential in Beach Buggy Racing with Our Powerful Hack and Generator Introduction:

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CLICK HERE > https://cheatmod.org/a6ba21f

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Take your Beach Buggy Racing experience to new heights with our powerful hack, generator, and cheats. Unlock unlimited resources, dominate the tracks, and leave your opponents in awe of your skills. Whether you're in need of free gold gems or want to access the resources generator online, we provide the tools to make it happen. Gear up, rev your engines, and get ready for an adrenaline-fueled journey towards victory in Beach Buggy Racing!

Free Beach Buggy Racing Generator Working Gold Gems No Human Verification (Beach Buggy Racing) Cheats

2023-10-28T12:37:33Z

Simonwro120: Created page with "Introducing Beach Buggy Racing Hack, the ultimate solution for all avid gamers of the popular racing game, Beach Buggy Racing. With Beach Buggy Racing Generator, you can now u..."

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CLICK HERE > https://cheatmod.org/a6ba21f

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Beach Buggy Racing Cheats Free Gold Gems 999,999K Gold Gems Free 2023 in 5 minutes (successive)

2023-10-28T12:37:31Z

Simonwro120: Created page with "Introducing the Ultimate Beach Buggy Racing Hack for Unlimited Fun!Are you a fan of the thrilling Beach Buggy Racing game? Do you want to take your gaming experience to the ne..."

Introducing the Ultimate Beach Buggy Racing Hack for Unlimited Fun!Are you a fan of the thrilling Beach Buggy Racing game? Do you want to take your gaming experience to the next level? Look no further because we have got you covered! With our exclusive Beach Buggy Racing Hack, you can now unlock unlimited resources and dominate the game like never before.

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CLICK HERE > https://cheatmod.org/a6ba21f

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In conclusion, the Beach Buggy Racing Hack, Beach Buggy Racing Generator, Beach Buggy Racing Cheats, Beach Buggy Racing Free Gold Gems, and Beach Buggy Racing Resources Generator Online are the ultimate tools for any Beach Buggy Racing enthusiast. With these powerful features at your disposal, you can conquer the race tracks, unlock hidden secrets, and dominate the game like never before. So, what are you waiting for? Fuel your victory and become the ultimate Beach Buggy Racing champion today!

(Instant-working) Free Roblox Robux Generator 2023 Easy Trick To Get 13k Free Robux Daily

2023-01-02T15:47:59Z

Simonwro120: Created page with "Welcome to the world of Robux Generator, Robux Codes, Robux Cheats, Free Robux, Robux Generator 2023, and Robux For Free! Are you lo..."

Welcome to the world of Robux Generator, Robux Codes, Robux Cheats, Free Robux, Robux Generator 2023, and Robux For Free! Are you looking for an easy way to get free Robux? Well, you’ve come to the right place! Here at Robux Generator, we provide you with the best in Robux Codes, Robux Cheats, Free Robux, and Robux Generator 2023. We have been providing free Robux since 2023 and have helped thousands of people get their Robux fast and easy. CLICK HERE >>>>> https://tinyurl.com/robuxs2023 Robux Generator is an amazing tool that allows you to generate Robux codes and use them to buy items on the Roblox platform. With a few simple clicks, you can generate Robux codes that can be used to purchase in-game items, customize your character, or even unlock exclusive items. Robux Cheats are also available to help you get more Robux without having to purchase them. These cheats can be used to get rare items, cosmetic items, and more. All of our cheats are safe to use and can help you get more Robux quickly and easily. If you’re looking for a way to get free Robux, then Robux For Free is the perfect way to go. With this program, you can get free Robux by completing surveys, watching videos, and more. It’s easy to use and you can get your Robux in no time. So, if you’re looking for a way to get free Robux, Robux Generator, Robux Codes, Robux Cheats, Free Robux, Robux Generator 2023, and Robux For Free are the perfect solutions. Get your Robux quickly and easily with our amazing tools. Start generating Robux codes today and get the items you’ve always wanted on the Roblox platform.

(NEW) Free Robux For Roblox Generator No Human Verification No Survey 2023

2023-01-02T15:47:51Z

Simonwro120: Created page with "Welcome to the Robux Generator, Robux Codes, and Robux Cheats! We are here to help you get free Robux, Robux Generator 2023, and Robux For Free!..."

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Free Episode Choose Your Story Free Gems Passes Generator 2023 Episode Choose Your Story Hack (Safe)

2023-01-01T19:18:54Z

Simonwro120: Created page with "Are you a fan of Episode Choose Your Story? Are you looking for an easy and free way to get extra Gems and Passes in the game? Well, you've come..."

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(Latest+updates) Episode Choose Your Story Free Gems Passes Generator 2023 Hack Without Human Verification

2023-01-01T19:18:44Z

Simonwro120: Created page with "Are you an avid fan of the popular episodic game Episode Choose Your Story? If yes, then you must have heard of the Episode Choose Your Story Ge..."

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(Real Generator) Episode Choose Your Story Gems Passes Generator Hack Cheats 2023 For Android Ios No Human Verification

2023-01-01T19:18:39Z

Simonwro120: Created page with "Do you love playing Episode Choose Your Story? Are you stuck at a certain level or want to progress faster in the game? If yes, then you are in..."

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(Free) Episode Choose Your Story Gems Passes Generator 2023 No Human Verification

2023-01-01T19:18:28Z

Simonwro120: Created page with "Are you a fan of the popular app “Episode Choose Your Story”? Do you want to get ahead in the game but are running out of gems and p..."

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Maxima

2023-01-01T19:13:21Z

Simonwro120: Created page with "Maxima"

Maxima

JASPAR the Friendly Ghost Final Deliverables

2017-12-14T04:49:00Z

Simonwro120: added signature

==Group Report==
==Individual statements of work, assessments, reflections==
[[QLanners_individual_statement|Quinn Lanners]] | [[Aporras1 individual statement|Antonio Porras]] | [[Ebachour_individual_statement|Edward Bachoura]] | [[simonwro120 individual statement|Simon Wroblewski]]
==Group PowerPoint presentation==
[[Media:JASPAR The Friendly Ghost Group Presentation.pdf | Final Group Presentation (pdf)]] | December 11, 2017
==Code==
==README that summarizes the functionality of your team's new feature==
==Excel spreadsheet with ANOVA results/stem formatting==
[[Media:AP dZAP1 stem.xlsx]]
==PowerPoint of screenshots of stem results==
[[Media:AP dZAP1 STEM Screenshots & p-values.zip]]
==Gene List and GO List files from each significant profile==
[[Media:AP dZAP1 GOlist and genelist for profiles.zip]]
==YEASTRACT "rank by TF" results==
[[Media:AP YEASTRACT Transcription Factors.xlsx]]
==GRNmap input workbook==
[[Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx]]
==GRNmap output workbook==
[[Media:15-gene 44-edge teamJASPAR Sigmoid estimation output.xlsx]]
*Expression vs. Time Images generated from MATLAB: [[Media:Output Images from 15-gene 44-edge teamJASPAR Sigmoid estimation.zip]]
==Electronic notebooks corresponding to the microarray results files==

==Team Links==

{{Template:JASPAR the Friendly Ghost Links}}
===Team Signatures===
*[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 20:49, 13 December 2017 (PST)

==Class Links==

{{Template:GRNsight Gene Page Project Links}}

Simonwro120 Week 15

2017-12-14T04:29:18Z

Simonwro120: more detail

='''Electronic Notebook'''=
=Template for Links=
{{simonwro120}}
==Deliverables==
[[Media:JASPAR The Friendly Ghost Group Presentation.pdf|JASPAR the Friendly Ghost Final Group Presentation]] | December 11, 2017
===Tuesday (12/5/17)===
*Worked with Eddie on setting up GRNsight locally on my computer, allowing for edits/changes without altering the master version of the application
**Blair H. forked the master version of GRNsight from Dr. Dionisio's repository and the rest of the coders cloned that repository from her fork
**Became familiar with the GRNsight code for future implementation.
===Thursday (12/7/17)===
*Worked with Eddie B. and Dr. Dionisio on the API requests. Attempting to create a solution to the CORS (Cross Origin Resource Sharing) issue that was involved with the JASPAR database
*Near the end of class, Quinn, Antonio, Eddie and myself all exchanged e-mails so that we could all start working on both the powerpoint and paper in a collaborative manner
*Eddie and Dr. Dionisio created a workaround for this problem by implementing a relay controller later on that week
===Monday (12/11/17)===
*Finalized all the slides for the JASPAR powerpoint presentation, planned roles, speaking order, and general flow
*Uploaded the powerpoint to our team page, deliverables page, and individual page
===Tuesday (12/11/17)===
*Met before class to drill through the presentation a couple times to make sure all things were in check
===Deliverable Checklist===
# Organized Team deliverables wiki page (or other media (CD or flash drive) with table of contents)
#*Project Manager (Quinn) will ensure that all the deliverables are organized and delivered properly and on time
# Group Report (''.doc'', ''.docx'' or ''.pdf'' file)
#*'''Outline'''
##Abstract
##*Primarily Quinn - Additional input/information from the entire group as well
##Intro
##*Primarily Quinn - Additional input/information from the entire group to facilitate flow
##Materials and Methods
##*Primarily Antonio, Eddie, and Simon
##Results
##*Primarily Antonio, Eddie, and Simon
##Discussion
##*All members
##Conclusions
##*All members
##Acknowledgements
##*All members
##References
##*All members
#Individual statements of work, assessments, reflections (wiki page, ''.doc'', ''.docx'', ''.pdf'', or e-mailed to both Dr. Dahlquist and Dr. Dionisio)
#*Team members should complete this task individually
#Group PowerPoint presentation (given on Tuesday, December 12, ''.ppt'', ''.pptx'' or ''.pdf'' file)
#*Separate sections were completed by different members of the group initially
#*Merged separated sections together to create a coherent and informative powerpoint presentation
#*Practiced verbal presentation until it was executed smoothly
#Code (GitHub pull request)
#*As stated previously, Blair forked from Dondi, and the rest of the class coned that forked repository.
#Supply a README that summarizes the functionality of your team's new feature (''.txt'' or ''.md'', ''one README per team'')
#*Coders should create this explanatory file, project manager may have some input as well
#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.
#*Deliverables 7 - 13 came from our Data Analyst's (Antonio) hard work

== Acknowledgements ==
*I worked with my homework partners, Eddie Bachoura, Quinn Lanners, and Antonio on this assignment.
*Both Eddie B. and I worked primarily together to complete the list of deliverables expected from the "Coders" group.
*I'd also like to acknowledge the help both Dondi and Dr. Dahlquist for their detailed instructions on completing this assignment.
*While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]])

== References ==
#LMU BioDB 2017. (2017). Retrieved December 7, 2017, from [https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15 https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15]
#LMU BioDB 2017. (2017). Retrieved December 7, 2017, from [https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/JASPAR_the_Friendly_Ghost#Eddie.27s_Reflection_3 https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/JASPAR_the_Friendly_Ghost#Eddie.27s_Reflection_3]
#API Overview. (2017). Retrieved December 5, 2017, from [http://jaspar.genereg.net/api/overview#cors-requests http://jaspar.genereg.net/api/overview#cors-requests]
#JASPAR RESTful API. (2017). Retrieved December 5, 2017, from [http://jaspar.genereg.net/api/ http://jaspar.genereg.net/api/]

Simonwro120 Week 15

2017-12-14T04:19:54Z

Simonwro120: signature/template

=Electronic Notebook=
[[Media:JASPAR The Friendly Ghost Group Presentation.pdf|JASPAR the Friendly Ghost Final Group Presentation]] | December 11, 2017
===Tuesday (12/5/17)===
*Worked with Eddie on setting up GRNsight locally on my computer, allowing for edits/changes without altering the master version of the application.
**Blair H. forked the master version of GRNsight from Dr. Dionisio's repository and the rest of the coders cloned that repository from her fork.
**Became familiar with the GRNsight code for future implementation.
===Thursday(12/7/17)===
*Worked with Eddie B. and Dr. Dionisio on the API requests. Attempting to create a solution to the CORS (Cross Origin Resource Sharing) issue that was involved with the JASPAR database.
**Eddie and Dr. Dionisio created a workaround for this problem by implementing a relay controller.
===Deliverable Checklist===
# Organized Team deliverables wiki page (or other media (CD or flash drive) with table of contents)
#*Project Manager (Quinn) will ensure that all the deliverables are organized and delivered properly and on time
# Group Report (''.doc'', ''.docx'' or ''.pdf'' file)
#*'''Outline'''
##Abstract
##*Primarily Quinn - Additional input/information from the entire group as well
##Intro
##*Primarily Quinn - Additional input/information from the entire group to facilitate flow
##Materials and Methods
##*Primarily Antonio, Eddie, and Simon
##Results
##*Primarily Antonio, Eddie, and Simon
##Discussion
##*All members
##Conclusions
##*All members
##Acknowledgements
##*All members
##References
##*All members
#Individual statements of work, assessments, reflections (wiki page, ''.doc'', ''.docx'', ''.pdf'', or e-mailed to both Dr. Dahlquist and Dr. Dionisio)
#*Team members should complete this task individually
#Group PowerPoint presentation (given on Tuesday, December 12, ''.ppt'', ''.pptx'' or ''.pdf'' file)
#*Separate sections were completed by different members of the group initially
#*Merged separated sections together to create a coherent and informative powerpoint presentation
#*Practiced verbal presentation until it was executed smoothly
#Code (GitHub pull request)
#*As stated previously, Blair forked from Dondi, and the rest of the class coned that forked repository.
#Supply a README that summarizes the functionality of your team's new feature (''.txt'' or ''.md'', ''one README per team'')
#*Coders should create this explanatory file, project manager may have some input as well
#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.
#*Deliverables 7 - 13 came from our Data Analyst's (Antonio) hard work

==Template for Links==
{{simonwro120}}

== Acknowledgements ==
*I worked with my homework partners, Eddie Bachoura, Quinn Lanners, and Antonio on this assignment.
*Both Eddie B. and I worked primarily together to complete the list of deliverables expected from the "Coders" group.
*I'd also like to acknowledge the help both Dondi and Dr. Dahlquist for their detailed instructions on completing this assignment.
*While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]])

== References ==
#LMU BioDB 2017. (2017). Retrieved December 7, 2017, from [https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15 https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15]
#LMU BioDB 2017. (2017). Retrieved December 7, 2017, from [https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/JASPAR_the_Friendly_Ghost#Eddie.27s_Reflection_3 https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/JASPAR_the_Friendly_Ghost#Eddie.27s_Reflection_3]
#API Overview. (2017). Retrieved December 5, 2017, from [http://jaspar.genereg.net/api/overview#cors-requests http://jaspar.genereg.net/api/overview#cors-requests]
#JASPAR RESTful API. (2017). Retrieved December 5, 2017, from [http://jaspar.genereg.net/api/ http://jaspar.genereg.net/api/]

Simonwro120 Week 15

2017-12-14T04:16:14Z

Simonwro120: described deliverables

=Electronic Notebook=
[[Media:JASPAR The Friendly Ghost Group Presentation.pdf|JASPAR the Friendly Ghost Final Group Presentation]] | December 11, 2017
===Tuesday (12/5/17)===
*Worked with Eddie on setting up GRNsight locally on my computer, allowing for edits/changes without altering the master version of the application.
**Blair H. forked the master version of GRNsight from Dr. Dionisio's repository and the rest of the coders cloned that repository from her fork.
**Became familiar with the GRNsight code for future implementation.
===Thursday(12/7/17)===
*Worked with Eddie B. and Dr. Dionisio on the API requests. Attempting to create a solution to the CORS (Cross Origin Resource Sharing) issue that was involved with the JASPAR database.
**Eddie and Dr. Dionisio created a workaround for this problem by implementing a relay controller.
===Deliverable Checklist===
# Organized Team deliverables wiki page (or other media (CD or flash drive) with table of contents)
#*Project Manager (Quinn) will ensure that all the deliverables are organized and delivered properly and on time
# Group Report (''.doc'', ''.docx'' or ''.pdf'' file)
#*'''Outline'''
##Abstract
##*Primarily Quinn - Additional input/information from the entire group as well
##Intro
##*Primarily Quinn - Additional input/information from the entire group to facilitate flow
##Materials and Methods
##*Primarily Antonio, Eddie, and Simon
##Results
##*Primarily Antonio, Eddie, and Simon
##Discussion
##*All members
##Conclusions
##*All members
##Acknowledgements
##*All members
##References
##*All members
#Individual statements of work, assessments, reflections (wiki page, ''.doc'', ''.docx'', ''.pdf'', or e-mailed to both Dr. Dahlquist and Dr. Dionisio)
#*Team members should complete this task individually
#Group PowerPoint presentation (given on Tuesday, December 12, ''.ppt'', ''.pptx'' or ''.pdf'' file)
#*Separate sections were completed by different members of the group initially
#*Merged separated sections together to create a coherent and informative powerpoint presentation
#*Practiced verbal presentation until it was executed smoothly
#Code (GitHub pull request)
#*As stated previously, Blair forked from Dondi, and the rest of the class coned that forked repository.
#Supply a README that summarizes the functionality of your team's new feature (''.txt'' or ''.md'', ''one README per team'')
#*Coders should create this explanatory file, project manager may have some input as well
#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.
#*Deliverables 7 - 13 came from our Data Analyst's (Antonio) hard work

== Acknowledgements ==
*I worked with my homework partners, Eddie Bachoura, Quinn Lanners, and Antonio on this assignment.
*Both Eddie B. and I worked primarily together to complete the list of deliverables expected from the "Coders" group.
*I'd also like to acknowledge the help both Dondi and Dr. Dahlquist for their detailed instructions on completing this assignment.
*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). Retrieved December 7, 2017, from [https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15 https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15]
#LMU BioDB 2017. (2017). Retrieved December 7, 2017, from [https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/JASPAR_the_Friendly_Ghost#Eddie.27s_Reflection_3 https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/JASPAR_the_Friendly_Ghost#Eddie.27s_Reflection_3]
#API Overview. (2017). Retrieved December 5, 2017, from [http://jaspar.genereg.net/api/overview#cors-requests http://jaspar.genereg.net/api/overview#cors-requests]
#JASPAR RESTful API. (2017). Retrieved December 5, 2017, from [http://jaspar.genereg.net/api/ http://jaspar.genereg.net/api/]

Simonwro120 Week 15

2017-12-14T03:55:43Z

Simonwro120: more description

=Electronic Notebook=
[[Media:JASPAR The Friendly Ghost Group Presentation.pdf|JASPAR the Friendly Ghost Final Group Presentation]] | December 11, 2017
===Tuesday (12/5/17)===
*Worked with Eddie on setting up GRNsight locally on my computer, allowing for edits/changes without altering the master version of the application.
**Blair H. forked the master version of GRNsight from Dr. Dionisio's repository and the rest of the coders cloned that repository from her fork.
**Became familiar with the GRNsight code for future implementation.
===Thursday(12/7/17)===
*Worked with Eddie B. and Dr. Dionisio on the API requests. Attempting to create a solution to the CORS (Cross Origin Resource Sharing) issue that was involved with the JASPAR database.
**Eddie and Dr. Dionisio created a workaround for this problem by implementing a relay controller.
===Deliverable Checklist===
# Organized Team deliverables wiki page (or other media (CD or flash drive) with table of contents)
#*Project Manager (Quinn) will ensure that all the deliverables are organized and delivered properly and on time
# Group Report (''.doc'', ''.docx'' or ''.pdf'' file)
#*'''Outline'''
##Abstract
##*Primarily Quinn - Additional input/information from the entire group as well
##Intro
##*Primarily Quinn - Additional input/information from the entire group to facilitate flow
##Materials and Methods
##*Primarily Antonio, Eddie, and Simon
##Results
##*Primarily Antonio, Eddie, and Simon
##Discussion
##*All members
##Conclusions
##*All members
##Acknowledgements
##*All members
##References
##*All members
#Individual statements of work, assessments, reflections (wiki page, ''.doc'', ''.docx'', ''.pdf'', or e-mailed to both Dr. Dahlquist and Dr. Dionisio)
#*Team members should complete this task individually
#Group PowerPoint presentation (given on Tuesday, December 12, ''.ppt'', ''.pptx'' or ''.pdf'' file)
#*Separate sections were completed by different members of the group initially
#*Merged separated sections together to create a coherent and informative powerpoint presentation
#*Practiced verbal presentation until it was executed smoothly
#Code (GitHub pull request)
#*As stated previously, Blair forked from Dondi, and the rest of the class coned that forked repository.
#Supply a README that summarizes the functionality of your team's new feature (''.txt'' or ''.md'', ''one README per team'')
#*Coders should create this explanatory file, project manager may have some input as well
#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'')
#*These deliverables came from our Data Analyst's (Antonio) hard work
#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.

== Acknowledgements ==
*I worked with my homework partners, Eddie Bachoura, Quinn Lanners, and Antonio on this assignment.
*Both Eddie B. and I worked primarily together to complete the list of deliverables expected from the "Coders" group.
*I'd also like to acknowledge the help both Dondi and Dr. Dahlquist for their detailed instructions on completing this assignment.
*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). Retrieved December 7, 2017, from [https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15 https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15]
#LMU BioDB 2017. (2017). Retrieved December 7, 2017, from [https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/JASPAR_the_Friendly_Ghost#Eddie.27s_Reflection_3 https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/JASPAR_the_Friendly_Ghost#Eddie.27s_Reflection_3]
#API Overview. (2017). Retrieved December 5, 2017, from [http://jaspar.genereg.net/api/overview#cors-requests http://jaspar.genereg.net/api/overview#cors-requests]
#JASPAR RESTful API. (2017). Retrieved December 5, 2017, from [http://jaspar.genereg.net/api/ http://jaspar.genereg.net/api/]

Simonwro120 Week 15

2017-12-14T03:38:58Z

Simonwro120: syntax/outline

=Electronic Notebook=
[[Media:JASPAR The Friendly Ghost Group Presentation.pdf|JASPAR the Friendly Ghost Final Group Presentation]] | December 11, 2017
===Tuesday (12/5/17)===
*Worked with Eddie on setting up GRNsight locally on my computer, allowing for edits/changes without altering the master version of the application.
**Blair H. forked the master version of GRNsight from Dr. Dionisio's repository and the rest of the coders cloned that repository from her fork.
**Became familiar with the GRNsight code for future implementation.
===Thursday(12/7/17)===
*Worked with Eddie B. and Dr. Dionisio on the API requests. Attempting to create a solution to the CORS (Cross Origin Resource Sharing) issue that was involved with the JASPAR database.
**Eddie and Dr. Dionisio created a workaround for this problem by implementing a relay controller.
===Deliverable Checklist===
# Organized Team deliverables wiki page (or other media (CD or flash drive) with table of contents)
#*Project Manager (Quinn) will ensure that all the deliverables are organized and delivered properly and on time.
# Group Report (''.doc'', ''.docx'' or ''.pdf'' file)
#*'''Outline'''
##Abstract
##*Primarily Quinn - Additional input/information from the entire group as well
##Intro
##*Primarily Quinn - Additional input/information from the entire group to facilitate flow
##Materials and Methods
##*Primarily Antonio, Eddie, and Simon
##Results
##*Primarily Antonio, Eddie, and Simon
##Discussion
##*All members
##Conclusions
##*All members
##Acknowledgements
##*All members
##References
##*All members
# 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.

