LMU BioDB 2013 - User contributions [en]

Team Name Deliverables

2013-12-14T00:38:36Z

Mpetredi: added final report

=Group=
:GenMAPP Gene Database:[[Media:Sinorhizobium_meliloti_1021_mpetredi_2013123-2.gdb]]
:ReadMe file: [[Media:ReadMe-SM.pdf|ReadME_S.meliloti]]
:Gene Database Schema diagram: [[Media:S.Meliloti_schema_20131205.pdf|S.meliloti_schema_20131205.pdf]]
:Gene Database Testing Report: [[Media:Match Test Sheet1.pdf]]
:Processed and analyzed DNA microarray dataset:
* .3 M: [[Media:Complete_processed_Data_MPM.xls|300mm NaCl XLS Version]]
* .7 M: [[Media:SinorhizobiumMeliloti_LM_GenMapp_FinalFile.txt]]
:GenMAPP Expression Dataset file: [[Media:SinorhizobiumMeliloti_LM_GenMapp_FinalFile.gex]]

[[Media:T30.gex|Gene expression set for 300mm NaCl]]

:Filtered MAPPFinder Results: .7 M files:
*[[Media:700s1-3-t15-Decreased-Criterion-GO.xls]]
*[[Media:700s1-3-t15-Increased-Criterion-GO.xls]]

*[[Media:MAPPFinder_results_T15-Criterion_Increased-GO.txt|Increased expression at T15 300mm NaCl]]

*[[Media:MAPPFinder_results_T15-Criterion_Decreased-GO.txt|Decreased expression at T15 300mm NaCl]]

*[[Media:T30_increased-Criterion0-GO.txt|Increased expression at t30 300mm NaCl]]

*[[Media:T30_MAPP_results-Criterion_Decreased-GO.txt|Decreased expression at t30 300mm NaCl]]

*[[Media:MAPPFinder_t60-Criterion_Increased-GO.txt|Increased expression at t60 300mm NaCl]]

*[[Media:MAPPFinder_t60-Criterion_Decreasaed-GO.txt|Decreased expression at t60 300mm NaCl]]
*[[Media:300N_T240_MAPPFINDER-Criterion_Increased-GO.txt|Increased expression t240 300mmNaCl]]
*[[Media:300N_T240_MAPPFINDER-Criterion_Decreased-GO.txt|decreased expression at t240 300mmNaCl]]

:Sample MAPP file of a relevant biological pathway for your species:

[[Media:regulation of transcription, DNA-dependent.mapp]]

[[Media:Structural_constituent_of_Ribosome.mapp| Structural constituents of ribosome 300mm NaCl]]

:Group Report: [[Media: BiologicalDatabasesFinalReport.pdf | S. meliloti Final Report]]
:PowerPoint presentation: [[Media:Sinorhizobium_Meliloti_(Strain_1021)_FINAL_PRESENTATION.pdf | Sinorhizobium meliloti (Strain_1021) FINAL_PRESENTATION (PDF)]]
*Note: Wiki page is not accepting our converted .ppt format. The PDF version should suffice.

=Individual=

*[[Miles Malefyt deliverables]]
*[[https://xmlpipedb.cs.lmu.edu/biodb/fall2013/index.php/Individual_Assessment_and_Reflection Mitchell Petredis deliverables]]
*[[Stephen Louie Deliverables]]

File:BiologicalDatabasesFinalReport.pdf

2013-12-14T00:35:00Z

Mpetredi: S. meliloti final report

S. meliloti final report

Individual Assessment and Reflection

2013-12-14T00:16:13Z

Mpetredi: added link to prompt

{{User Page Link}}

Reference page for this assignment: [[Gene Database Project Report Guidelines]]

==Statement of Work==

*As coder of [[[[Team Name]]]], I was responsible for creating and tweaking versions of gmbuilder under the provision of Dr. Dionisio to help create a proper analysis tool for our species ''Sinorhizobium Meliloti'' (Strain 1021). Additionally, I imported the unique UniProt XML, GO OBO-XML, and GOA files into the PostgreSQL database for our species using my custom versions of gmbuilder and exported the .gdb files necessary for the quality assurance and GenMAPP users to do their respective roles.
*In total, 3 versions of gmbuilder were created and produced the following .gdb files (in order of oldest to newest):
**[[Media: gmbuilder-2.0b71.zip | gmbuilder-2.0b71.zip]]
***[[Media:Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_2013117.gdb | Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_2013117.gdb]]
**[[Media:GenMAPP_Builder_2.0b72 S. meliloti.zip|GenMAPP_Builder_2.0b72 S. meliloti.zip]]
***[[Media:Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_20131121.gdb|Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_20131121.gdb]]
**[[Media: SmelilotiGenMAPP_Builder_2.0b73.zip]]
***[[Media:Sinorhizobium_meliloti_1021_mpetredi_2013123-2.gdb]]

*My lab progression is listed below:
*[[mpetredi Week 12]]
*[[mpetredi Week 13]]
*[[mpetredi Week 14]]

NOTE: "Important Files 3" does not have a .gdb file because of accidentally importing duplicate data into PostgreSQL; I decided it would be a hindrance to use that .gdb file for analysis and therefore discarded it. A new database and .gdb file were created under "Important Files 4" to resolve this issue.

==Assessment of Project==

*Our project was somewhat successful, but it is still a work in progress. I believe my team displayed dedication to the quality of the project, and while we were not able to create an error-free database this semester, our work-ethic significantly contributed to the further completion of the gene database. If my team's schedule outside of this class weren't as complex, I believe we could have delivered a finished product.
*If I could do it all over again, I'd start the project earlier. Additionally, having a laptop with all the lab software would have made it more convenient to organize the project and work on it away from the lab.
*Gene Database Project and Group Report Evaluation
*#Content: We described our methods with as much detail as we could and provided explanations for our results and discussion.
*#Organization: We followed the prompt given to us, and reading the report over again it seems like it's structured well.
*#Completeness: Considering the challenges we had with this project, I'd say our report feels as complete as it can be.

==Reflection on the Process==

*I learned the following
**With my head: Biology and Computer Science can drastically benefit from each other. As technology improves, scientists can discover new things that previously could not be comprehended or understood.
**With my heart: Close communication and flexibility in scheduling with team members is critical to achieving project goals.
**With your hands: I gained a better understanding of how database management and organization works, and even learned some coding.
*A year from now, I'll remember the various SQL queries and how to utilize filtering mechanisms in large datasets.

Individual Assessment and Reflection

2013-12-14T00:11:41Z

Mpetredi: /* Assessment of Project */ added assessment of project

{{User Page Link}}

==Statement of Work==

*As coder of [[[[Team Name]]]], I was responsible for creating and tweaking versions of gmbuilder under the provision of Dr. Dionisio to help create a proper analysis tool for our species ''Sinorhizobium Meliloti'' (Strain 1021). Additionally, I imported the unique UniProt XML, GO OBO-XML, and GOA files into the PostgreSQL database for our species using my custom versions of gmbuilder and exported the .gdb files necessary for the quality assurance and GenMAPP users to do their respective roles.
*In total, 3 versions of gmbuilder were created and produced the following .gdb files (in order of oldest to newest):
**[[Media: gmbuilder-2.0b71.zip | gmbuilder-2.0b71.zip]]
***[[Media:Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_2013117.gdb | Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_2013117.gdb]]
**[[Media:GenMAPP_Builder_2.0b72 S. meliloti.zip|GenMAPP_Builder_2.0b72 S. meliloti.zip]]
***[[Media:Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_20131121.gdb|Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_20131121.gdb]]
**[[Media: SmelilotiGenMAPP_Builder_2.0b73.zip]]
***[[Media:Sinorhizobium_meliloti_1021_mpetredi_2013123-2.gdb]]

*My lab progression is listed below:
*[[mpetredi Week 12]]
*[[mpetredi Week 13]]
*[[mpetredi Week 14]]

NOTE: "Important Files 3" does not have a .gdb file because of accidentally importing duplicate data into PostgreSQL; I decided it would be a hindrance to use that .gdb file for analysis and therefore discarded it. A new database and .gdb file were created under "Important Files 4" to resolve this issue.

==Assessment of Project==

*Our project was somewhat successful, but it is still a work in progress. I believe my team displayed dedication to the quality of the project, and while we were not able to create an error-free database this semester, our work-ethic significantly contributed to the further completion of the gene database. If my team's schedule outside of this class weren't as complex, I believe we could have delivered a finished product.
*If I could do it all over again, I'd start the project earlier. Additionally, having a laptop with all the lab software would have made it more convenient to organize the project and work on it away from the lab.
*Gene Database Project and Group Report Evaluation
*#Content: We described our methods with as much detail as we could and provided explanations for our results and discussion.
*#Organization: We followed the prompt given to us, and reading the report over again it seems like it's structured well.
*#Completeness: Considering the challenges we had with this project, I'd say our report feels as complete as it can be.

==Reflection on the Process==

*I learned the following
**With my head: Biology and Computer Science can drastically benefit from each other. As technology improves, scientists can discover new things that previously could not be comprehended or understood.
**With my heart: Close communication and flexibility in scheduling with team members is critical to achieving project goals.
**With your hands: I gained a better understanding of how database management and organization works, and even learned some coding.
*A year from now, I'll remember the various SQL queries and how to utilize filtering mechanisms in large datasets.

Team Name Deliverables

2013-12-13T23:31:13Z

Mpetredi: added note about PowerPoint Presentation

=Group=
:GenMAPP Gene Database:[[Media:Sinorhizobium_meliloti_1021_mpetredi_2013123-2.gdb]]
:ReadMe file: [[Media:ReadMe-SM.pdf|ReadME_S.meliloti]]
:Gene Database Schema diagram: [[Media:S.Meliloti_schema_20131205.pdf|S.meliloti_schema_20131205.pdf]]
:Gene Database Testing Report: [[Media:Match Test Sheet1.pdf]]
:Processed and analyzed DNA microarray dataset:
* .3 M: [[Media:Complete_processed_Data_MPM.xls|300mm NaCl XLS Version]]
* .7 M: [[Media:SinorhizobiumMeliloti_LM_GenMapp_FinalFile.txt]]
:GenMAPP Expression Dataset file: [[Media:SinorhizobiumMeliloti_LM_GenMapp_FinalFile.gex]]

[[Media:T30.gex|Gene expression set for 300mm NaCl]]

:Filtered MAPPFinder Results: .7 M files:
*[[Media:700s1-3-t15-Decreased-Criterion-GO.xls]]
*[[Media:700s1-3-t15-Increased-Criterion-GO.xls]]

*[[Media:MAPPFinder_results_T15-Criterion_Increased-GO.txt|Increased expression at T15 300mm NaCl]]

*[[Media:MAPPFinder_results_T15-Criterion_Decreased-GO.txt|Decreased expression at T15 300mm NaCl]]

*[[Media:T30_increased-Criterion0-GO.txt|Increased expression at t30 300mm NaCl]]

*[[Media:T30_MAPP_results-Criterion_Decreased-GO.txt|Decreased expression at t30 300mm NaCl]]

*[[Media:MAPPFinder_t60-Criterion_Increased-GO.txt|Increased expression at t60 300mm NaCl]]

*[[Media:MAPPFinder_t60-Criterion_Decreasaed-GO.txt|Decreased expression at t60 300mm NaCl]]
*[[Media:300N_T240_MAPPFINDER-Criterion_Increased-GO.txt|Increased expression t240 300mmNaCl]]
*[[Media:300N_T240_MAPPFINDER-Criterion_Decreased-GO.txt|decreased expression at t240 300mmNaCl]]

:Sample MAPP file of a relevant biological pathway for your species:

[[Media:regulation of transcription, DNA-dependent.mapp]]

[[Media:Structural_constituent_of_Ribosome.mapp| Structural constituents of ribosome 300mm NaCl]]

:Group Report:
:PowerPoint presentation: [[Media:Sinorhizobium_Meliloti_(Strain_1021)_FINAL_PRESENTATION.pdf | Sinorhizobium meliloti (Strain_1021) FINAL_PRESENTATION (PDF)]]
*Note: Wiki page is not accepting our converted .ppt format. The PDF version should suffice.

