Template:Gene hAPI - Revision history

Cwong34: /* Project Deliverables Checklist */ added check

2017-12-15T05:32:14Z

‎Project Deliverables Checklist: added check

Cwong34: Checked off some deliverables items

2017-12-13T23:53:22Z

Checked off some deliverables items

Cwong34: Deleted Milestone 5 for coders

2017-12-12T02:55:22Z

Deleted Milestone 5 for coders

Cwong34: Removed links from template - added to actual page

2017-12-12T02:47:41Z

Removed links from template - added to actual page

Cazinge: /* Coders */ updated list

2017-12-08T21:03:49Z

‎Coders: updated list

Cwong34: Deleted milestones related to other team groups

2017-11-30T23:37:18Z

Deleted milestones related to other team groups

Cwong34: Deleted QA milestones for teams other than Gene API

2017-11-30T23:34:33Z

Deleted QA milestones for teams other than Gene API

Cwong34: Created checkboxes for milestones

2017-11-30T23:22:08Z

Created checkboxes for milestones

Cwong34: Added deliverables page link to template

2017-11-30T23:11:23Z

Added deliverables page link to template

Dbashour: /* Project Schedule Checklist */

2017-11-23T08:27:32Z

‎Project Schedule Checklist

@@ Line 14: / Line 14: @@
 [ ]GRNmap input workbook (with network adjacency matrix, .xlsx) <br>
 [ ]GRNmap output workbook (.xlsx) <br>
-[ ]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. <br>
+[X]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. <br>
 =Project Manager=

@@ Line 1: / Line 1: @@
 =Project Deliverables Checklist=
-[ ]Organized Team deliverables wiki page (or other media (CD or flash drive) with table of contents) <br>
+[X]Organized Team deliverables wiki page (or other media (CD or flash drive) with table of contents) <br>
 [ ]Group Report (.doc, .docx or .pdf file) <br>
 [ ]Individual statements of work, assessments, reflections (wiki page, .doc, .docx, .pdf, or e-mailed to both Dr. Dahlquist and Dr. Dionisio) <br>
-[ ]Group PowerPoint presentation (given on Tuesday, December 12, .ppt, .pptx or .pdf file) <br>
+[X]Group PowerPoint presentation (given on Tuesday, December 12, .ppt, .pptx or .pdf file) <br>
 [ ]Code (GitHub pull request) <br>
 [ ]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  <br>

← Older revision		Revision as of 02:55, 12 December 2017
Line 146:		Line 146:

	Teams should perform their own internal testing (both manual and automated) on their respective files throughout development. Commit and push your work to your designated branch at appropriate intervals. Coders who are not familiar with this style of working should consult with fellow guild members or talk to Dr. Dionisio.		Teams should perform their own internal testing (both manual and automated) on their respective files throughout development. Commit and push your work to your designated branch at appropriate intervals. Coders who are not familiar with this style of working should consult with fellow guild members or talk to Dr. Dionisio.
−
−	~~[X]'''Milestone 5: Integration and Integration Testing'''~~
−
−	Integration and integration testing should take place periodically to make sure that the overall gene page project is coming together well. Most of the Coders’ work for the remainder of the semester will be a cycle of the development and integration milestones. The Interaction and Integration team is in charge of coordinating when these integrations take place. The first integration will likely be the most difficult one to perform, but it is hoped that later iterations will proceed more smoothly.
−
−	When the other teams have reached the following sub-milestones, the first integration cycle can take place. Future iterations are at the discretion of the Interaction and Integration team in coordination with how the other teams are progressing:
−	* Page Design: first working version of the gene page
−	* Gene Database APIs: first working version of the <code>getGeneInformation</code> function
−	* JASPAR: This team’s work does not have to participate in the first integration cycle; instead, they should integrate their work with the Gene Database APIs team whenever they have a working prototype. JASPAR functionality simply “shows up” at some future integration cycle.
−	* Interaction and Integration: You are not blocked from working prior to the first integration; you can work on exploring the existing GRNsight code to implement the right-click functionality that will open the gene page in a new tab or window. You can start by making this code open a blank page. Upon the first integration iteration, you can then connect that page to the gene page provided by the Page Design team.
−
−	~~An individual integration iteration proceeds in this way:~~
−	~~# The Page Design and Gene Database APIs teams issue ''pull requests'' to merge their branches with the ''master'' branch.~~
−	~~# The Coders guild reviews each other’s code and points out any needed revisions.~~
−	~~# Once all revision requests are fulfilled, the Interaction and Integration team merges the pull requests into ''master''.~~
−	~~# The Coders guild resolves any merge conflicts then tests the combined code.~~
−	# The combined code is allowed to be ''unfinished'', but it should not be ''broken''. The combined GRNsight build should still run and show steady progress toward the fully-envisioned gene page functionality.
−	~~# Code revisions at this stage are committed and pushed to ''master''.~~
−	# When the Interaction and Integration team is satisfied with the state of the combined code, the other teams can then merge ''master'' back into their respective branches, and localized development and testing can proceed to the next phase.
−	~~# When the teams feel that they have reached another integration point, they notify the Interaction and Integration team of this and another integration iteration can take place.~~
−	~~# Rinse and repeat until the project is done!~~