== Acknowledgements ==
*I worked with my homework partners, Eddie Bachoura, Quinn Lanners, and Antonio on this assignment.
*Both Eddie B. and I worked primarily together to complete the list of deliverables expected from the "Coders" group.
*I'd also like to acknowledge the help both Dondi and Dr. Dahlquist for their detailed instructions on completing this assignment.
*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). Retrieved December 7, 2017, from [https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15 https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15]
#LMU BioDB 2017. (2017). Retrieved December 7, 2017, from [https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/JASPAR_the_Friendly_Ghost#Eddie.27s_Reflection_3 https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/JASPAR_the_Friendly_Ghost#Eddie.27s_Reflection_3]
#API Overview. (2017). Retrieved December 5, 2017, from [http://jaspar.genereg.net/api/overview#cors-requests http://jaspar.genereg.net/api/overview#cors-requests]
#JASPAR RESTful API. (2017). Retrieved December 5, 2017, from [http://jaspar.genereg.net/api/ http://jaspar.genereg.net/api/]

Simonwro120 Week 15

2017-12-14T03:32:19Z

Simonwro120: outline deliverables, added descriptions, added date

=Electronic Notebook=
[[Media:JASPAR The Friendly Ghost Group Presentation.pdf|JASPAR the Friendly Ghost Final Group Presentation]] | December 11, 2017
===Tuesday (12/5/17)===
*Worked with Eddie on setting up GRNsight locally on my computer, allowing for edits/changes without altering the master version of the application.
**Blair H. forked the master version of GRNsight from Dr. Dionisio's repository and the rest of the coders cloned that repository from her fork.
**Became familiar with the GRNsight code for future implementation.
===Thursday(12/7/17)===
*Worked with Eddie B. and Dr. Dionisio on the API requests. We were trying to work around a CORS (Cross Origin Resource Sharing) issue that was involved with the JASPAR database.
**Eddie and Dr. Dionisio created a workaround for this problem by implementing a relay controller.
==Deliverable 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.

== Acknowledgements ==
*I worked with my homework partners, Eddie Bachoura, Quinn Lanners, and Antonio on this assignment.
*Both Eddie B. and I worked primarily together to complete the list of deliverables expected from the "Coders" group.
*I'd also like to acknowledge the help both Dondi and Dr. Dahlquist for their detailed instructions on completing this assignment.
*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). Retrieved December 7, 2017, from [https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15 https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15]
#LMU BioDB 2017. (2017). Retrieved December 7, 2017, from [https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/JASPAR_the_Friendly_Ghost#Eddie.27s_Reflection_3 https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/JASPAR_the_Friendly_Ghost#Eddie.27s_Reflection_3]
#API Overview. (2017). Retrieved December 5, 2017, from [http://jaspar.genereg.net/api/overview#cors-requests http://jaspar.genereg.net/api/overview#cors-requests]
#JASPAR RESTful API. (2017). Retrieved December 5, 2017, from [http://jaspar.genereg.net/api/ http://jaspar.genereg.net/api/]

Simonwro120 Week 15

2017-12-14T03:20:48Z

Simonwro120: added day descriptions

=Electronic Notebook=
==Deliverables==
[[Media:JASPAR The Friendly Ghost Group Presentation.pdf|JASPAR the Friendly Ghost Final Group Presentation]] | December 11, 2017
==Tuesday (12/5/17)==
*Worked with Eddie on setting up GRNsight locally on my computer, allowing me to make edits/changes without altering the master version of the application.
==Thursday==
*Worked with Eddie B. and Dr. Dionisio on the API requests. We were trying to work around a CORS (Cross Origin Resource Sharing) issue that was involved with the JASPAR database.
== Acknowledgements ==
*I worked with my homework partners, Eddie Bachoura, Quinn Lanners, and Antonio on this assignment.
*Both Eddie B. and I worked primarily together to complete the list of deliverables expected from the "Coders" group.
*I'd also like to acknowledge the help both Dondi and Dr. Dahlquist for their detailed instructions on completing this assignment.
*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). Retrieved December 7, 2017, from [https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15 https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15]
#LMU BioDB 2017. (2017). Retrieved December 7, 2017, from [https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/JASPAR_the_Friendly_Ghost#Eddie.27s_Reflection_3 https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/JASPAR_the_Friendly_Ghost#Eddie.27s_Reflection_3]
#API Overview. (2017). Retrieved December 5, 2017, from [http://jaspar.genereg.net/api/overview#cors-requests http://jaspar.genereg.net/api/overview#cors-requests]
#JASPAR RESTful API. (2017). Retrieved December 5, 2017, from [http://jaspar.genereg.net/api/ http://jaspar.genereg.net/api/]

Simonwro120 Week 15

2017-12-08T00:00:54Z

Simonwro120: added JASPAR api reference

=Electronic Notebook=

==Tuesday==

==Thursday==

== Acknowledgements ==
*I worked with my homework partner, Eddie Bachoura, on this assignment.
*I'd also like to acknowledge the help both Dondi and Dr. Dahlquist for their detailed instructions on completing this assignment.
*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). Retrieved December 7, 2017, from [https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15 https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15]
#LMU BioDB 2017. (2017). Retrieved December 7, 2017, from [https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/JASPAR_the_Friendly_Ghost#Eddie.27s_Reflection_3 https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/JASPAR_the_Friendly_Ghost#Eddie.27s_Reflection_3]
#API Overview. (2017). Retrieved December 5, 2017, from [http://jaspar.genereg.net/api/overview#cors-requests http://jaspar.genereg.net/api/overview#cors-requests]
#JASPAR RESTful API. (2017). Retrieved December 5, 2017, from [http://jaspar.genereg.net/api/ http://jaspar.genereg.net/api/]

Simonwro120 Week 15

2017-12-07T23:53:38Z

Simonwro120: outline

=Electronic Notebook=

==Tuesday==

==Thursday==

== Acknowledgements ==
*I worked with my homework partner, Eddie Bachoura, on this assignment.
*I'd also like to acknowledge the help both Dondi and Dr. Dahlquist for their detailed instructions on completing this assignment.
*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 15 Retrieved December 7, 2017, from [https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15 https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15]
#LMU BioDB 2017. (2017). Week 15 Retrieved December 7, 2017, from [https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/JASPAR_the_Friendly_Ghost#Eddie.27s_Reflection_3 https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/JASPAR_the_Friendly_Ghost#Eddie.27s_Reflection_3]

JASPAR the Friendly Ghost

2017-12-05T05:59:13Z

Simonwro120: syntax

==Deliverables==
[[Media:Genome-wide_analysis_of_the_yeast_transcriptome_upon_heat_and_cold_shock._QL_AP.zip|Antonio and Quinn Journal Club Presentation]] | November 21, 2017 
[[Media:e_and_s_presentation_2.pdf|Eddie and Simon Chapter 6 Presentation]] | November 14, 2017 
[https://github.com/bhamilton18/GRNsight GitHub fork] 
[https://github.com/bhamilton18/GRNsight/tree/gene-database-apis GitHub api branch] (in collaboration with [[Gene_hAPI|Gene_hAPI team]])
==Working Files==

===Antonio's Working Files===
# Gene list for profile 22 of dZAP1 Excel file: [[Media:AP dZAP1 profile22 genelist.xlsx]]
# YEASTRACT Transcription Factor Data: [[Media:AP YEASTRACT Transcription Factors.xlsx]]
# YEASTRACT Regulation Matrix Profile: [[Media:AP Regulation Matrix profile22 dZAP1.xlsx]]
# YEASTRACT Adjacency Matrix: [[Media:AP Adjacency Matrix profile22 dZAP1.xlsx]]
# YEASTRACT Adjacency Matrix with Network for GRNsight: [[Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx]]
# Screenshot of GRNsight Regulatory Network: [[Media:AP Regulation Matrix profile22 GRNsight Network.PNG]]

==Calendar==
{| class ="wikitable"
|+November & December
|-
|Sunday
|Monday
|Tuesday
|Wednesday
|Thursday
|Friday
|Saturday
|-
|
|
|
|'''1'''
|'''2'''
|'''3'''
|'''4'''
|-
|'''5'''
|'''6'''
|'''7'''
|'''8'''
|'''9'''
|'''10'''
|'''11'''
|-
|'''12'''
|'''13'''
|'''14''' C: PPT Presentation PM/DA: Journal Articles
|'''15'''
|'''16'''
|'''17'''
|'''18'''
|-
|'''19'''
|'''20'''
|'''21''' C: Complete setup steps (Milestones 1-3) PM/DA: Journal Club Presentations
|'''22''' ''Thanksgiving Break''
|'''23''' ''Thanksgiving Break''
|'''24''' ''Thanksgiving Break''
|'''25'''
|-
|'''26'''
|'''27'''
|'''28''' C: Fimilariaze self with file structure PM: Chose application data fields from JASPAR DA: Review ANOVA Results
|'''29'''
|'''30''' C: Tests for API PM: Share info to be used from JASPAR with other teams DA: Determine transcription factors, develop candidate gene reg network, and fix edits from week 8 & 10
|'''1'''
|'''2'''
|-
|'''3'''
|'''4'''
|'''5''' C: Retrieval code for API PM: Begin Final Group Paper and PPT DA:Model gene reg network Visualize Results
|'''6'''
|'''7''' C: Review and Test Code PM: Review and Test code PM&DA:Work on Paper and PPT
|'''8'''
|'''9''' Complete Group PPT
|-
|'''10''' Practice Group Presentation
|'''11''' Final group Presentation ''2:00-4:00PM''
|'''12'''
|'''13''' Final Group Paper Completely Written
|'''14''' Edit Final Group Paper
|'''15''' All deliverables due ''4:30PM''
|'''16'''
|}

==Executive Summaries==

===Week 11===

====Quinn's Executive Summary====
Created citations for two entries in the annotated bibliography for papers that report microarray data from yeast subjected to cold shock: 
Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6 
Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, 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 
Also completed a search activity to compare the results found from PubMed, GoogleScholar, and Web of Science using both basic and advanced search tools. 
Individual Journal Page: [[QLanners Week 11]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Executive Summary====
For this assignment, I spent most of my time reading and re-reading Paul Ford's article on how apps are made. It was chapter 6 in a larger work called ''What is Code?'' After absorbing the information laid out in this chapter, Eddie and I made a presentation about it. The presentation summarizes the article, which is about technique, methods, practices, and tools that expedite and simplify the programming process. In addition to making the presentation, I finished my 10 terms and made an outline for the article on my individual journal page. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 13:45, 14 November 2017 (PST)

====Antonio's Executive Summary====

Created two citations for the bibliography for the following articles:

#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#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.

I also completed the basic keyword searches on PubMed, Google Scholar, and Web of Science along with the advanced searches and the respective results. Lastly, I completed the prospective searches and collected the results of how many articles the article cites and how many articles cite the article. Totaling to the 3 articles.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 15:51, 14 November 2017 (PST)

Individual Journal Week 11: [[Aporras1_Week_11|Aporras1 Week 11]]

====Eddie Bachoura's Executive Summary====
This week, I spent my time for this class reading the Paul Ford article, chapter 6, which was about how to write applications and the modern practices and tools which are used to aid in cutting down some of the tedious nature of coding. Then, Simon and I spent the rest of the time working on our presentation. Team's progress: I believe that Simon and I worked well this weekend. The only issue that I found was that we didn't start until pretty late (Monday), but that was all at my own fault because I wasn't here for this weekend. We should fix that by starting earlier next weekend!

Individual Journal Week 11: [[Ebachour_Week_11|Eddie Bachoura Week 11]] 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:29, 13 November 2017 (PST)

===Week 12===

====Quinn's Executive Summary====
Worked closely with Antonio to summarize the results of the journal article Becerra et al. (2003) into a journal club presentation. In order to do so, we both completed the outline provided on the [[Week_12|Week 12]] assignment page on our wiki. We then took this information and used it to create our journal club presentations, which we practiced together and will share in class on Tuesday, November 21. 
Individual Journal Page: [[QLanners Week 12]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Executive Summary====
This week, I met with my coding partner [[User:Ebachour|Eddie Bachoura]] and he helped me clone the code that [[User:Bhamilton18|Blair Hamilton]] forked from the master branch.
After that, Eddie and I helped put together a list of milestones with dates that they should be completed. Using that, Quinn was able to put together a calendar like scheduale for our team to refer to. The last thing I did was open up the cloned files from Blair's fork on my text editor so that I could familiarize myself with the code. 
Individual Journal Page: [[simonwro120 Week 12]] 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:44, 20 November 2017 (PST)

====Antonio's Executive Summary====
Worked throughout the assignment with Quinn to complete the powerpoint presentation on the journal article: ''Genome-wide analysis of the yeast transcriptome upon heat and cold shock''. We both worked closely together on the outline of the article while maintaining our own style of completing the outline. We then practiced our presentation once the information was finalized and are looking forward to sharing on Tuesday the 21st of November.

Individual journal page: [[Aporras1_Week_12|Aporras 1 Week 12]]

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:19, 20 November 2017 (PST)
====Eddie Bachoura's Executive Summary====
This week, most of my time was spent setting up the branch on github and then getting my local version up and running so that I can write and test code on my own laptop. After that, I helped Simon out with doing the same. I also sent Quinn a list of our milestones for this project, as well as letting him know which ones were already completed. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 19:09, 20 November 2017 (PST) 
Week 12 Journal Page: [[ebachour_Week_12| Edward Bachoura]]

===Week 14===

====Quinn's Executive Summary====
This week, I worked closely with the other QAs and [[User:Kdahlquist|Dr. Dahlquist]] to determine what information should be pulled from each of the five databases. I then communicated this information to our coders. Along with this task, I worked communicated closely with both the data analyst and the coders to ensure that they were on track, and to make modifications to their respective milestones on the team calender. Finally, I added additional team milestones to the calendar to reflect all of the steps that need to be taken to complete the deliverables that we have due at the end of the semester. All of this progress can be seen in my [[QLanners_Week_14|individual weekly journal]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:05, 4 December 2017 (PST)

====Simon's Executive Summary====
This week our coding group hit a bit of wall, not just for one, but for multiple reasons. One reason was caused by the fact that one of the coding group members worked in a language that would not be compatible with GRNsight. Another problem our coding group encountered was caused by a complexity in the the JASPAR API relating CORS (Cross-Oirgin Resource Sharing). Although these complications did occur, both me and Eddie B. know where the API guidelines are for JASPAR and what content we need to produce. In addition to that, an api file has been made as well which will be augmented soon. 
Individual Journal Page: [[simonwro120 Week 14]] 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 21:45, 4 December 2017 (PST)

====Antonio's Executive Summary====
This week, I made edits to both my individual [[Aporras1 Week 8]] and [[Aporras1 Week 10]] pages based from feedback received from [[User:Kdahlquist|Dr. Dahlquist]] and [[User:Dondi|Dr. Dionisio]]. The outline for these edits can be found on my [[Aporras1 Week 14]] page along with the continuation of the [[Week 10|Week 10]] assignment. In this continuation, I selected transcription factors from [[Media:AP dZAP1 profile22 genelist.xlsx]] and put them into YEASTRACT to find the most significant ones and found 49 significant transcription factors found in [[Media:AP YEASTRACT Transcription Factors.xlsx]]. Then I selected 22 of the most significant, 2 additional ones (HAP4 and GLN3) as instructed, to put back into YEASTRACT and create a regulation matrix uploaded as: [[Media:AP Regulation Matrix profile22 dZAP1.xlsx]]. I then created a "network" worksheet, found in [[Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx]], from the matrix and used GRNsight to generate a regulation network visualization: [[Media:AP Regulation Matrix profile22 GRNsight Network.PNG]]. These media downloads can also be found on my [[Aporras1 Week 14|Week 14]] journal entry in the
"Deliverables" section.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 18:31, 3 December 2017 (PST)

====Eddie's Executive Summary====

==Weekly Reflections==

===Week 11===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a good job of staying on task and working together to make sure that we both understood the whole assignment. So there was good communication between the Bibliography group.
#What didn't work?
#*I felt a bit disconnected with my other teammates Eddie and Simon. There was not very good communication with them about whether they needed any help and if they were on progress.
#What to improve upon going forward?
#*Going forward all of the members of the team need to do a better job of communicating. Also, we need to do a better job of properly communicating about how to fill out the team page ahead of time, so that we aren't frantically figuring that out last second. I will work to fix this by initiating communication earlier on in the week.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Reflection====
#What worked?
#*Both me and Eddie were able to put together a powerpoint and present in time for the presentation date
#What didn't work?
#*Due to traveling, Eddie could not be back in LA to help with the project until Monday, which did not give us much time, resulting in our presentation being a bit late as far as submission on our wiki pages.
#How will to improve upon going forward?
#*Going forward I'd like to start early and finish early, that way we can be prepared for any unexpected complications. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:48, 20 November 2017 (PST)

====Antonio's Reflection====
1. What worked? Quinn and I were able to get our work done on time without overlap. We communicated well.

2. What didn't work? Nothing specific prevented us from working efficiently.

3. What will I do next to fix what didn't work? Complete work ahead of time to be more thorough. Maintain a growth mindset.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:06, 20 November 2017 (PST)

====Eddie's Reflection====
Found in Week 11 summary ^^^

===Week 12===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a very good job of working ahead and getting our presentation done in a timely manner. In this way, we were able to ask the instructors any questions we had as they came up, and also allowed for ample time to practice.
#What didn't work?
#*Once again, I felt a bit disconnected from my other partners Eddie and Simon. While I texted Eddie a couple times about their progress, I still never got a chance to see exactly what they were doing.
#What to improve upon going forward?
#*While I feel like this will start to come together once we all start working on our assigned portion of the project together, we still do need to improve our communication between the coders and the PM/DA. In order to do so, I will make sure to continue to check base with each team member each day in class, and also text in the group message when I have questions for the whole team.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Reflection====
#What worked?
#*With Eddie's help, we were both able to set up GRNsight on our laptops.
#What didn't work?
#*Nothing in specific stopped us from working efficiently.
#How will to improve upon going forward?
#*Going forward I'd like to get my summaries in earlier, as well as my individual page and reflections. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:48, 20 November 2017 (PST)

====Antonio's Reflection====
#What worked?
#*Worked closely with Quinn and we kept regular contact through text as we worked through the assignment. Troubleshooting was easy as we were both very capable to take initiative and work to finish the presentation earlier rather than later in the time given.
#What didn't work?
#*I could definitely improve on mastering certain aspects of the assignment. I didn't really communicate with Eddie or Simon but I'd attribute that to having different assignments and parts to complete rather than a team issue.
#What to will I do next to fix what didn't work?
#*Communicate more. I'm hoping we'll have opportunities to work more closely together in the future.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:12, 20 November 2017 (PST)

====Eddie's Reflection====
# What worked?
#: Our work session was successful in setting up GRNsight on my laptop (again) and on Simon's.
# What didn't work?
#: Nothing :D
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 21:47, 20 November 2017 (PST)

===Week 14===

====Quinn's Reflection====
#What Worked?
#*This week our team did a much better job of communicating and keeping each other in the loop. Also, the collaboration between all of the QAs was a very effective way to determine which information should be pulled from each database
#What didn't work?
#*I was still a bit confused as to how all of the teams should be working together as we approach the end of the semester
#What will I do next to fix what didn't work>
#*I will make sure to ask about this concern in the next stand up review between the QAs. This will help clear this question up for me and the rest of the class. 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:05, 4 December 2017 (PST)

====Simon's Reflection====
#What Worked?
#*Our class was able to produce a solid list of data items, specified to each database. This meant that as a coder for the JASPAR team, I knew which pieces of data to retrireve and produce from the JASPAR database.
#What didn't work?
#*There were some complications with the language some of the new code was written. There was also a problem with the JASPAR API relating to CORS (Cross-Oirgin Resource Sharing).
#What will I do next to fix what didn't work?
#*I hope to be more knowledgeable about these type of things in reference to computer science.
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 21:57, 4 December 2017 (PST)

====Antonio's Reflection====
# What worked? This week, I worked ahead and was able to complete, at least to my knowledge, this week's assignment ahead of time rather than waiting until the last minute. It was extremely helpful to have a group chat with the other data analysts as we had questions throughout the assignment.
# What didn't work? Everything seems to have run smoothly except I don't really know what the coders are assigned to do and most likely because it goes over my head.
# What will I do next to fix what didn't work? Try to see what the coders are doing, mostly out of curiosity.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 18:36, 3 December 2017 (PST)

====Eddie's Reflection====

==Acknowledgements==

==References==
===Week 11===
#LMU BioDB 2017. (2017). Week 11. Retrieved November 07, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_11
#Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6
#Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, 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
#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#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.
#Top Integrated Development Environment index. (n.d.). Retrieved November 13, 2017, from http://pypl.github.io/IDE.html
#What is an API?. (2016). Retrieved November 13, 2017, from https://medium.freecodecamp.org/what-is-an-api-in-english-please-b880a3214a82
#What's the difference between an API vs SDK?. (2012). Retrieved November 13, 2017, from https://blogs.vmware.com/vsphere/2012/01/whats-the-difference-between-an-api-vs-sdk.html
#Xcode. (2017). Retrieved November 13, 2017, from https://itunes.apple.com/us/app/xcode/id497799835
#What Is Code? (2015). Retrieved November 13, 2017, from https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#how-are-apps-made
#Shrinkwrapped Software. (n.d.). Retrieved November 13, 2017, from http://www.businessdictionary.com/definition/shrinkwrapped-software.html
#Web Application Framework. (2015). Retrieved November 13, 2017, from https://web.archive.org/web/20150723163302/http://docforge.com/wiki/Web_application_framework

===Week 12===
#LMU BioDB 2017. (2017). Week 12. Retrieved November 16, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
#Anneal. (n.d.). ''Genscript''. Retrieved on November 19, 2017 from https://www.genscript.com/molecular-biology-glossary/11896/anneal
#Assay.(2005). ''Biology-Online''. Retrieved on November 19, 2017 http://www.biology-online.org/dictionary/Assay
#Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, 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
#Causton HC, Ren B, Koh SS, et al. 2001. Remodelling of yeast genome expression in response to environmental changes. Mol Biol Cell 12: 323–337.
#Chomczynski, P., & Sacchi, N. (1987). Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Analytical biochemistry, 162(1), 156-159.
#Cluster analysis. BusinessDictionary.com. Retrieved November 19, 2017, from BusinessDictionary.com website: http://www.businessdictionary.com/definition/cluster-analysis.html
#Consensus sequence | Definition of consensus sequence in English by Oxford Dictionaries. (n.d.). Retrieved November 20, 2017, from https://en.oxforddictionaries.com/definition/consensus_sequence
#Cyclins. (n.d.). ''BioNinja''. Retrieved on November 19, 2017 from http://ib.bioninja.com.au/standard-level/topic-1-cell-biology/16-cell-division/cyclins.html
#Differences between in vitro, in vivo, and in silico studies. (n.d.). Retrieved November 20, 2017, from https://mpkb.org/home/patients/assessing_literature/in_vitro_studies
#Donzeau M, Bourdineaud JP, Lauquin GJ. 1996. Regulation by low temperatures and anaerobiosis of a yeast gene specifying a putative GPI-anchored plasma membrane protein. Mol Microbiol 20: 449–459.
#Gasch AP, Spellman PT, Kao CM, et al. 2000. Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11: 4241–4257.
#Glutathione. (n.d.). Retrieved November 20, 2017, from https://www.merriam-webster.com/dictionary/glutathione
#Haploid. (n.d.). Retrieved November 20, 2017, from http://www.biology-online.org/dictionary/Haploid
#HAW. (2011). Difference Between Haploid and Diploid. ''Difference Between.com''. Retrieved on November 19, 2017 from http://www.differencebetween.com/difference-between-haploid-and-vs-diploid/
#Hybridization. (2008). ''Biology-Online''. Retrieved on November 19, 2017 from http://www.biology-online.org/dictionary/Hybridization
#Kondo K, Inouye M. 1991. Cold-induction of yeast NSR1 protein and its role in pre-rRNA processing. J Biol Chem 267: 16 259–16 265.
#Kowalski LR, Kondo K, Inouye M. 1995. Cold-shock induction of a family of TIP1-related proteins associated with the membrane in Saccharomyces cerevisiae. Mol Microbiol 15: 341 – 353.
#LMU BioDB 2017. (2017). Week 12. Retrieved November 16, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
#Mai B, Breeden L. 1997. Xbp1, a stress-upregulated transcrip- tional repressor of the Saccharomyces cerevisae Swi4/Mbp1 family. Mol Cell Biol 17: 6491–6501.
#(n.d.). Retrieved November 19, 2017, from http://fg.cns.utexas.edu/fg/protocol%3A_YPD_plates.html
#(n.d.). Retrieved November 20, 2017, from https://www.nature.com/scitable/definition/diploid-310
#Oligonucleotide. (2014). ''News Medical Life Sciences''. Retrieved on November 19, 2017 from https://www.news-medical.net/life-sciences/What-is-an-Oligonucleotide.aspx
#Polypropylene. (n.d.). ''Dictionary.com''. Retrieved on November 19, 2017 from http://www.dictionary.com/browse/polypropylene
#Putative. (2014). ''Biology-Online''. Retrieved on November 19, 2017 from http://www.biology-online.org/dictionary/Putative
#Study.com. (2017). What is Annealing? - Definition, Biology & Process | Study.com. [online] Available at: http://study.com/academy/lesson/what-is-annealing-definition-biology-process.html [Accessed 21 Nov. 2017].
#Transcriptome. (n.d.). ''Nature''. Retrieved on November 19, 2017 from https://www.nature.com/scitable/definition/transcriptome-296
#Yelland, P. M. (2010). An introduction to correspondence analysis. Math. J, 12, 1-23.
#Young, F.W. (1999). Principle Components. ''forrest.psych.unc.edu''. Retrieved on November 19, 2017 from http://forrest.psych.unc.edu/research/vista-frames/help/lecturenotes/lecture13/biplot.html
#Zhang L, Ohta A, Horiuchi H, Takagi M, Imai R. 2001. Multiple mechanisms regulate expression of low temperature responsive (LOT) genes in Saccharomyces cerevisiae. Biochem Biophys Res Commun 283: 531 – 535.

