View source for Ksherbina Project Notebook

==Week 12==

===Starting the Set Up of the Testing Environment===

#Downloaded the following software onto my personal computer:
#*Latest version of GenMAPP Builder (gmbuilder2.0-b71) from [http://sourceforge.net/projects/xmlpipedb/files/?source=navbar SourceForge]
#*[http://www.oracle.com/technetwork/java/javase/downloads/index.html Java SE 7u45]
#*[http://www.eclipse.org/downloads/ Eclipse IDE for Java EE Developers]
#Created an account on [http://sourceforge.net/ SourceForge].

===Import/Export of Gene Database===

#Downloaded the [http://www.uniprot.org/uniprot/?query=organism:315277+keyword:181 UniProt XML] for ''C. trachomatis'' serovar A strain HAR-13: [[Media:Uniprot XML C.trachomatis serovar A KS 20131114.xml|Uniprot XML C.trachomatis serovar A KS 20131114.xml]]
#Downloaded the [ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/ GOA file] for ''C. trachomatis'' serovar A: [[Media:22183.C trachomatis A KS 20131114.goa|22183.C trachomatis A KS 20131114.goa]]
#Created a new database in pgAdminIII: CT_KS_20131114_gmb2b71
#*Created tables in the database by executing the script in the file ''gmbuilder.sql''.
#Launched ''gmbuilder-32bit.bat'':
#Configured the database in gmbuilder:
#*Host or address: localhost
#*Port number: 5432
#*Database name: CT_KS_20131114_gmb2b71
#*Username: postgres
#*Password: <password of the PostgreSQL database created above>
#Imported the UniProt XML file into the PostgreSQL database through gmbuilder.
#Imported the OBO-XML file into the PostgreSQL database through gmbuilder.
#*gmbuilder was not able to completely process the data. See the testing report below for details.
#Imported the GOA file into into the PostgreSQL database through gmbuilder.
#*I did not begin the actual export of the database due to the problem with processing the OBO-XML file.

====Testing Report====

Version of GenMAPP Builder: 2.0b71

Computer on which export was run: Personal computer

Postgres Database name: CT_KS_20131114_gmb2b71

UniProt XML filename: Uniprot_XML_C.trachomatis_serovar_A_KS_20131114.xml
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_11
* Time taken to import: 1.70 min

GO OBO-XML filename: Go_daily-termdb_v2_HD_20131107.obo-xml
* GO OBO-XML version (The version information can be found in the file properties after the file downloaded from the [http://beta.geneontology.org/page/download-ontology GO Download page] has been unzipped):
* Time taken to import: 9.29 min
* Time taken to process: '''Could no complete the process. The following error came up when gmbuilder was processing the 81000 term:'''
 ERROR edu.lmu.xmlpipedb.gmbuilder.GenMAPPBuilder  - java.util.concurrent.ExecutionException:java.lang.OutOfMemoryError:
 Java heap space

GOA filename: 22183.C_trachomatis_A_KS_20131114.goa
* GOA version (News on [http://www.ebi.ac.uk/GOA/ this page] records past releases; current information can be found in the Last modified field on the [ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/ FTP site]):
* Time taken to import: 0.02 min

Name of .gdb file:
* Time taken to export .gdb:
* Upload your file and link to it here.

Note:

===Creating Custom Species Profile===

#On one of the class computers in the first row, I launched Eclipse with Subclipse.
#Went to Window > Open Perspective > Other > SVN Repository Exploring.
#Defined a new subversion by clicking on ''Add Repository'' and adding the URL https://svn.code.sf.net/p/xmlpipedb/code. Clicked Finish.
#Double-clicked on trunk, right-clicked on gmbuilder, and chose Checkout....
#Created a new project (chose Check out as a project configured using the New Project Wizard).
#Went to Window > Preferences > Java > Installed JREs. Added a new environment with JDK.
#Double-clicked on the project folder.
#Double-clicked on the lib folder.
#Shift-clicked and selected all files in the lib folder and then control-clicked on every file inside the lib folder whose name does not end in .jar. Right-click on one of them and choose Build Path > Add to Build Path from the popup menu that comes up.
#Created a species profile called ChlamydiaTrachomatisSerovarA.
#*Dondi modified the name to ChlamydiaTrachomatisSerovarAUniProtSpeciesProfile.
#Customized the species profile.
#*Opened the new profile and added the lines of code as specified in [[Coder|"Customize the Species Profile"]] directions.
#**Still need to insert the species-specific URL that returns a web page describing a gene for that species.
#Committed the profile following the directions in [[Coder|"Updating and Committing Code"]].

===Reflection===

#What were the week’s key accomplishments?
#*One of this week's key accomplishments was downloading the files necessary to run a import/export gene database cycle and the microarray files that will be analyzed. Also this week, we were able to start an import/export cycle.
#What are next week’s target accomplishments?
#*Next week, I would like to complete an import/export cycle and vet it with the QA person. In addition, I hope that we can download the software necessary to open the microarray files, format the files, and perform statistical analysis.
#What team strengths were seen this week?
#*I believe our strength this week as a team was meeting outside of class to create milestones. This meeting results in a detailed calendar of intermediate milestones that we plan to meet accomplish in order to meet the file deadline.
#What team weaknesses were seen this week?
#*It was difficult to set up the aforementioned meeting due to our busy schedules. Additionally, we did not have a clear plan for working on the project until the middle/end of the week. In the coming weeks, our goal will be to improve our work plan for each class period so as to minimize the difficulty of scheduling work meetings outside of class.