@@ Line 1: / Line 1: @@
 =Project Deliverables Checklist=
 [ ]Organized Team deliverables wiki page (or other media (CD or flash drive) with table of contents) <br>
@@ Line 26: / Line 17: @@
 =Project Manager=
-[ ]'''Milestone 1: Project “Scaffolding”'''
+[X]'''Milestone 1: Project “Scaffolding”'''
 This milestone pertains to setting up an initial schedule and any resources that your team will use for the duration of the project. It will be useful to get an overview of every team member’s own milestones so that you have an accurate big picture view.
@@ Line 38: / Line 29: @@
 #** Question/answer sequences
-[ ]'''Milestone 2: Periodic Updates'''
+[X]'''Milestone 2: Periodic Updates'''
 Not as much a milestone as an on-going task, once the project is up and running the Project Manager is responsible for keeping track of everyone’s progress.
@@ Line 56: / Line 47: @@
 * For the [[Week 12]] assignment, the Data Analysts will work with the QAs to prepare a PowerPoint presentation to be delivered in class on Tuesday, November 21.
-[ ]'''Milestone 3: Complete Data Analysis of Dahlquist Lab Data for Visualization with GRNsight'''
+[X]'''Milestone 3: Complete Data Analysis of Dahlquist Lab Data for Visualization with GRNsight'''
 * For [[Week 14]] and [[Week 15]], the Data Analysts will review and complete the microarray data analysis begun with the [[Week 8]] and [[Week 10]] assignments with the eventual goal of visualizing a gene regulatory network derived from their dataset in GRNsight.  Specifically:
@@ Line 76: / Line 67: @@
 * For the [[Week 12]] assignment, the Data Analysts will work with the QAs to prepare a PowerPoint presentation to be delivered in class on Tuesday, November 21.
-[ ]'''Milestone 3: Requirements Analysis'''
+[X]'''Milestone 3: Requirements Analysis'''
 As the Coders begin their development work and the Data Analysts start working with their assigned microarray data sets, the QA team members should familiarize themselves with and help specify the expected correct functionalities of their respective teams.
@@ Line 83: / Line 74: @@
 * ''Gene Database APIs team'': QA should get to know how the four web service APIs are to be used in order to retrieve gene data given a gene symbol. They should be able to perform these steps themselves using '''curl''' or a web browser, so that they can provide independent verification that the Coders’ work is functioning correctly.
-[ ]'''Milestone 4: On-going Testing of Respective Team Deliverables'''
+[X]'''Milestone 4: On-going Testing of Respective Team Deliverables'''
 The rest of the semester is expected to be an on-going process of verifying and validating the correctness of a QA member’s assigned team. Specific concerns include but are not limited to the following:
@@ Line 138: / Line 129: @@
 If anyone runs into problems with this procedure, please consult with your fellow guild members or notify Dr. Dionisio.
-[ ]'''Milestone 4: Development, Implementation, and Localized Testing'''
+[X]'''Milestone 4: Development, Implementation, and Localized Testing'''
 At this point, each team proceeds with their own development work. In general, each team will do most of their work (and place most of their files) in the following locations within the GRNsight repository. Some files may need to go elsewhere; check in with Dr. Dionisio if there are any file organization/location issues:
@@ Line 156: / Line 147: @@
 Teams should perform their own internal testing (both manual and automated) on their respective files throughout development. Commit and push your work to your designated branch at appropriate intervals. Coders who are not familiar with this style of working should consult with fellow guild members or talk to Dr. Dionisio.
-[ ]'''Milestone 5: Integration and Integration Testing'''
+[X]'''Milestone 5: Integration and Integration Testing'''
 Integration and integration testing should take place periodically to make sure that the overall gene page project is coming together well. Most of the Coders’ work for the remainder of the semester will be a cycle of the development and integration milestones. The Interaction and Integration team is in charge of coordinating when these integrations take place. The first integration will likely be the most difficult one to perform, but it is hoped that later iterations will proceed more smoothly.