===Week 14===
Ensembl. (2017). "Gene: HSF1". Retrieved November 28, 2017, from https://www.ensembl.org/Saccharomyces_cerevisiae/Gene/Summary?db=core;g=YGL073W;r=VII:368753-371254;t=YGL073W 
JASPAR. (2017). "Detailed information of matrix profile MA0319.1". Retrieved on November 28, 2017, from http://jaspar.genereg.net/matrix/MA0319.1/ 
LMU BioDB 2017. (2017). Week 14. Retrieved November 28, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_14 
NCBI. (2017). "HSF1 stress-responsive transcription factor HSF1 [ Saccharomyces cerevisiae S288C ]". Retrieved November 28, 2017, from https://www.ncbi.nlm.nih.gov/gene/852806 
Saccharomyces Genome Database. (2017). "HSF1 / YGL073W Overview". Retrieved November 28, 2017, from https://www.yeastgenome.org/locus/S000003041 
UniProt. (2017). "UniProtKB - P10961 (HSF_YEAST)". Retrieved November 28, 2017 from http://www.uniprot.org/uniprot/P10961

==Team Links==

{{Template:JASPAR the Friendly Ghost Links}}

==Class Links==

{{Template:GRNsight Gene Page Project Links}}

JASPAR the Friendly Ghost

2017-12-05T05:57:27Z

Simonwro120: reflection

==Deliverables==
[[Media:Genome-wide_analysis_of_the_yeast_transcriptome_upon_heat_and_cold_shock._QL_AP.zip|Antonio and Quinn Journal Club Presentation]] | November 21, 2017 
[[Media:e_and_s_presentation_2.pdf|Eddie and Simon Chapter 6 Presentation]] | November 14, 2017 
[https://github.com/bhamilton18/GRNsight GitHub fork] 
[https://github.com/bhamilton18/GRNsight/tree/gene-database-apis GitHub api branch] (in collaboration with [[Gene_hAPI|Gene_hAPI team]])
==Working Files==

===Antonio's Working Files===
# Gene list for profile 22 of dZAP1 Excel file: [[Media:AP dZAP1 profile22 genelist.xlsx]]
# YEASTRACT Transcription Factor Data: [[Media:AP YEASTRACT Transcription Factors.xlsx]]
# YEASTRACT Regulation Matrix Profile: [[Media:AP Regulation Matrix profile22 dZAP1.xlsx]]
# YEASTRACT Adjacency Matrix: [[Media:AP Adjacency Matrix profile22 dZAP1.xlsx]]
# YEASTRACT Adjacency Matrix with Network for GRNsight: [[Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx]]
# Screenshot of GRNsight Regulatory Network: [[Media:AP Regulation Matrix profile22 GRNsight Network.PNG]]

==Calendar==
{| class ="wikitable"
|+November & December
|-
|Sunday
|Monday
|Tuesday
|Wednesday
|Thursday
|Friday
|Saturday
|-
|
|
|
|'''1'''
|'''2'''
|'''3'''
|'''4'''
|-
|'''5'''
|'''6'''
|'''7'''
|'''8'''
|'''9'''
|'''10'''
|'''11'''
|-
|'''12'''
|'''13'''
|'''14''' C: PPT Presentation PM/DA: Journal Articles
|'''15'''
|'''16'''
|'''17'''
|'''18'''
|-
|'''19'''
|'''20'''
|'''21''' C: Complete setup steps (Milestones 1-3) PM/DA: Journal Club Presentations
|'''22''' ''Thanksgiving Break''
|'''23''' ''Thanksgiving Break''
|'''24''' ''Thanksgiving Break''
|'''25'''
|-
|'''26'''
|'''27'''
|'''28''' C: Fimilariaze self with file structure PM: Chose application data fields from JASPAR DA: Review ANOVA Results
|'''29'''
|'''30''' C: Tests for API PM: Share info to be used from JASPAR with other teams DA: Determine transcription factors, develop candidate gene reg network, and fix edits from week 8 & 10
|'''1'''
|'''2'''
|-
|'''3'''
|'''4'''
|'''5''' C: Retrieval code for API PM: Begin Final Group Paper and PPT DA:Model gene reg network Visualize Results
|'''6'''
|'''7''' C: Review and Test Code PM: Review and Test code PM&DA:Work on Paper and PPT
|'''8'''
|'''9''' Complete Group PPT
|-
|'''10''' Practice Group Presentation
|'''11''' Final group Presentation ''2:00-4:00PM''
|'''12'''
|'''13''' Final Group Paper Completely Written
|'''14''' Edit Final Group Paper
|'''15''' All deliverables due ''4:30PM''
|'''16'''
|}

==Executive Summaries==

===Week 11===

====Quinn's Executive Summary====
Created citations for two entries in the annotated bibliography for papers that report microarray data from yeast subjected to cold shock: 
Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6 
Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, 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 
Also completed a search activity to compare the results found from PubMed, GoogleScholar, and Web of Science using both basic and advanced search tools. 
Individual Journal Page: [[QLanners Week 11]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Executive Summary====
For this assignment, I spent most of my time reading and re-reading Paul Ford's article on how apps are made. It was chapter 6 in a larger work called ''What is Code?'' After absorbing the information laid out in this chapter, Eddie and I made a presentation about it. The presentation summarizes the article, which is about technique, methods, practices, and tools that expedite and simplify the programming process. In addition to making the presentation, I finished my 10 terms and made an outline for the article on my individual journal page. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 13:45, 14 November 2017 (PST)

====Antonio's Executive Summary====

Created two citations for the bibliography for the following articles:

#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#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.

I also completed the basic keyword searches on PubMed, Google Scholar, and Web of Science along with the advanced searches and the respective results. Lastly, I completed the prospective searches and collected the results of how many articles the article cites and how many articles cite the article. Totaling to the 3 articles.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 15:51, 14 November 2017 (PST)

Individual Journal Week 11: [[Aporras1_Week_11|Aporras1 Week 11]]

====Eddie Bachoura's Executive Summary====
This week, I spent my time for this class reading the Paul Ford article, chapter 6, which was about how to write applications and the modern practices and tools which are used to aid in cutting down some of the tedious nature of coding. Then, Simon and I spent the rest of the time working on our presentation. Team's progress: I believe that Simon and I worked well this weekend. The only issue that I found was that we didn't start until pretty late (Monday), but that was all at my own fault because I wasn't here for this weekend. We should fix that by starting earlier next weekend!

Individual Journal Week 11: [[Ebachour_Week_11|Eddie Bachoura Week 11]] 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:29, 13 November 2017 (PST)

===Week 12===

====Quinn's Executive Summary====
Worked closely with Antonio to summarize the results of the journal article Becerra et al. (2003) into a journal club presentation. In order to do so, we both completed the outline provided on the [[Week_12|Week 12]] assignment page on our wiki. We then took this information and used it to create our journal club presentations, which we practiced together and will share in class on Tuesday, November 21. 
Individual Journal Page: [[QLanners Week 12]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Executive Summary====
This week, I met with my coding partner [[User:Ebachour|Eddie Bachoura]] and he helped me clone the code that [[User:Bhamilton18|Blair Hamilton]] forked from the master branch.
After that, Eddie and I helped put together a list of milestones with dates that they should be completed. Using that, Quinn was able to put together a calendar like scheduale for our team to refer to. The last thing I did was open up the cloned files from Blair's fork on my text editor so that I could familiarize myself with the code. 
Individual Journal Page: [[simonwro120 Week 12]] 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:44, 20 November 2017 (PST)

====Antonio's Executive Summary====
Worked throughout the assignment with Quinn to complete the powerpoint presentation on the journal article: ''Genome-wide analysis of the yeast transcriptome upon heat and cold shock''. We both worked closely together on the outline of the article while maintaining our own style of completing the outline. We then practiced our presentation once the information was finalized and are looking forward to sharing on Tuesday the 21st of November.

Individual journal page: [[Aporras1_Week_12|Aporras 1 Week 12]]

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:19, 20 November 2017 (PST)
====Eddie Bachoura's Executive Summary====
This week, most of my time was spent setting up the branch on github and then getting my local version up and running so that I can write and test code on my own laptop. After that, I helped Simon out with doing the same. I also sent Quinn a list of our milestones for this project, as well as letting him know which ones were already completed. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 19:09, 20 November 2017 (PST) 
Week 12 Journal Page: [[ebachour_Week_12| Edward Bachoura]]

===Week 14===

====Quinn's Executive Summary====
This week, I worked closely with the other QAs and [[User:Kdahlquist|Dr. Dahlquist]] to determine what information should be pulled from each of the five databases. I then communicated this information to our coders. Along with this task, I worked communicated closely with both the data analyst and the coders to ensure that they were on track, and to make modifications to their respective milestones on the team calender. Finally, I added additional team milestones to the calendar to reflect all of the steps that need to be taken to complete the deliverables that we have due at the end of the semester. All of this progress can be seen in my [[QLanners_Week_14|individual weekly journal]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:05, 4 December 2017 (PST)

====Simon's Executive Summary====
This week our coding group hit a bit of wall, not just for one, but for multiple reasons. One reason was caused by the fact that one of the coding group members worked in a language that would not be compatible with GRNsight. Another problem our coding group encountered was caused by a complexity in the the JASPAR API relating CORS (Cross-Oirgin Resource Sharing). Although these complications did occur, both me and Eddie B. know where the API guidelines are for JASPAR and what content we need to produce. In addition to that, an api file has been made as well which will be augmented soon. 
Individual Journal Page: [[simonwro120 Week 14]] 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 21:45, 4 December 2017 (PST)

====Antonio's Executive Summary====
This week, I made edits to both my individual [[Aporras1 Week 8]] and [[Aporras1 Week 10]] pages based from feedback received from [[User:Kdahlquist|Dr. Dahlquist]] and [[User:Dondi|Dr. Dionisio]]. The outline for these edits can be found on my [[Aporras1 Week 14]] page along with the continuation of the [[Week 10|Week 10]] assignment. In this continuation, I selected transcription factors from [[Media:AP dZAP1 profile22 genelist.xlsx]] and put them into YEASTRACT to find the most significant ones and found 49 significant transcription factors found in [[Media:AP YEASTRACT Transcription Factors.xlsx]]. Then I selected 22 of the most significant, 2 additional ones (HAP4 and GLN3) as instructed, to put back into YEASTRACT and create a regulation matrix uploaded as: [[Media:AP Regulation Matrix profile22 dZAP1.xlsx]]. I then created a "network" worksheet, found in [[Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx]], from the matrix and used GRNsight to generate a regulation network visualization: [[Media:AP Regulation Matrix profile22 GRNsight Network.PNG]]. These media downloads can also be found on my [[Aporras1 Week 14|Week 14]] journal entry in the
"Deliverables" section.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 18:31, 3 December 2017 (PST)

====Eddie's Executive Summary====

==Weekly Reflections==

===Week 11===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a good job of staying on task and working together to make sure that we both understood the whole assignment. So there was good communication between the Bibliography group.
#What didn't work?
#*I felt a bit disconnected with my other teammates Eddie and Simon. There was not very good communication with them about whether they needed any help and if they were on progress.
#What to improve upon going forward?
#*Going forward all of the members of the team need to do a better job of communicating. Also, we need to do a better job of properly communicating about how to fill out the team page ahead of time, so that we aren't frantically figuring that out last second. I will work to fix this by initiating communication earlier on in the week.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Reflection====
#What worked?
#*Both me and Eddie were able to put together a powerpoint and present in time for the presentation date
#What didn't work?
#*Due to traveling, Eddie could not be back in LA to help with the project until Monday, which did not give us much time, resulting in our presentation being a bit late as far as submission on our wiki pages.
#How will to improve upon going forward?
#*Going forward I'd like to start early and finish early, that way we can be prepared for any unexpected complications. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:48, 20 November 2017 (PST)

====Antonio's Reflection====
1. What worked? Quinn and I were able to get our work done on time without overlap. We communicated well.

2. What didn't work? Nothing specific prevented us from working efficiently.

3. What will I do next to fix what didn't work? Complete work ahead of time to be more thorough. Maintain a growth mindset.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:06, 20 November 2017 (PST)

====Eddie's Reflection====
Found in Week 11 summary ^^^

===Week 12===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a very good job of working ahead and getting our presentation done in a timely manner. In this way, we were able to ask the instructors any questions we had as they came up, and also allowed for ample time to practice.
#What didn't work?
#*Once again, I felt a bit disconnected from my other partners Eddie and Simon. While I texted Eddie a couple times about their progress, I still never got a chance to see exactly what they were doing.
#What to improve upon going forward?
#*While I feel like this will start to come together once we all start working on our assigned portion of the project together, we still do need to improve our communication between the coders and the PM/DA. In order to do so, I will make sure to continue to check base with each team member each day in class, and also text in the group message when I have questions for the whole team.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Reflection====
#What worked?
#*With Eddie's help, we were both able to set up GRNsight on our laptops.
#What didn't work?
#*Nothing in specific stopped us from working efficiently.
#How will to improve upon going forward?
#*Going forward I'd like to get my summaries in earlier, as well as my individual page and reflections. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:48, 20 November 2017 (PST)

====Antonio's Reflection====
#What worked?
#*Worked closely with Quinn and we kept regular contact through text as we worked through the assignment. Troubleshooting was easy as we were both very capable to take initiative and work to finish the presentation earlier rather than later in the time given.
#What didn't work?
#*I could definitely improve on mastering certain aspects of the assignment. I didn't really communicate with Eddie or Simon but I'd attribute that to having different assignments and parts to complete rather than a team issue.
#What to will I do next to fix what didn't work?
#*Communicate more. I'm hoping we'll have opportunities to work more closely together in the future.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:12, 20 November 2017 (PST)

====Eddie's Reflection====
# What worked?
#: Our work session was successful in setting up GRNsight on my laptop (again) and on Simon's.
# What didn't work?
#: Nothing :D
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 21:47, 20 November 2017 (PST)

===Week 14===

====Quinn's Reflection====
#What Worked?
#*This week our team did a much better job of communicating and keeping each other in the loop. Also, the collaboration between all of the QAs was a very effective way to determine which information should be pulled from each database
#What didn't work?
#*I was still a bit confused as to how all of the teams should be working together as we approach the end of the semester
#What will I do next to fix what didn't work>
#*I will make sure to ask about this concern in the next stand up review between the QAs. This will help clear this question up for me and the rest of the class. 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:05, 4 December 2017 (PST)

====Simon's Reflection====
#What Worked?
*Our class was able to produce a solid list of data items, specified to each database. This meant that as a coder for the JASPAR team, I knew which pieces of data to retrireve and produce from the JASPAR database.
#What didn't work?
*There were some complications with the language some of the new code was written. There was also a problem with the JASPAR API relating to CORS (Cross-Oirgin Resource Sharing).
#What will I do next to fix what didn't work?
*I hope to be more knowledgeable about these type of things in reference to computer science.
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 21:57, 4 December 2017 (PST)

====Antonio's Reflection====
# What worked? This week, I worked ahead and was able to complete, at least to my knowledge, this week's assignment ahead of time rather than waiting until the last minute. It was extremely helpful to have a group chat with the other data analysts as we had questions throughout the assignment.
# What didn't work? Everything seems to have run smoothly except I don't really know what the coders are assigned to do and most likely because it goes over my head.
# What will I do next to fix what didn't work? Try to see what the coders are doing, mostly out of curiosity.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 18:36, 3 December 2017 (PST)

====Eddie's Reflection====

==Acknowledgements==

==References==
===Week 11===
#LMU BioDB 2017. (2017). Week 11. Retrieved November 07, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_11
#Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6
#Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, 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
#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#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.
#Top Integrated Development Environment index. (n.d.). Retrieved November 13, 2017, from http://pypl.github.io/IDE.html
#What is an API?. (2016). Retrieved November 13, 2017, from https://medium.freecodecamp.org/what-is-an-api-in-english-please-b880a3214a82
#What's the difference between an API vs SDK?. (2012). Retrieved November 13, 2017, from https://blogs.vmware.com/vsphere/2012/01/whats-the-difference-between-an-api-vs-sdk.html
#Xcode. (2017). Retrieved November 13, 2017, from https://itunes.apple.com/us/app/xcode/id497799835
#What Is Code? (2015). Retrieved November 13, 2017, from https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#how-are-apps-made
#Shrinkwrapped Software. (n.d.). Retrieved November 13, 2017, from http://www.businessdictionary.com/definition/shrinkwrapped-software.html
#Web Application Framework. (2015). Retrieved November 13, 2017, from https://web.archive.org/web/20150723163302/http://docforge.com/wiki/Web_application_framework

===Week 12===
#LMU BioDB 2017. (2017). Week 12. Retrieved November 16, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
#Anneal. (n.d.). ''Genscript''. Retrieved on November 19, 2017 from https://www.genscript.com/molecular-biology-glossary/11896/anneal
#Assay.(2005). ''Biology-Online''. Retrieved on November 19, 2017 http://www.biology-online.org/dictionary/Assay
#Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, 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
#Causton HC, Ren B, Koh SS, et al. 2001. Remodelling of yeast genome expression in response to environmental changes. Mol Biol Cell 12: 323–337.
#Chomczynski, P., & Sacchi, N. (1987). Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Analytical biochemistry, 162(1), 156-159.
#Cluster analysis. BusinessDictionary.com. Retrieved November 19, 2017, from BusinessDictionary.com website: http://www.businessdictionary.com/definition/cluster-analysis.html
#Consensus sequence | Definition of consensus sequence in English by Oxford Dictionaries. (n.d.). Retrieved November 20, 2017, from https://en.oxforddictionaries.com/definition/consensus_sequence
#Cyclins. (n.d.). ''BioNinja''. Retrieved on November 19, 2017 from http://ib.bioninja.com.au/standard-level/topic-1-cell-biology/16-cell-division/cyclins.html
#Differences between in vitro, in vivo, and in silico studies. (n.d.). Retrieved November 20, 2017, from https://mpkb.org/home/patients/assessing_literature/in_vitro_studies
#Donzeau M, Bourdineaud JP, Lauquin GJ. 1996. Regulation by low temperatures and anaerobiosis of a yeast gene specifying a putative GPI-anchored plasma membrane protein. Mol Microbiol 20: 449–459.
#Gasch AP, Spellman PT, Kao CM, et al. 2000. Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11: 4241–4257.
#Glutathione. (n.d.). Retrieved November 20, 2017, from https://www.merriam-webster.com/dictionary/glutathione
#Haploid. (n.d.). Retrieved November 20, 2017, from http://www.biology-online.org/dictionary/Haploid
#HAW. (2011). Difference Between Haploid and Diploid. ''Difference Between.com''. Retrieved on November 19, 2017 from http://www.differencebetween.com/difference-between-haploid-and-vs-diploid/
#Hybridization. (2008). ''Biology-Online''. Retrieved on November 19, 2017 from http://www.biology-online.org/dictionary/Hybridization
#Kondo K, Inouye M. 1991. Cold-induction of yeast NSR1 protein and its role in pre-rRNA processing. J Biol Chem 267: 16 259–16 265.
#Kowalski LR, Kondo K, Inouye M. 1995. Cold-shock induction of a family of TIP1-related proteins associated with the membrane in Saccharomyces cerevisiae. Mol Microbiol 15: 341 – 353.
#LMU BioDB 2017. (2017). Week 12. Retrieved November 16, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
#Mai B, Breeden L. 1997. Xbp1, a stress-upregulated transcrip- tional repressor of the Saccharomyces cerevisae Swi4/Mbp1 family. Mol Cell Biol 17: 6491–6501.
#(n.d.). Retrieved November 19, 2017, from http://fg.cns.utexas.edu/fg/protocol%3A_YPD_plates.html
#(n.d.). Retrieved November 20, 2017, from https://www.nature.com/scitable/definition/diploid-310
#Oligonucleotide. (2014). ''News Medical Life Sciences''. Retrieved on November 19, 2017 from https://www.news-medical.net/life-sciences/What-is-an-Oligonucleotide.aspx
#Polypropylene. (n.d.). ''Dictionary.com''. Retrieved on November 19, 2017 from http://www.dictionary.com/browse/polypropylene
#Putative. (2014). ''Biology-Online''. Retrieved on November 19, 2017 from http://www.biology-online.org/dictionary/Putative
#Study.com. (2017). What is Annealing? - Definition, Biology & Process | Study.com. [online] Available at: http://study.com/academy/lesson/what-is-annealing-definition-biology-process.html [Accessed 21 Nov. 2017].
#Transcriptome. (n.d.). ''Nature''. Retrieved on November 19, 2017 from https://www.nature.com/scitable/definition/transcriptome-296
#Yelland, P. M. (2010). An introduction to correspondence analysis. Math. J, 12, 1-23.
#Young, F.W. (1999). Principle Components. ''forrest.psych.unc.edu''. Retrieved on November 19, 2017 from http://forrest.psych.unc.edu/research/vista-frames/help/lecturenotes/lecture13/biplot.html
#Zhang L, Ohta A, Horiuchi H, Takagi M, Imai R. 2001. Multiple mechanisms regulate expression of low temperature responsive (LOT) genes in Saccharomyces cerevisiae. Biochem Biophys Res Commun 283: 531 – 535.