=Individual=

*[[Miles Malefyt deliverables]]
*[[https://xmlpipedb.cs.lmu.edu/biodb/fall2013/index.php/Individual_Assessment_and_Reflection Mitchell Petredis deliverables]]
*[[Stephen Louie Deliverables]]

Team Name Deliverables

2013-12-13T23:26:11Z

Mpetredi:

=Group=
:GenMAPP Gene Database:[[Media:Sinorhizobium_meliloti_1021_mpetredi_2013123-2.gdb]]
:ReadMe file: [[Media:ReadMe-SM.pdf|ReadME_S.meliloti]]
:Gene Database Schema diagram: [[Media:S.Meliloti_schema_20131205.pdf|S.meliloti_schema_20131205.pdf]]
:Gene Database Testing Report: [[Media:Match Test Sheet1.pdf]]
:Processed and analyzed DNA microarray dataset:
* .3 M: [[Media:Complete_processed_Data_MPM.xls|300mm NaCl XLS Version]]
* .7 M: [[Media:SinorhizobiumMeliloti_LM_GenMapp_FinalFile.txt]]
:GenMAPP Expression Dataset file: [[Media:SinorhizobiumMeliloti_LM_GenMapp_FinalFile.gex]]

[[Media:T30.gex|Gene expression set for 300mm NaCl]]

:Filtered MAPPFinder Results: .7 M files:
*[[Media:700s1-3-t15-Decreased-Criterion-GO.xls]]
*[[Media:700s1-3-t15-Increased-Criterion-GO.xls]]

*[[Media:MAPPFinder_results_T15-Criterion_Increased-GO.txt|Increased expression at T15 300mm NaCl]]

*[[Media:MAPPFinder_results_T15-Criterion_Decreased-GO.txt|Decreased expression at T15 300mm NaCl]]

*[[Media:T30_increased-Criterion0-GO.txt|Increased expression at t30 300mm NaCl]]

*[[Media:MAPPFinder_t60-Criterion_Increased-GO.txt|Increased expression at t60 300mm NaCl]]

*[[Media:MAPPFinder_t60-Criterion_Decreasaed-GO.txt|Decreased expression at t60 300mm NaCl]]
*[[Media:300N_T240_MAPPFINDER-Criterion_Increased-GO.txt|Increased expression t240 300mmNaCl]]
*[[Media:300N_T240_MAPPFINDER-Criterion_Decreased-GO.txt|decreased expression at t240 300mmNaCl]]

:Sample MAPP file of a relevant biological pathway for your species:[[Media:regulation of transcription, DNA-dependent.mapp]]
:Group Report:
:PowerPoint presentation: [[Media:Sinorhizobium_Meliloti_(Strain_1021)_FINAL_PRESENTATION.pdf | Sinorhizobium meliloti (Strain_1021) FINAL_PRESENTATION (PDF)]]

=Individual=

*[[Miles Malefyt deliverables]]
*[[https://xmlpipedb.cs.lmu.edu/biodb/fall2013/index.php/Individual_Assessment_and_Reflection Mitchell Petredis deliverables]]
*[[Stephen Louie Deliverables]]

File:Sinorhizobium Meliloti (Strain 1021) FINAL PRESENTATION.pdf

2013-12-13T23:24:23Z

Mpetredi: PDF of presentation given on December 13, 2013.

PDF of presentation given on December 13, 2013.

Team Name Deliverables

2013-12-13T23:13:32Z

Mpetredi: created a bulleted list

Team Name Deliverables

2013-12-13T22:34:39Z

Mpetredi: added bulleted list for deliverables

Team Name Deliverables

2013-12-13T22:34:16Z

Mpetredi: added my contributions to the deliverables page

User:Mpetredi

2013-12-13T22:11:49Z

Mpetredi: /* Contact Information */ erased one of the email addresses

{{mpetredi}}

==Contact Information==
:Loyola Marymount University
:1 LMU Drive MSB-5957
:Los Angeles, CA 90045-2659

*mpetredi at lion dot lmu dot edu

==[[Individual Assessment and Reflection]]==

==Weekly Assignments==
*[[Week 1]]
*[[Week 2]]
*[[Week 3]]
*[[Week 4]]
*[[Week 5]]
*[[Week 6]]
*[[Week 7]]
*[[Week 8]]
*[[Week 9]]
*[[Week 10]]
*[[Week 11]]
*[[Week 12]]
*[[Week 13]]
*[[Week 14]]
*[[Week 15]]

==Journals==

===Class 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]]

====My Class Journal Entries====
#[[Class_Journal_Week_1#Mitchell Petredis|Response to Class Journal 1]]
#[[Class_Journal_Week_2#Mitchell Petredis|Response to Class Journal 2]]
#[[Class_Journal_Week_3#Mitchell Petredis|Response to Class Journal 3]]
#[[Class_Journal_Week_4#Mitchell Petredis|Response to Class Journal 4]]
#[[Class_Journal_Week_5#Mitchell Petredis|Response to Class Journal 5]]
#*[[Protegen]]
#[[Class_Journal_Week_6#Mitchell Petredis|Response to Class Journal 6]]
#[[Class_Journal_Week_7#Mitchell Petredis|Response to Class Journal 7]]
#[[Class_Journal_Week_8#Mitchell Petredis|Response to Class Journal 8]]
#[[Class_Journal_Week_9#Mitchell Petredis|Response to Class Journal 9]]

===Individual Class Journals===
*[[mpetredi Week 2]]
*[[mpetredi Week 3]]
*[[mpetredi Week 4]]
*[[mpetredi Week 5]]
*[[mpetredi Week 6]]
*[[mpetredi Week 7]]
*[[mpetredi Week 8]]
*[[mpetredi Week 9]]
*[[mpetredi Week 10]]
*[[mpetredi Week 11]]
*[[mpetredi Week 12]]
*[[mpetredi Week 13]]
*[[mpetredi Week 14]]

==Education==

===Loyola Marymount University===

:Major: Biology
:Expected Graduation: 2015

*Started taking upper division classes this year.

===Research Projects===
:*[http://phagesdb.org/phages/MePac/ MePac Bacteriophage]
[[Image:MePac EMPic (1).jpg | thumb | border | right]] 
:**Mentors
:***Dr. Yiwen Fang
:***Dr. Carl Urbinati
:***Dr. Gary Kuleck
:**Presentations
:***2012 LMU Undergraduate Research Symposium
:***[[Media:WCBSURC+Proceedings+2012.pdf|37th Annual West Coast Biological Sciences Undergraduate Research Conference]]

==Work Experience==

===Loyola Marymount University===
:'''Information Technology Services'''
:*2011-2012
:#Lab Assistant: Diagnose and troubleshoot issues in computer labs.
:*2012-2013
:#Foley 220 Lab Manager: Maintain logs of supply usage and assist with computer issues.
:#Student Innovation Center Technician: Diagnose and troubleshoot student and teacher technology issues.

===Withers Dental===
:'''Dental Technician'''
:*Summer 2013
:**Stocked and sanitized operating rooms
:**Sterilized and bagged dental instruments according to function.
:**Assisted in creating 40 sport guards for the entire Mira Costa High School Varsity football team.

==Personal Interests and Hobbies==
*Technology
*Gaming
*Photography
*Art
*Swimming
*Gardening



==Templates==

*[[Template:mpetredi]]
*[[Template: mpetredi Week 2 Journal Entry]]
*[[Template: mpetredi Week 4 Journal Entry]]
*[[Template: Hilda and Mitchell Week 5 Journal Entry]]
*[[Template: Individual Assignment Categories]]
*[[Template: User Page Link]]

==Wiki Pages==
*[[Week 1 Journal Entry]]
*[[Week 2 Journal Entry]]
*[[Week 3 Journal Entry]]
*[[mpetredi Week 2]]
*[[mpetredi Week 3]]
*[[Class Notes]]
*[[Class Notes 2]]
*[[Class Notes 3]]

==Useful Links==
[[http://libguides.lmu.edu/BIOL367 BIOL 367 LibGuide]]

[[Category: Individual Homework]]
[[Category: User Page]]

Team Name

2013-12-13T22:11:24Z

Mpetredi: /* Mitchell Petredis */ erased one of the email addresses

Species: ''Sinorhizobium Meliloti'' (Strain 1021)
==Group Project==
[[media:Sinorhizobium_Meliloti_group_project.pdf|Group Project]]

==Personnel==
===Stephen Louie===
Project Manager, Quality Assurance
:slouie4 at lion.lmu.edu
:1 LMU Drive MSB 5194
:Los Angeles, CA 90045
:[[Stephen Louie Project Notebook|Stephen Louie Project Notebook]]

===Lauren Magee===
GenMAPP Expert
:lmagee1 at lion.lmu.edu
:1 LMU Drive MSB-5258,
:Los Angeles, CA 90045
===Mitchell Petredis===
Coding Supervisor
:mpetredi at lion dot lmu dot edu
:Loyola Marymount University
:1 LMU Drive MSB-5957
:Los Angeles, CA 90045-2659

===Miles Malefyt===
GenMAPP Coordinator
:milesm@malefyt.com
:mmalefyt@lion.lmu.edu
:8416 Campion drive
:Westchester, CA 90045
cell: 831-236-5402

[[User:Mmalefyt|Mmalefyt]] ([[User talk:Mmalefyt|talk]]) 10:31, 31 October 2013 (PDT)

==Micro Array paper==

[[http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-785/?keywords=&organism=Sinorhizobium%20meliloti&array=&exptype Osmotic upshift elicited by salt and sucrose]]
*[[http://jb.asm.org/content/188/21/7617 HTML version]]
*[[http://jb.asm.org/content/188/21/7617.full.pdf+html PDF version]]
*[[Media:A-MEXP-230.adf.txt]]
*[[Media:E-MEXP-785.eSet.r]]-unable to download, because the file is too big
*[[Media:E-MEXP-785.processed.1.zip]]
*[[Media:E-MEXP-785.raw.2.zip]]
*[[Media:E-MEXP-785.idf.txt]]
*[[Media:E-MEXP-785.raw.1.zip]]-unable to download, because the file is too big
*[[Media:E-MEXP-785.sdrf.txt]]
*Raw Data File for 700S (1-3): [[File:Full Raw Data.xls]]
*[[Media:Compiled Ratios and Logs.xls]]
*[[Media:SinorhizobiumMeliloti_LM_GenMapp_DataSheet.txt]]
*[[Media:SinorhizobiumMeliloti_LM_GenMapp_DataSheet.xls]]
*[[Media:SinorhizobiumMeliloti_LM_GenMapp_FinalFile.txt]]
*[[Media:SinorhizobiumMeliloti_LM_GenMapp_FinalFile.EX.txt]]
*[[Media:SinorhizobiumMeliloti_LM_GenMapp_FinalFile.gex]]
*[[Media:ColorSets.mapp]]
*[[Media:SinorhizobiumMeliloti_LM_GenMapp_FinalFile.gmf]]
*[[Media:700S1-3-t15-Decreased-Criterion0-GO.txt]]
*[[Media:700S1-3-t15-Increased-Criterion0-GO.txt]]
Domínguez-Ferreras, A., Pérez-Arnedo, R., Becker, A., Olivares, J., Soto, M.J., Sanjuán, J. (2006) Transcriptome Profiling Reveals the Importance of Plasmid pSymB for Osmoadaptation of Sinorhizobium meliloti ''Journal of Bacteriology'' 188:7617-7625

==Genome Paper==

[http://search.proquest.com/docview/213572450?accountid=7418 The composite genome of the legume symbiont Sinorhizobium meliloti. Science 293, 668–672.]

Galibert, F., Finan, T.M., Long, S., Puhler, A., et al. (2001) The composite genome of the legume symbiont Sinorhizobium meliloti ''Science'' 293:668-672

[[Category: Sinorhizobium meliloti]]
[[Category: Group Projects]]

==Model Organism Database==
Link: http://cmr.jcvi.org/tigr-scripts/CMR/GenomePage.cgi?org=ntsm01

==Compiled raw Data==
[[Media:Team_Name_NaCl_compiled_raw_Data.xls|300 NaCl compiled data set]]
==Compiled processed data==
[[Media:Complete_processed_Data.xls|Processed Data]]

==Data ready for GenMAPP==
[[Media:Complete_processed_Data_MPM.xls|XLS Version]]

[[Media:Complete_processed_Data_MPM.txt|TXT version, USE THIS]]

==Important Files==

Taxon ID: 266834

Version of GenMAPP Builder: [[Media: gmbuilder-2.0b71.zip | gmbuilder-2.0b71.zip]]

Computer on which export was run: Keck Lab Computer, back computer (furthest from the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import:19.17 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import: 17.81 minutes
* Time taken to process: 15.54 minutes

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import: 0.21 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file: [[Media:Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_2013117.gdb | Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_2013117.gdb]]
* Time taken to export .gdb: Started at 2pm on 11-7-2013, finished at 9:47pm
* Upload your file and link to it here.

