Difference between revisions of "Team H(oo)KD Week 12 Status Report"
From LMU BioDB 2013
(→Coder Status Update: Added some details regarding creating the custom species profile) |
(→GenMAPP User Status Update: Editted signature to be consistent with (general) time status report was actually submitted) |
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*Began the gene database import export cycle: | *Began the gene database import export cycle: | ||
:*Downloaded the UniProt XML file for ''Chlamydia trachomatis'' serovar A strain HAR-13. | :*Downloaded the UniProt XML file for ''Chlamydia trachomatis'' serovar A strain HAR-13. | ||
| − | :*Downloaded the GOA file for ''Chlamydia trachomatis | + | :*Downloaded the GOA file for ''Chlamydia trachomatis'' serovar A. |
:*Created a PostgreSQl database for the species. | :*Created a PostgreSQl database for the species. | ||
:*I was able to import both the UniProt XML file and the GOA file for the ''C. trachomatis'' into the PostgreSQL database through gmbuilder-32bit.bat. While I was also able to import the OBO-XML file, I could not finish processing the data. After gmbuilder processed the 81000 term, I received the following error after which gmbuilder ceased the processing of the OBO-XML file: | :*I was able to import both the UniProt XML file and the GOA file for the ''C. trachomatis'' into the PostgreSQL database through gmbuilder-32bit.bat. While I was also able to import the OBO-XML file, I could not finish processing the data. After gmbuilder processed the 81000 term, I received the following error after which gmbuilder ceased the processing of the OBO-XML file: | ||
ERROR edu.lmu.xmlpipedb.gmbuilder.GenMAPPBuilder - java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError: | ERROR edu.lmu.xmlpipedb.gmbuilder.GenMAPPBuilder - java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError: | ||
Java heap space | Java heap space | ||
| − | :* | + | :*Per Dondi's advice, tomorrow (November 15) I will try to increase the java heap space and rerun the import/export cycle. |
*Created a custom species profile and committed it to SourceForge. However, this profile still needs work. I will need to work with the QA analyst to add to the profile a species-specific URL that returns a web page describing a gene for the species. | *Created a custom species profile and committed it to SourceForge. However, this profile still needs work. I will need to work with the QA analyst to add to the profile a species-specific URL that returns a web page describing a gene for the species. | ||
| Line 24: | Line 24: | ||
==GenMAPP User Status Update== | ==GenMAPP User Status Update== | ||
| + | #Found and acquired the microarray paper the team. | ||
| + | #*Provided all necessary links. | ||
| + | #Downloaded microarray data in the rawest possible form. | ||
| + | #Working on verifying the gene IDs in the microarray data match the chosen species and strain that is being used to create the .gdb. | ||
| + | #*This will be done in conjunction with the Quality Assurance person and Coder. | ||
| + | #Created categories for file management on team page. | ||
| + | #*Linked to the source of the microarray data | ||
| + | #*Uploaded the microarray data files to the wiki | ||
| − | + | -[[User:Dwilliams|Dwilliams]] ([[User talk:Dwilliams|talk]]) 21:28, 14 November 2013 (PST) | |
| − | + | ||
[[Category:Journal Entry]] | [[Category:Journal Entry]] | ||
| + | [[Category:Team H(oo)KD]] | ||
Latest revision as of 05:29, 22 November 2013
| Project Manager/Coder: Katrina Sherbina | Quality Assurance: Hilda Delgadillo | GenMAPP User: Dillon Williams |
| Project Guidelines: | Gene Database Project | Report Guidelines | |
| Team Journal Assignments | Week 12 Status Report | Week 13 Status Report | Week 15 Status Report |
| Individual Status Reports: | HDelgadi Project Notebook | dwilliams Project Notebook | Ksherbina Project Notebook |
| Useful Links: | Class Page | Team Home Page |
| Final Product | Project Deliverables |
Refer to the calendar on the team home page to see the milestones for this week.
[edit] Coder Status Update
- Began the gene database import export cycle:
- Downloaded the UniProt XML file for Chlamydia trachomatis serovar A strain HAR-13.
- Downloaded the GOA file for Chlamydia trachomatis serovar A.
- Created a PostgreSQl database for the species.
- I was able to import both the UniProt XML file and the GOA file for the C. trachomatis into the PostgreSQL database through gmbuilder-32bit.bat. While I was also able to import the OBO-XML file, I could not finish processing the data. After gmbuilder processed the 81000 term, I received the following error after which gmbuilder ceased the processing of the OBO-XML file:
ERROR edu.lmu.xmlpipedb.gmbuilder.GenMAPPBuilder - java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError: Java heap space
- Per Dondi's advice, tomorrow (November 15) I will try to increase the java heap space and rerun the import/export cycle.
- Created a custom species profile and committed it to SourceForge. However, this profile still needs work. I will need to work with the QA analyst to add to the profile a species-specific URL that returns a web page describing a gene for the species.
Ksherbina (talk) 23:04, 14 November 2013 (PST)
[edit] QA Status Update
- Obtaining the files GOA file, UniProt XML file, and the GO OBO-XML file were essential to obtain this week. With these files we will begin the importing and exporting of the files Friday November 15th, so we may continue with the exporting of files into the GenMAPP Gene Database next week.
HDelgadi (talk) 10:46, 14 November 2013 (PST)
[edit] GenMAPP User Status Update
- Found and acquired the microarray paper the team.
- Provided all necessary links.
- Downloaded microarray data in the rawest possible form.
- Working on verifying the gene IDs in the microarray data match the chosen species and strain that is being used to create the .gdb.
- This will be done in conjunction with the Quality Assurance person and Coder.
- Created categories for file management on team page.
- Linked to the source of the microarray data
- Uploaded the microarray data files to the wiki