===Week 14===
Ensembl. (2017). "Gene: HSF1". Retrieved November 28, 2017, from https://www.ensembl.org/Saccharomyces_cerevisiae/Gene/Summary?db=core;g=YGL073W;r=VII:368753-371254;t=YGL073W 
JASPAR. (2017). "Detailed information of matrix profile MA0319.1". Retrieved on November 28, 2017, from http://jaspar.genereg.net/matrix/MA0319.1/ 
LMU BioDB 2017. (2017). Week 14. Retrieved November 28, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_14 
NCBI. (2017). "HSF1 stress-responsive transcription factor HSF1 [ Saccharomyces cerevisiae S288C ]". Retrieved November 28, 2017, from https://www.ncbi.nlm.nih.gov/gene/852806 
Saccharomyces Genome Database. (2017). "HSF1 / YGL073W Overview". Retrieved November 28, 2017, from https://www.yeastgenome.org/locus/S000003041 
UniProt. (2017). "UniProtKB - P10961 (HSF_YEAST)". Retrieved November 28, 2017 from http://www.uniprot.org/uniprot/P10961

==Team Links==

{{Template:JASPAR the Friendly Ghost Links}}

==Class Links==

{{Template:GRNsight Gene Page Project Links}}

JASPAR the Friendly Ghost

2017-12-05T05:48:46Z

Simonwro120: outline

==Deliverables==
[[Media:Genome-wide_analysis_of_the_yeast_transcriptome_upon_heat_and_cold_shock._QL_AP.zip|Antonio and Quinn Journal Club Presentation]] | November 21, 2017 
[[Media:e_and_s_presentation_2.pdf|Eddie and Simon Chapter 6 Presentation]] | November 14, 2017 
[https://github.com/bhamilton18/GRNsight GitHub fork] 
[https://github.com/bhamilton18/GRNsight/tree/gene-database-apis GitHub api branch] (in collaboration with [[Gene_hAPI|Gene_hAPI team]])
==Working Files==

===Antonio's Working Files===
# Gene list for profile 22 of dZAP1 Excel file: [[Media:AP dZAP1 profile22 genelist.xlsx]]
# YEASTRACT Transcription Factor Data: [[Media:AP YEASTRACT Transcription Factors.xlsx]]
# YEASTRACT Regulation Matrix Profile: [[Media:AP Regulation Matrix profile22 dZAP1.xlsx]]
# YEASTRACT Adjacency Matrix: [[Media:AP Adjacency Matrix profile22 dZAP1.xlsx]]
# YEASTRACT Adjacency Matrix with Network for GRNsight: [[Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx]]
# Screenshot of GRNsight Regulatory Network: [[Media:AP Regulation Matrix profile22 GRNsight Network.PNG]]

==Calendar==
{| class ="wikitable"
|+November & December
|-
|Sunday
|Monday
|Tuesday
|Wednesday
|Thursday
|Friday
|Saturday
|-
|
|
|
|'''1'''
|'''2'''
|'''3'''
|'''4'''
|-
|'''5'''
|'''6'''
|'''7'''
|'''8'''
|'''9'''
|'''10'''
|'''11'''
|-
|'''12'''
|'''13'''
|'''14''' C: PPT Presentation PM/DA: Journal Articles
|'''15'''
|'''16'''
|'''17'''
|'''18'''
|-
|'''19'''
|'''20'''
|'''21''' C: Complete setup steps (Milestones 1-3) PM/DA: Journal Club Presentations
|'''22''' ''Thanksgiving Break''
|'''23''' ''Thanksgiving Break''
|'''24''' ''Thanksgiving Break''
|'''25'''
|-
|'''26'''
|'''27'''
|'''28''' C: Fimilariaze self with file structure PM: Chose application data fields from JASPAR DA: Review ANOVA Results
|'''29'''
|'''30''' C: Tests for API PM: Share info to be used from JASPAR with other teams DA: Determine transcription factors, develop candidate gene reg network, and fix edits from week 8 & 10
|'''1'''
|'''2'''
|-
|'''3'''
|'''4'''
|'''5''' C: Retrieval code for API PM: Begin Final Group Paper and PPT DA:Model gene reg network Visualize Results
|'''6'''
|'''7''' C: Review and Test Code PM: Review and Test code PM&DA:Work on Paper and PPT
|'''8'''
|'''9''' Complete Group PPT
|-
|'''10''' Practice Group Presentation
|'''11''' Final group Presentation ''2:00-4:00PM''
|'''12'''
|'''13''' Final Group Paper Completely Written
|'''14''' Edit Final Group Paper
|'''15''' All deliverables due ''4:30PM''
|'''16'''
|}

==Executive Summaries==

===Week 11===

====Quinn's Executive Summary====
Created citations for two entries in the annotated bibliography for papers that report microarray data from yeast subjected to cold shock: 
Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6 
Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, 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 
Also completed a search activity to compare the results found from PubMed, GoogleScholar, and Web of Science using both basic and advanced search tools. 
Individual Journal Page: [[QLanners Week 11]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Executive Summary====
For this assignment, I spent most of my time reading and re-reading Paul Ford's article on how apps are made. It was chapter 6 in a larger work called ''What is Code?'' After absorbing the information laid out in this chapter, Eddie and I made a presentation about it. The presentation summarizes the article, which is about technique, methods, practices, and tools that expedite and simplify the programming process. In addition to making the presentation, I finished my 10 terms and made an outline for the article on my individual journal page. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 13:45, 14 November 2017 (PST)

====Antonio's Executive Summary====

Created two citations for the bibliography for the following articles:

#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#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.

I also completed the basic keyword searches on PubMed, Google Scholar, and Web of Science along with the advanced searches and the respective results. Lastly, I completed the prospective searches and collected the results of how many articles the article cites and how many articles cite the article. Totaling to the 3 articles.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 15:51, 14 November 2017 (PST)

Individual Journal Week 11: [[Aporras1_Week_11|Aporras1 Week 11]]

====Eddie Bachoura's Executive Summary====
This week, I spent my time for this class reading the Paul Ford article, chapter 6, which was about how to write applications and the modern practices and tools which are used to aid in cutting down some of the tedious nature of coding. Then, Simon and I spent the rest of the time working on our presentation. Team's progress: I believe that Simon and I worked well this weekend. The only issue that I found was that we didn't start until pretty late (Monday), but that was all at my own fault because I wasn't here for this weekend. We should fix that by starting earlier next weekend!

Individual Journal Week 11: [[Ebachour_Week_11|Eddie Bachoura Week 11]] 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:29, 13 November 2017 (PST)

===Week 12===

====Quinn's Executive Summary====
Worked closely with Antonio to summarize the results of the journal article Becerra et al. (2003) into a journal club presentation. In order to do so, we both completed the outline provided on the [[Week_12|Week 12]] assignment page on our wiki. We then took this information and used it to create our journal club presentations, which we practiced together and will share in class on Tuesday, November 21. 
Individual Journal Page: [[QLanners Week 12]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Executive Summary====
This week, I met with my coding partner [[User:Ebachour|Eddie Bachoura]] and he helped me clone the code that [[User:Bhamilton18|Blair Hamilton]] forked from the master branch.
After that, Eddie and I helped put together a list of milestones with dates that they should be completed. Using that, Quinn was able to put together a calendar like scheduale for our team to refer to. The last thing I did was open up the cloned files from Blair's fork on my text editor so that I could familiarize myself with the code. 
Individual Journal Page: [[simonwro120 Week 12]] 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:44, 20 November 2017 (PST)

====Antonio's Executive Summary====
Worked throughout the assignment with Quinn to complete the powerpoint presentation on the journal article: ''Genome-wide analysis of the yeast transcriptome upon heat and cold shock''. We both worked closely together on the outline of the article while maintaining our own style of completing the outline. We then practiced our presentation once the information was finalized and are looking forward to sharing on Tuesday the 21st of November.

Individual journal page: [[Aporras1_Week_12|Aporras 1 Week 12]]

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:19, 20 November 2017 (PST)
====Eddie Bachoura's Executive Summary====
This week, most of my time was spent setting up the branch on github and then getting my local version up and running so that I can write and test code on my own laptop. After that, I helped Simon out with doing the same. I also sent Quinn a list of our milestones for this project, as well as letting him know which ones were already completed. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 19:09, 20 November 2017 (PST) 
Week 12 Journal Page: [[ebachour_Week_12| Edward Bachoura]]

===Week 14===

====Quinn's Executive Summary====
This week, I worked closely with the other QAs and [[User:Kdahlquist|Dr. Dahlquist]] to determine what information should be pulled from each of the five databases. I then communicated this information to our coders. Along with this task, I worked communicated closely with both the data analyst and the coders to ensure that they were on track, and to make modifications to their respective milestones on the team calender. Finally, I added additional team milestones to the calendar to reflect all of the steps that need to be taken to complete the deliverables that we have due at the end of the semester. All of this progress can be seen in my [[QLanners_Week_14|individual weekly journal]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:05, 4 December 2017 (PST)

====Simon's Executive Summary====
This week our coding group hit a bit of wall, not just for one, but for multiple reasons. One reason was caused by the fact that one of the coding group members worked in a language that would not be compatible with GRNsight. Another problem our coding group encountered was caused by a complexity in the the JASPAR API relating CORS (Cross-Oirgin Resource Sharing). Although these complications did occur, both me and Eddie B. know where the API guidelines are for JASPAR and what content we need to produce. In addition to that, an api file has been made as well which will be augmented soon. 
Individual Journal Page: [[simonwro120 Week 14]] 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 21:45, 4 December 2017 (PST)

====Antonio's Executive Summary====
This week, I made edits to both my individual [[Aporras1 Week 8]] and [[Aporras1 Week 10]] pages based from feedback received from [[User:Kdahlquist|Dr. Dahlquist]] and [[User:Dondi|Dr. Dionisio]]. The outline for these edits can be found on my [[Aporras1 Week 14]] page along with the continuation of the [[Week 10|Week 10]] assignment. In this continuation, I selected transcription factors from [[Media:AP dZAP1 profile22 genelist.xlsx]] and put them into YEASTRACT to find the most significant ones and found 49 significant transcription factors found in [[Media:AP YEASTRACT Transcription Factors.xlsx]]. Then I selected 22 of the most significant, 2 additional ones (HAP4 and GLN3) as instructed, to put back into YEASTRACT and create a regulation matrix uploaded as: [[Media:AP Regulation Matrix profile22 dZAP1.xlsx]]. I then created a "network" worksheet, found in [[Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx]], from the matrix and used GRNsight to generate a regulation network visualization: [[Media:AP Regulation Matrix profile22 GRNsight Network.PNG]]. These media downloads can also be found on my [[Aporras1 Week 14|Week 14]] journal entry in the
"Deliverables" section.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 18:31, 3 December 2017 (PST)

====Eddie's Executive Summary====

==Weekly Reflections==

===Week 11===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a good job of staying on task and working together to make sure that we both understood the whole assignment. So there was good communication between the Bibliography group.
#What didn't work?
#*I felt a bit disconnected with my other teammates Eddie and Simon. There was not very good communication with them about whether they needed any help and if they were on progress.
#What to improve upon going forward?
#*Going forward all of the members of the team need to do a better job of communicating. Also, we need to do a better job of properly communicating about how to fill out the team page ahead of time, so that we aren't frantically figuring that out last second. I will work to fix this by initiating communication earlier on in the week.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Reflection====
#What worked?
#*Both me and Eddie were able to put together a powerpoint and present in time for the presentation date
#What didn't work?
#*Due to traveling, Eddie could not be back in LA to help with the project until Monday, which did not give us much time, resulting in our presentation being a bit late as far as submission on our wiki pages.
#How will to improve upon going forward?
#*Going forward I'd like to start early and finish early, that way we can be prepared for any unexpected complications. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:48, 20 November 2017 (PST)

====Antonio's Reflection====
1. What worked? Quinn and I were able to get our work done on time without overlap. We communicated well.

2. What didn't work? Nothing specific prevented us from working efficiently.

3. What will I do next to fix what didn't work? Complete work ahead of time to be more thorough. Maintain a growth mindset.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:06, 20 November 2017 (PST)

====Eddie's Reflection====
Found in Week 11 summary ^^^

===Week 12===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a very good job of working ahead and getting our presentation done in a timely manner. In this way, we were able to ask the instructors any questions we had as they came up, and also allowed for ample time to practice.
#What didn't work?
#*Once again, I felt a bit disconnected from my other partners Eddie and Simon. While I texted Eddie a couple times about their progress, I still never got a chance to see exactly what they were doing.
#What to improve upon going forward?
#*While I feel like this will start to come together once we all start working on our assigned portion of the project together, we still do need to improve our communication between the coders and the PM/DA. In order to do so, I will make sure to continue to check base with each team member each day in class, and also text in the group message when I have questions for the whole team.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Reflection====
#What worked?
#*With Eddie's help, we were both able to set up GRNsight on our laptops.
#What didn't work?
#*Nothing in specific stopped us from working efficiently.
#How will to improve upon going forward?
#*Going forward I'd like to get my summaries in earlier, as well as my individual page and reflections. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:48, 20 November 2017 (PST)

====Antonio's Reflection====
#What worked?
#*Worked closely with Quinn and we kept regular contact through text as we worked through the assignment. Troubleshooting was easy as we were both very capable to take initiative and work to finish the presentation earlier rather than later in the time given.
#What didn't work?
#*I could definitely improve on mastering certain aspects of the assignment. I didn't really communicate with Eddie or Simon but I'd attribute that to having different assignments and parts to complete rather than a team issue.
#What to will I do next to fix what didn't work?
#*Communicate more. I'm hoping we'll have opportunities to work more closely together in the future.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:12, 20 November 2017 (PST)

====Eddie's Reflection====
# What worked?
#: Our work session was successful in setting up GRNsight on my laptop (again) and on Simon's.
# What didn't work?
#: Nothing :D
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 21:47, 20 November 2017 (PST)

===Week 14===

====Quinn's Reflection====
#What Worked?
#*This week our team did a much better job of communicating and keeping each other in the loop. Also, the collaboration between all of the QAs was a very effective way to determine which information should be pulled from each database
#What didn't work?
#*I was still a bit confused as to how all of the teams should be working together as we approach the end of the semester
#What will I do next to fix what didn't work>
#*I will make sure to ask about this concern in the next stand up review between the QAs. This will help clear this question up for me and the rest of the class. 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:05, 4 December 2017 (PST)

====Simon's Reflection====
#What Worked?
#What didn't work?
#What will I do next to fix what didn't work?

====Antonio's Reflection====
# What worked? This week, I worked ahead and was able to complete, at least to my knowledge, this week's assignment ahead of time rather than waiting until the last minute. It was extremely helpful to have a group chat with the other data analysts as we had questions throughout the assignment.
# What didn't work? Everything seems to have run smoothly except I don't really know what the coders are assigned to do and most likely because it goes over my head.
# What will I do next to fix what didn't work? Try to see what the coders are doing, mostly out of curiosity.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 18:36, 3 December 2017 (PST)

====Eddie's Reflection====

==Acknowledgements==

==References==
===Week 11===
#LMU BioDB 2017. (2017). Week 11. Retrieved November 07, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_11
#Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6
#Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, 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
#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#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.
#Top Integrated Development Environment index. (n.d.). Retrieved November 13, 2017, from http://pypl.github.io/IDE.html
#What is an API?. (2016). Retrieved November 13, 2017, from https://medium.freecodecamp.org/what-is-an-api-in-english-please-b880a3214a82
#What's the difference between an API vs SDK?. (2012). Retrieved November 13, 2017, from https://blogs.vmware.com/vsphere/2012/01/whats-the-difference-between-an-api-vs-sdk.html
#Xcode. (2017). Retrieved November 13, 2017, from https://itunes.apple.com/us/app/xcode/id497799835
#What Is Code? (2015). Retrieved November 13, 2017, from https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#how-are-apps-made
#Shrinkwrapped Software. (n.d.). Retrieved November 13, 2017, from http://www.businessdictionary.com/definition/shrinkwrapped-software.html
#Web Application Framework. (2015). Retrieved November 13, 2017, from https://web.archive.org/web/20150723163302/http://docforge.com/wiki/Web_application_framework

===Week 12===
#LMU BioDB 2017. (2017). Week 12. Retrieved November 16, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
#Anneal. (n.d.). ''Genscript''. Retrieved on November 19, 2017 from https://www.genscript.com/molecular-biology-glossary/11896/anneal
#Assay.(2005). ''Biology-Online''. Retrieved on November 19, 2017 http://www.biology-online.org/dictionary/Assay
#Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, 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
#Causton HC, Ren B, Koh SS, et al. 2001. Remodelling of yeast genome expression in response to environmental changes. Mol Biol Cell 12: 323–337.
#Chomczynski, P., & Sacchi, N. (1987). Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Analytical biochemistry, 162(1), 156-159.
#Cluster analysis. BusinessDictionary.com. Retrieved November 19, 2017, from BusinessDictionary.com website: http://www.businessdictionary.com/definition/cluster-analysis.html
#Consensus sequence | Definition of consensus sequence in English by Oxford Dictionaries. (n.d.). Retrieved November 20, 2017, from https://en.oxforddictionaries.com/definition/consensus_sequence
#Cyclins. (n.d.). ''BioNinja''. Retrieved on November 19, 2017 from http://ib.bioninja.com.au/standard-level/topic-1-cell-biology/16-cell-division/cyclins.html
#Differences between in vitro, in vivo, and in silico studies. (n.d.). Retrieved November 20, 2017, from https://mpkb.org/home/patients/assessing_literature/in_vitro_studies
#Donzeau M, Bourdineaud JP, Lauquin GJ. 1996. Regulation by low temperatures and anaerobiosis of a yeast gene specifying a putative GPI-anchored plasma membrane protein. Mol Microbiol 20: 449–459.
#Gasch AP, Spellman PT, Kao CM, et al. 2000. Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11: 4241–4257.
#Glutathione. (n.d.). Retrieved November 20, 2017, from https://www.merriam-webster.com/dictionary/glutathione
#Haploid. (n.d.). Retrieved November 20, 2017, from http://www.biology-online.org/dictionary/Haploid
#HAW. (2011). Difference Between Haploid and Diploid. ''Difference Between.com''. Retrieved on November 19, 2017 from http://www.differencebetween.com/difference-between-haploid-and-vs-diploid/
#Hybridization. (2008). ''Biology-Online''. Retrieved on November 19, 2017 from http://www.biology-online.org/dictionary/Hybridization
#Kondo K, Inouye M. 1991. Cold-induction of yeast NSR1 protein and its role in pre-rRNA processing. J Biol Chem 267: 16 259–16 265.
#Kowalski LR, Kondo K, Inouye M. 1995. Cold-shock induction of a family of TIP1-related proteins associated with the membrane in Saccharomyces cerevisiae. Mol Microbiol 15: 341 – 353.
#LMU BioDB 2017. (2017). Week 12. Retrieved November 16, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
#Mai B, Breeden L. 1997. Xbp1, a stress-upregulated transcrip- tional repressor of the Saccharomyces cerevisae Swi4/Mbp1 family. Mol Cell Biol 17: 6491–6501.
#(n.d.). Retrieved November 19, 2017, from http://fg.cns.utexas.edu/fg/protocol%3A_YPD_plates.html
#(n.d.). Retrieved November 20, 2017, from https://www.nature.com/scitable/definition/diploid-310
#Oligonucleotide. (2014). ''News Medical Life Sciences''. Retrieved on November 19, 2017 from https://www.news-medical.net/life-sciences/What-is-an-Oligonucleotide.aspx
#Polypropylene. (n.d.). ''Dictionary.com''. Retrieved on November 19, 2017 from http://www.dictionary.com/browse/polypropylene
#Putative. (2014). ''Biology-Online''. Retrieved on November 19, 2017 from http://www.biology-online.org/dictionary/Putative
#Study.com. (2017). What is Annealing? - Definition, Biology & Process | Study.com. [online] Available at: http://study.com/academy/lesson/what-is-annealing-definition-biology-process.html [Accessed 21 Nov. 2017].
#Transcriptome. (n.d.). ''Nature''. Retrieved on November 19, 2017 from https://www.nature.com/scitable/definition/transcriptome-296
#Yelland, P. M. (2010). An introduction to correspondence analysis. Math. J, 12, 1-23.
#Young, F.W. (1999). Principle Components. ''forrest.psych.unc.edu''. Retrieved on November 19, 2017 from http://forrest.psych.unc.edu/research/vista-frames/help/lecturenotes/lecture13/biplot.html
#Zhang L, Ohta A, Horiuchi H, Takagi M, Imai R. 2001. Multiple mechanisms regulate expression of low temperature responsive (LOT) genes in Saccharomyces cerevisiae. Biochem Biophys Res Commun 283: 531 – 535.