Note:

replace geneID with ~ when you find MOD link

==Important Files 2==

Info based on export done on 11/21/2013

Taxon ID: 266834

Version of GenMAPP Builder: [[Media:GenMAPP_Builder_2.0b72 S. meliloti.zip|GenMAPP_Builder_2.0b72 S. meliloti.zip]]

Computer on which export was run: Keck Lab Computer, front computer (closest to the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import: 7.34 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import: 6.31 minutes
* Time taken to process: 4.60 minutes

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import: 0.07 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file: [[Media:Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_20131121.gdb|Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_20131121.gdb]]
* Time taken to export .gdb: Started at 10:18 AM on 11/21/2013; ended at 1:34 PM

==Important Files 3==

'''From Week 14, December 3-5, 2013'''

NOTE: Forgot that I cannot import data into the same database. I will continue to do an export based on what I have, and will do another import/export cycle on another computer using the same version of gmbuilder that I used here.

Taxon ID: 266834

Version of GenMAPP Builder: [[Media: SmelilotiGenMAPP_Builder_2.0b73.zip]]

Computer on which export was run: Keck Lab Computer, front computer (closest to the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import: 6.27 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import: 6.07 minutes
* Time taken to process: 12.42 minutes
**NOTE: gmbuilder told me that the GO OBO-XML file was already processed in the database, and wanted to know if I wanted to process the information again. I chose yes.

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import: 0.07 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file:
* Time taken to export .gdb: started around 10am
* Upload your file and link to it here.

==Important Files 4==

'''From Week 14, December 3-5, 2013'''

NOTE: Here is the other import/export, using a new database on a different Keck Lab computer

Taxon ID: 266834

Version of GenMAPP Builder: [[Media: SmelilotiGenMAPP_Builder_2.0b73.zip]]

Computer on which export was run: Keck Lab Computer, front computer (closest to the whiteboard)

Postgres Database name: S meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import: 6.25 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import: 6.21 minutes
* Time taken to process: 4.50 minutes

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import: 0.07 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file: [[Media:Sinorhizobium_meliloti_1021_mpetredi_2013123-2.gdb]]
* Time taken to export .gdb: Started at 10:28am. Finished at 1:36pm

* Upload your file and link to it here.

GEX File
*[[Media:2013125-Complete_processed_Data_MPM.gex]]

==Wiki Navigation==
[[Template:Team Name]]
{{Team Name}}
*[[Teamname Week 13 Status Report]]
*[[Laurmagee: Week 13]]
*[[Teamname Week 15 Status Report]]
*[[Laurmagee: Week 15]]
*[[Electronic notebook: sinorhizobium meliloti|Miles Malefyt electronic notebook]]

Individual Assessment and Reflection

2013-12-11T20:49:38Z

Mpetredi: /* Reflection on the Process */ finished Reflection on the Process

{{User Page Link}}

==Statement of Work==

*As coder of [[[[Team Name]]]], I was responsible for creating and tweaking versions of gmbuilder under the provision of Dr. Dionisio to help create a proper analysis tool for our species ''Sinorhizobium Meliloti'' (Strain 1021). Additionally, I imported the unique UniProt XML, GO OBO-XML, and GOA files into the PostgreSQL database for our species using my custom versions of gmbuilder and exported the .gdb files necessary for the quality assurance and GenMAPP users to do their respective roles.
*In total, 3 versions of gmbuilder were created and produced the following .gdb files (in order of oldest to newest):
**[[Media: gmbuilder-2.0b71.zip | gmbuilder-2.0b71.zip]]
***[[Media:Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_2013117.gdb | Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_2013117.gdb]]
**[[Media:GenMAPP_Builder_2.0b72 S. meliloti.zip|GenMAPP_Builder_2.0b72 S. meliloti.zip]]
***[[Media:Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_20131121.gdb|Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_20131121.gdb]]
**[[Media: SmelilotiGenMAPP_Builder_2.0b73.zip]]
***[[Media:Sinorhizobium_meliloti_1021_mpetredi_2013123-2.gdb]]

*My lab progression is listed below:
*[[mpetredi Week 12]]
*[[mpetredi Week 13]]
*[[mpetredi Week 14]]

NOTE: "Important Files 3" does not have a .gdb file because of accidentally importing duplicate data into PostgreSQL; I decided it would be a hindrance to use that .gdb file for analysis and therefore discarded it. A new database and .gdb file were created under "Important Files 4" to resolve this issue.

==Assessment of Project==

*Our project was somewhat successful, but it is still a work in progress. I believe my team displayed dedication to the quality of the project, and while we were not able to create an error-free database this semester, our work-ethic significantly contributed to the further completion of the gene database. If my team's schedule outside of this class weren't as complex, I believe we could have delivered a finished product.
*If I could do it all over again, I'd start the project earlier. Additionally, having a laptop with all the lab software would have made it more convenient to organize the project and work on it away from the lab.
*Gene Database Project and Group Report Evaluation
*#Content:
*#Organization:
*#Completeness:

==Reflection on the Process==

*I learned the following
**With my head: Biology and Computer Science can drastically benefit from each other. As technology improves, scientists can discover new things that previously could not be comprehended or understood.
**With my heart: Close communication and flexibility in scheduling with team members is critical to achieving project goals.
**With your hands: I gained a better understanding of how database management and organization works, and even learned some coding.
*A year from now, I'll remember the various SQL queries and how to utilize filtering mechanisms in large datasets.

Individual Assessment and Reflection

2013-12-11T20:40:12Z

Mpetredi: added lab note references

{{User Page Link}}

==Statement of Work==

*As coder of [[[[Team Name]]]], I was responsible for creating and tweaking versions of gmbuilder under the provision of Dr. Dionisio to help create a proper analysis tool for our species ''Sinorhizobium Meliloti'' (Strain 1021). Additionally, I imported the unique UniProt XML, GO OBO-XML, and GOA files into the PostgreSQL database for our species using my custom versions of gmbuilder and exported the .gdb files necessary for the quality assurance and GenMAPP users to do their respective roles.
*In total, 3 versions of gmbuilder were created and produced the following .gdb files (in order of oldest to newest):
**[[Media: gmbuilder-2.0b71.zip | gmbuilder-2.0b71.zip]]
***[[Media:Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_2013117.gdb | Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_2013117.gdb]]
**[[Media:GenMAPP_Builder_2.0b72 S. meliloti.zip|GenMAPP_Builder_2.0b72 S. meliloti.zip]]
***[[Media:Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_20131121.gdb|Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_20131121.gdb]]
**[[Media: SmelilotiGenMAPP_Builder_2.0b73.zip]]
***[[Media:Sinorhizobium_meliloti_1021_mpetredi_2013123-2.gdb]]

*My lab progression is listed below:
*[[mpetredi Week 12]]
*[[mpetredi Week 13]]
*[[mpetredi Week 14]]

NOTE: "Important Files 3" does not have a .gdb file because of accidentally importing duplicate data into PostgreSQL; I decided it would be a hindrance to use that .gdb file for analysis and therefore discarded it. A new database and .gdb file were created under "Important Files 4" to resolve this issue.

==Assessment of Project==

*Our project was somewhat successful, but it is still a work in progress. I believe my team displayed dedication to the quality of the project, and while we were not able to create an error-free database this semester, our work-ethic significantly contributed to the further completion of the gene database. If my team's schedule outside of this class weren't as complex, I believe we could have delivered a finished product.
*If I could do it all over again, I'd start the project earlier. Additionally, having a laptop with all the lab software would have made it more convenient to organize the project and work on it away from the lab.
*Gene Database Project and Group Report Evaluation
*#Content:
*#Organization:
*#Completeness:

==Reflection on the Process==

*I learned the following
**Biology and Computer Science can drastically benefit from each other

Individual Assessment and Reflection

2013-12-11T20:37:45Z

Mpetredi: more statement of work

{{User Page Link}}

==Statement of Work==

*As coder of [[[[Team Name]]]], I was responsible for creating and tweaking versions of gmbuilder under the provision of Dr. Dionisio to help create a proper analysis tool for our species ''Sinorhizobium Meliloti'' (Strain 1021). Additionally, I imported the unique UniProt XML, GO OBO-XML, and GOA files into the PostgreSQL database for our species using my custom versions of gmbuilder and exported the .gdb files necessary for the quality assurance and GenMAPP users to do their respective roles.
*In total, 3 versions of gmbuilder were created and produced the following .gdb files (in order of oldest to newest):
**[[Media: gmbuilder-2.0b71.zip | gmbuilder-2.0b71.zip]]
***[[Media:Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_2013117.gdb | Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_2013117.gdb]]
**[[Media:GenMAPP_Builder_2.0b72 S. meliloti.zip|GenMAPP_Builder_2.0b72 S. meliloti.zip]]
***[[Media:Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_20131121.gdb|Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_20131121.gdb]]
**[[Media: SmelilotiGenMAPP_Builder_2.0b73.zip]]
***[[Media:Sinorhizobium_meliloti_1021_mpetredi_2013123-2.gdb]]

NOTE: "Important Files 3" does not have a .gdb file because of accidentally importing duplicate data into PostgreSQL; I decided it would be a hindrance to use that .gdb file for analysis and therefore discarded it. A new database and .gdb file were created under "Important Files 4" to resolve this issue.

==Assessment of Project==

*Our project was somewhat successful, but it is still a work in progress. I believe my team displayed dedication to the quality of the project, and while we were not able to create an error-free database this semester, our work-ethic significantly contributed to the further completion of the gene database. If my team's schedule outside of this class weren't as complex, I believe we could have delivered a finished product.
*If I could do it all over again, I'd start the project earlier. Additionally, having a laptop with all the lab software would have made it more convenient to organize the project and work on it away from the lab.
*Gene Database Project and Group Report Evaluation
*#Content:
*#Organization:
*#Completeness:

==Reflection on the Process==

*I learned the following
**Biology and Computer Science can drastically benefit from each other

Individual Assessment and Reflection

2013-12-10T23:44:20Z

Mpetredi: added some responses to individual assessment and reflection

{{User Page Link}}

==Statement of Work==

==Assessment of Project==

*Our project was somewhat successful, but it is still a work in progress. I believe my team displayed dedication to the quality of the project, and while we were not able to create an error-free database this semester, our work-ethic significantly contributed to the further completion of the gene database. If my team's schedule outside of this class weren't as complex, I believe we could have delivered a finished product.
*If I could do it all over again, I'd start the project earlier. Additionally, having a laptop with all the lab software would have made it more convenient to organize the project and work on it away from the lab.
*Gene Database Project and Group Report Evaluation
*#Content:
*#Organization:
*#Completeness:

==Reflection on the Process==

*I learned the following
**Biology and Computer Science can drastically benefit from each other

User:Mpetredi

2013-12-10T23:30:36Z

Mpetredi: created individual assessment and reflection page

{{mpetredi}}

==Contact Information==
:Loyola Marymount University
:1 LMU Drive MSB-5957
:Los Angeles, CA 90045-2659

*mrpetredis at gmail dot com
*mpetredi at lion dot lmu dot edu

==[[Individual Assessment and Reflection]]==

==Weekly Assignments==
*[[Week 1]]
*[[Week 2]]
*[[Week 3]]
*[[Week 4]]
*[[Week 5]]
*[[Week 6]]
*[[Week 7]]
*[[Week 8]]
*[[Week 9]]
*[[Week 10]]
*[[Week 11]]
*[[Week 12]]
*[[Week 13]]
*[[Week 14]]
*[[Week 15]]

==Journals==

===Class 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]]

====My Class Journal Entries====
#[[Class_Journal_Week_1#Mitchell Petredis|Response to Class Journal 1]]
#[[Class_Journal_Week_2#Mitchell Petredis|Response to Class Journal 2]]
#[[Class_Journal_Week_3#Mitchell Petredis|Response to Class Journal 3]]
#[[Class_Journal_Week_4#Mitchell Petredis|Response to Class Journal 4]]
#[[Class_Journal_Week_5#Mitchell Petredis|Response to Class Journal 5]]
#*[[Protegen]]
#[[Class_Journal_Week_6#Mitchell Petredis|Response to Class Journal 6]]
#[[Class_Journal_Week_7#Mitchell Petredis|Response to Class Journal 7]]
#[[Class_Journal_Week_8#Mitchell Petredis|Response to Class Journal 8]]
#[[Class_Journal_Week_9#Mitchell Petredis|Response to Class Journal 9]]

===Individual Class Journals===
*[[mpetredi Week 2]]
*[[mpetredi Week 3]]
*[[mpetredi Week 4]]
*[[mpetredi Week 5]]
*[[mpetredi Week 6]]
*[[mpetredi Week 7]]
*[[mpetredi Week 8]]
*[[mpetredi Week 9]]
*[[mpetredi Week 10]]
*[[mpetredi Week 11]]
*[[mpetredi Week 12]]
*[[mpetredi Week 13]]
*[[mpetredi Week 14]]

==Education==

===Loyola Marymount University===

:Major: Biology
:Expected Graduation: 2015

*Started taking upper division classes this year.