@@ Line 93: / Line 93: @@
 * For the [[Week 11]] assignment, the Coders (including Designers) of each team will prepare a PowerPoint presentation of their respective assigned software design/development/engineering/best practices reading to be delivered in class on Tuesday, November 14.
-[ ]'''Milestone 1: Working Environment Setup'''
+[X]'''Milestone 1: Working Environment Setup'''
 Coder work will require the following software. The Seaver 120 lab computers are already set up for this; this list is provided for Coders who need to work on a different computer or outside of the lab.
@@ Line 104: / Line 104: @@
 Make sure that this software is installed and operational before beginning. If any Coder needs help with any of these packages, please consult your fellow guild members or ask Dr. Dionisio.
-[ ]'''Milestone 2: Version Control Setup'''
+[X]'''Milestone 2: Version Control Setup'''
 Coding work will be done on a ''fork'' of the open source [https://github.com/dondi/GRNsight GRNsight project], which is hosted on [https://github.com GitHub]. The software that interacts with GitHub to perform version control is '''git'''. If any Coder needs help with '''git''' or version control concepts in general, please consult your fellow guild members or ask Dr. Dionisio.
@@ Line 122: / Line 122: @@
 The structure described in this milestone is a typical GitHub fork-and-branch approach which some Coders are already familiar with. If any Coder needs help with this methodology, please consult your fellow guild members or ask Dr. Dionisio.
-[ ]'''Milestone 3: “Developer Rig” Setup and Initial As-Is Build'''
+[X]'''Milestone 3: “Developer Rig” Setup and Initial As-Is Build'''
 Before development can begin in earnest, the following initial setup steps must be performed ''per Coder'' after version control setup is complete:

@@ Line 86: / Line 86: @@
 The rest of the semester is expected to be an on-going process of verifying and validating the correctness of a QA member’s assigned team. Specific concerns include but are not limited to the following:
 * ''Gene Database APIs and JASPAR teams'': Manual testing will involve some combination of '''curl''' and web browser developer tool use in order to get to know the data returned by the various web services. The Coder members should find ways to show the Quality Assurance members the work-in-progress data returned by <code>getGeneInformation</code>, which QA can then compare to the raw web service API calls for accuracy. After the first integration milestone, QA members can examine the behavior of the prototype gene page at both the end-user and Developer Tools levels (i.e., examining network traffic to make sure the correct requests are going out with the expected responses coming in; inspecting the gene page elements to make sure that they received the correct data).
 =Coders=