===Week 14===
Ensembl. (2017). "Gene: HSF1". Retrieved November 28, 2017, from https://www.ensembl.org/Saccharomyces_cerevisiae/Gene/Summary?db=core;g=YGL073W;r=VII:368753-371254;t=YGL073W 
JASPAR. (2017). "Detailed information of matrix profile MA0319.1". Retrieved on November 28, 2017, from http://jaspar.genereg.net/matrix/MA0319.1/ 
LMU BioDB 2017. (2017). Week 14. Retrieved November 28, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_14 
NCBI. (2017). "HSF1 stress-responsive transcription factor HSF1 [ Saccharomyces cerevisiae S288C ]". Retrieved November 28, 2017, from https://www.ncbi.nlm.nih.gov/gene/852806 
Saccharomyces Genome Database. (2017). "HSF1 / YGL073W Overview". Retrieved November 28, 2017, from https://www.yeastgenome.org/locus/S000003041 
UniProt. (2017). "UniProtKB - P10961 (HSF_YEAST)". Retrieved November 28, 2017 from http://www.uniprot.org/uniprot/P10961

==Team Links==

{{Template:JASPAR the Friendly Ghost Links}}

==Class Links==

{{Template:GRNsight Gene Page Project Links}}

JASPAR the Friendly Ghost

2017-12-05T05:45:09Z

Simonwro120: finished summary

==Deliverables==
[[Media:Genome-wide_analysis_of_the_yeast_transcriptome_upon_heat_and_cold_shock._QL_AP.zip|Antonio and Quinn Journal Club Presentation]] | November 21, 2017 
[[Media:e_and_s_presentation_2.pdf|Eddie and Simon Chapter 6 Presentation]] | November 14, 2017 
[https://github.com/bhamilton18/GRNsight GitHub fork] 
[https://github.com/bhamilton18/GRNsight/tree/gene-database-apis GitHub api branch] (in collaboration with [[Gene_hAPI|Gene_hAPI team]])
==Working Files==

===Antonio's Working Files===
# Gene list for profile 22 of dZAP1 Excel file: [[Media:AP dZAP1 profile22 genelist.xlsx]]
# YEASTRACT Transcription Factor Data: [[Media:AP YEASTRACT Transcription Factors.xlsx]]
# YEASTRACT Regulation Matrix Profile: [[Media:AP Regulation Matrix profile22 dZAP1.xlsx]]
# YEASTRACT Adjacency Matrix: [[Media:AP Adjacency Matrix profile22 dZAP1.xlsx]]
# YEASTRACT Adjacency Matrix with Network for GRNsight: [[Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx]]
# Screenshot of GRNsight Regulatory Network: [[Media:AP Regulation Matrix profile22 GRNsight Network.PNG]]

==Calendar==
{| class ="wikitable"
|+November & December
|-
|Sunday
|Monday
|Tuesday
|Wednesday
|Thursday
|Friday
|Saturday
|-
|
|
|
|'''1'''
|'''2'''
|'''3'''
|'''4'''
|-
|'''5'''
|'''6'''
|'''7'''
|'''8'''
|'''9'''
|'''10'''
|'''11'''
|-
|'''12'''
|'''13'''
|'''14''' C: PPT Presentation PM/DA: Journal Articles
|'''15'''
|'''16'''
|'''17'''
|'''18'''
|-
|'''19'''
|'''20'''
|'''21''' C: Complete setup steps (Milestones 1-3) PM/DA: Journal Club Presentations
|'''22''' ''Thanksgiving Break''
|'''23''' ''Thanksgiving Break''
|'''24''' ''Thanksgiving Break''
|'''25'''
|-
|'''26'''
|'''27'''
|'''28''' C: Fimilariaze self with file structure PM: Chose application data fields from JASPAR DA: Review ANOVA Results
|'''29'''
|'''30''' C: Tests for API PM: Share info to be used from JASPAR with other teams DA: Determine transcription factors, develop candidate gene reg network, and fix edits from week 8 & 10
|'''1'''
|'''2'''
|-
|'''3'''
|'''4'''
|'''5''' C: Retrieval code for API PM: Begin Final Group Paper and PPT DA:Model gene reg network Visualize Results
|'''6'''
|'''7''' C: Review and Test Code PM: Review and Test code PM&DA:Work on Paper and PPT
|'''8'''
|'''9''' Complete Group PPT
|-
|'''10''' Practice Group Presentation
|'''11''' Final group Presentation ''2:00-4:00PM''
|'''12'''
|'''13''' Final Group Paper Completely Written
|'''14''' Edit Final Group Paper
|'''15''' All deliverables due ''4:30PM''
|'''16'''
|}

==Executive Summaries==

===Week 11===

====Quinn's Executive Summary====
Created citations for two entries in the annotated bibliography for papers that report microarray data from yeast subjected to cold shock: 
Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6 
Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, 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 
Also completed a search activity to compare the results found from PubMed, GoogleScholar, and Web of Science using both basic and advanced search tools. 
Individual Journal Page: [[QLanners Week 11]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Executive Summary====
For this assignment, I spent most of my time reading and re-reading Paul Ford's article on how apps are made. It was chapter 6 in a larger work called ''What is Code?'' After absorbing the information laid out in this chapter, Eddie and I made a presentation about it. The presentation summarizes the article, which is about technique, methods, practices, and tools that expedite and simplify the programming process. In addition to making the presentation, I finished my 10 terms and made an outline for the article on my individual journal page. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 13:45, 14 November 2017 (PST)

====Antonio's Executive Summary====

Created two citations for the bibliography for the following articles:

#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#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.

I also completed the basic keyword searches on PubMed, Google Scholar, and Web of Science along with the advanced searches and the respective results. Lastly, I completed the prospective searches and collected the results of how many articles the article cites and how many articles cite the article. Totaling to the 3 articles.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 15:51, 14 November 2017 (PST)

Individual Journal Week 11: [[Aporras1_Week_11|Aporras1 Week 11]]

====Eddie Bachoura's Executive Summary====
This week, I spent my time for this class reading the Paul Ford article, chapter 6, which was about how to write applications and the modern practices and tools which are used to aid in cutting down some of the tedious nature of coding. Then, Simon and I spent the rest of the time working on our presentation. Team's progress: I believe that Simon and I worked well this weekend. The only issue that I found was that we didn't start until pretty late (Monday), but that was all at my own fault because I wasn't here for this weekend. We should fix that by starting earlier next weekend!

Individual Journal Week 11: [[Ebachour_Week_11|Eddie Bachoura Week 11]] 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:29, 13 November 2017 (PST)

===Week 12===

====Quinn's Executive Summary====
Worked closely with Antonio to summarize the results of the journal article Becerra et al. (2003) into a journal club presentation. In order to do so, we both completed the outline provided on the [[Week_12|Week 12]] assignment page on our wiki. We then took this information and used it to create our journal club presentations, which we practiced together and will share in class on Tuesday, November 21. 
Individual Journal Page: [[QLanners Week 12]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Executive Summary====
This week, I met with my coding partner [[User:Ebachour|Eddie Bachoura]] and he helped me clone the code that [[User:Bhamilton18|Blair Hamilton]] forked from the master branch.
After that, Eddie and I helped put together a list of milestones with dates that they should be completed. Using that, Quinn was able to put together a calendar like scheduale for our team to refer to. The last thing I did was open up the cloned files from Blair's fork on my text editor so that I could familiarize myself with the code. 
Individual Journal Page: [[simonwro120 Week 12]] 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:44, 20 November 2017 (PST)

====Antonio's Executive Summary====
Worked throughout the assignment with Quinn to complete the powerpoint presentation on the journal article: ''Genome-wide analysis of the yeast transcriptome upon heat and cold shock''. We both worked closely together on the outline of the article while maintaining our own style of completing the outline. We then practiced our presentation once the information was finalized and are looking forward to sharing on Tuesday the 21st of November.

Individual journal page: [[Aporras1_Week_12|Aporras 1 Week 12]]

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:19, 20 November 2017 (PST)
====Eddie Bachoura's Executive Summary====
This week, most of my time was spent setting up the branch on github and then getting my local version up and running so that I can write and test code on my own laptop. After that, I helped Simon out with doing the same. I also sent Quinn a list of our milestones for this project, as well as letting him know which ones were already completed. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 19:09, 20 November 2017 (PST) 
Week 12 Journal Page: [[ebachour_Week_12| Edward Bachoura]]

===Week 14===

====Quinn's Executive Summary====
This week, I worked closely with the other QAs and [[User:Kdahlquist|Dr. Dahlquist]] to determine what information should be pulled from each of the five databases. I then communicated this information to our coders. Along with this task, I worked communicated closely with both the data analyst and the coders to ensure that they were on track, and to make modifications to their respective milestones on the team calender. Finally, I added additional team milestones to the calendar to reflect all of the steps that need to be taken to complete the deliverables that we have due at the end of the semester. All of this progress can be seen in my [[QLanners_Week_14|individual weekly journal]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:05, 4 December 2017 (PST)

====Simon's Executive Summary====
This week our coding group hit a bit of wall, not just for one, but for multiple reasons. One reason was caused by the fact that one of the coding group members worked in a language that would not be compatible with GRNsight. Another problem our coding group encountered was caused by a complexity in the the JASPAR API relating CORS (Cross-Oirgin Resource Sharing). Although these complications did occur, both me and Eddie B. know where the API guidelines are for JASPAR and what content we need to produce. In addition to that, an api file has been made as well which will be augmented soon. 
Individual Journal Page: [[simonwro120 Week 14]] 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 21:45, 4 December 2017 (PST)

====Antonio's Executive Summary====
This week, I made edits to both my individual [[Aporras1 Week 8]] and [[Aporras1 Week 10]] pages based from feedback received from [[User:Kdahlquist|Dr. Dahlquist]] and [[User:Dondi|Dr. Dionisio]]. The outline for these edits can be found on my [[Aporras1 Week 14]] page along with the continuation of the [[Week 10|Week 10]] assignment. In this continuation, I selected transcription factors from [[Media:AP dZAP1 profile22 genelist.xlsx]] and put them into YEASTRACT to find the most significant ones and found 49 significant transcription factors found in [[Media:AP YEASTRACT Transcription Factors.xlsx]]. Then I selected 22 of the most significant, 2 additional ones (HAP4 and GLN3) as instructed, to put back into YEASTRACT and create a regulation matrix uploaded as: [[Media:AP Regulation Matrix profile22 dZAP1.xlsx]]. I then created a "network" worksheet, found in [[Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx]], from the matrix and used GRNsight to generate a regulation network visualization: [[Media:AP Regulation Matrix profile22 GRNsight Network.PNG]]. These media downloads can also be found on my [[Aporras1 Week 14|Week 14]] journal entry in the
"Deliverables" section.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 18:31, 3 December 2017 (PST)

====Eddie's Executive Summary====

==Weekly Reflections==

===Week 11===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a good job of staying on task and working together to make sure that we both understood the whole assignment. So there was good communication between the Bibliography group.
#What didn't work?
#*I felt a bit disconnected with my other teammates Eddie and Simon. There was not very good communication with them about whether they needed any help and if they were on progress.
#What to improve upon going forward?
#*Going forward all of the members of the team need to do a better job of communicating. Also, we need to do a better job of properly communicating about how to fill out the team page ahead of time, so that we aren't frantically figuring that out last second. I will work to fix this by initiating communication earlier on in the week.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Reflection====
#What worked?
#*Both me and Eddie were able to put together a powerpoint and present in time for the presentation date
#What didn't work?
#*Due to traveling, Eddie could not be back in LA to help with the project until Monday, which did not give us much time, resulting in our presentation being a bit late as far as submission on our wiki pages.
#How will to improve upon going forward?
#*Going forward I'd like to start early and finish early, that way we can be prepared for any unexpected complications. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:48, 20 November 2017 (PST)

====Antonio's Reflection====
1. What worked? Quinn and I were able to get our work done on time without overlap. We communicated well.

2. What didn't work? Nothing specific prevented us from working efficiently.

3. What will I do next to fix what didn't work? Complete work ahead of time to be more thorough. Maintain a growth mindset.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:06, 20 November 2017 (PST)

====Eddie's Reflection====
Found in Week 11 summary ^^^

===Week 12===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a very good job of working ahead and getting our presentation done in a timely manner. In this way, we were able to ask the instructors any questions we had as they came up, and also allowed for ample time to practice.
#What didn't work?
#*Once again, I felt a bit disconnected from my other partners Eddie and Simon. While I texted Eddie a couple times about their progress, I still never got a chance to see exactly what they were doing.
#What to improve upon going forward?
#*While I feel like this will start to come together once we all start working on our assigned portion of the project together, we still do need to improve our communication between the coders and the PM/DA. In order to do so, I will make sure to continue to check base with each team member each day in class, and also text in the group message when I have questions for the whole team.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Reflection====
#What worked?
#*With Eddie's help, we were both able to set up GRNsight on our laptops.
#What didn't work?
#*Nothing in specific stopped us from working efficiently.
#How will to improve upon going forward?
#*Going forward I'd like to get my summaries in earlier, as well as my individual page and reflections. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:48, 20 November 2017 (PST)

====Antonio's Reflection====
#What worked?
#*Worked closely with Quinn and we kept regular contact through text as we worked through the assignment. Troubleshooting was easy as we were both very capable to take initiative and work to finish the presentation earlier rather than later in the time given.
#What didn't work?
#*I could definitely improve on mastering certain aspects of the assignment. I didn't really communicate with Eddie or Simon but I'd attribute that to having different assignments and parts to complete rather than a team issue.
#What to will I do next to fix what didn't work?
#*Communicate more. I'm hoping we'll have opportunities to work more closely together in the future.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:12, 20 November 2017 (PST)

====Eddie's Reflection====
# What worked?
#: Our work session was successful in setting up GRNsight on my laptop (again) and on Simon's.
# What didn't work?
#: Nothing :D
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 21:47, 20 November 2017 (PST)

===Week 14===

====Quinn's Reflection====
#What Worked?
#*This week our team did a much better job of communicating and keeping each other in the loop. Also, the collaboration between all of the QAs was a very effective way to determine which information should be pulled from each database
#What didn't work?
#*I was still a bit confused as to how all of the teams should be working together as we approach the end of the semester
#What will I do next to fix what didn't work>
#*I will make sure to ask about this concern in the next stand up review between the QAs. This will help clear this question up for me and the rest of the class. 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:05, 4 December 2017 (PST)

====Simon's Reflection====

====Antonio's Reflection====
# What worked? This week, I worked ahead and was able to complete, at least to my knowledge, this week's assignment ahead of time rather than waiting until the last minute. It was extremely helpful to have a group chat with the other data analysts as we had questions throughout the assignment.
# What didn't work? Everything seems to have run smoothly except I don't really know what the coders are assigned to do and most likely because it goes over my head.
# What will I do next to fix what didn't work? Try to see what the coders are doing, mostly out of curiosity.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 18:36, 3 December 2017 (PST)

====Eddie's Reflection====

==Acknowledgements==

==References==
===Week 11===
#LMU BioDB 2017. (2017). Week 11. Retrieved November 07, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_11
#Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6
#Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, 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
#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#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.
#Top Integrated Development Environment index. (n.d.). Retrieved November 13, 2017, from http://pypl.github.io/IDE.html
#What is an API?. (2016). Retrieved November 13, 2017, from https://medium.freecodecamp.org/what-is-an-api-in-english-please-b880a3214a82
#What's the difference between an API vs SDK?. (2012). Retrieved November 13, 2017, from https://blogs.vmware.com/vsphere/2012/01/whats-the-difference-between-an-api-vs-sdk.html
#Xcode. (2017). Retrieved November 13, 2017, from https://itunes.apple.com/us/app/xcode/id497799835
#What Is Code? (2015). Retrieved November 13, 2017, from https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#how-are-apps-made
#Shrinkwrapped Software. (n.d.). Retrieved November 13, 2017, from http://www.businessdictionary.com/definition/shrinkwrapped-software.html
#Web Application Framework. (2015). Retrieved November 13, 2017, from https://web.archive.org/web/20150723163302/http://docforge.com/wiki/Web_application_framework

===Week 12===
#LMU BioDB 2017. (2017). Week 12. Retrieved November 16, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
#Anneal. (n.d.). ''Genscript''. Retrieved on November 19, 2017 from https://www.genscript.com/molecular-biology-glossary/11896/anneal
#Assay.(2005). ''Biology-Online''. Retrieved on November 19, 2017 http://www.biology-online.org/dictionary/Assay
#Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, 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
#Causton HC, Ren B, Koh SS, et al. 2001. Remodelling of yeast genome expression in response to environmental changes. Mol Biol Cell 12: 323–337.
#Chomczynski, P., & Sacchi, N. (1987). Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Analytical biochemistry, 162(1), 156-159.
#Cluster analysis. BusinessDictionary.com. Retrieved November 19, 2017, from BusinessDictionary.com website: http://www.businessdictionary.com/definition/cluster-analysis.html
#Consensus sequence | Definition of consensus sequence in English by Oxford Dictionaries. (n.d.). Retrieved November 20, 2017, from https://en.oxforddictionaries.com/definition/consensus_sequence
#Cyclins. (n.d.). ''BioNinja''. Retrieved on November 19, 2017 from http://ib.bioninja.com.au/standard-level/topic-1-cell-biology/16-cell-division/cyclins.html
#Differences between in vitro, in vivo, and in silico studies. (n.d.). Retrieved November 20, 2017, from https://mpkb.org/home/patients/assessing_literature/in_vitro_studies
#Donzeau M, Bourdineaud JP, Lauquin GJ. 1996. Regulation by low temperatures and anaerobiosis of a yeast gene specifying a putative GPI-anchored plasma membrane protein. Mol Microbiol 20: 449–459.
#Gasch AP, Spellman PT, Kao CM, et al. 2000. Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11: 4241–4257.
#Glutathione. (n.d.). Retrieved November 20, 2017, from https://www.merriam-webster.com/dictionary/glutathione
#Haploid. (n.d.). Retrieved November 20, 2017, from http://www.biology-online.org/dictionary/Haploid
#HAW. (2011). Difference Between Haploid and Diploid. ''Difference Between.com''. Retrieved on November 19, 2017 from http://www.differencebetween.com/difference-between-haploid-and-vs-diploid/
#Hybridization. (2008). ''Biology-Online''. Retrieved on November 19, 2017 from http://www.biology-online.org/dictionary/Hybridization
#Kondo K, Inouye M. 1991. Cold-induction of yeast NSR1 protein and its role in pre-rRNA processing. J Biol Chem 267: 16 259–16 265.
#Kowalski LR, Kondo K, Inouye M. 1995. Cold-shock induction of a family of TIP1-related proteins associated with the membrane in Saccharomyces cerevisiae. Mol Microbiol 15: 341 – 353.
#LMU BioDB 2017. (2017). Week 12. Retrieved November 16, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
#Mai B, Breeden L. 1997. Xbp1, a stress-upregulated transcrip- tional repressor of the Saccharomyces cerevisae Swi4/Mbp1 family. Mol Cell Biol 17: 6491–6501.
#(n.d.). Retrieved November 19, 2017, from http://fg.cns.utexas.edu/fg/protocol%3A_YPD_plates.html
#(n.d.). Retrieved November 20, 2017, from https://www.nature.com/scitable/definition/diploid-310
#Oligonucleotide. (2014). ''News Medical Life Sciences''. Retrieved on November 19, 2017 from https://www.news-medical.net/life-sciences/What-is-an-Oligonucleotide.aspx
#Polypropylene. (n.d.). ''Dictionary.com''. Retrieved on November 19, 2017 from http://www.dictionary.com/browse/polypropylene
#Putative. (2014). ''Biology-Online''. Retrieved on November 19, 2017 from http://www.biology-online.org/dictionary/Putative
#Study.com. (2017). What is Annealing? - Definition, Biology & Process | Study.com. [online] Available at: http://study.com/academy/lesson/what-is-annealing-definition-biology-process.html [Accessed 21 Nov. 2017].
#Transcriptome. (n.d.). ''Nature''. Retrieved on November 19, 2017 from https://www.nature.com/scitable/definition/transcriptome-296
#Yelland, P. M. (2010). An introduction to correspondence analysis. Math. J, 12, 1-23.
#Young, F.W. (1999). Principle Components. ''forrest.psych.unc.edu''. Retrieved on November 19, 2017 from http://forrest.psych.unc.edu/research/vista-frames/help/lecturenotes/lecture13/biplot.html
#Zhang L, Ohta A, Horiuchi H, Takagi M, Imai R. 2001. Multiple mechanisms regulate expression of low temperature responsive (LOT) genes in Saccharomyces cerevisiae. Biochem Biophys Res Commun 283: 531 – 535.

===Week 14===
Ensembl. (2017). "Gene: HSF1". Retrieved November 28, 2017, from https://www.ensembl.org/Saccharomyces_cerevisiae/Gene/Summary?db=core;g=YGL073W;r=VII:368753-371254;t=YGL073W 
JASPAR. (2017). "Detailed information of matrix profile MA0319.1". Retrieved on November 28, 2017, from http://jaspar.genereg.net/matrix/MA0319.1/ 
LMU BioDB 2017. (2017). Week 14. Retrieved November 28, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_14 
NCBI. (2017). "HSF1 stress-responsive transcription factor HSF1 [ Saccharomyces cerevisiae S288C ]". Retrieved November 28, 2017, from https://www.ncbi.nlm.nih.gov/gene/852806 
Saccharomyces Genome Database. (2017). "HSF1 / YGL073W Overview". Retrieved November 28, 2017, from https://www.yeastgenome.org/locus/S000003041 
UniProt. (2017). "UniProtKB - P10961 (HSF_YEAST)". Retrieved November 28, 2017 from http://www.uniprot.org/uniprot/P10961

==Team Links==

{{Template:JASPAR the Friendly Ghost Links}}

==Class Links==

{{Template:GRNsight Gene Page Project Links}}

Simonwro120 Week 14

2017-12-05T03:02:27Z

Simonwro120: syntax

=Electronic Notebook=
The coding team for JASPAR was given a list of deliverables on which need to be retrieved from the JASPAR API.
*'''They Include:'''
*#Matrix ID
*#Class Heat shock factors
*#Family HSF factors
*#Sequence Logo ''(First Image)''
*#Frequency Matrix ''(Second Image)''
[[File:Jasper seq log and freq matrix.png]]

Simonwro120 Week 14

2017-12-05T03:00:05Z

Simonwro120: added image

=Electronic Notebook=
The coding team for JASPAR was given a list of deliverables on which need to be retrieved from the JASPAR API.
*'''They Include:'''
*#Matrix ID
*#Class Heat shock factors
*#Family HSF factors
*#Sequence Logo ''First Image''
*#Frequency Matrix ''Second Image''

[[File:Jasper seq log and freq matrix.png]]

Simonwro120 Week 14

2017-12-05T02:44:25Z

Simonwro120: syntax

Simonwro120 Week 14

2017-12-05T02:42:43Z

Simonwro120: start

=Electronic Notebook=
The coding team for JASPAR was given a list of deliverables on which need to be retrieved from the JASPAR API.
*'''They Include:'''
*#Matrix ID MA0319.1
*#Class Heat shock factors
*#Family HSF factors
*#Sequence Logo image below
*#Frequency Matrix image below

JASPAR the Friendly Ghost

2017-12-05T02:27:44Z

Simonwro120: added more summary

==Deliverables==
[[Media:Genome-wide_analysis_of_the_yeast_transcriptome_upon_heat_and_cold_shock._QL_AP.zip|Antonio and Quinn Journal Club Presentation]] | November 21, 2017 
[[Media:e_and_s_presentation_2.pdf|Eddie and Simon Chapter 6 Presentation]] | November 14, 2017 
[https://github.com/bhamilton18/GRNsight GitHub fork] 
[https://github.com/bhamilton18/GRNsight/tree/gene-database-apis GitHub api branch] (in collaboration with [[Gene_hAPI|Gene_hAPI team]])
==Working Files==

===Antonio's Working Files===
# Gene list for profile 22 of dZAP1 Excel file: [[Media:AP dZAP1 profile22 genelist.xlsx]]
# YEASTRACT Transcription Factor Data: [[Media:AP YEASTRACT Transcription Factors.xlsx]]
# YEASTRACT Regulation Matrix Profile: [[Media:AP Regulation Matrix profile22 dZAP1.xlsx]]
# YEASTRACT Adjacency Matrix: [[Media:AP Adjacency Matrix profile22 dZAP1.xlsx]]
# YEASTRACT Adjacency Matrix with Network for GRNsight: [[Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx]]
# Screenshot of GRNsight Regulatory Network: [[Media:AP Regulation Matrix profile22 GRNsight Network.PNG]]

==Calendar==
{| class ="wikitable"
|+November & December
|-
|Sunday
|Monday
|Tuesday
|Wednesday
|Thursday
|Friday
|Saturday
|-
|
|
|
|'''1'''
|'''2'''
|'''3'''
|'''4'''
|-
|'''5'''
|'''6'''
|'''7'''
|'''8'''
|'''9'''
|'''10'''
|'''11'''
|-
|'''12'''
|'''13'''
|'''14''' C: PPT Presentation PM/DA: Journal Articles
|'''15'''
|'''16'''
|'''17'''
|'''18'''
|-
|'''19'''
|'''20'''
|'''21''' C: Complete setup steps (Milestones 1-3) PM/DA: Journal Club Presentations
|'''22''' ''Thanksgiving Break''
|'''23''' ''Thanksgiving Break''
|'''24''' ''Thanksgiving Break''
|'''25'''
|-
|'''26'''
|'''27'''
|'''28''' C: Fimilariaze self with file structure PM: Chose application data fields from JASPAR DA: Review ANOVA Results
|'''29'''
|'''30''' C: Tests for API PM: Share info to be used from JASPAR with other teams DA: Determine transcription factors, develop candidate gene reg network, and fix edits from week 8 & 10
|'''1'''
|'''2'''
|-
|'''3'''
|'''4'''
|'''5''' C: Retrieval code for API PM: Begin Final Group Paper and PPT DA:Model gene reg network Visualize Results
|'''6'''
|'''7''' C: Review and Test Code PM: Review and Test code PM&DA:Work on Paper and PPT
|'''8'''
|'''9''' Complete Group PPT
|-
|'''10''' Practice Group Presentation
|'''11''' Final group Presentation ''2:00-4:00PM''
|'''12'''
|'''13''' Final Group Paper Completely Written
|'''14''' Edit Final Group Paper
|'''15''' All deliverables due ''4:30PM''
|'''16'''
|}

==Executive Summaries==

===Week 11===

====Quinn's Executive Summary====
Created citations for two entries in the annotated bibliography for papers that report microarray data from yeast subjected to cold shock: 
Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6 
Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, 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 
Also completed a search activity to compare the results found from PubMed, GoogleScholar, and Web of Science using both basic and advanced search tools. 
Individual Journal Page: [[QLanners Week 11]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Executive Summary====
For this assignment, I spent most of my time reading and re-reading Paul Ford's article on how apps are made. It was chapter 6 in a larger work called ''What is Code?'' After absorbing the information laid out in this chapter, Eddie and I made a presentation about it. The presentation summarizes the article, which is about technique, methods, practices, and tools that expedite and simplify the programming process. In addition to making the presentation, I finished my 10 terms and made an outline for the article on my individual journal page. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 13:45, 14 November 2017 (PST)

====Antonio's Executive Summary====

Created two citations for the bibliography for the following articles:

#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#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.