===Research Projects===
:*[http://phagesdb.org/phages/MePac/ MePac Bacteriophage]
[[Image:MePac EMPic (1).jpg | thumb | border | right]] 
:**Mentors
:***Dr. Yiwen Fang
:***Dr. Carl Urbinati
:***Dr. Gary Kuleck
:**Presentations
:***2012 LMU Undergraduate Research Symposium
:***[[Media:WCBSURC+Proceedings+2012.pdf|37th Annual West Coast Biological Sciences Undergraduate Research Conference]]

==Work Experience==

===Loyola Marymount University===
:'''Information Technology Services'''
:*2011-2012
:#Lab Assistant: Diagnose and troubleshoot issues in computer labs.
:*2012-2013
:#Foley 220 Lab Manager: Maintain logs of supply usage and assist with computer issues.
:#Student Innovation Center Technician: Diagnose and troubleshoot student and teacher technology issues.

===Withers Dental===
:'''Dental Technician'''
:*Summer 2013
:**Stocked and sanitized operating rooms
:**Sterilized and bagged dental instruments according to function.
:**Assisted in creating 40 sport guards for the entire Mira Costa High School Varsity football team.

==Personal Interests and Hobbies==
*Technology
*Gaming
*Photography
*Art
*Swimming
*Gardening



==Templates==

*[[Template:mpetredi]]
*[[Template: mpetredi Week 2 Journal Entry]]
*[[Template: mpetredi Week 4 Journal Entry]]
*[[Template: Hilda and Mitchell Week 5 Journal Entry]]
*[[Template: Individual Assignment Categories]]
*[[Template: User Page Link]]

==Wiki Pages==
*[[Week 1 Journal Entry]]
*[[Week 2 Journal Entry]]
*[[Week 3 Journal Entry]]
*[[mpetredi Week 2]]
*[[mpetredi Week 3]]
*[[Class Notes]]
*[[Class Notes 2]]
*[[Class Notes 3]]

==Useful Links==
[[http://libguides.lmu.edu/BIOL367 BIOL 367 LibGuide]]

[[Category: Individual Homework]]
[[Category: User Page]]

Team Name

2013-12-05T18:18:41Z

Mpetredi: /* Important Files 4 */ added gex file

Species: ''Sinorhizobium Meliloti'' (Strain 1021)
==Group Project==
[[media:Sinorhizobium_Meliloti_group_project.pdf|Group Project]]

==Personnel==
===Stephen Louie===
Project Manager, Quality Assurance
:slouie4 at lion.lmu.edu
:1 LMU Drive MSB 5194
:Los Angeles, CA 90045
:[[Stephen Louie Project Notebook|Stephen Louie Project Notebook]]

===Lauren Magee===
GenMAPP Expert
:lmagee1 at lion.lmu.edu
:1 LMU Drive MSB-5258,
:Los Angeles, CA 90045
===Mitchell Petredis===
Coding Supervisor
:mrpetredis at gmail dot com
:mpetredi at lion dot lmu dot edu
:Loyola Marymount University
:1 LMU Drive MSB-5957
:Los Angeles, CA 90045-2659
===Miles Malefyt===
GenMAPP Coordinator
:milesm@malefyt.com
:mmalefyt@lion.lmu.edu
:8416 Campion drive
:Westchester, CA 90045
cell: 831-236-5402

[[User:Mmalefyt|Mmalefyt]] ([[User talk:Mmalefyt|talk]]) 10:31, 31 October 2013 (PDT)

==Micro Array paper==

[[http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-785/?keywords=&organism=Sinorhizobium%20meliloti&array=&exptype Osmotic upshift elicited by salt and sucrose]]
*[[http://jb.asm.org/content/188/21/7617 HTML version]]
*[[http://jb.asm.org/content/188/21/7617.full.pdf+html PDF version]]
*[[Media:A-MEXP-230.adf.txt]]
*[[Media:E-MEXP-785.eSet.r]]
*[[Media:E-MEXP-785.processed.1.zip]]
*[[Media:E-MEXP-785.raw.2.zip]]
*[[Media:E-MEXP-785.idf.txt]]
*[[Media:E-MEXP-785.raw.1.zip]]
*[[Media:E-MEXP-785.sdrf.txt]]
*Raw Data File for 700S (1-3): [[File:Full Raw Data.xls]]
*[[File:Compiled Ratios and Logs.xls]]
*[[File:SinorhizobiumMeliloti_LM_GenMapp_DataSheet.txt]]
*[[File:SinorhizobiumMeliloti_LM_GenMapp_DataSheet.xls]]

Domínguez-Ferreras, A., Pérez-Arnedo, R., Becker, A., Olivares, J., Soto, M.J., Sanjuán, J. (2006) Transcriptome Profiling Reveals the Importance of Plasmid pSymB for Osmoadaptation of Sinorhizobium meliloti ''Journal of Bacteriology'' 188:7617-7625

==Genome Paper==

[http://search.proquest.com/docview/213572450?accountid=7418 The composite genome of the legume symbiont Sinorhizobium meliloti. Science 293, 668–672.]

Galibert, F., Finan, T.M., Long, S., Puhler, A., et al. (2001) The composite genome of the legume symbiont Sinorhizobium meliloti ''Science'' 293:668-672

[[Category: Sinorhizobium meliloti]]
[[Category: Group Projects]]

==Model Organism Database==
Link: http://cmr.jcvi.org/tigr-scripts/CMR/GenomePage.cgi?org=ntsm01

==Compiled raw Data==
[[Media:Team_Name_NaCl_compiled_raw_Data.xls|300 NaCl compiled data set]]
==Compiled processed data==
[[Media:Complete_processed_Data.xls|Processed Data]]

==Data ready for GenMAPP==
[[Media:Complete_processed_Data_MPM.xls|XLS Version]]

[[Media:Complete_processed_Data_MPM.txt|TXT version, USE THIS]]

==Important Files==

Taxon ID: 266834

Version of GenMAPP Builder: [[Media: gmbuilder-2.0b71.zip | gmbuilder-2.0b71.zip]]

Computer on which export was run: Keck Lab Computer, back computer (furthest from the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import:19.17 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import: 17.81 minutes
* Time taken to process: 15.54 minutes

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import: 0.21 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file: [[Media:Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_2013117.gdb | Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_2013117.gdb]]
* Time taken to export .gdb: Started at 2pm on 11-7-2013, finished at 9:47pm
* Upload your file and link to it here.

Note:

replace geneID with ~ when you find MOD link

==Important Files 2==

Info based on export done on 11/21/2013

Taxon ID: 266834

Version of GenMAPP Builder: [[Media:GenMAPP_Builder_2.0b72 S. meliloti.zip|GenMAPP_Builder_2.0b72 S. meliloti.zip]]

Computer on which export was run: Keck Lab Computer, front computer (closest to the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import: 7.34 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import: 6.31 minutes
* Time taken to process: 4.60 minutes

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import: 0.07 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file: [[Media:Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_20131121.gdb|Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_20131121.gdb]]
* Time taken to export .gdb: Started at 10:18 AM on 11/21/2013; ended at 1:34 PM

==Important Files 3==

'''From Week 14, December 3-5, 2013'''

NOTE: Forgot that I cannot import data into the same database. I will continue to do an export based on what I have, and will do another import/export cycle on another computer using the same version of gmbuilder that I used here.

Taxon ID: 266834

Version of GenMAPP Builder: [[Media: SmelilotiGenMAPP_Builder_2.0b73.zip]]

Computer on which export was run: Keck Lab Computer, front computer (closest to the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import: 6.27 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import: 6.07 minutes
* Time taken to process: 12.42 minutes
**NOTE: gmbuilder told me that the GO OBO-XML file was already processed in the database, and wanted to know if I wanted to process the information again. I chose yes.

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import: 0.07 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file:
* Time taken to export .gdb: started around 10am
* Upload your file and link to it here.

==Important Files 4==

'''From Week 14, December 3-5, 2013'''

NOTE: Here is the other import/export, using a new database on a different Keck Lab computer

Taxon ID: 266834

Version of GenMAPP Builder: [[Media: SmelilotiGenMAPP_Builder_2.0b73.zip]]

Computer on which export was run: Keck Lab Computer, front computer (closest to the whiteboard)

Postgres Database name: S meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import: 6.25 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import: 6.21 minutes
* Time taken to process: 4.50 minutes

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import: 0.07 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file: [[Media:Sinorhizobium_meliloti_1021_mpetredi_2013123-2.gdb]]
* Time taken to export .gdb: Started at 10:28am. Finished at 1:36pm

* Upload your file and link to it here.

GEX File
*[[Media:2013125-Complete_processed_Data_MPM.gex]]

==Wiki Navigation==
{{Team Name}}
*[[Teamname Week 13 Status Report]]
*[[Laurmagee: Week 13]]

File:2013125-Complete processed Data MPM.gex

2013-12-05T18:17:56Z

Mpetredi: GEX file created with 5535 errors

GEX file created with 5535 errors

File:SmelilotiGenMAPP Builder 2.0b73.zip

2013-12-04T06:31:16Z

Mpetredi: custom gmbuilder created on 12/3/2013

custom gmbuilder created on 12/3/2013

Team Name

2013-12-04T06:30:58Z

Mpetredi: /* Important Files 4 */ changed database name to reflect accuracy

Species: ''Sinorhizobium Meliloti'' (Strain 1021)
==Group Project==
[[media:Sinorhizobium_Meliloti_group_project.pdf|Group Project]]

==Personnel==
===Stephen Louie===
Project Manager, Quality Assurance
:slouie4 at lion.lmu.edu
:1 LMU Drive MSB 5194
:Los Angeles, CA 90045
:[[Stephen Louie Project Notebook|Stephen Louie Project Notebook]]

===Lauren Magee===
GenMAPP Expert
:lmagee1 at lion.lmu.edu
:1 LMU Drive MSB-5258,
:Los Angeles, CA 90045
===Mitchell Petredis===
Coding Supervisor
:mrpetredis at gmail dot com
:mpetredi at lion dot lmu dot edu
:Loyola Marymount University
:1 LMU Drive MSB-5957
:Los Angeles, CA 90045-2659
===Miles Malefyt===
GenMAPP Coordinator
:milesm@malefyt.com
:mmalefyt@lion.lmu.edu
:8416 Campion drive
:Westchester, CA 90045
cell: 831-236-5402

[[User:Mmalefyt|Mmalefyt]] ([[User talk:Mmalefyt|talk]]) 10:31, 31 October 2013 (PDT)

==Micro Array paper==

[[http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-785/?keywords=&organism=Sinorhizobium%20meliloti&array=&exptype Osmotic upshift elicited by salt and sucrose]]
*[[http://jb.asm.org/content/188/21/7617 HTML version]]
*[[http://jb.asm.org/content/188/21/7617.full.pdf+html PDF version]]
*[[Media:A-MEXP-230.adf.txt]]
*[[Media:E-MEXP-785.eSet.r]]
*[[Media:E-MEXP-785.processed.1.zip]]
*[[Media:E-MEXP-785.raw.2.zip]]
*[[Media:E-MEXP-785.idf.txt]]
*[[Media:E-MEXP-785.raw.1.zip]]
*[[Media:E-MEXP-785.sdrf.txt]]
*Raw Data File for 700S (1-3): [[File:Full Raw Data.xls]]
*[[File:Compiled Ratios and Logs.xls]]
*[[File:SinorhizobiumMeliloti_LM_GenMapp_DataSheet.txt]]
*[[File:SinorhizobiumMeliloti_LM_GenMapp_DataSheet.xls]]

Domínguez-Ferreras, A., Pérez-Arnedo, R., Becker, A., Olivares, J., Soto, M.J., Sanjuán, J. (2006) Transcriptome Profiling Reveals the Importance of Plasmid pSymB for Osmoadaptation of Sinorhizobium meliloti ''Journal of Bacteriology'' 188:7617-7625

==Genome Paper==

[http://search.proquest.com/docview/213572450?accountid=7418 The composite genome of the legume symbiont Sinorhizobium meliloti. Science 293, 668–672.]

