Difference between revisions of "Bklein7 Week 12"

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==Files Asked for in the Gene Database Testing Report==
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==Genome Sequencing Paper PowerPoint Presentation==
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For convenience, all of the files explicitly asked for in the "Gene Database Testing Report" section were compressed together in this file: [[File:Bklein7 Week9 Files.zip]].
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Presentation File (PDF): [[File:Genomepaper cw20151116.pdf]]
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==Quality Assurance Work==
 +
I created and tested our first ''Bordetella pertussis'' gene database, tagged '''cw20151119'''.
 +
*Gene Database v1: [[File:Bpertussis-std cw20151119.zip]]
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*[[Gene Database Testing Report- cw20151119]] (I authored sections 1-4.6. Lena authored sections 4.7 & 4.8)
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Work Log:
 +
*Thursday, November 19: I followed the import-export process for the creation of our first ''Bordetella pertussis'' gene database. My protocol was documented on the Gene Database Testing Report page for this database.
 +
*Monday, November 23: I accessed the exported database and went through counting protocols to evaluate its content. Results were posted on the Gene Database Testing Report page for this database.
  
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==Pre-requisites==
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==Coder Work==
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The following set of software was used in the creation and testing of the ''Vibrio cholerae'' gene database:
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Before proceeding, I designated my personal laptop as my development computer.
 +
=== GitHub Repository Clone Setup ===
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GitHub Information:
 +
*My GitHub account: [https://github.com/bklein7 bklein7]
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*Projects in which I am listed as a developer: [https://github.com/lmu-bioinformatics/xmlpipedb LMU Bioinformatics XMLPipeDB Project]
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**My Team: [https://github.com/orgs/lmu-bioinformatics/teams/the-class-whoopers The Class Whoopers]
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**My Branch: [https://github.com/lmu-bioinformatics/xmlpipedb/tree/b-pertussis b-pertussis]
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GitHub Clone Setup:
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#I designated a folder on my Desktop entitled "B. pertussis Project" as the location for my local copy of the [https://github.com/lmu-bioinformatics/xmlpipedb XMLPipeDB GitHub repository]. To enter this location, I opened Terminal and used the following command: <pre>cd /Users/brandonklein/Desktop/B.\ pertussis\ Project</pre>
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#I cloned the repository:<pre>git clone https://github.com/lmu-bioinformatics/xmlpipedb.git</pre>
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#I entered the clone folder: <pre>cd xmlpipedb</pre>
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#I switched to my branch:<pre>git checkout b-pertussis</pre>
  
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# [http://www.7-zip.org/ 7-zip]tool that for unpacking .gz and .zip files
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=== “Developer Rig” Setup and Initial As-Is Build ===
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# [http://www.postgresql.org PostgreSQL] on Windows (version 9.4.x)
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Necessary software was downloaded:
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# [https://sourceforge.net/projects/xmlpipedb/files/ GenMAPP Builder]
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* Java developer tools: [http://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html JDK 8] (which, at this writing, is ''JDK 8u65'')
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# Java JDK 1.8 64-bit
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* Any tool that can unpack .gz and .zip files: [http://www.kekaosx.com/en/ Keka] (listed as an equivalent software to [http://www.7-zip.org/ 7-zip] for Mac OS X)
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# [https://github.com/GenMAPPCS/genmapp GenMAPP 2]
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* ''XMLPipeDB Match'' utility
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# [https://sourceforge.net/projects/xmlpipedb/files/ XMLPipeDB match utility] for counting IDs in XML files
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* Development environment: [http://www.eclipse.org Eclipse IDE for Java EE Developers]
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# Microsoft Access for reading .mdb files
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==== Eclipse Workspace Setup ====
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# I ran Eclipse.
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# When prompted to specify a Workspace, I selected my "xmlpipedb" repository clone folder and clicked "Open".
 +
# I verified that my repository clone folder was listed as the ''Workspace:'' and clicked ''OK''.
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# When presented with the introductory display, I clicked the ''Workbench'' button.
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#* This took me to an empty developer area:
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#* [[File:Screen Shot 2015-11-23 at 5.10.28 PM.png]]
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==== Java Project Setup ====
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# I right-clicked within the empty ''Project Explorer'' tab and chose '''New > Project…''' from the menu that appeared.
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# I chose ''Java Project'' from the list of “wizards” and clicked on the ''Next >'' button.
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# On the next panel, I entered <code>gmbuilder</code> as the ''Project name:''.
 +
#* The ''JRE'' section showed Java 1.8, confirming that my version of Java was up to date.
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# I click on the ''Finish'' button.
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#* When asked if I wanted to open the “Java perspective,” I responded with ''Yes''.
 +
# The ''gmbuilder'' project folder was now visible in the ''Project Explorer'' tab.
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#* The ''gmbuilder'' project folder did not show a red ''x'' icon.
  