I also completed the basic keyword searches on PubMed, Google Scholar, and Web of Science along with the advanced searches and the respective results. Lastly, I completed the prospective searches and collected the results of how many articles the article cites and how many articles cite the article. Totaling to the 3 articles.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 15:51, 14 November 2017 (PST)

Individual Journal Week 11: [[Aporras1_Week_11|Aporras1 Week 11]]

====Eddie Bachoura's Executive Summary====
This week, I spent my time for this class reading the Paul Ford article, chapter 6, which was about how to write applications and the modern practices and tools which are used to aid in cutting down some of the tedious nature of coding. Then, Simon and I spent the rest of the time working on our presentation. Team's progress: I believe that Simon and I worked well this weekend. The only issue that I found was that we didn't start until pretty late (Monday), but that was all at my own fault because I wasn't here for this weekend. We should fix that by starting earlier next weekend!

Individual Journal Week 11: [[Ebachour_Week_11|Eddie Bachoura Week 11]] 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:29, 13 November 2017 (PST)

===Week 12===

====Quinn's Executive Summary====
Worked closely with Antonio to summarize the results of the journal article Becerra et al. (2003) into a journal club presentation. In order to do so, we both completed the outline provided on the [[Week_12|Week 12]] assignment page on our wiki. We then took this information and used it to create our journal club presentations, which we practiced together and will share in class on Tuesday, November 21. 
Individual Journal Page: [[QLanners Week 12]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Executive Summary====
This week, I met with my coding partner [[User:Ebachour|Eddie Bachoura]] and he helped me clone the code that [[User:Bhamilton18|Blair Hamilton]] forked from the master branch.
After that, Eddie and I helped put together a list of milestones with dates that they should be completed. Using that, Quinn was able to put together a calendar like scheduale for our team to refer to. The last thing I did was open up the cloned files from Blair's fork on my text editor so that I could familiarize myself with the code. 
Individual Journal Page: [[simonwro120 Week 12]] 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:44, 20 November 2017 (PST)

====Antonio's Executive Summary====
Worked throughout the assignment with Quinn to complete the powerpoint presentation on the journal article: ''Genome-wide analysis of the yeast transcriptome upon heat and cold shock''. We both worked closely together on the outline of the article while maintaining our own style of completing the outline. We then practiced our presentation once the information was finalized and are looking forward to sharing on Tuesday the 21st of November.

Individual journal page: [[Aporras1_Week_12|Aporras 1 Week 12]]

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:19, 20 November 2017 (PST)
====Eddie Bachoura's Executive Summary====
This week, most of my time was spent setting up the branch on github and then getting my local version up and running so that I can write and test code on my own laptop. After that, I helped Simon out with doing the same. I also sent Quinn a list of our milestones for this project, as well as letting him know which ones were already completed. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 19:09, 20 November 2017 (PST) 
Week 12 Journal Page: [[ebachour_Week_12| Edward Bachoura]]

===Week 14===

====Quinn's Executive Summary====

====Simon's Executive Summary====
This week our coding group hit a bit of wall, not just for one, but for multiple reasons. One reason was caused by the fact that one of the coding group members worked in a language that would not be compatible with GRNsight. Another problem our coding group encountered was caused by a complexity in the the JASPAR API relating CORS (Cross-Oirgin Resource Sharing). Although these complications did occur, we both me and Eddie B. know where the API guidelines are for for JASPAR and what content we need to produce.

====Antonio's Executive Summary====
This week, I made edits to both my individual [[Aporras1 Week 8]] and [[Aporras1 Week 10]] pages based from feedback received from [[User:Kdahlquist|Dr. Dahlquist]] and [[User:Dondi|Dr. Dionisio]]. The outline for these edits can be found on my [[Aporras1 Week 14]] page along with the continuation of the [[Week 10|Week 10]] assignment. In this continuation, I selected transcription factors from [[Media:AP dZAP1 profile22 genelist.xlsx]] and put them into YEASTRACT to find the most significant ones and found 49 significant transcription factors found in [[Media:AP YEASTRACT Transcription Factors.xlsx]]. Then I selected 22 of the most significant, 2 additional ones (HAP4 and GLN3) as instructed, to put back into YEASTRACT and create a regulation matrix uploaded as: [[Media:AP Regulation Matrix profile22 dZAP1.xlsx]]. I then created a "network" worksheet, found in [[Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx]], from the matrix and used GRNsight to generate a regulation network visualization: [[Media:AP Regulation Matrix profile22 GRNsight Network.PNG]]. These media downloads can also be found on my [[Aporras1 Week 14|Week 14]] journal entry in the
"Deliverables" section.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 18:31, 3 December 2017 (PST)

====Eddie's Executive Summary====

==Weekly Reflections==

===Week 11===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a good job of staying on task and working together to make sure that we both understood the whole assignment. So there was good communication between the Bibliography group.
#What didn't work?
#*I felt a bit disconnected with my other teammates Eddie and Simon. There was not very good communication with them about whether they needed any help and if they were on progress.
#What to improve upon going forward?
#*Going forward all of the members of the team need to do a better job of communicating. Also, we need to do a better job of properly communicating about how to fill out the team page ahead of time, so that we aren't frantically figuring that out last second. I will work to fix this by initiating communication earlier on in the week.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Reflection====
#What worked?
#*Both me and Eddie were able to put together a powerpoint and present in time for the presentation date
#What didn't work?
#*Due to traveling, Eddie could not be back in LA to help with the project until Monday, which did not give us much time, resulting in our presentation being a bit late as far as submission on our wiki pages.
#How will to improve upon going forward?
#*Going forward I'd like to start early and finish early, that way we can be prepared for any unexpected complications. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:48, 20 November 2017 (PST)

====Antonio's Reflection====
1. What worked? Quinn and I were able to get our work done on time without overlap. We communicated well.

2. What didn't work? Nothing specific prevented us from working efficiently.

3. What will I do next to fix what didn't work? Complete work ahead of time to be more thorough. Maintain a growth mindset.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:06, 20 November 2017 (PST)

====Eddie's Reflection====
Found in Week 11 summary ^^^

===Week 12===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a very good job of working ahead and getting our presentation done in a timely manner. In this way, we were able to ask the instructors any questions we had as they came up, and also allowed for ample time to practice.
#What didn't work?
#*Once again, I felt a bit disconnected from my other partners Eddie and Simon. While I texted Eddie a couple times about their progress, I still never got a chance to see exactly what they were doing.
#What to improve upon going forward?
#*While I feel like this will start to come together once we all start working on our assigned portion of the project together, we still do need to improve our communication between the coders and the PM/DA. In order to do so, I will make sure to continue to check base with each team member each day in class, and also text in the group message when I have questions for the whole team.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Reflection====
#What worked?
#*With Eddie's help, we were both able to set up GRNsight on our laptops.
#What didn't work?
#*Nothing in specific stopped us from working efficiently.
#How will to improve upon going forward?
#*Going forward I'd like to get my summaries in earlier, as well as my individual page and reflections. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:48, 20 November 2017 (PST)

====Antonio's Reflection====
#What worked?
#*Worked closely with Quinn and we kept regular contact through text as we worked through the assignment. Troubleshooting was easy as we were both very capable to take initiative and work to finish the presentation earlier rather than later in the time given.
#What didn't work?
#*I could definitely improve on mastering certain aspects of the assignment. I didn't really communicate with Eddie or Simon but I'd attribute that to having different assignments and parts to complete rather than a team issue.
#What to will I do next to fix what didn't work?
#*Communicate more. I'm hoping we'll have opportunities to work more closely together in the future.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:12, 20 November 2017 (PST)

====Eddie's Reflection====
# What worked?
#: Our work session was successful in setting up GRNsight on my laptop (again) and on Simon's.
# What didn't work?
#: Nothing :D
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 21:47, 20 November 2017 (PST)

===Week 14===

====Quinn's Reflection====

====Simon's Reflection====

====Antonio's Reflection====
# What worked? This week, I worked ahead and was able to complete, at least to my knowledge, this week's assignment ahead of time rather than waiting until the last minute. It was extremely helpful to have a group chat with the other data analysts as we had questions throughout the assignment.
# What didn't work? Everything seems to have run smoothly except I don't really know what the coders are assigned to do and most likely because it goes over my head.
# What will I do next to fix what didn't work? Try to see what the coders are doing, mostly out of curiosity.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 18:36, 3 December 2017 (PST)

====Eddie's Reflection====

==Acknowledgements==

==References==
===Week 11===
#LMU BioDB 2017. (2017). Week 11. Retrieved November 07, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_11
#Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6
#Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, 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
#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#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.
#Top Integrated Development Environment index. (n.d.). Retrieved November 13, 2017, from http://pypl.github.io/IDE.html
#What is an API?. (2016). Retrieved November 13, 2017, from https://medium.freecodecamp.org/what-is-an-api-in-english-please-b880a3214a82
#What's the difference between an API vs SDK?. (2012). Retrieved November 13, 2017, from https://blogs.vmware.com/vsphere/2012/01/whats-the-difference-between-an-api-vs-sdk.html
#Xcode. (2017). Retrieved November 13, 2017, from https://itunes.apple.com/us/app/xcode/id497799835
#What Is Code? (2015). Retrieved November 13, 2017, from https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#how-are-apps-made
#Shrinkwrapped Software. (n.d.). Retrieved November 13, 2017, from http://www.businessdictionary.com/definition/shrinkwrapped-software.html
#Web Application Framework. (2015). Retrieved November 13, 2017, from https://web.archive.org/web/20150723163302/http://docforge.com/wiki/Web_application_framework

===Week 12===
#LMU BioDB 2017. (2017). Week 12. Retrieved November 16, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
#Anneal. (n.d.). ''Genscript''. Retrieved on November 19, 2017 from https://www.genscript.com/molecular-biology-glossary/11896/anneal
#Assay.(2005). ''Biology-Online''. Retrieved on November 19, 2017 http://www.biology-online.org/dictionary/Assay
#Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, 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
#Causton HC, Ren B, Koh SS, et al. 2001. Remodelling of yeast genome expression in response to environmental changes. Mol Biol Cell 12: 323–337.
#Chomczynski, P., & Sacchi, N. (1987). Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Analytical biochemistry, 162(1), 156-159.
#Cluster analysis. BusinessDictionary.com. Retrieved November 19, 2017, from BusinessDictionary.com website: http://www.businessdictionary.com/definition/cluster-analysis.html
#Consensus sequence | Definition of consensus sequence in English by Oxford Dictionaries. (n.d.). Retrieved November 20, 2017, from https://en.oxforddictionaries.com/definition/consensus_sequence
#Cyclins. (n.d.). ''BioNinja''. Retrieved on November 19, 2017 from http://ib.bioninja.com.au/standard-level/topic-1-cell-biology/16-cell-division/cyclins.html
#Differences between in vitro, in vivo, and in silico studies. (n.d.). Retrieved November 20, 2017, from https://mpkb.org/home/patients/assessing_literature/in_vitro_studies
#Donzeau M, Bourdineaud JP, Lauquin GJ. 1996. Regulation by low temperatures and anaerobiosis of a yeast gene specifying a putative GPI-anchored plasma membrane protein. Mol Microbiol 20: 449–459.
#Gasch AP, Spellman PT, Kao CM, et al. 2000. Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11: 4241–4257.
#Glutathione. (n.d.). Retrieved November 20, 2017, from https://www.merriam-webster.com/dictionary/glutathione
#Haploid. (n.d.). Retrieved November 20, 2017, from http://www.biology-online.org/dictionary/Haploid
#HAW. (2011). Difference Between Haploid and Diploid. ''Difference Between.com''. Retrieved on November 19, 2017 from http://www.differencebetween.com/difference-between-haploid-and-vs-diploid/
#Hybridization. (2008). ''Biology-Online''. Retrieved on November 19, 2017 from http://www.biology-online.org/dictionary/Hybridization
#Kondo K, Inouye M. 1991. Cold-induction of yeast NSR1 protein and its role in pre-rRNA processing. J Biol Chem 267: 16 259–16 265.
#Kowalski LR, Kondo K, Inouye M. 1995. Cold-shock induction of a family of TIP1-related proteins associated with the membrane in Saccharomyces cerevisiae. Mol Microbiol 15: 341 – 353.
#LMU BioDB 2017. (2017). Week 12. Retrieved November 16, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
#Mai B, Breeden L. 1997. Xbp1, a stress-upregulated transcrip- tional repressor of the Saccharomyces cerevisae Swi4/Mbp1 family. Mol Cell Biol 17: 6491–6501.
#(n.d.). Retrieved November 19, 2017, from http://fg.cns.utexas.edu/fg/protocol%3A_YPD_plates.html
#(n.d.). Retrieved November 20, 2017, from https://www.nature.com/scitable/definition/diploid-310
#Oligonucleotide. (2014). ''News Medical Life Sciences''. Retrieved on November 19, 2017 from https://www.news-medical.net/life-sciences/What-is-an-Oligonucleotide.aspx
#Polypropylene. (n.d.). ''Dictionary.com''. Retrieved on November 19, 2017 from http://www.dictionary.com/browse/polypropylene
#Putative. (2014). ''Biology-Online''. Retrieved on November 19, 2017 from http://www.biology-online.org/dictionary/Putative
#Study.com. (2017). What is Annealing? - Definition, Biology & Process | Study.com. [online] Available at: http://study.com/academy/lesson/what-is-annealing-definition-biology-process.html [Accessed 21 Nov. 2017].
#Transcriptome. (n.d.). ''Nature''. Retrieved on November 19, 2017 from https://www.nature.com/scitable/definition/transcriptome-296
#Yelland, P. M. (2010). An introduction to correspondence analysis. Math. J, 12, 1-23.
#Young, F.W. (1999). Principle Components. ''forrest.psych.unc.edu''. Retrieved on November 19, 2017 from http://forrest.psych.unc.edu/research/vista-frames/help/lecturenotes/lecture13/biplot.html
#Zhang L, Ohta A, Horiuchi H, Takagi M, Imai R. 2001. Multiple mechanisms regulate expression of low temperature responsive (LOT) genes in Saccharomyces cerevisiae. Biochem Biophys Res Commun 283: 531 – 535.

==Team Links==

{{Template:JASPAR the Friendly Ghost Links}}

==Class Links==

{{Template:GRNsight Gene Page Project Links}}

JASPAR the Friendly Ghost

2017-12-05T02:22:02Z

Simonwro120: some summary

==Deliverables==
[[Media:Genome-wide_analysis_of_the_yeast_transcriptome_upon_heat_and_cold_shock._QL_AP.zip|Antonio and Quinn Journal Club Presentation]] | November 21, 2017 
[[Media:e_and_s_presentation_2.pdf|Eddie and Simon Chapter 6 Presentation]] | November 14, 2017 
[https://github.com/bhamilton18/GRNsight GitHub fork] 
[https://github.com/bhamilton18/GRNsight/tree/gene-database-apis GitHub api branch] (in collaboration with [[Gene_hAPI|Gene_hAPI team]])
==Working Files==

===Antonio's Working Files===
# Gene list for profile 22 of dZAP1 Excel file: [[Media:AP dZAP1 profile22 genelist.xlsx]]
# YEASTRACT Transcription Factor Data: [[Media:AP YEASTRACT Transcription Factors.xlsx]]
# YEASTRACT Regulation Matrix Profile: [[Media:AP Regulation Matrix profile22 dZAP1.xlsx]]
# YEASTRACT Adjacency Matrix: [[Media:AP Adjacency Matrix profile22 dZAP1.xlsx]]
# YEASTRACT Adjacency Matrix with Network for GRNsight: [[Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx]]
# Screenshot of GRNsight Regulatory Network: [[Media:AP Regulation Matrix profile22 GRNsight Network.PNG]]

==Calendar==
{| class ="wikitable"
|+November & December
|-
|Sunday
|Monday
|Tuesday
|Wednesday
|Thursday
|Friday
|Saturday
|-
|
|
|
|'''1'''
|'''2'''
|'''3'''
|'''4'''
|-
|'''5'''
|'''6'''
|'''7'''
|'''8'''
|'''9'''
|'''10'''
|'''11'''
|-
|'''12'''
|'''13'''
|'''14''' C: PPT Presentation PM/DA: Journal Articles
|'''15'''
|'''16'''
|'''17'''
|'''18'''
|-
|'''19'''
|'''20'''
|'''21''' C: Complete setup steps (Milestones 1-3) PM/DA: Journal Club Presentations
|'''22''' ''Thanksgiving Break''
|'''23''' ''Thanksgiving Break''
|'''24''' ''Thanksgiving Break''
|'''25'''
|-
|'''26'''
|'''27'''
|'''28''' C: Fimilariaze self with file structure PM: Chose application data fields from JASPAR DA: Review ANOVA Results
|'''29'''
|'''30''' C: Tests for API PM: Share info to be used from JASPAR with other teams DA: Determine transcription factors, develop candidate gene reg network, and fix edits from week 8 & 10
|'''1'''
|'''2'''
|-
|'''3'''
|'''4'''
|'''5''' C: Retrieval code for API PM: Begin Final Group Paper and PPT DA:Model gene reg network Visualize Results
|'''6'''
|'''7''' C: Review and Test Code PM: Review and Test code PM&DA:Work on Paper and PPT
|'''8'''
|'''9''' Complete Group PPT
|-
|'''10''' Practice Group Presentation
|'''11''' Final group Presentation ''2:00-4:00PM''
|'''12'''
|'''13''' Final Group Paper Completely Written
|'''14''' Edit Final Group Paper
|'''15''' All deliverables due ''4:30PM''
|'''16'''
|}

==Executive Summaries==

===Week 11===

====Quinn's Executive Summary====
Created citations for two entries in the annotated bibliography for papers that report microarray data from yeast subjected to cold shock: 
Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6 
Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, 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 
Also completed a search activity to compare the results found from PubMed, GoogleScholar, and Web of Science using both basic and advanced search tools. 
Individual Journal Page: [[QLanners Week 11]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Executive Summary====
For this assignment, I spent most of my time reading and re-reading Paul Ford's article on how apps are made. It was chapter 6 in a larger work called ''What is Code?'' After absorbing the information laid out in this chapter, Eddie and I made a presentation about it. The presentation summarizes the article, which is about technique, methods, practices, and tools that expedite and simplify the programming process. In addition to making the presentation, I finished my 10 terms and made an outline for the article on my individual journal page. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 13:45, 14 November 2017 (PST)

====Antonio's Executive Summary====

Created two citations for the bibliography for the following articles:

#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#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.

I also completed the basic keyword searches on PubMed, Google Scholar, and Web of Science along with the advanced searches and the respective results. Lastly, I completed the prospective searches and collected the results of how many articles the article cites and how many articles cite the article. Totaling to the 3 articles.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 15:51, 14 November 2017 (PST)

Individual Journal Week 11: [[Aporras1_Week_11|Aporras1 Week 11]]

====Eddie Bachoura's Executive Summary====
This week, I spent my time for this class reading the Paul Ford article, chapter 6, which was about how to write applications and the modern practices and tools which are used to aid in cutting down some of the tedious nature of coding. Then, Simon and I spent the rest of the time working on our presentation. Team's progress: I believe that Simon and I worked well this weekend. The only issue that I found was that we didn't start until pretty late (Monday), but that was all at my own fault because I wasn't here for this weekend. We should fix that by starting earlier next weekend!

Individual Journal Week 11: [[Ebachour_Week_11|Eddie Bachoura Week 11]] 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:29, 13 November 2017 (PST)

===Week 12===

====Quinn's Executive Summary====
Worked closely with Antonio to summarize the results of the journal article Becerra et al. (2003) into a journal club presentation. In order to do so, we both completed the outline provided on the [[Week_12|Week 12]] assignment page on our wiki. We then took this information and used it to create our journal club presentations, which we practiced together and will share in class on Tuesday, November 21. 
Individual Journal Page: [[QLanners Week 12]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Executive Summary====
This week, I met with my coding partner [[User:Ebachour|Eddie Bachoura]] and he helped me clone the code that [[User:Bhamilton18|Blair Hamilton]] forked from the master branch.
After that, Eddie and I helped put together a list of milestones with dates that they should be completed. Using that, Quinn was able to put together a calendar like scheduale for our team to refer to. The last thing I did was open up the cloned files from Blair's fork on my text editor so that I could familiarize myself with the code. 
Individual Journal Page: [[simonwro120 Week 12]] 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:44, 20 November 2017 (PST)

====Antonio's Executive Summary====
Worked throughout the assignment with Quinn to complete the powerpoint presentation on the journal article: ''Genome-wide analysis of the yeast transcriptome upon heat and cold shock''. We both worked closely together on the outline of the article while maintaining our own style of completing the outline. We then practiced our presentation once the information was finalized and are looking forward to sharing on Tuesday the 21st of November.

Individual journal page: [[Aporras1_Week_12|Aporras 1 Week 12]]

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:19, 20 November 2017 (PST)
====Eddie Bachoura's Executive Summary====
This week, most of my time was spent setting up the branch on github and then getting my local version up and running so that I can write and test code on my own laptop. After that, I helped Simon out with doing the same. I also sent Quinn a list of our milestones for this project, as well as letting him know which ones were already completed. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 19:09, 20 November 2017 (PST) 
Week 12 Journal Page: [[ebachour_Week_12| Edward Bachoura]]

===Week 14===

====Quinn's Executive Summary====

====Simon's Executive Summary====
This week our coding group hit a bit of wall, not just for one, but for multiple reasons. One reason was caused by the fact that one of the coding group members worked in a language that would not be compatible with GRNsight. Another problem our coding group encountered was caused by a complexity in the the JASPAR API relating CORS (Cross-Oirgin Resource Sharing).