Galibert, F., Finan, T.M., Long, S., Puhler, A., et al. (2001) The composite genome of the legume symbiont Sinorhizobium meliloti ''Science'' 293:668-672

[[Category: Sinorhizobium meliloti]]
[[Category: Group Projects]]

==Model Organism Database==
Link: http://cmr.jcvi.org/tigr-scripts/CMR/GenomePage.cgi?org=ntsm01

==Compiled raw Data==
[[Media:Team_Name_NaCl_compiled_raw_Data.xls|300 NaCl compiled data set]]
==Compiled processed data==
[[Media:Complete_processed_Data.xls|Processed Data]]

==Data ready for GenMAPP==
[[Media:Data_Sets_ratio2.xls|NaCl 300mm XLS version]]

[[Media:Data_Sets_ratio2.txt|NaCl 300mm TXT Version]]

==Important Files==

Taxon ID: 266834

Version of GenMAPP Builder: [[Media: gmbuilder-2.0b71.zip | gmbuilder-2.0b71.zip]]

Computer on which export was run: Keck Lab Computer, back computer (furthest from the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import:19.17 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import: 17.81 minutes
* Time taken to process: 15.54 minutes

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import: 0.21 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file: [[Media:Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_2013117.gdb | Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_2013117.gdb]]
* Time taken to export .gdb: Started at 2pm on 11-7-2013, finished at 9:47pm
* Upload your file and link to it here.

Note:

replace geneID with ~ when you find MOD link

==Important Files 2==

Info based on export done on 11/21/2013

Taxon ID: 266834

Version of GenMAPP Builder: [[Media:GenMAPP_Builder_2.0b72 S. meliloti.zip|GenMAPP_Builder_2.0b72 S. meliloti.zip]]

Computer on which export was run: Keck Lab Computer, front computer (closest to the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import: 7.34 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import: 6.31 minutes
* Time taken to process: 4.60 minutes

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import: 0.07 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file: [[Media:Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_20131121.gdb|Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_20131121.gdb]]
* Time taken to export .gdb: Started at 10:18 AM on 11/21/2013; ended at 1:34 PM

==Important Files 3==

'''From Week 14, December 3-5, 2013'''

NOTE: Forgot that I cannot import data into the same database. I will continue to do an export based on what I have, and will do another import/export cycle on another computer using the same version of gmbuilder that I used here.

Taxon ID: 266834

Version of GenMAPP Builder: [[Media: SmelilotiGenMAPP_Builder_2.0b73.zip]]

Computer on which export was run: Keck Lab Computer, front computer (closest to the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import: 6.27 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import: 6.07 minutes
* Time taken to process: 12.42 minutes
**NOTE: gmbuilder told me that the GO OBO-XML file was already processed in the database, and wanted to know if I wanted to process the information again. I chose yes.

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import: 0.07 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file:
* Time taken to export .gdb: started around 10am
* Upload your file and link to it here.

==Important Files 4==

'''From Week 14, December 3-5, 2013'''

NOTE: Here is the other import/export, using a new database on a different Keck Lab computer

Taxon ID: 266834

Version of GenMAPP Builder: [[Media: SmelilotiGenMAPP_Builder_2.0b73.zip]]

Computer on which export was run: Keck Lab Computer, front computer (closest to the whiteboard)

Postgres Database name: S meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import: 6.25 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import: 6.21 minutes
* Time taken to process: 4.50 minutes

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import: 0.07 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file: [[Media:Sinorhizobium_meliloti_1021_mpetredi_2013123-2.gdb]]
* Time taken to export .gdb: Started at 10:28am. Finished at 1:36pm

* Upload your file and link to it here.

==Wiki Navigation==
{{Team Name}}
*[[Teamname Week 13 Status Report]]
*[[Laurmagee: Week 13]]

Team Name

2013-12-04T06:30:27Z

Mpetredi: /* Important Files 3 */ added gmbuilder version

Species: ''Sinorhizobium Meliloti'' (Strain 1021)
==Group Project==
[[media:Sinorhizobium_Meliloti_group_project.pdf|Group Project]]

==Personnel==
===Stephen Louie===
Project Manager, Quality Assurance
:slouie4 at lion.lmu.edu
:1 LMU Drive MSB 5194
:Los Angeles, CA 90045
:[[Stephen Louie Project Notebook|Stephen Louie Project Notebook]]

===Lauren Magee===
GenMAPP Expert
:lmagee1 at lion.lmu.edu
:1 LMU Drive MSB-5258,
:Los Angeles, CA 90045
===Mitchell Petredis===
Coding Supervisor
:mrpetredis at gmail dot com
:mpetredi at lion dot lmu dot edu
:Loyola Marymount University
:1 LMU Drive MSB-5957
:Los Angeles, CA 90045-2659
===Miles Malefyt===
GenMAPP Coordinator
:milesm@malefyt.com
:mmalefyt@lion.lmu.edu
:8416 Campion drive
:Westchester, CA 90045
cell: 831-236-5402

[[User:Mmalefyt|Mmalefyt]] ([[User talk:Mmalefyt|talk]]) 10:31, 31 October 2013 (PDT)

==Micro Array paper==

[[http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-785/?keywords=&organism=Sinorhizobium%20meliloti&array=&exptype Osmotic upshift elicited by salt and sucrose]]
*[[http://jb.asm.org/content/188/21/7617 HTML version]]
*[[http://jb.asm.org/content/188/21/7617.full.pdf+html PDF version]]
*[[Media:A-MEXP-230.adf.txt]]
*[[Media:E-MEXP-785.eSet.r]]
*[[Media:E-MEXP-785.processed.1.zip]]
*[[Media:E-MEXP-785.raw.2.zip]]
*[[Media:E-MEXP-785.idf.txt]]
*[[Media:E-MEXP-785.raw.1.zip]]
*[[Media:E-MEXP-785.sdrf.txt]]
*Raw Data File for 700S (1-3): [[File:Full Raw Data.xls]]
*[[File:Compiled Ratios and Logs.xls]]
*[[File:SinorhizobiumMeliloti_LM_GenMapp_DataSheet.txt]]
*[[File:SinorhizobiumMeliloti_LM_GenMapp_DataSheet.xls]]

Domínguez-Ferreras, A., Pérez-Arnedo, R., Becker, A., Olivares, J., Soto, M.J., Sanjuán, J. (2006) Transcriptome Profiling Reveals the Importance of Plasmid pSymB for Osmoadaptation of Sinorhizobium meliloti ''Journal of Bacteriology'' 188:7617-7625

==Genome Paper==

[http://search.proquest.com/docview/213572450?accountid=7418 The composite genome of the legume symbiont Sinorhizobium meliloti. Science 293, 668–672.]

Galibert, F., Finan, T.M., Long, S., Puhler, A., et al. (2001) The composite genome of the legume symbiont Sinorhizobium meliloti ''Science'' 293:668-672

[[Category: Sinorhizobium meliloti]]
[[Category: Group Projects]]

==Model Organism Database==
Link: http://cmr.jcvi.org/tigr-scripts/CMR/GenomePage.cgi?org=ntsm01

==Compiled raw Data==
[[Media:Team_Name_NaCl_compiled_raw_Data.xls|300 NaCl compiled data set]]
==Compiled processed data==
[[Media:Complete_processed_Data.xls|Processed Data]]

==Data ready for GenMAPP==
[[Media:Data_Sets_ratio2.xls|NaCl 300mm XLS version]]

[[Media:Data_Sets_ratio2.txt|NaCl 300mm TXT Version]]

==Important Files==

Taxon ID: 266834

Version of GenMAPP Builder: [[Media: gmbuilder-2.0b71.zip | gmbuilder-2.0b71.zip]]

Computer on which export was run: Keck Lab Computer, back computer (furthest from the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import:19.17 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import: 17.81 minutes
* Time taken to process: 15.54 minutes

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import: 0.21 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file: [[Media:Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_2013117.gdb | Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_2013117.gdb]]
* Time taken to export .gdb: Started at 2pm on 11-7-2013, finished at 9:47pm
* Upload your file and link to it here.

Note:

replace geneID with ~ when you find MOD link

==Important Files 2==

Info based on export done on 11/21/2013

Taxon ID: 266834

Version of GenMAPP Builder: [[Media:GenMAPP_Builder_2.0b72 S. meliloti.zip|GenMAPP_Builder_2.0b72 S. meliloti.zip]]

Computer on which export was run: Keck Lab Computer, front computer (closest to the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import: 7.34 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import: 6.31 minutes
* Time taken to process: 4.60 minutes

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import: 0.07 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file: [[Media:Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_20131121.gdb|Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_20131121.gdb]]
* Time taken to export .gdb: Started at 10:18 AM on 11/21/2013; ended at 1:34 PM

==Important Files 3==

'''From Week 14, December 3-5, 2013'''

NOTE: Forgot that I cannot import data into the same database. I will continue to do an export based on what I have, and will do another import/export cycle on another computer using the same version of gmbuilder that I used here.

Taxon ID: 266834

Version of GenMAPP Builder: [[Media: SmelilotiGenMAPP_Builder_2.0b73.zip]]

Computer on which export was run: Keck Lab Computer, front computer (closest to the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import: 6.27 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import: 6.07 minutes
* Time taken to process: 12.42 minutes
**NOTE: gmbuilder told me that the GO OBO-XML file was already processed in the database, and wanted to know if I wanted to process the information again. I chose yes.

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import: 0.07 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file:
* Time taken to export .gdb: started around 10am
* Upload your file and link to it here.

==Important Files 4==

'''From Week 14, December 3-5, 2013'''

NOTE: Here is the other import/export, using a new database on a different Keck Lab computer

Taxon ID: 266834

Version of GenMAPP Builder: [[Media: SmelilotiGenMAPP_Builder_2.0b73.zip]]

Computer on which export was run: Keck Lab Computer, front computer (closest to the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import: 6.25 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import: 6.21 minutes
* Time taken to process: 4.50 minutes

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import: 0.07 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file: [[Media:Sinorhizobium_meliloti_1021_mpetredi_2013123-2.gdb]]
* Time taken to export .gdb: Started at 10:28am. Finished at 1:36pm

* Upload your file and link to it here.

