Anuvarsh Week 12

Electronic Lab Notebook

Goals

• Start an export in class
• Complete milestone 1: Version Control Setup
• Complete milestone 2: “Developer Rig” Setup and Initial As-Is Build

GenMAPP Builder Project Setup and Initial Build

• Began on Thursday, November 19, 2015
• During the guild huddle with Dr. Dionisio, I was added to the lmu-bioinfomatics/xmlpipedb repository and created a branch called b-cenocepacia according to the species that my team is working on.
• After the guild meeting, I proceeded to the GenMAPP Builder Project Setup and Initial Build heading and completed the following:

GitHub Repository Clone Setup

1. cd to the desktop of my development computer (my laptop - MacBook Pro).
2. Cloned the repository:

   git clone https://github.com/lmu-bioinformatics/xmlpipedb.git

3. cd into the clone folder xmlpipedb:

   cd xmlpipedb

4. Switched to my branch:

   git checkout b-cenocepacia

5. I saw the following message:

   Branch b-cenocepacia set up to track remote branch b-cenocepacia from origin. Switched to a new branch 'b-cenocepacia'

Eclipse Workspace Setup

1. Ran Eclipse.
2. Selected Desktop/xmlpipedb when Eclipse asked me to select a workspace using Browse... and then clicked on Open followed by OK.
3. An introductory displace window appeared, and I clicked on the Workbench button (upper-right corner, with a 3D arrow for an icon).
4. My repository clone folder opened in the window with a tab titled Project Explorer on the left of the window.

Java Project Setup

1. Right-clicked within the Project Explorer tab and chose New > Project… from the menu that appears.
2. Chose Java Project from the list of “wizards” and clicked on the Next > button.
3. On the next panel, I entered gmbuilder as the Project name:.
4. Clicked on the Finish button.
5. Clicked Yes when Eclipse asked whether I want to open the "Java perspective."
6. You should now see a gmbuilder project folder in the Project Explorer tab.

Initial Build

1. Opened the gmbuilder project by clicking on the gray triangle to the left of its name.
2. Right-clicked on build.xml and choose Run As > Ant Build... (the one with the ellipses) from the menu that appears.
3. In the Edit Configuration dialog that appeared, I unchecked dist.
4. Checked on the clean and dist items in the Targets tab. The Target execution order section near the bottom of the dialog said clean, dist.
5. Clicked the Run button.
6. When it finished, I right-clicked on the gmbuilder project folder and chose Refresh from the menu that appeared).
7. A dist folder appeared inside the gmbuilder project folder. This folder is my personally-built copy of GenMAPP Builder.
   • Result when build finished:
   • 

Adding a Species Profile to GenMAPP Builder

• Began on Monday, November 23, 2015.

Create the Species Profile

1. Exposed the contents of the src folder.
2. Right-clicked on the edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles package and chose New > Class from the popup menu.
3. In the dialog that appeared, I entered the following:
   • Name: bCenocepaciaUniProtSpeciesProfile
   • Superclass: edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles.UniProtSpeciesProfile
4. Clicked Finish. The new .java file I created appeared within the edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles package.
   • Eclipse window after clicking "Finish":
   • 

Customize the Species Profile

• Opened the file that I just created. It appeared in the editor area of Eclipse.
• Added the following code:
• 
• At this point, I was unsure about the species link that I needed to add, so I commented a second option. Before proceeding, I will need to talk to Brandon or Dr. Dionisio.

Update on Nov. 24, 2015

• Dr. Dionisio and I played around with the links and determined that the feature_id URL and the locusID URL lead to the same page, so we will use the locusID URL because it uses the gene name in the url while the other uses a key.

Other Links

User Page: Anindita Varshneya
Class Page: BIOL/CMSI 367: Biological Databases, Fall 2015
Group Page: GÉNialOMICS

Assignment Pages

Week 1 Assignment
Week 2 Assignment
Week 3 Assignment
Week 4 Assignment
Week 5 Assignment
Week 6 Assignment
Week 7 Assignment
Week 8 Assignment
Week 9 Assignment
Week 10 Assignment
Week 11 Assignment
Week 12 Assignment
No Week 13 Assignment
Week 14 Assignment
Week 15 Assignment

Individual Journals

Individual Journal Week 2
Individual Journal Week 3
Individual Journal Week 4
Individual Journal Week 5
Individual Journal Week 6
Individual Journal Week 7
Individual Journal Week 8
Individual Journal Week 9
Individual Journal Week 10
Individual Journal Week 11
Individual Journal Week 12
Individual Journal Week 14
Individual Journal Week 15

Shared Journals

Class Journal Week 1
Class Journal Week 2
Class Journal Week 3
Class Journal Week 4
Class Journal Week 5
Class Journal Week 6
Class Journal Week 7
Class Journal Week 8
Class Journal Week 9
GÉNialOMICS Journal Week 10
GÉNialOMICS Journal Week 11
GÉNialOMICS Journal Week 12
GÉNialOMICS Journal Week 14
GÉNialOMICS Journal Week 15

GÉNialOMICS Links

Weekly Group Assignments	Shared Group Journals	Project Links	Team Members
Week 10 Week 11 Week 12 Week 14 Week 15	GÉNialOMICS Week 10 GÉNialOMICS Week 11 GÉNialOMICS Week 12 GÉNialOMICS Week 14 GÉNialOMICS Week 15	GENialOMICS Home Page GENialOMICS Deliverables Gene Database Project Overview Instructions for Project Deliverables Project Manager Guild Page GenMAPP User Guild Page Quality Assurance Guild Page Coder Guild Page	Project Manager/Coder: Anu Varshneya Quality Assurance: Brandon Litvak GenMAPP User: Veronica Pacheco GenMAPP User: Kevin Wyllie