====Antonio's Executive Summary====
This week, I made edits to both my individual [[Aporras1 Week 8]] and [[Aporras1 Week 10]] pages based from feedback received from [[User:Kdahlquist|Dr. Dahlquist]] and [[User:Dondi|Dr. Dionisio]]. The outline for these edits can be found on my [[Aporras1 Week 14]] page along with the continuation of the [[Week 10|Week 10]] assignment. In this continuation, I selected transcription factors from [[Media:AP dZAP1 profile22 genelist.xlsx]] and put them into YEASTRACT to find the most significant ones and found 49 significant transcription factors found in [[Media:AP YEASTRACT Transcription Factors.xlsx]]. Then I selected 22 of the most significant, 2 additional ones (HAP4 and GLN3) as instructed, to put back into YEASTRACT and create a regulation matrix uploaded as: [[Media:AP Regulation Matrix profile22 dZAP1.xlsx]]. I then created a "network" worksheet, found in [[Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx]], from the matrix and used GRNsight to generate a regulation network visualization: [[Media:AP Regulation Matrix profile22 GRNsight Network.PNG]]. These media downloads can also be found on my [[Aporras1 Week 14|Week 14]] journal entry in the
"Deliverables" section.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 18:31, 3 December 2017 (PST)

====Eddie's Executive Summary====

==Weekly Reflections==

===Week 11===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a good job of staying on task and working together to make sure that we both understood the whole assignment. So there was good communication between the Bibliography group.
#What didn't work?
#*I felt a bit disconnected with my other teammates Eddie and Simon. There was not very good communication with them about whether they needed any help and if they were on progress.
#What to improve upon going forward?
#*Going forward all of the members of the team need to do a better job of communicating. Also, we need to do a better job of properly communicating about how to fill out the team page ahead of time, so that we aren't frantically figuring that out last second. I will work to fix this by initiating communication earlier on in the week.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Reflection====
#What worked?
#*Both me and Eddie were able to put together a powerpoint and present in time for the presentation date
#What didn't work?
#*Due to traveling, Eddie could not be back in LA to help with the project until Monday, which did not give us much time, resulting in our presentation being a bit late as far as submission on our wiki pages.
#How will to improve upon going forward?
#*Going forward I'd like to start early and finish early, that way we can be prepared for any unexpected complications. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:48, 20 November 2017 (PST)

====Antonio's Reflection====
1. What worked? Quinn and I were able to get our work done on time without overlap. We communicated well.

2. What didn't work? Nothing specific prevented us from working efficiently.

3. What will I do next to fix what didn't work? Complete work ahead of time to be more thorough. Maintain a growth mindset.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:06, 20 November 2017 (PST)

====Eddie's Reflection====
Found in Week 11 summary ^^^

===Week 12===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a very good job of working ahead and getting our presentation done in a timely manner. In this way, we were able to ask the instructors any questions we had as they came up, and also allowed for ample time to practice.
#What didn't work?
#*Once again, I felt a bit disconnected from my other partners Eddie and Simon. While I texted Eddie a couple times about their progress, I still never got a chance to see exactly what they were doing.
#What to improve upon going forward?
#*While I feel like this will start to come together once we all start working on our assigned portion of the project together, we still do need to improve our communication between the coders and the PM/DA. In order to do so, I will make sure to continue to check base with each team member each day in class, and also text in the group message when I have questions for the whole team.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Reflection====
#What worked?
#*With Eddie's help, we were both able to set up GRNsight on our laptops.
#What didn't work?
#*Nothing in specific stopped us from working efficiently.
#How will to improve upon going forward?
#*Going forward I'd like to get my summaries in earlier, as well as my individual page and reflections. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:48, 20 November 2017 (PST)

====Antonio's Reflection====
#What worked?
#*Worked closely with Quinn and we kept regular contact through text as we worked through the assignment. Troubleshooting was easy as we were both very capable to take initiative and work to finish the presentation earlier rather than later in the time given.
#What didn't work?
#*I could definitely improve on mastering certain aspects of the assignment. I didn't really communicate with Eddie or Simon but I'd attribute that to having different assignments and parts to complete rather than a team issue.
#What to will I do next to fix what didn't work?
#*Communicate more. I'm hoping we'll have opportunities to work more closely together in the future.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:12, 20 November 2017 (PST)

====Eddie's Reflection====
# What worked?
#: Our work session was successful in setting up GRNsight on my laptop (again) and on Simon's.
# What didn't work?
#: Nothing :D
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 21:47, 20 November 2017 (PST)

===Week 14===

====Quinn's Reflection====

====Simon's Reflection====

====Antonio's Reflection====
# What worked? This week, I worked ahead and was able to complete, at least to my knowledge, this week's assignment ahead of time rather than waiting until the last minute. It was extremely helpful to have a group chat with the other data analysts as we had questions throughout the assignment.
# What didn't work? Everything seems to have run smoothly except I don't really know what the coders are assigned to do and most likely because it goes over my head.
# What will I do next to fix what didn't work? Try to see what the coders are doing, mostly out of curiosity.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 18:36, 3 December 2017 (PST)

====Eddie's Reflection====

==Acknowledgements==

==References==
===Week 11===
#LMU BioDB 2017. (2017). Week 11. Retrieved November 07, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_11
#Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6
#Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, 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
#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#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.
#Top Integrated Development Environment index. (n.d.). Retrieved November 13, 2017, from http://pypl.github.io/IDE.html
#What is an API?. (2016). Retrieved November 13, 2017, from https://medium.freecodecamp.org/what-is-an-api-in-english-please-b880a3214a82
#What's the difference between an API vs SDK?. (2012). Retrieved November 13, 2017, from https://blogs.vmware.com/vsphere/2012/01/whats-the-difference-between-an-api-vs-sdk.html
#Xcode. (2017). Retrieved November 13, 2017, from https://itunes.apple.com/us/app/xcode/id497799835
#What Is Code? (2015). Retrieved November 13, 2017, from https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#how-are-apps-made
#Shrinkwrapped Software. (n.d.). Retrieved November 13, 2017, from http://www.businessdictionary.com/definition/shrinkwrapped-software.html
#Web Application Framework. (2015). Retrieved November 13, 2017, from https://web.archive.org/web/20150723163302/http://docforge.com/wiki/Web_application_framework

===Week 12===
#LMU BioDB 2017. (2017). Week 12. Retrieved November 16, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
#Anneal. (n.d.). ''Genscript''. Retrieved on November 19, 2017 from https://www.genscript.com/molecular-biology-glossary/11896/anneal
#Assay.(2005). ''Biology-Online''. Retrieved on November 19, 2017 http://www.biology-online.org/dictionary/Assay
#Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, 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
#Causton HC, Ren B, Koh SS, et al. 2001. Remodelling of yeast genome expression in response to environmental changes. Mol Biol Cell 12: 323–337.
#Chomczynski, P., & Sacchi, N. (1987). Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Analytical biochemistry, 162(1), 156-159.
#Cluster analysis. BusinessDictionary.com. Retrieved November 19, 2017, from BusinessDictionary.com website: http://www.businessdictionary.com/definition/cluster-analysis.html
#Consensus sequence | Definition of consensus sequence in English by Oxford Dictionaries. (n.d.). Retrieved November 20, 2017, from https://en.oxforddictionaries.com/definition/consensus_sequence
#Cyclins. (n.d.). ''BioNinja''. Retrieved on November 19, 2017 from http://ib.bioninja.com.au/standard-level/topic-1-cell-biology/16-cell-division/cyclins.html
#Differences between in vitro, in vivo, and in silico studies. (n.d.). Retrieved November 20, 2017, from https://mpkb.org/home/patients/assessing_literature/in_vitro_studies
#Donzeau M, Bourdineaud JP, Lauquin GJ. 1996. Regulation by low temperatures and anaerobiosis of a yeast gene specifying a putative GPI-anchored plasma membrane protein. Mol Microbiol 20: 449–459.
#Gasch AP, Spellman PT, Kao CM, et al. 2000. Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11: 4241–4257.
#Glutathione. (n.d.). Retrieved November 20, 2017, from https://www.merriam-webster.com/dictionary/glutathione
#Haploid. (n.d.). Retrieved November 20, 2017, from http://www.biology-online.org/dictionary/Haploid
#HAW. (2011). Difference Between Haploid and Diploid. ''Difference Between.com''. Retrieved on November 19, 2017 from http://www.differencebetween.com/difference-between-haploid-and-vs-diploid/
#Hybridization. (2008). ''Biology-Online''. Retrieved on November 19, 2017 from http://www.biology-online.org/dictionary/Hybridization
#Kondo K, Inouye M. 1991. Cold-induction of yeast NSR1 protein and its role in pre-rRNA processing. J Biol Chem 267: 16 259–16 265.
#Kowalski LR, Kondo K, Inouye M. 1995. Cold-shock induction of a family of TIP1-related proteins associated with the membrane in Saccharomyces cerevisiae. Mol Microbiol 15: 341 – 353.
#LMU BioDB 2017. (2017). Week 12. Retrieved November 16, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
#Mai B, Breeden L. 1997. Xbp1, a stress-upregulated transcrip- tional repressor of the Saccharomyces cerevisae Swi4/Mbp1 family. Mol Cell Biol 17: 6491–6501.
#(n.d.). Retrieved November 19, 2017, from http://fg.cns.utexas.edu/fg/protocol%3A_YPD_plates.html
#(n.d.). Retrieved November 20, 2017, from https://www.nature.com/scitable/definition/diploid-310
#Oligonucleotide. (2014). ''News Medical Life Sciences''. Retrieved on November 19, 2017 from https://www.news-medical.net/life-sciences/What-is-an-Oligonucleotide.aspx
#Polypropylene. (n.d.). ''Dictionary.com''. Retrieved on November 19, 2017 from http://www.dictionary.com/browse/polypropylene
#Putative. (2014). ''Biology-Online''. Retrieved on November 19, 2017 from http://www.biology-online.org/dictionary/Putative
#Study.com. (2017). What is Annealing? - Definition, Biology & Process | Study.com. [online] Available at: http://study.com/academy/lesson/what-is-annealing-definition-biology-process.html [Accessed 21 Nov. 2017].
#Transcriptome. (n.d.). ''Nature''. Retrieved on November 19, 2017 from https://www.nature.com/scitable/definition/transcriptome-296
#Yelland, P. M. (2010). An introduction to correspondence analysis. Math. J, 12, 1-23.
#Young, F.W. (1999). Principle Components. ''forrest.psych.unc.edu''. Retrieved on November 19, 2017 from http://forrest.psych.unc.edu/research/vista-frames/help/lecturenotes/lecture13/biplot.html
#Zhang L, Ohta A, Horiuchi H, Takagi M, Imai R. 2001. Multiple mechanisms regulate expression of low temperature responsive (LOT) genes in Saccharomyces cerevisiae. Biochem Biophys Res Commun 283: 531 – 535.

==Team Links==

{{Template:JASPAR the Friendly Ghost Links}}

==Class Links==

{{Template:GRNsight Gene Page Project Links}}

Simonwro120 Week 12

2017-11-21T07:02:18Z

Simonwro120: added individual journal

==Electronic Laboratory Journal==
'''Almost all of our work for this week was done in class.'''
#Creating branch:
#*We waited for Blair and Zac to make the fork, and then for John and Eddie A. to make their branch.
#*Then, Eddie cloned the fork, switched to their branch, and made a new branch from there. After that he helped me create a branch of my own.
#*At this point, an issue appeared while trying to get the branch on my laptop.
#**What had happened was; Eddie forgot to push his code after making the branch and therefore the branch didn't exist anywhere other than on his laptop. After he pushed his latest branch, I was good to go.
#Cloning and getting GRNsight working locally:
#*Cloning was smooth for the both of us.
#*npm installed well.
#*npm started well.
#Writing the list of Milestones:
#*Both me and Eddie read through our list of tasks as Coders and then Eddie translated it all into a summarized list.
#*We then had that list sent to Quinn so that he could add it to our website.
#Added the executive summary and more to our shared journal Jaspar Page.
#Looking through GRNsight's code to familiarize myself with it.
==Acknowledgements==
*I worked with my homework partner in class, [[User:Ebachour|Eddie Bachoura]]. We also met face-to-face one time outside of class. We texted outside of class and met to work on the presentation part of the assignment together.
*While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.''' 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 23:02, 20 November 2017 (PST)

=References=
* LMU BioDB 2017. (2017). Week 15. Retrieved November 20, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15
{{simonwro120}}

Simonwro120 Week 12

2017-11-21T06:54:59Z

Simonwro120: outline

JASPAR the Friendly Ghost

2017-11-21T06:48:34Z

Simonwro120: syntax

JASPAR the Friendly Ghost

2017-11-21T06:44:23Z

Simonwro120: added reflection

JASPAR the Friendly Ghost

2017-11-21T06:37:09Z

Simonwro120: adding reflection

Template:JASPAR the Friendly Ghost Links

2017-11-16T23:19:28Z

Simonwro120: syntax fix

Template:JASPAR the Friendly Ghost Links

2017-11-16T23:18:55Z

Simonwro120: added my individual journal page to template

JASPAR the Friendly Ghost

2017-11-14T21:45:12Z

Simonwro120: Added executive summar

==Executive Summaries==

===Week 11===

====Quinn's Executive Summary====
Created citations for two entries in the annotated bibliography for papers that report microarray data from yeast subjected to cold shock: 
Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6 
Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, 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 
Also completed a search activity to compare the results found from PubMed, GoogleScholar, and Web of Science using both basic and advanced search tools. 
Individual Journal Page: [[QLanners Week 11]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Executive Summary====
For this assignment, I spent most of my time reading and re-reading Paul Ford's article on how apps are made. It was chapter 6 in a larger work called ''What is Code?'' After absorbing the information laid out in this chapter, Eddie and I made a presentation about it. The presentation summarizes the article, which is about technique, methods, practices, and tools that expedite and simplify the programming process. In addition to making the presentation, I finished my 10 terms and made an outline for the article on my individual journal page. 
Individual Journal Page: [[simonwro120 Week 11]] 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 13:45, 14 November 2017 (PST)

====Antonio's Executive Summary====

Created two citations for the bibliography for the following articles:

#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#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.

I also completed the basic keyword searches on PubMed, Google Scholar, and Web of Science along with the advanced searches and the respective results. Lastly, I completed the prospective searches and collected the results of how many articles the article cites and how many articles cite the article. Totaling to the 3 articles.

Individual Journal Week 11: [[Aporras1_Week_11|Aporras1 Week 11]]

====Eddie Bachoura's Executive Summary====
This week, I spent my time for this class reading the Paul Ford article, chapter 6, which was about how to write applications and the modern practices and tools which are used to aid in cutting down some of the tedious nature of coding. Then, Simon and I spent the rest of the time working on our presentation. Team's progress: I believe that Simon and I worked well this weekend. The only issue that I found was that we didn't start until pretty late (Monday), but that was all at my own fault because I wasn't here for this weekend. We should fix that by starting earlier next weekend!

Individual Journal Week 11: [[Ebachour_Week_11|Eddie Bachoura Week 11]] 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:29, 13 November 2017 (PST)
==Acknowledgements==

==References==
#LMU BioDB 2017. (2017). Week 11. Retrieved November 07, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_11

==Links==

{{Template:JASPAR the Friendly Ghost Links}}

Simonwro120 Week 11

2017-11-14T21:31:06Z

Simonwro120: changed link to .pdf

== Individual Journal Page ==

== Design and Development Terms ==
#IDE (Integrated Development Environment) - An application software which provides helpful tips and tricks for programmers when they are developing software. Usually, an IDE contains three things: <code>[http://pypl.github.io/IDE.html http://pypl.github.io/IDE.html]</code>
#*A source code editor
#*Build automation tools
#*A debugger
#API (Application Programming Interface) - It is a specification within a source code meant to be used as an interface component that receives requests and sends responses. <code>[https://medium.freecodecamp.org/what-is-an-api-in-english-please-b880a3214a82 https://medium.freecodecamp.org/what-is-an-api-in-english-please-b880a3214a82]</code> <code>[https://blogs.vmware.com/vsphere/2012/01/whats-the-difference-between-an-api-vs-sdk.html https://blogs.vmware.com/vsphere/2012/01/whats-the-difference-between-an-api-vs-sdk.html]</code>
#SDK - Commonly referred to as "devkits", an SDK is a set of tools for software developers which aid in the creation of applications for certain platforms. <code>[https://blogs.vmware.com/vsphere/2012/01/whats-the-difference-between-an-api-vs-sdk.html https://blogs.vmware.com/vsphere/2012/01/whats-the-difference-between-an-api-vs-sdk.html]</code>
#Xcode - An IDE which includes devkits for software developers. These devkits are for creating applications in iOS for iOS devices. <code>[https://itunes.apple.com/us/app/xcode/id497799835 https://itunes.apple.com/us/app/xcode/id497799835]</code>
#Premature Optimization - The act of wasting time and other resources trying optimize your code which will not result in a difference in the functionality of the code. <code>[https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#how-are-apps-made https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#how-are-apps-made]</code>
#Polymer - A "Web Components" library, which is a resource for bits and pieces of reusable code to aid in software development. Bootstrap is an example of this. <code>[https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#how-are-apps-made https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#how-are-apps-made]</code>
#SQLite - One of the most respected, widely used, and best-tested pieces of software, SQLite is a database that is completely free and open to use. <code>[https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#how-are-apps-made https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#how-are-apps-made]</code>
#Shrinkwrapped Software - Commercially sold software in retail off the shelf which requires a code to activate. <code>[http://www.businessdictionary.com/definition/shrinkwrapped-software.html http://www.businessdictionary.com/definition/shrinkwrapped-software.html]</code>
#Build Servers - Also called a continuous integration server (CI server), a build server is a stable and reliable environment where software developers can build, share, and distribute projects they are working on. <code>[http://searchsoftwarequality.techtarget.com/definition/Build-Server http://searchsoftwarequality.techtarget.com/definition/Build-Server]</code>
#Web Framework - Commonly referred to as a web application framework (WAF), a web framework is a software application that is made for aiding software developers create web applications such as web services, web resources, and web APIs. <code>[https://web.archive.org/web/20150723163302/http://docforge.com/wiki/Web_application_framework https://web.archive.org/web/20150723163302/http://docforge.com/wiki/Web_application_framework]</code>

== Article Outline ==
===How Are Apps Made?===
'''Integrated Development Environment (IDE)'''
*IDEs are application software, which provide helpful facilities for programmers when they are developing their own software.
*Xcode - Apple’s IDE; used for creating software for Mac and iPhone.
'''Software Development Kit (SDK)'''
*Within Xcode there are many SDK’s, one of which is the iOS SDK.
**The iOS SDK is used for making iPhone and iPad apps and is made up of dozens and dozens of APIs.
*Application Programming Interface (API) – Is a specification within a source code; used as an interface component that receives requests and sends responses.
*Software designed to create software is commonly free because it stimulates the creation of more software
'''Frameworks'''
*There are hundreds of different frameworks and just about every language has one.
*Web Frameworks - Commonly referred to as a web application framework (WAF), a web framework is a software application that is made for aiding software developers create web applications such as web services, web resources, and web APIs.
*These frameworks expedite the programming process, however they also limit and influence it in certain ways as well.
'''Testing and Debugging'''
*Debugging is the process of running and examining your code to find and fix the code that isn’t working as intended and tests are code.
*Testing is the process of using test programs either written by yourself or by others to test the functionality and integrity of a different program that you are working on.
'''Version control'''
*Version control – The control programmers have over the evolution of their program.
*GitHub is an environment where code can be controlled this way, a master version is created and then people can clone the code (repository) and make their own edits, then ask for permission to merge their version back to the master.
'''Main Message'''
*The main message is that there are many ways to aid programmers’ development of software.
'''Importance/Significance'''
*The implications of these practices, processes, techniques, and methods allow for programmers to create programs faster and with higher quality because they are specified for certain platforms.

== Link to Presentation ==
[[Media:e_and_s_presentation_2.pdf|Eddie and Simon Presentation]]

== Acknowledgements ==
*I worked with my homework partner, Eddie Bachoura, on this assignment.
*I'd also like to acknowledge the help both Dondi and Dr. Dahlquist for their detailed instructions on completing this assignment.
*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 11 Retrieved November 9, 2017, from [https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_11 https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_11]
#Top Integrated Development Environment index. (n.d.). Retrieved November 13, 2017, from [http://pypl.github.io/IDE.html http://pypl.github.io/IDE.html]
#What is an API?. (2016). Retrieved November 13, 2017, from https://medium.freecodecamp.org/what-is-an-api-in-english-please-b880a3214a82
#What's the difference between an API vs SDK?. (2012). Retrieved November 13, 2017, from [https://blogs.vmware.com/vsphere/2012/01/whats-the-difference-between-an-api-vs-sdk.html https://blogs.vmware.com/vsphere/2012/01/whats-the-difference-between-an-api-vs-sdk.html]
#Xcode. (2017). Retrieved November 13, 2017, from [https://itunes.apple.com/us/app/xcode/id497799835 https://itunes.apple.com/us/app/xcode/id497799835]
#What Is Code? (2015). Retrieved November 13, 2017, from [https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#how-are-apps-made https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#how-are-apps-made]
#Shrinkwrapped Software. (n.d.). Retrieved November 13, 2017, from [http://www.businessdictionary.com/definition/shrinkwrapped-software.html http://www.businessdictionary.com/definition/shrinkwrapped-software.html]
#Web Application Framework. (2015). Retrieved November 13, 2017, from [https://web.archive.org/web/20150723163302/http://docforge.com/wiki/Web_application_framework https://web.archive.org/web/20150723163302/http://docforge.com/wiki/Web_application_framework]

Simonwro120 Week 11

2017-11-14T07:46:07Z

Simonwro120: added link to presentation

== Individual Journal Page ==

== Design and Development Terms ==
#IDE (Integrated Development Environment) - An application software which provides helpful tips and tricks for programmers when they are developing software. Usually, an IDE contains three things: <code>[http://pypl.github.io/IDE.html http://pypl.github.io/IDE.html]</code>
#*A source code editor
#*Build automation tools
#*A debugger
#API (Application Programming Interface) - It is a specification within a source code meant to be used as an interface component that receives requests and sends responses. <code>[https://medium.freecodecamp.org/what-is-an-api-in-english-please-b880a3214a82 https://medium.freecodecamp.org/what-is-an-api-in-english-please-b880a3214a82]</code> <code>[https://blogs.vmware.com/vsphere/2012/01/whats-the-difference-between-an-api-vs-sdk.html https://blogs.vmware.com/vsphere/2012/01/whats-the-difference-between-an-api-vs-sdk.html]</code>
#SDK - Commonly referred to as "devkits", an SDK is a set of tools for software developers which aid in the creation of applications for certain platforms. <code>[https://blogs.vmware.com/vsphere/2012/01/whats-the-difference-between-an-api-vs-sdk.html https://blogs.vmware.com/vsphere/2012/01/whats-the-difference-between-an-api-vs-sdk.html]</code>
#Xcode - An IDE which includes devkits for software developers. These devkits are for creating applications in iOS for iOS devices. <code>[https://itunes.apple.com/us/app/xcode/id497799835 https://itunes.apple.com/us/app/xcode/id497799835]</code>
#Premature Optimization - The act of wasting time and other resources trying optimize your code which will not result in a difference in the functionality of the code. <code>[https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#how-are-apps-made https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#how-are-apps-made]</code>
#Polymer - A "Web Components" library, which is a resource for bits and pieces of reusable code to aid in software development. Bootstrap is an example of this. <code>[https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#how-are-apps-made https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#how-are-apps-made]</code>
#SQLite - One of the most respected, widely used, and best-tested pieces of software, SQLite is a database that is completely free and open to use. <code>[https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#how-are-apps-made https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#how-are-apps-made]</code>
#Shrinkwrapped Software - Commercially sold software in retail off the shelf which requires a code to activate. <code>[http://www.businessdictionary.com/definition/shrinkwrapped-software.html http://www.businessdictionary.com/definition/shrinkwrapped-software.html]</code>
#Build Servers - Also called a continuous integration server (CI server), a build server is a stable and reliable environment where software developers can build, share, and distribute projects they are working on. <code>[http://searchsoftwarequality.techtarget.com/definition/Build-Server http://searchsoftwarequality.techtarget.com/definition/Build-Server]</code>
#Web Framework - Commonly referred to as a web application framework (WAF), a web framework is a software application that is made for aiding software developers create web applications such as web services, web resources, and web APIs. <code>[https://web.archive.org/web/20150723163302/http://docforge.com/wiki/Web_application_framework https://web.archive.org/web/20150723163302/http://docforge.com/wiki/Web_application_framework]</code>

== Article Outline ==
===How Are Apps Made?===
'''Integrated Development Environment (IDE)'''
*IDEs are application software, which provide helpful facilities for programmers when they are developing their own software.
*Xcode - Apple’s IDE; used for creating software for Mac and iPhone.
'''Software Development Kit (SDK)'''
*Within Xcode there are many SDK’s, one of which is the iOS SDK.
**The iOS SDK is used for making iPhone and iPad apps and is made up of dozens and dozens of APIs.
*Application Programming Interface (API) – Is a specification within a source code; used as an interface component that receives requests and sends responses.
*Software designed to create software is commonly free because it stimulates the creation of more software
'''Frameworks'''
*There are hundreds of different frameworks and just about every language has one.
*Web Frameworks - Commonly referred to as a web application framework (WAF), a web framework is a software application that is made for aiding software developers create web applications such as web services, web resources, and web APIs.
*These frameworks expedite the programming process, however they also limit and influence it in certain ways as well.
'''Testing and Debugging'''
*Debugging is the process of running and examining your code to find and fix the code that isn’t working as intended and tests are code.
*Testing is the process of using test programs either written by yourself or by others to test the functionality and integrity of a different program that you are working on.
'''Version control'''
*Version control – The control programmers have over the evolution of their program.
*GitHub is an environment where code can be controlled this way, a master version is created and then people can clone the code (repository) and make their own edits, then ask for permission to merge their version back to the master.
'''Main Message'''
*The main message is that there are many ways to aid programmers’ development of software.
'''Importance/Significance'''
*The implications of these practices, processes, techniques, and methods allow for programmers to create programs faster and with higher quality because they are specified for certain platforms.