==Wiki Navigation==
{{Team Name}}
*[[Teamname Week 13 Status Report]]
*[[Laurmagee: Week 13]]

Team Name

2013-12-04T06:29:36Z

Mpetredi: /* Important Files 4 */ added gmbuilder version

Species: ''Sinorhizobium Meliloti'' (Strain 1021)
==Group Project==
[[media:Sinorhizobium_Meliloti_group_project.pdf|Group Project]]

==Personnel==
===Stephen Louie===
Project Manager, Quality Assurance
:slouie4 at lion.lmu.edu
:1 LMU Drive MSB 5194
:Los Angeles, CA 90045
:[[Stephen Louie Project Notebook|Stephen Louie Project Notebook]]

===Lauren Magee===
GenMAPP Expert
:lmagee1 at lion.lmu.edu
:1 LMU Drive MSB-5258,
:Los Angeles, CA 90045
===Mitchell Petredis===
Coding Supervisor
:mrpetredis at gmail dot com
:mpetredi at lion dot lmu dot edu
:Loyola Marymount University
:1 LMU Drive MSB-5957
:Los Angeles, CA 90045-2659
===Miles Malefyt===
GenMAPP Coordinator
:milesm@malefyt.com
:mmalefyt@lion.lmu.edu
:8416 Campion drive
:Westchester, CA 90045
cell: 831-236-5402

[[User:Mmalefyt|Mmalefyt]] ([[User talk:Mmalefyt|talk]]) 10:31, 31 October 2013 (PDT)

==Micro Array paper==

[[http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-785/?keywords=&organism=Sinorhizobium%20meliloti&array=&exptype Osmotic upshift elicited by salt and sucrose]]
*[[http://jb.asm.org/content/188/21/7617 HTML version]]
*[[http://jb.asm.org/content/188/21/7617.full.pdf+html PDF version]]
*[[Media:A-MEXP-230.adf.txt]]
*[[Media:E-MEXP-785.eSet.r]]
*[[Media:E-MEXP-785.processed.1.zip]]
*[[Media:E-MEXP-785.raw.2.zip]]
*[[Media:E-MEXP-785.idf.txt]]
*[[Media:E-MEXP-785.raw.1.zip]]
*[[Media:E-MEXP-785.sdrf.txt]]
*Raw Data File for 700S (1-3): [[File:Full Raw Data.xls]]
*[[File:Compiled Ratios and Logs.xls]]
*[[File:SinorhizobiumMeliloti_LM_GenMapp_DataSheet.txt]]
*[[File:SinorhizobiumMeliloti_LM_GenMapp_DataSheet.xls]]

Domínguez-Ferreras, A., Pérez-Arnedo, R., Becker, A., Olivares, J., Soto, M.J., Sanjuán, J. (2006) Transcriptome Profiling Reveals the Importance of Plasmid pSymB for Osmoadaptation of Sinorhizobium meliloti ''Journal of Bacteriology'' 188:7617-7625

==Genome Paper==

[http://search.proquest.com/docview/213572450?accountid=7418 The composite genome of the legume symbiont Sinorhizobium meliloti. Science 293, 668–672.]

Galibert, F., Finan, T.M., Long, S., Puhler, A., et al. (2001) The composite genome of the legume symbiont Sinorhizobium meliloti ''Science'' 293:668-672

[[Category: Sinorhizobium meliloti]]
[[Category: Group Projects]]

==Model Organism Database==
Link: http://cmr.jcvi.org/tigr-scripts/CMR/GenomePage.cgi?org=ntsm01

==Compiled raw Data==
[[Media:Team_Name_NaCl_compiled_raw_Data.xls|300 NaCl compiled data set]]
==Compiled processed data==
[[Media:Complete_processed_Data.xls|Processed Data]]

==Data ready for GenMAPP==
[[Media:Data_Sets_ratio2.xls|NaCl 300mm XLS version]]

[[Media:Data_Sets_ratio2.txt|NaCl 300mm TXT Version]]

==Important Files==

Taxon ID: 266834

Version of GenMAPP Builder: [[Media: gmbuilder-2.0b71.zip | gmbuilder-2.0b71.zip]]

Computer on which export was run: Keck Lab Computer, back computer (furthest from the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import:19.17 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import: 17.81 minutes
* Time taken to process: 15.54 minutes

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import: 0.21 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file: [[Media:Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_2013117.gdb | Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_2013117.gdb]]
* Time taken to export .gdb: Started at 2pm on 11-7-2013, finished at 9:47pm
* Upload your file and link to it here.

Note:

replace geneID with ~ when you find MOD link

==Important Files 2==

Info based on export done on 11/21/2013

Taxon ID: 266834

Version of GenMAPP Builder: [[Media:GenMAPP_Builder_2.0b72 S. meliloti.zip|GenMAPP_Builder_2.0b72 S. meliloti.zip]]

Computer on which export was run: Keck Lab Computer, front computer (closest to the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import: 7.34 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import: 6.31 minutes
* Time taken to process: 4.60 minutes

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import: 0.07 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file: [[Media:Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_20131121.gdb|Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_20131121.gdb]]
* Time taken to export .gdb: Started at 10:18 AM on 11/21/2013; ended at 1:34 PM

==Important Files 3==

'''From Week 14, December 3-5, 2013'''

NOTE: Forgot that I cannot import data into the same database. I will continue to do an export based on what I have, and will do another import/export cycle on another computer using the same version of gmbuilder that I used here.

Taxon ID: 266834

Version of GenMAPP Builder:

Computer on which export was run: Keck Lab Computer, front computer (closest to the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import: 6.27 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import: 6.07 minutes
* Time taken to process: 12.42 minutes
**NOTE: gmbuilder told me that the GO OBO-XML file was already processed in the database, and wanted to know if I wanted to process the information again. I chose yes.

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import: 0.07 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file:
* Time taken to export .gdb: started around 10am
* Upload your file and link to it here.

==Important Files 4==

'''From Week 14, December 3-5, 2013'''

NOTE: Here is the other import/export, using a new database on a different Keck Lab computer

Taxon ID: 266834

Version of GenMAPP Builder: [[Media: SmelilotiGenMAPP_Builder_2.0b73.zip]]

Computer on which export was run: Keck Lab Computer, front computer (closest to the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import: 6.25 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import: 6.21 minutes
* Time taken to process: 4.50 minutes

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import: 0.07 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file: [[Media:Sinorhizobium_meliloti_1021_mpetredi_2013123-2.gdb]]
* Time taken to export .gdb: Started at 10:28am. Finished at 1:36pm

* Upload your file and link to it here.

==Wiki Navigation==
{{Team Name}}
*[[Teamname Week 13 Status Report]]
*[[Laurmagee: Week 13]]

File:Sinorhizobium meliloti 1021 mpetredi 2013123-2.gdb

2013-12-04T06:24:38Z

Mpetredi: Fourth export done, using gmbuilder "b73" on a new database

Fourth export done, using gmbuilder "b73" on a new database

Team Name

2013-12-04T06:20:54Z

Mpetredi: /* Important Files 4 */ added link to 4th gdb file

Species: ''Sinorhizobium Meliloti'' (Strain 1021)
==Group Project==
[[media:Sinorhizobium_Meliloti_group_project.pdf|Group Project]]

==Personnel==
===Stephen Louie===
Project Manager, Quality Assurance
:slouie4 at lion.lmu.edu
:1 LMU Drive MSB 5194
:Los Angeles, CA 90045
:[[Stephen Louie Project Notebook|Stephen Louie Project Notebook]]

===Lauren Magee===
GenMAPP Expert
:lmagee1 at lion.lmu.edu
:1 LMU Drive MSB-5258,
:Los Angeles, CA 90045
===Mitchell Petredis===
Coding Supervisor
:mrpetredis at gmail dot com
:mpetredi at lion dot lmu dot edu
:Loyola Marymount University
:1 LMU Drive MSB-5957
:Los Angeles, CA 90045-2659
===Miles Malefyt===
GenMAPP Coordinator
:milesm@malefyt.com
:mmalefyt@lion.lmu.edu
:8416 Campion drive
:Westchester, CA 90045
cell: 831-236-5402

[[User:Mmalefyt|Mmalefyt]] ([[User talk:Mmalefyt|talk]]) 10:31, 31 October 2013 (PDT)

==Micro Array paper==

[[http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-785/?keywords=&organism=Sinorhizobium%20meliloti&array=&exptype Osmotic upshift elicited by salt and sucrose]]
*[[http://jb.asm.org/content/188/21/7617 HTML version]]
*[[http://jb.asm.org/content/188/21/7617.full.pdf+html PDF version]]
*[[Media:A-MEXP-230.adf.txt]]
*[[Media:E-MEXP-785.eSet.r]]
*[[Media:E-MEXP-785.processed.1.zip]]
*[[Media:E-MEXP-785.raw.2.zip]]
*[[Media:E-MEXP-785.idf.txt]]
*[[Media:E-MEXP-785.raw.1.zip]]
*[[Media:E-MEXP-785.sdrf.txt]]
*Raw Data File for 700S (1-3): [[File:Full Raw Data.xls]]
*[[File:Compiled Ratios and Logs.xls]]
*[[File:SinorhizobiumMeliloti_LM_GenMapp_DataSheet.txt]]
*[[File:SinorhizobiumMeliloti_LM_GenMapp_DataSheet.xls]]

Domínguez-Ferreras, A., Pérez-Arnedo, R., Becker, A., Olivares, J., Soto, M.J., Sanjuán, J. (2006) Transcriptome Profiling Reveals the Importance of Plasmid pSymB for Osmoadaptation of Sinorhizobium meliloti ''Journal of Bacteriology'' 188:7617-7625

==Genome Paper==

[http://search.proquest.com/docview/213572450?accountid=7418 The composite genome of the legume symbiont Sinorhizobium meliloti. Science 293, 668–672.]

Galibert, F., Finan, T.M., Long, S., Puhler, A., et al. (2001) The composite genome of the legume symbiont Sinorhizobium meliloti ''Science'' 293:668-672

[[Category: Sinorhizobium meliloti]]
[[Category: Group Projects]]

==Model Organism Database==
Link: http://cmr.jcvi.org/tigr-scripts/CMR/GenomePage.cgi?org=ntsm01

==Compiled raw Data==
[[Media:Team_Name_NaCl_compiled_raw_Data.xls|300 NaCl compiled data set]]
==Compiled processed data==
[[Media:Complete_processed_Data.xls|Processed Data]]

==Data ready for GenMAPP==
[[Media:Data_Sets_ratio2.xls|NaCl 300mm XLS version]]

[[Media:Data_Sets_ratio2.txt|NaCl 300mm TXT Version]]

==Important Files==

Taxon ID: 266834

Version of GenMAPP Builder: [[Media: gmbuilder-2.0b71.zip | gmbuilder-2.0b71.zip]]

Computer on which export was run: Keck Lab Computer, back computer (furthest from the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import:19.17 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import: 17.81 minutes
* Time taken to process: 15.54 minutes

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import: 0.21 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file: [[Media:Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_2013117.gdb | Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_2013117.gdb]]
* Time taken to export .gdb: Started at 2pm on 11-7-2013, finished at 9:47pm
* Upload your file and link to it here.

Note:

replace geneID with ~ when you find MOD link

==Important Files 2==

Info based on export done on 11/21/2013

Taxon ID: 266834

Version of GenMAPP Builder: [[Media:GenMAPP_Builder_2.0b72 S. meliloti.zip|GenMAPP_Builder_2.0b72 S. meliloti.zip]]

Computer on which export was run: Keck Lab Computer, front computer (closest to the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import: 7.34 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import: 6.31 minutes
* Time taken to process: 4.60 minutes

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import: 0.07 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file: [[Media:Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_20131121.gdb|Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_20131121.gdb]]
* Time taken to export .gdb: Started at 10:18 AM on 11/21/2013; ended at 1:34 PM

==Important Files 3==

'''From Week 14, December 3-5, 2013'''

NOTE: Forgot that I cannot import data into the same database. I will continue to do an export based on what I have, and will do another import/export cycle on another computer using the same version of gmbuilder that I used here.

Taxon ID: 266834

Version of GenMAPP Builder:

Computer on which export was run: Keck Lab Computer, front computer (closest to the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import: 6.27 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import: 6.07 minutes
* Time taken to process: 12.42 minutes
**NOTE: gmbuilder told me that the GO OBO-XML file was already processed in the database, and wanted to know if I wanted to process the information again. I chose yes.

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import: 0.07 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file:
* Time taken to export .gdb: started around 10am
* Upload your file and link to it here.

==Important Files 4==

'''From Week 14, December 3-5, 2013'''

NOTE: Here is the other import/export, using a new database on a different Keck Lab computer

Taxon ID: 266834

Version of GenMAPP Builder:

Computer on which export was run: Keck Lab Computer, front computer (closest to the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import: 6.25 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import: 6.21 minutes
* Time taken to process: 4.50 minutes

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import: 0.07 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file: [[Media:Sinorhizobium_meliloti_1021_mpetredi_2013123-2.gdb]]
* Time taken to export .gdb: Started at 10:28am. Finished at 1:36pm

* Upload your file and link to it here.