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==Gene Database Creation==
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=== Initial Build ===
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===Downloading Data Source Files and GenMAPP Builder===
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# I opened the ''gmbuilder'' project by clicking on the gray triangle to the left of its name.
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# I right-clicked on ''build.xml'' listing and chose '''Run As > Ant Build...''' from the menu that appears.
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*I download the UniProt XML, GOA, and GO OBO-XML files for ''Vibrio cholerae'' along with the GenMAPP Builder program.
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# In the ''Edit Configuration'' dialog that appears, I entered the "Targets" tab. There, I checked on the ''clean'' and ''dist'' items in the ''Targets'' tab. The ''Target execution order'' section near the bottom of the dialog displayed ''clean, dist''.
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**All files were saved to the folder ''Bklein7_Week9'' on my computer's ThawSpace.
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# I clicked the ''Run'' button. After 3 seconds of processing, the build was successful.
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**Files that required extraction were unzipped using [http://www.7-zip.org/ 7-zip].
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# When this was done, I right-clicked on the ''gmbuilder'' project folder and chose '''Refresh''' from the menu that appears.
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**Data files that remained in a folder after unzipping were removed from their folders to facilitate organization and command line processing.
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# A ''dist'' folder was now present inside the ''gmbuilder'' project folder. This was my personally-built copy of ''GenMAPP Builder''. Its contents correspond to the extracted contents of the ''gmbuilder-3.0.0-build-5.zip'' file that was downloaded in class.
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#*Screenshot of my copy of gmbuilder within the Eclipse working environment:
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====UniProt XML====
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#*[[File:Eclipse gmbuilder Ant Build.png]]
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* I went to the [http://www.uniprot.org/taxonomy/complete-proteomes UniProt Complete Proteomes] page.
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**From there, I navigated to the complete proteome download page for [http://www.uniprot.org/uniprot/?query=organism:243277 Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)].
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** I clicked on the "Download" button at the top of the page above and selected the following options:
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***"Download all"
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***"XML" from the "Format" drop-down menu
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***"Compressed" format
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**I extracted the file using [http://www.7-zip.org/ 7-zip].
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====GOA====
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* UniProt-GOA files can be downloaded from the [http://ftp.ebi.ac.uk/pub/databases/GO/goa/ UniProt-GOA ftp site].
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*Within the above site, I navigated to the [http://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/46.V_cholerae_ATCC_39315.goa GO annotations for ''Vibrio cholerae''].
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**This text file was automatically opened by my browser. Therefore, I had to manually download the file.
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====GO OBO-XML====
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* I downloaded the GO OBO-XML formatted file from the [http://geneontology.org/page/download-ontology#Legacy_Downloads Gene Ontology legacy download page].
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*I extracted the file using [http://www.7-zip.org/ 7-zip].
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====Downloaded GenMAPP Builder====
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# I downloaded the GenMAPP Builder zip folder: [https://github.com/lmu-bioinformatics/xmlpipedb/releases/download/untagged-bd04fffc4da853fedf30/gmbuilder-3.0.0-build-5.zip Download gmbuilder-3.0.0-build-5.zip].
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# I extracted the GenMAPP Builder folder using [http://www.7-zip.org/ 7-zip].
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===Creating the New Database in PostgreSQL===
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* I launched ''pgAdmin III'' and connected to the PostgreSQL 9.4 server (localhost:5432).
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** On this server, I created a new database: ''V.cholerae_20151027_gmb3build5''.
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** I opened the SQL Editor tab to use an XMLPipeDB query to create the tables in the database.
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*** I clicked on the Open File icon and selected the file ''gmbuilder.sql''. This imported a series of SQL commands into the editor tab.
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*** I clicked on the Execute Query icon to run this command.
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***In viewing the schema for this database, I confirmed that there were 167 tables after running the above command.
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===Configuring GenMAPP Builder to Connect to the PostgreSQL Database===
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* To begin, I launched gmbuilder.bat.
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* I selected the "Configure Database" option and entered the following information into the fields below:
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** Host or address: localhost
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** Port number: 5432
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** Database name: V.cholerae_20151027_gmb3build5
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** Username: postgres
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** Password: Welcome1
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===Importing Data into the PostgreSQL Database===
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*The downloaded data files for ''Vibrio cholerea'' were specified and imported into the database by clicking on the following buttons:
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** Selected File > Import UniProt XML...
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** Selected File > Import GO OBO-XML...
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** Clicked OK to the message asking to process the GO data.
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** Selected File > Import GOA...
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===Exporting a GenMAPP Gene Database (.gdb)===
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* I selected File > Export to GenMAPP Gene Database... to begin the export process.
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* I typed my name in the owner field (Brandon Klein).
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* I selected''Vibrio cholerae'' as the gene database species and then clicked ''Next''.
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* The database was saved as ''Vc-Std_BK_20151027''.
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* I checked the boxes for exporting all Molecular Function, Cellular Component, and Biological Process Gene Ontology Terms.
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* Finally, I clicked the "Next" button to begin the export process.
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==Gene Database Testing Report==
+
  