== Link to Presentation ==
[[Media:e_and_s_presentation_2.pptx|Eddie and Simon Presentation]]

== Acknowledgements ==
*I worked with my homework partner, Eddie Bachoura, on this assignment.
*I'd also like to acknowledge the help both Dondi and Dr. Dahlquist for their detailed instructions on completing this assignment.
*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 11 Retrieved November 9, 2017, from [https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_11 https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_11]
#Top Integrated Development Environment index. (n.d.). Retrieved November 13, 2017, from [http://pypl.github.io/IDE.html http://pypl.github.io/IDE.html]
#What is an API?. (2016). Retrieved November 13, 2017, from https://medium.freecodecamp.org/what-is-an-api-in-english-please-b880a3214a82
#What's the difference between an API vs SDK?. (2012). Retrieved November 13, 2017, from [https://blogs.vmware.com/vsphere/2012/01/whats-the-difference-between-an-api-vs-sdk.html https://blogs.vmware.com/vsphere/2012/01/whats-the-difference-between-an-api-vs-sdk.html]
#Xcode. (2017). Retrieved November 13, 2017, from [https://itunes.apple.com/us/app/xcode/id497799835 https://itunes.apple.com/us/app/xcode/id497799835]
#What Is Code? (2015). Retrieved November 13, 2017, from [https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#how-are-apps-made https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#how-are-apps-made]
#Shrinkwrapped Software. (n.d.). Retrieved November 13, 2017, from [http://www.businessdictionary.com/definition/shrinkwrapped-software.html http://www.businessdictionary.com/definition/shrinkwrapped-software.html]
#Web Application Framework. (2015). Retrieved November 13, 2017, from [https://web.archive.org/web/20150723163302/http://docforge.com/wiki/Web_application_framework https://web.archive.org/web/20150723163302/http://docforge.com/wiki/Web_application_framework]

Simonwro120 Week 11

2017-11-14T06:27:32Z

Simonwro120: Added Acknowledgements

== Individual Journal Page ==

=== Design and Development Terms ===
#IDE (Integrated Development Environment) - An application software which provides helpful tips and tricks for programmers when they are developing software. Usually, an IDE contains three things: <code>[http://pypl.github.io/IDE.html http://pypl.github.io/IDE.html]</code>
#*A source code editor
#*Build automation tools
#*A debugger
#API (Application Programming Interface) - It is a specification within a source code meant to be used as an interface component that receives requests and sends responses. <code>[https://medium.freecodecamp.org/what-is-an-api-in-english-please-b880a3214a82 https://medium.freecodecamp.org/what-is-an-api-in-english-please-b880a3214a82]</code> <code>[https://blogs.vmware.com/vsphere/2012/01/whats-the-difference-between-an-api-vs-sdk.html https://blogs.vmware.com/vsphere/2012/01/whats-the-difference-between-an-api-vs-sdk.html]</code>
#SDK - Commonly referred to as "devkits", an SDK is a set of tools for software developers which aid in the creation of applications for certain platforms. <code>[https://blogs.vmware.com/vsphere/2012/01/whats-the-difference-between-an-api-vs-sdk.html https://blogs.vmware.com/vsphere/2012/01/whats-the-difference-between-an-api-vs-sdk.html]</code>
#Xcode - An IDE which includes devkits for software developers. These devkits are for creating applications in iOS for iOS devices. <code>[https://itunes.apple.com/us/app/xcode/id497799835 https://itunes.apple.com/us/app/xcode/id497799835]</code>
#Premature Optimization - The act of wasting time and other resources trying optimize your code which will not result in a difference in the functionality of the code. <code>[https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#how-are-apps-made https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#how-are-apps-made]</code>
#Polymer - A "Web Components" library, which is a resource for bits and pieces of reusable code to aid in software development. Bootstrap is an example of this. <code>[https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#how-are-apps-made https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#how-are-apps-made]</code>
#SQLite - One of the most respected, widely used, and best-tested pieces of software, SQLite is a database that is completely free and open to use. <code>[https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#how-are-apps-made https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#how-are-apps-made]</code>
#Shrinkwrapped Software - Commercially sold software in retail off the shelf which requires a code to activate. <code>[http://www.businessdictionary.com/definition/shrinkwrapped-software.html http://www.businessdictionary.com/definition/shrinkwrapped-software.html]</code>
#Build Servers - Also called a continuous integration server (CI server), a build server is a stable and reliable environment where software developers can build, share, and distribute projects they are working on. <code>[http://searchsoftwarequality.techtarget.com/definition/Build-Server http://searchsoftwarequality.techtarget.com/definition/Build-Server]</code>
#Web Framework - Commonly referred to as a web application framework (WAF), a web framework is a software application that is made for aiding software developers create web applications such as web services, web resources, and web APIs. <code>[https://web.archive.org/web/20150723163302/http://docforge.com/wiki/Web_application_framework https://web.archive.org/web/20150723163302/http://docforge.com/wiki/Web_application_framework]</code>

=== Article Outline ===
====How Are Apps Made?====
'''Integrated Development Environment (IDE)'''
*IDEs are application software, which provide helpful facilities for programmers when they are developing their own software.
*Xcode - Apple’s IDE; used for creating software for Mac and iPhone.
'''Software Development Kit (SDK)'''
*Within Xcode there are many SDK’s, one of which is the iOS SDK.
**The iOS SDK is used for making iPhone and iPad apps and is made up of dozens and dozens of APIs.
*Application Programming Interface (API) – Is a specification within a source code; used as an interface component that receives requests and sends responses.
*Software designed to create software is commonly free because it stimulates the creation of more software
'''Frameworks'''
*There are hundreds of different frameworks and just about every language has one.
*Web Frameworks - Commonly referred to as a web application framework (WAF), a web framework is a software application that is made for aiding software developers create web applications such as web services, web resources, and web APIs.
*These frameworks expedite the programming process, however they also limit and influence it in certain ways as well.
'''Testing and Debugging'''
*Debugging is the process of running and examining your code to find and fix the code that isn’t working as intended and tests are code.
*Testing is the process of using test programs either written by yourself or by others to test the functionality and integrity of a different program that you are working on.
'''Version control'''
*Version control – The control programmers have over the evolution of their program.
*GitHub is an environment where code can be controlled this way, a master version is created and then people can clone the code (repository) and make their own edits, then ask for permission to merge their version back to the master.
'''Main Message'''
*The main message is that there are many ways to aid programmers’ development of software.
'''Importance/Significance'''
*The implications of these practices, processes, techniques, and methods allow for programmers to create programs faster and with higher quality because they are specified for certain platforms.

== Acknowledgements ==
*I worked with my homework partner, Eddie Bachoura, on this assignment.
*I'd also like to acknowledge the help both Dondi and Dr. Dahlquist for their detailed instructions on completing this assignment.
*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 11 Retrieved November 9, 2017, from [https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_11 https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_11]
#Top Integrated Development Environment index. (n.d.). Retrieved November 13, 2017, from [http://pypl.github.io/IDE.html http://pypl.github.io/IDE.html]
#What is an API?. (2016). Retrieved November 13, 2017, from https://medium.freecodecamp.org/what-is-an-api-in-english-please-b880a3214a82
#What's the difference between an API vs SDK?. (2012). Retrieved November 13, 2017, from [https://blogs.vmware.com/vsphere/2012/01/whats-the-difference-between-an-api-vs-sdk.html https://blogs.vmware.com/vsphere/2012/01/whats-the-difference-between-an-api-vs-sdk.html]
#Xcode. (2017). Retrieved November 13, 2017, from [https://itunes.apple.com/us/app/xcode/id497799835 https://itunes.apple.com/us/app/xcode/id497799835]
#What Is Code? (2015). Retrieved November 13, 2017, from [https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#how-are-apps-made https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#how-are-apps-made]
#Shrinkwrapped Software. (n.d.). Retrieved November 13, 2017, from [http://www.businessdictionary.com/definition/shrinkwrapped-software.html http://www.businessdictionary.com/definition/shrinkwrapped-software.html]
#Web Application Framework. (2015). Retrieved November 13, 2017, from [https://web.archive.org/web/20150723163302/http://docforge.com/wiki/Web_application_framework https://web.archive.org/web/20150723163302/http://docforge.com/wiki/Web_application_framework]

Simonwro120 Week 11

2017-11-14T06:25:36Z

Simonwro120: syntax fix

== Individual Journal Page ==

=== Design and Development Terms ===
#IDE (Integrated Development Environment) - An application software which provides helpful tips and tricks for programmers when they are developing software. Usually, an IDE contains three things: <code>[http://pypl.github.io/IDE.html http://pypl.github.io/IDE.html]</code>
#*A source code editor
#*Build automation tools
#*A debugger
#API (Application Programming Interface) - It is a specification within a source code meant to be used as an interface component that receives requests and sends responses. <code>[https://medium.freecodecamp.org/what-is-an-api-in-english-please-b880a3214a82 https://medium.freecodecamp.org/what-is-an-api-in-english-please-b880a3214a82]</code> <code>[https://blogs.vmware.com/vsphere/2012/01/whats-the-difference-between-an-api-vs-sdk.html https://blogs.vmware.com/vsphere/2012/01/whats-the-difference-between-an-api-vs-sdk.html]</code>
#SDK - Commonly referred to as "devkits", an SDK is a set of tools for software developers which aid in the creation of applications for certain platforms. <code>[https://blogs.vmware.com/vsphere/2012/01/whats-the-difference-between-an-api-vs-sdk.html https://blogs.vmware.com/vsphere/2012/01/whats-the-difference-between-an-api-vs-sdk.html]</code>
#Xcode - An IDE which includes devkits for software developers. These devkits are for creating applications in iOS for iOS devices. <code>[https://itunes.apple.com/us/app/xcode/id497799835 https://itunes.apple.com/us/app/xcode/id497799835]</code>
#Premature Optimization - The act of wasting time and other resources trying optimize your code which will not result in a difference in the functionality of the code. <code>[https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#how-are-apps-made https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#how-are-apps-made]</code>
#Polymer - A "Web Components" library, which is a resource for bits and pieces of reusable code to aid in software development. Bootstrap is an example of this. <code>[https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#how-are-apps-made https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#how-are-apps-made]</code>
#SQLite - One of the most respected, widely used, and best-tested pieces of software, SQLite is a database that is completely free and open to use. <code>[https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#how-are-apps-made https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#how-are-apps-made]</code>
#Shrinkwrapped Software - Commercially sold software in retail off the shelf which requires a code to activate. <code>[http://www.businessdictionary.com/definition/shrinkwrapped-software.html http://www.businessdictionary.com/definition/shrinkwrapped-software.html]</code>
#Build Servers - Also called a continuous integration server (CI server), a build server is a stable and reliable environment where software developers can build, share, and distribute projects they are working on. <code>[http://searchsoftwarequality.techtarget.com/definition/Build-Server http://searchsoftwarequality.techtarget.com/definition/Build-Server]</code>
#Web Framework - Commonly referred to as a web application framework (WAF), a web framework is a software application that is made for aiding software developers create web applications such as web services, web resources, and web APIs. <code>[https://web.archive.org/web/20150723163302/http://docforge.com/wiki/Web_application_framework https://web.archive.org/web/20150723163302/http://docforge.com/wiki/Web_application_framework]</code>

=== Article Outline ===
====How Are Apps Made?====
'''Integrated Development Environment (IDE)'''
*IDEs are application software, which provide helpful facilities for programmers when they are developing their own software.
*Xcode - Apple’s IDE; used for creating software for Mac and iPhone.
'''Software Development Kit (SDK)'''
*Within Xcode there are many SDK’s, one of which is the iOS SDK.
**The iOS SDK is used for making iPhone and iPad apps and is made up of dozens and dozens of APIs.
*Application Programming Interface (API) – Is a specification within a source code; used as an interface component that receives requests and sends responses.
*Software designed to create software is commonly free because it stimulates the creation of more software
'''Frameworks'''
*There are hundreds of different frameworks and just about every language has one.
*Web Frameworks - Commonly referred to as a web application framework (WAF), a web framework is a software application that is made for aiding software developers create web applications such as web services, web resources, and web APIs.
*These frameworks expedite the programming process, however they also limit and influence it in certain ways as well.
'''Testing and Debugging'''
*Debugging is the process of running and examining your code to find and fix the code that isn’t working as intended and tests are code.
*Testing is the process of using test programs either written by yourself or by others to test the functionality and integrity of a different program that you are working on.
'''Version control'''
*Version control – The control programmers have over the evolution of their program.
*GitHub is an environment where code can be controlled this way, a master version is created and then people can clone the code (repository) and make their own edits, then ask for permission to merge their version back to the master.
'''Main Message'''
*The main message is that there are many ways to aid programmers’ development of software.
'''Importance/Significance'''
*The implications of these practices, processes, techniques, and methods allow for programmers to create programs faster and with higher quality because they are specified for certain platforms.

== Acknowledgements ==

== References ==
#LMU BioDB 2017. (2017). Week 11 Retrieved November 9, 2017, from [https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_11 https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_11]
#Top Integrated Development Environment index. (n.d.). Retrieved November 13, 2017, from [http://pypl.github.io/IDE.html http://pypl.github.io/IDE.html]
#What is an API?. (2016). Retrieved November 13, 2017, from https://medium.freecodecamp.org/what-is-an-api-in-english-please-b880a3214a82
#What's the difference between an API vs SDK?. (2012). Retrieved November 13, 2017, from [https://blogs.vmware.com/vsphere/2012/01/whats-the-difference-between-an-api-vs-sdk.html https://blogs.vmware.com/vsphere/2012/01/whats-the-difference-between-an-api-vs-sdk.html]
#Xcode. (2017). Retrieved November 13, 2017, from [https://itunes.apple.com/us/app/xcode/id497799835 https://itunes.apple.com/us/app/xcode/id497799835]
#What Is Code? (2015). Retrieved November 13, 2017, from [https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#how-are-apps-made https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#how-are-apps-made]
#Shrinkwrapped Software. (n.d.). Retrieved November 13, 2017, from [http://www.businessdictionary.com/definition/shrinkwrapped-software.html http://www.businessdictionary.com/definition/shrinkwrapped-software.html]
#Web Application Framework. (2015). Retrieved November 13, 2017, from [https://web.archive.org/web/20150723163302/http://docforge.com/wiki/Web_application_framework https://web.archive.org/web/20150723163302/http://docforge.com/wiki/Web_application_framework]

Simonwro120 Week 11

2017-11-14T06:19:34Z

Simonwro120: outline

== Individual Journal Page ==

=== Design and Development Terms ===
#IDE (Integrated Development Environment) - An application software which provides helpful tips and tricks for programmers when they are developing software. Usually, an IDE contains three things: <code>[http://pypl.github.io/IDE.html http://pypl.github.io/IDE.html]</code>
#*A source code editor
#*Build automation tools
#*A debugger
#API (Application Programming Interface) - It is a specification within a source code meant to be used as an interface component that receives requests and sends responses. <code>[https://medium.freecodecamp.org/what-is-an-api-in-english-please-b880a3214a82 https://medium.freecodecamp.org/what-is-an-api-in-english-please-b880a3214a82]</code> <code>[https://blogs.vmware.com/vsphere/2012/01/whats-the-difference-between-an-api-vs-sdk.html https://blogs.vmware.com/vsphere/2012/01/whats-the-difference-between-an-api-vs-sdk.html]</code>
#SDK - Commonly referred to as "devkits", an SDK is a set of tools for software developers which aid in the creation of applications for certain platforms. <code>[https://blogs.vmware.com/vsphere/2012/01/whats-the-difference-between-an-api-vs-sdk.html https://blogs.vmware.com/vsphere/2012/01/whats-the-difference-between-an-api-vs-sdk.html]</code>
#Xcode - An IDE which includes devkits for software developers. These devkits are for creating applications in iOS for iOS devices. <code>[https://itunes.apple.com/us/app/xcode/id497799835 https://itunes.apple.com/us/app/xcode/id497799835]</code>
#Premature Optimization - The act of wasting time and other resources trying optimize your code which will not result in a difference in the functionality of the code. <code>[https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#how-are-apps-made https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#how-are-apps-made]</code>
#Polymer - A "Web Components" library, which is a resource for bits and pieces of reusable code to aid in software development. Bootstrap is an example of this. <code>[https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#how-are-apps-made https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#how-are-apps-made]</code>
#SQLite - One of the most respected, widely used, and best-tested pieces of software, SQLite is a database that is completely free and open to use. <code>[https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#how-are-apps-made https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#how-are-apps-made]</code>
#Shrinkwrapped Software - Commercially sold software in retail off the shelf which requires a code to activate. <code>[http://www.businessdictionary.com/definition/shrinkwrapped-software.html http://www.businessdictionary.com/definition/shrinkwrapped-software.html]</code>
#Build Servers - Also called a continuous integration server (CI server), a build server is a stable and reliable environment where software developers can build, share, and distribute projects they are working on. <code>[http://searchsoftwarequality.techtarget.com/definition/Build-Server http://searchsoftwarequality.techtarget.com/definition/Build-Server]</code>
#Web Framework - Commonly referred to as a web application framework (WAF), a web framework is a software application that is made for aiding software developers create web applications such as web services, web resources, and web APIs. <code>[https://web.archive.org/web/20150723163302/http://docforge.com/wiki/Web_application_framework https://web.archive.org/web/20150723163302/http://docforge.com/wiki/Web_application_framework]</code>

=== Article Outline ===
How Are Apps Made?
''Integrated Development Environment (IDE)''
*IDEs are application software, which provide helpful facilities for programmers when they are developing their own software.
*Xcode - Apple’s IDE; used for creating software for Mac and iPhone.
Software Development Kit (SDK)
*Within Xcode there are many SDK’s, one of which is the iOS SDK.
**The iOS SDK is used for making iPhone and iPad apps and is made up of dozens and dozens of APIs.
*Application Programming Interface (API) – Is a specification within a source code; used as an interface component that receives requests and sends responses.
*Software designed to create software is commonly free because it stimulates the creation of more software
''Frameworks''
*There are hundreds of different frameworks and just about every language has one.
*Web Frameworks - Commonly referred to as a web application framework (WAF), a web framework is a software application that is made for aiding software developers create web applications such as web services, web resources, and web APIs.
*These frameworks expedite the programming process, however they also limit and influence it in certain ways as well.
''Testing and Debugging''
*Debugging is the process of running and examining your code to find and fix the code that isn’t working as intended and tests are code.
*Testing is the process of using test programs either written by yourself or by others to test the functionality and integrity of a different program that you are working on.
''Version control''
*Version control – The control programmers have over the evolution of their program.
*GitHub is an environment where code can be controlled this way, a master version is created and then people can clone the code (repository) and make their own edits, then ask for permission to merge their version back to the master.
''Main Message''
*The main message is that there are many ways to aid programmers’ development of software.
''Importance/Significance''
*The implications of these practices, processes, techniques, and methods allow for programmers to create programs faster and with higher quality because they are specified for certain platforms.

== Acknowledgements ==

== References ==
#LMU BioDB 2017. (2017). Week 11 Retrieved November 9, 2017, from [https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_11 https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_11]
#Top Integrated Development Environment index. (n.d.). Retrieved November 13, 2017, from [http://pypl.github.io/IDE.html http://pypl.github.io/IDE.html]
#What is an API?. (2016). Retrieved November 13, 2017, from https://medium.freecodecamp.org/what-is-an-api-in-english-please-b880a3214a82
#What's the difference between an API vs SDK?. (2012). Retrieved November 13, 2017, from [https://blogs.vmware.com/vsphere/2012/01/whats-the-difference-between-an-api-vs-sdk.html https://blogs.vmware.com/vsphere/2012/01/whats-the-difference-between-an-api-vs-sdk.html]
#Xcode. (2017). Retrieved November 13, 2017, from [https://itunes.apple.com/us/app/xcode/id497799835 https://itunes.apple.com/us/app/xcode/id497799835]
#What Is Code? (2015). Retrieved November 13, 2017, from [https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#how-are-apps-made https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#how-are-apps-made]
#Shrinkwrapped Software. (n.d.). Retrieved November 13, 2017, from [http://www.businessdictionary.com/definition/shrinkwrapped-software.html http://www.businessdictionary.com/definition/shrinkwrapped-software.html]
#Web Application Framework. (2015). Retrieved November 13, 2017, from [https://web.archive.org/web/20150723163302/http://docforge.com/wiki/Web_application_framework https://web.archive.org/web/20150723163302/http://docforge.com/wiki/Web_application_framework]

Simonwro120 Week 11

2017-11-14T01:35:43Z

Simonwro120: syntax fix