==Wiki Navigation==
{{Team Name}}
*[[Teamname Week 13 Status Report]]
*[[Laurmagee: Week 13]]

Team Name

2013-12-03T22:40:56Z

Mpetredi: /* Important Files 4 */ added time to export gdb

Species: ''Sinorhizobium Meliloti'' (Strain 1021)
==Group Project==
[[media:Sinorhizobium_Meliloti_group_project.pdf|Group Project]]

==Personnel==
===Stephen Louie===
Project Manager, Quality Assurance
:slouie4 at lion.lmu.edu
:1 LMU Drive MSB 5194
:Los Angeles, CA 90045
:[[Stephen Louie Project Notebook|Stephen Louie Project Notebook]]

===Lauren Magee===
GenMAPP Expert
:lmagee1 at lion.lmu.edu
:1 LMU Drive MSB-5258,
:Los Angeles, CA 90045
===Mitchell Petredis===
Coding Supervisor
:mrpetredis at gmail dot com
:mpetredi at lion dot lmu dot edu
:Loyola Marymount University
:1 LMU Drive MSB-5957
:Los Angeles, CA 90045-2659
===Miles Malefyt===
GenMAPP Coordinator
:milesm@malefyt.com
:mmalefyt@lion.lmu.edu
:8416 Campion drive
:Westchester, CA 90045
cell: 831-236-5402

[[User:Mmalefyt|Mmalefyt]] ([[User talk:Mmalefyt|talk]]) 10:31, 31 October 2013 (PDT)

==Micro Array paper==

[[http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-785/?keywords=&organism=Sinorhizobium%20meliloti&array=&exptype Osmotic upshift elicited by salt and sucrose]]
*[[http://jb.asm.org/content/188/21/7617 HTML version]]
*[[http://jb.asm.org/content/188/21/7617.full.pdf+html PDF version]]
*[[Media:A-MEXP-230.adf.txt]]
*[[Media:E-MEXP-785.eSet.r]]
*[[Media:E-MEXP-785.processed.1.zip]]
*[[Media:E-MEXP-785.raw.2.zip]]
*[[Media:E-MEXP-785.idf.txt]]
*[[Media:E-MEXP-785.raw.1.zip]]
*[[Media:E-MEXP-785.sdrf.txt]]
*Raw Data File for 700S (1-3): [[File:Full Raw Data.xls]]
*[[File:Compiled Ratios and Logs.xls]]
*[[File:SinorhizobiumMeliloti_LM_GenMapp_DataSheet.txt]]
*[[File:SinorhizobiumMeliloti_LM_GenMapp_DataSheet.xls]]

Domínguez-Ferreras, A., Pérez-Arnedo, R., Becker, A., Olivares, J., Soto, M.J., Sanjuán, J. (2006) Transcriptome Profiling Reveals the Importance of Plasmid pSymB for Osmoadaptation of Sinorhizobium meliloti ''Journal of Bacteriology'' 188:7617-7625

==Genome Paper==

[http://search.proquest.com/docview/213572450?accountid=7418 The composite genome of the legume symbiont Sinorhizobium meliloti. Science 293, 668–672.]

Galibert, F., Finan, T.M., Long, S., Puhler, A., et al. (2001) The composite genome of the legume symbiont Sinorhizobium meliloti ''Science'' 293:668-672

[[Category: Sinorhizobium meliloti]]
[[Category: Group Projects]]

==Model Organism Database==
Link: http://cmr.jcvi.org/tigr-scripts/CMR/GenomePage.cgi?org=ntsm01

==Compiled raw Data==
[[Media:Team_Name_NaCl_compiled_raw_Data.xls|300 NaCl compiled data set]]
==Compiled processed data==
[[Media:Complete_processed_Data.xls|Processed Data]]

==Data ready for GenMAPP==
[[Media:Data_Sets_ratio2.xls|NaCl 300mm XLS version]]

[[Media:Data_Sets_ratio2.txt|NaCl 300mm TXT Version]]

==Important Files==

Taxon ID: 266834

Version of GenMAPP Builder: [[Media: gmbuilder-2.0b71.zip | gmbuilder-2.0b71.zip]]

Computer on which export was run: Keck Lab Computer, back computer (furthest from the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import:19.17 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import: 17.81 minutes
* Time taken to process: 15.54 minutes

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import: 0.21 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file: [[Media:Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_2013117.gdb | Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_2013117.gdb]]
* Time taken to export .gdb: Started at 2pm on 11-7-2013, finished at 9:47pm
* Upload your file and link to it here.

Note:

replace geneID with ~ when you find MOD link

==Important Files 2==

Info based on export done on 11/21/2013

Taxon ID: 266834

Version of GenMAPP Builder: [[Media:GenMAPP_Builder_2.0b72 S. meliloti.zip|GenMAPP_Builder_2.0b72 S. meliloti.zip]]

Computer on which export was run: Keck Lab Computer, front computer (closest to the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import: 7.34 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import: 6.31 minutes
* Time taken to process: 4.60 minutes

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import: 0.07 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file: [[Media:Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_20131121.gdb|Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_20131121.gdb]]
* Time taken to export .gdb: Started at 10:18 AM on 11/21/2013; ended at 1:34 PM

==Important Files 3==

'''From Week 14, December 3-5, 2013'''

NOTE: Forgot that I cannot import data into the same database. I will continue to do an export based on what I have, and will do another import/export cycle on another computer using the same version of gmbuilder that I used here.

Taxon ID: 266834

Version of GenMAPP Builder:

Computer on which export was run: Keck Lab Computer, front computer (closest to the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import: 6.27 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import: 6.07 minutes
* Time taken to process: 12.42 minutes
**NOTE: gmbuilder told me that the GO OBO-XML file was already processed in the database, and wanted to know if I wanted to process the information again. I chose yes.

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import: 0.07 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file:
* Time taken to export .gdb: started around 10am
* Upload your file and link to it here.

==Important Files 4==

'''From Week 14, December 3-5, 2013'''

NOTE: Here is the other import/export, using a new database on a different Keck Lab computer

Taxon ID: 266834

Version of GenMAPP Builder:

Computer on which export was run: Keck Lab Computer, front computer (closest to the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import: 6.25 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import: 6.21 minutes
* Time taken to process: 4.50 minutes

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import: 0.07 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file:
* Time taken to export .gdb: Started at 10:28am. Finished at 1:36pm

* Upload your file and link to it here.

==Wiki Navigation==
{{Team Name}}
*[[Teamname Week 13 Status Report]]
*[[Laurmagee: Week 13]]

Mpetredi Week 14

2013-12-03T18:31:12Z

Mpetredi: added image of new string of code

==[[user:mpetredi|'''Mitchell Petredis''']]==

'''Lab Progression'''

==December 3, 2013==
*Added the following string of code in Eclipse (line is highlighted)
**[[Image:2013123_New_String_of_Code.PNG]]
**String of code also available below as text:

@Override
public TableManager getSystemTableManagerCustomizations(TableManager tableManager, TableManager primarySystemTableManager, Date version) throws SQLException, InvalidParameterException {
List<String> comparisonList = new ArrayList<String>();
comparisonList.add("ordered locus");
comparisonList.add("ORF");

return systemTableManagerCustomizationsHelper(tableManager, primarySystemTableManager, version, "OrderedLocusNames", comparisonList);
}
*Used all files except for the .gdb to run another import/export, using the latest version of gmbuilder
*All information pertaining to import/export 3 can be found under [[[[Team Name]]]] in "Important Files 3".

[[[[Team Name]]]]

File:2013123 New String of Code.PNG

2013-12-03T18:29:55Z

Mpetredi: shows the string of code added on December 3, 2013 and where it was placed in Eclipse

shows the string of code added on December 3, 2013 and where it was placed in Eclipse

Team Name

2013-12-03T18:28:43Z

Mpetredi: /* Important Files 3 */ note about start time of gdb export

Species: ''Sinorhizobium Meliloti'' (Strain 1021)
==Group Project==
[[media:Sinorhizobium_Meliloti_group_project.pdf|Group Project]]

==Personnel==
===Stephen Louie===
Project Manager, Quality Assurance
:slouie4 at lion.lmu.edu
:1 LMU Drive MSB 5194
:Los Angeles, CA 90045
:[[Stephen Louie Project Notebook|Stephen Louie Project Notebook]]

===Lauren Magee===
GenMAPP Expert
:lmagee1 at lion.lmu.edu
:1 LMU Drive MSB-5258,
:Los Angeles, CA 90045
===Mitchell Petredis===
Coding Supervisor
:mrpetredis at gmail dot com
:mpetredi at lion dot lmu dot edu
:Loyola Marymount University
:1 LMU Drive MSB-5957
:Los Angeles, CA 90045-2659
===Miles Malefyt===
GenMAPP Coordinator
:milesm@malefyt.com
:mmalefyt@lion.lmu.edu
:8416 Campion drive
:Westchester, CA 90045
cell: 831-236-5402

[[User:Mmalefyt|Mmalefyt]] ([[User talk:Mmalefyt|talk]]) 10:31, 31 October 2013 (PDT)

==Micro Array paper==

[[http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-785/?keywords=&organism=Sinorhizobium%20meliloti&array=&exptype Osmotic upshift elicited by salt and sucrose]]
*[[http://jb.asm.org/content/188/21/7617 HTML version]]
*[[http://jb.asm.org/content/188/21/7617.full.pdf+html PDF version]]
*[[Media:A-MEXP-230.adf.txt]]
*[[Media:E-MEXP-785.eSet.r]]
*[[Media:E-MEXP-785.processed.1.zip]]
*[[Media:E-MEXP-785.raw.2.zip]]
*[[Media:E-MEXP-785.idf.txt]]
*[[Media:E-MEXP-785.raw.1.zip]]
*[[Media:E-MEXP-785.sdrf.txt]]
*Raw Data File for 700S (1-3): [[File:Full Raw Data.xls]]
*[[File:Compiled Ratios and Logs.xls]]
*[[File:SinorhizobiumMeliloti_LM_GenMapp_DataSheet.txt]]
*[[File:SinorhizobiumMeliloti_LM_GenMapp_DataSheet.xls]]

Domínguez-Ferreras, A., Pérez-Arnedo, R., Becker, A., Olivares, J., Soto, M.J., Sanjuán, J. (2006) Transcriptome Profiling Reveals the Importance of Plasmid pSymB for Osmoadaptation of Sinorhizobium meliloti ''Journal of Bacteriology'' 188:7617-7625

==Genome Paper==

[http://search.proquest.com/docview/213572450?accountid=7418 The composite genome of the legume symbiont Sinorhizobium meliloti. Science 293, 668–672.]

Galibert, F., Finan, T.M., Long, S., Puhler, A., et al. (2001) The composite genome of the legume symbiont Sinorhizobium meliloti ''Science'' 293:668-672

[[Category: Sinorhizobium meliloti]]
[[Category: Group Projects]]

==Model Organism Database==
Link: http://cmr.jcvi.org/tigr-scripts/CMR/GenomePage.cgi?org=ntsm01

==Compiled raw Data==
[[Media:Team_Name_NaCl_compiled_raw_Data.xls|300 NaCl compiled data set]]
==Compiled processed data==
[[Media:Complete_processed_Data.xls|Processed Data]]

==Data ready for GenMAPP==
[[Media:Data_Sets_ratio2.xls|NaCl 300mm XLS version]]

[[Media:Data_Sets_ratio2.txt|NaCl 300mm TXT Version]]

==Important Files==

Taxon ID: 266834

Version of GenMAPP Builder: [[Media: gmbuilder-2.0b71.zip | gmbuilder-2.0b71.zip]]

Computer on which export was run: Keck Lab Computer, back computer (furthest from the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import:19.17 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import: 17.81 minutes
* Time taken to process: 15.54 minutes

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import: 0.21 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file: [[Media:Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_2013117.gdb | Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_2013117.gdb]]
* Time taken to export .gdb: Started at 2pm on 11-7-2013, finished at 9:47pm
* Upload your file and link to it here.

Note:

replace geneID with ~ when you find MOD link

==Important Files 2==

Info based on export done on 11/21/2013

Taxon ID: 266834

Version of GenMAPP Builder: [[Media:GenMAPP_Builder_2.0b72 S. meliloti.zip|GenMAPP_Builder_2.0b72 S. meliloti.zip]]

Computer on which export was run: Keck Lab Computer, front computer (closest to the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import: 7.34 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import: 6.31 minutes
* Time taken to process: 4.60 minutes

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import: 0.07 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file: [[Media:Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_20131121.gdb|Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_20131121.gdb]]
* Time taken to export .gdb: Started at 10:18 AM on 11/21/2013; ended at 1:34 PM

==Important Files 3==

'''From Week 14, December 3-5, 2013'''

NOTE: Forgot that I cannot import data into the same database. I will continue to do an export based on what I have, and will do another import/export cycle on another computer using the same version of gmbuilder that I used here.