 
==Links==
 
==Links==

Latest revision as of 08:02, 24 November 2015

Genome Sequencing Paper PowerPoint Presentation

Presentation File (PDF): File:Genomepaper cw20151116.pdf

Quality Assurance Work

I created and tested our first Bordetella pertussis gene database, tagged cw20151119.

Work Log:

  • Thursday, November 19: I followed the import-export process for the creation of our first Bordetella pertussis gene database. My protocol was documented on the Gene Database Testing Report page for this database.
  • Monday, November 23: I accessed the exported database and went through counting protocols to evaluate its content. Results were posted on the Gene Database Testing Report page for this database.

Coder Work

Before proceeding, I designated my personal laptop as my development computer.

GitHub Repository Clone Setup

GitHub Information:

GitHub Clone Setup:

  1. I designated a folder on my Desktop entitled "B. pertussis Project" as the location for my local copy of the XMLPipeDB GitHub repository. To enter this location, I opened Terminal and used the following command: 
    cd /Users/brandonklein/Desktop/B.\ pertussis\ Project
  2. I cloned the repository:
    git clone https://github.com/lmu-bioinformatics/xmlpipedb.git
  3. I entered the clone folder: 
    cd xmlpipedb
  4. I switched to my branch:
    git checkout b-pertussis

“Developer Rig” Setup and Initial As-Is Build

Necessary software was downloaded:

  • Java developer tools: JDK 8 (which, at this writing, is JDK 8u65)
  • Any tool that can unpack .gz and .zip files: Keka (listed as an equivalent software to 7-zip for Mac OS X)
  • XMLPipeDB Match utility
  • Development environment: Eclipse IDE for Java EE Developers

Eclipse Workspace Setup

  1. I ran Eclipse.
  2. When prompted to specify a Workspace, I selected my "xmlpipedb" repository clone folder and clicked "Open".
  3. I verified that my repository clone folder was listed as the Workspace: and clicked OK.
  4. When presented with the introductory display, I clicked the Workbench button.
    • This took me to an empty developer area:
    • Screen Shot 2015-11-23 at 5.10.28 PM.png

Java Project Setup

  1. I right-clicked within the empty Project Explorer tab and chose New > Project… from the menu that appeared.
  2. I 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:.
    • The JRE section showed Java 1.8, confirming that my version of Java was up to date.
  4. I click on the Finish button.
    • When asked if I wanted to open the “Java perspective,” I responded with Yes.
  5. The gmbuilder project folder was now visible in the Project Explorer tab.
    • The gmbuilder project folder did not show a red x icon.

Initial Build

  1. I opened the gmbuilder project by clicking on the gray triangle to the left of its name.
  2. I right-clicked on build.xml listing and chose Run As > Ant Build... from the menu that appears.
  3. In the Edit Configuration dialog that appears, I entered the "Targets" tab. There, I checked on the clean and dist items in the Targets tab. The Target execution order section near the bottom of the dialog displayed clean, dist.
  4. I clicked the Run button. After 3 seconds of processing, the build was successful.
  5. When this was done, I right-clicked on the gmbuilder project folder and chose Refresh from the menu that appears.
  6. A dist folder was now present inside the gmbuilder project folder. This was my personally-built copy of GenMAPP Builder. Its contents correspond to the extracted contents of the gmbuilder-3.0.0-build-5.zip file that was downloaded in class.
    • Screenshot of my copy of gmbuilder within the Eclipse working environment:
    • Eclipse gmbuilder Ant Build.png

Links

Assignments Pages

Individual Journal Entries

Shared Journal Entries

Retrieved from "https://xmlpipedb.lmucs.io/biodb/fall2015/index.php?title=Bklein7_Week_12&oldid=6941"