@@ Line 26: / Line 26: @@
 =Project Manager=
-=== Milestone 1: Project “Scaffolding” ===
+[ ]'''Milestone 1: Project “Scaffolding”'''
 This milestone pertains to setting up an initial schedule and any resources that your team will use for the duration of the project. It will be useful to get an overview of every team member’s own milestones so that you have an accurate big picture view.
@@ Line 38: / Line 38: @@
 #** Question/answer sequences
-=== Milestone 2: Periodic Updates ===
+[ ]'''Milestone 2: Periodic Updates'''
 Not as much a milestone as an on-going task, once the project is up and running the Project Manager is responsible for keeping track of everyone’s progress.
@@ Line 48: / Line 48: @@
 =Data Analyst=
-=== Milestone 1: Annotated Bibliography ===
+[X]'''Milestone 1: Annotated Bibliography'''
 * For the [[Week 11]] assignment, the Data Analysts will work with the QAs to develop an annotated bibliography of papers that perform the global transcriptional analysis of DNA microarray data in yeast.
-=== Milestone 2: Journal Club Presentation ===
+[X]'''Milestone 2: Journal Club Presentation'''
 * For the [[Week 12]] assignment, the Data Analysts will work with the QAs to prepare a PowerPoint presentation to be delivered in class on Tuesday, November 21.
-=== Milestone 3: Complete Data Analysis of Dahlquist Lab Data for Visualization with GRNsight ===
+[ ]'''Milestone 3: Complete Data Analysis of Dahlquist Lab Data for Visualization with GRNsight'''
 * For [[Week 14]] and [[Week 15]], the Data Analysts will review and complete the microarray data analysis begun with the [[Week 8]] and [[Week 10]] assignments with the eventual goal of visualizing a gene regulatory network derived from their dataset in GRNsight.  Specifically:
@@ Line 68: / Line 68: @@
 =Quality Assurance=
-=== Milestone 1: Annotated Bibliography ===
+[X]'''Milestone 1: Annotated Bibliography'''
 * For the [[Week 11]] assignment, the Data Analysts will work with the QAs to develop an annotated bibliography of papers that perform the global transcriptional analysis of DNA microarray data in yeast.
-=== Milestone 2: Journal Club Presentation ===
+[X]'''Milestone 2: Journal Club Presentation'''
 * For the [[Week 12]] assignment, the Data Analysts will work with the QAs to prepare a PowerPoint presentation to be delivered in class on Tuesday, November 21.
-=== Milestone 3: Requirements Analysis ===
+[ ]'''Milestone 3: Requirements Analysis'''
 As the Coders begin their development work and the Data Analysts start working with their assigned microarray data sets, the QA team members should familiarize themselves with and help specify the expected correct functionalities of their respective teams.
@@ Line 86: / Line 86: @@
 * ''Interaction and integration team'': QA should be familiar with the vision of the project’s overall goal so that when they are presented with progressive builds of the project, they can test the functionality from end to end in order to detect flaws or points of improvement.
-=== Milestone 4: On-going Testing of Respective Team Deliverables ===
+[ ]'''Milestone 4: On-going Testing of Respective Team Deliverables'''
 The rest of the semester is expected to be an on-going process of verifying and validating the correctness of a QA member’s assigned team. Specific concerns include but are not limited to the following:
@@ Line 93: / Line 93: @@
 * For the Interaction and Integration team, prior to the first integration, QA can make sure that the “click-to-open-the-page” functionality works well and is bug-free. After the first integration, QA should work through the whole cycle of opening a gene page and examining the data that appear. QA should open multiple gene pages in the same session to make sure that successive gene page openings do not “step on” each other or leave behind obsolete data that “pollutes” future gene page loads.
-=Coder=
+=Coders=
-=== Milestone 0: Journal Club Presentation ===
+[X]'''Milestone 0: Journal Club Presentation'''
 * For the [[Week 11]] assignment, the Coders (including Designers) of each team will prepare a PowerPoint presentation of their respective assigned software design/development/engineering/best practices reading to be delivered in class on Tuesday, November 14.
-=== Milestone 1: Working Environment Setup ===
+[ ]'''Milestone 1: Working Environment Setup'''
 Coder work will require the following software. The Seaver 120 lab computers are already set up for this; this list is provided for Coders who need to work on a different computer or outside of the lab.
@@ Line 109: / Line 109: @@
 Make sure that this software is installed and operational before beginning. If any Coder needs help with any of these packages, please consult your fellow guild members or ask Dr. Dionisio.
-=== Milestone 2: Version Control Setup ===
+[ ]'''Milestone 2: Version Control Setup'''
 Coding work will be done on a ''fork'' of the open source [https://github.com/dondi/GRNsight GRNsight project], which is hosted on [https://github.com GitHub]. The software that interacts with GitHub to perform version control is '''git'''. If any Coder needs help with '''git''' or version control concepts in general, please consult your fellow guild members or ask Dr. Dionisio.
@@ Line 127: / Line 127: @@
 The structure described in this milestone is a typical GitHub fork-and-branch approach which some Coders are already familiar with. If any Coder needs help with this methodology, please consult your fellow guild members or ask Dr. Dionisio.
-=== Milestone 3: “Developer Rig” Setup and Initial As-Is Build ===
+[ ]'''Milestone 3: “Developer Rig” Setup and Initial As-Is Build'''
 Before development can begin in earnest, the following initial setup steps must be performed ''per Coder'' after version control setup is complete:
@@ Line 143: / Line 143: @@
 If anyone runs into problems with this procedure, please consult with your fellow guild members or notify Dr. Dionisio.
-=== Milestone 4: Development, Implementation, and Localized Testing ===
+[ ]'''Milestone 4: Development, Implementation, and Localized Testing'''
 At this point, each team proceeds with their own development work. In general, each team will do most of their work (and place most of their files) in the following locations within the GRNsight repository. Some files may need to go elsewhere; check in with Dr. Dionisio if there are any file organization/location issues:
@@ Line 161: / Line 161: @@
 Teams should perform their own internal testing (both manual and automated) on their respective files throughout development. Commit and push your work to your designated branch at appropriate intervals. Coders who are not familiar with this style of working should consult with fellow guild members or talk to Dr. Dionisio.
-=== Milestone 5: Integration and Integration Testing ===
+[ ]'''Milestone 5: Integration and Integration Testing'''
 Integration and integration testing should take place periodically to make sure that the overall gene page project is coming together well. Most of the Coders’ work for the remainder of the semester will be a cycle of the development and integration milestones. The Interaction and Integration team is in charge of coordinating when these integrations take place. The first integration will likely be the most difficult one to perform, but it is hoped that later iterations will proceed more smoothly.

← Older revision		Revision as of 23:11, 30 November 2017
Line 1:		Line 1:
	= Gene hAPI Helpful Links =		= Gene hAPI Helpful Links =
		+	Our Deliverables: [[Gene hAPI Deliverables]]
		+
	Main Page: [[Main Page]]		Main Page: [[Main Page]]