Taxon ID: 266834

Version of GenMAPP Builder:

Computer on which export was run: Keck Lab Computer, front computer (closest to the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import: 6.27 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import: 6.07 minutes
* Time taken to process: 12.42 minutes
**NOTE: gmbuilder told me that the GO OBO-XML file was already processed in the database, and wanted to know if I wanted to process the information again. I chose yes.

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import: 0.07 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file:
* Time taken to export .gdb: started around 10am
* Upload your file and link to it here.

==Important Files 4==

'''From Week 14, December 3-5, 2013'''

NOTE: Here is the other import/export, using a new database on a different Keck Lab computer

Taxon ID: 266834

Version of GenMAPP Builder:

Computer on which export was run: Keck Lab Computer, front computer (closest to the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import: 6.25 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import: 6.21 minutes
* Time taken to process: 4.50 minutes

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import: 0.07 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file:
* Time taken to export .gdb: Started at 10:28am

* Upload your file and link to it here.

==Wiki Navigation==
{{Team Name}}
*[[Teamname Week 13 Status Report]]
*[[Laurmagee: Week 13]]

Team Name

2013-12-03T18:27:08Z

Mpetredi: /* Important Files 4 */ added note about gdb export

Species: ''Sinorhizobium Meliloti'' (Strain 1021)
==Group Project==
[[media:Sinorhizobium_Meliloti_group_project.pdf|Group Project]]

==Personnel==
===Stephen Louie===
Project Manager, Quality Assurance
:slouie4 at lion.lmu.edu
:1 LMU Drive MSB 5194
:Los Angeles, CA 90045
:[[Stephen Louie Project Notebook|Stephen Louie Project Notebook]]

===Lauren Magee===
GenMAPP Expert
:lmagee1 at lion.lmu.edu
:1 LMU Drive MSB-5258,
:Los Angeles, CA 90045
===Mitchell Petredis===
Coding Supervisor
:mrpetredis at gmail dot com
:mpetredi at lion dot lmu dot edu
:Loyola Marymount University
:1 LMU Drive MSB-5957
:Los Angeles, CA 90045-2659
===Miles Malefyt===
GenMAPP Coordinator
:milesm@malefyt.com
:mmalefyt@lion.lmu.edu
:8416 Campion drive
:Westchester, CA 90045
cell: 831-236-5402

[[User:Mmalefyt|Mmalefyt]] ([[User talk:Mmalefyt|talk]]) 10:31, 31 October 2013 (PDT)

==Micro Array paper==

[[http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-785/?keywords=&organism=Sinorhizobium%20meliloti&array=&exptype Osmotic upshift elicited by salt and sucrose]]
*[[http://jb.asm.org/content/188/21/7617 HTML version]]
*[[http://jb.asm.org/content/188/21/7617.full.pdf+html PDF version]]
*[[Media:A-MEXP-230.adf.txt]]
*[[Media:E-MEXP-785.eSet.r]]
*[[Media:E-MEXP-785.processed.1.zip]]
*[[Media:E-MEXP-785.raw.2.zip]]
*[[Media:E-MEXP-785.idf.txt]]
*[[Media:E-MEXP-785.raw.1.zip]]
*[[Media:E-MEXP-785.sdrf.txt]]
*Raw Data File for 700S (1-3): [[File:Full Raw Data.xls]]
*[[File:Compiled Ratios and Logs.xls]]
*[[File:SinorhizobiumMeliloti_LM_GenMapp_DataSheet.txt]]
*[[File:SinorhizobiumMeliloti_LM_GenMapp_DataSheet.xls]]

Domínguez-Ferreras, A., Pérez-Arnedo, R., Becker, A., Olivares, J., Soto, M.J., Sanjuán, J. (2006) Transcriptome Profiling Reveals the Importance of Plasmid pSymB for Osmoadaptation of Sinorhizobium meliloti ''Journal of Bacteriology'' 188:7617-7625

==Genome Paper==

[http://search.proquest.com/docview/213572450?accountid=7418 The composite genome of the legume symbiont Sinorhizobium meliloti. Science 293, 668–672.]

Galibert, F., Finan, T.M., Long, S., Puhler, A., et al. (2001) The composite genome of the legume symbiont Sinorhizobium meliloti ''Science'' 293:668-672

[[Category: Sinorhizobium meliloti]]
[[Category: Group Projects]]

==Model Organism Database==
Link: http://cmr.jcvi.org/tigr-scripts/CMR/GenomePage.cgi?org=ntsm01

==Compiled raw Data==
[[Media:Team_Name_NaCl_compiled_raw_Data.xls|300 NaCl compiled data set]]
==Compiled processed data==
[[Media:Complete_processed_Data.xls|Processed Data]]

==Data ready for GenMAPP==
[[Media:Data_Sets_ratio2.xls|NaCl 300mm XLS version]]

[[Media:Data_Sets_ratio2.txt|NaCl 300mm TXT Version]]

==Important Files==

Taxon ID: 266834

Version of GenMAPP Builder: [[Media: gmbuilder-2.0b71.zip | gmbuilder-2.0b71.zip]]

Computer on which export was run: Keck Lab Computer, back computer (furthest from the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import:19.17 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import: 17.81 minutes
* Time taken to process: 15.54 minutes

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import: 0.21 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file: [[Media:Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_2013117.gdb | Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_2013117.gdb]]
* Time taken to export .gdb: Started at 2pm on 11-7-2013, finished at 9:47pm
* Upload your file and link to it here.

Note:

replace geneID with ~ when you find MOD link

==Important Files 2==

Info based on export done on 11/21/2013

Taxon ID: 266834

Version of GenMAPP Builder: [[Media:GenMAPP_Builder_2.0b72 S. meliloti.zip|GenMAPP_Builder_2.0b72 S. meliloti.zip]]

Computer on which export was run: Keck Lab Computer, front computer (closest to the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import: 7.34 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import: 6.31 minutes
* Time taken to process: 4.60 minutes

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import: 0.07 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file: [[Media:Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_20131121.gdb|Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_20131121.gdb]]
* Time taken to export .gdb: Started at 10:18 AM on 11/21/2013; ended at 1:34 PM

==Important Files 3==

'''From Week 14, December 3-5, 2013'''

NOTE: Forgot that I cannot import data into the same database. I will continue to do an export based on what I have, and will do another import/export cycle on another computer using the same version of gmbuilder that I used here.

Taxon ID: 266834

Version of GenMAPP Builder:

Computer on which export was run: Keck Lab Computer, front computer (closest to the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import: 6.27 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import: 6.07 minutes
* Time taken to process: 12.42 minutes
**NOTE: gmbuilder told me that the GO OBO-XML file was already processed in the database, and wanted to know if I wanted to process the information again. I chose yes.

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import: 0.07 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

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

==Important Files 4==

'''From Week 14, December 3-5, 2013'''

NOTE: Here is the other import/export, using a new database on a different Keck Lab computer

Taxon ID: 266834

Version of GenMAPP Builder:

Computer on which export was run: Keck Lab Computer, front computer (closest to the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import: 6.25 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import: 6.21 minutes
* Time taken to process: 4.50 minutes

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import: 0.07 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file:
* Time taken to export .gdb: Started at 10:28am

* Upload your file and link to it here.

==Wiki Navigation==
{{Team Name}}
*[[Teamname Week 13 Status Report]]
*[[Laurmagee: Week 13]]

Team Name

2013-12-03T18:25:47Z

Mpetredi: /* Important Files 4 */ added time to import goa file

Species: ''Sinorhizobium Meliloti'' (Strain 1021)
==Group Project==
[[media:Sinorhizobium_Meliloti_group_project.pdf|Group Project]]

==Personnel==
===Stephen Louie===
Project Manager, Quality Assurance
:slouie4 at lion.lmu.edu
:1 LMU Drive MSB 5194
:Los Angeles, CA 90045
:[[Stephen Louie Project Notebook|Stephen Louie Project Notebook]]

===Lauren Magee===
GenMAPP Expert
:lmagee1 at lion.lmu.edu
:1 LMU Drive MSB-5258,
:Los Angeles, CA 90045
===Mitchell Petredis===
Coding Supervisor
:mrpetredis at gmail dot com
:mpetredi at lion dot lmu dot edu
:Loyola Marymount University
:1 LMU Drive MSB-5957
:Los Angeles, CA 90045-2659
===Miles Malefyt===
GenMAPP Coordinator
:milesm@malefyt.com
:mmalefyt@lion.lmu.edu
:8416 Campion drive
:Westchester, CA 90045
cell: 831-236-5402

[[User:Mmalefyt|Mmalefyt]] ([[User talk:Mmalefyt|talk]]) 10:31, 31 October 2013 (PDT)

==Micro Array paper==

[[http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-785/?keywords=&organism=Sinorhizobium%20meliloti&array=&exptype Osmotic upshift elicited by salt and sucrose]]
*[[http://jb.asm.org/content/188/21/7617 HTML version]]
*[[http://jb.asm.org/content/188/21/7617.full.pdf+html PDF version]]
*[[Media:A-MEXP-230.adf.txt]]
*[[Media:E-MEXP-785.eSet.r]]
*[[Media:E-MEXP-785.processed.1.zip]]
*[[Media:E-MEXP-785.raw.2.zip]]
*[[Media:E-MEXP-785.idf.txt]]
*[[Media:E-MEXP-785.raw.1.zip]]
*[[Media:E-MEXP-785.sdrf.txt]]
*Raw Data File for 700S (1-3): [[File:Full Raw Data.xls]]
*[[File:Compiled Ratios and Logs.xls]]
*[[File:SinorhizobiumMeliloti_LM_GenMapp_DataSheet.txt]]
*[[File:SinorhizobiumMeliloti_LM_GenMapp_DataSheet.xls]]

Domínguez-Ferreras, A., Pérez-Arnedo, R., Becker, A., Olivares, J., Soto, M.J., Sanjuán, J. (2006) Transcriptome Profiling Reveals the Importance of Plasmid pSymB for Osmoadaptation of Sinorhizobium meliloti ''Journal of Bacteriology'' 188:7617-7625

==Genome Paper==

[http://search.proquest.com/docview/213572450?accountid=7418 The composite genome of the legume symbiont Sinorhizobium meliloti. Science 293, 668–672.]

Galibert, F., Finan, T.M., Long, S., Puhler, A., et al. (2001) The composite genome of the legume symbiont Sinorhizobium meliloti ''Science'' 293:668-672

[[Category: Sinorhizobium meliloti]]
[[Category: Group Projects]]

==Model Organism Database==
Link: http://cmr.jcvi.org/tigr-scripts/CMR/GenomePage.cgi?org=ntsm01

==Compiled raw Data==
[[Media:Team_Name_NaCl_compiled_raw_Data.xls|300 NaCl compiled data set]]
==Compiled processed data==
[[Media:Complete_processed_Data.xls|Processed Data]]

==Data ready for GenMAPP==
[[Media:Data_Sets_ratio2.xls|NaCl 300mm XLS version]]

[[Media:Data_Sets_ratio2.txt|NaCl 300mm TXT Version]]

==Important Files==

Taxon ID: 266834

Version of GenMAPP Builder: [[Media: gmbuilder-2.0b71.zip | gmbuilder-2.0b71.zip]]

Computer on which export was run: Keck Lab Computer, back computer (furthest from the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import:19.17 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import: 17.81 minutes
* Time taken to process: 15.54 minutes

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import: 0.21 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file: [[Media:Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_2013117.gdb | Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_2013117.gdb]]
* Time taken to export .gdb: Started at 2pm on 11-7-2013, finished at 9:47pm
* Upload your file and link to it here.

Note:

replace geneID with ~ when you find MOD link

==Important Files 2==

Info based on export done on 11/21/2013

Taxon ID: 266834

Version of GenMAPP Builder: [[Media:GenMAPP_Builder_2.0b72 S. meliloti.zip|GenMAPP_Builder_2.0b72 S. meliloti.zip]]

Computer on which export was run: Keck Lab Computer, front computer (closest to the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import: 7.34 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import: 6.31 minutes
* Time taken to process: 4.60 minutes

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import: 0.07 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file: [[Media:Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_20131121.gdb|Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_20131121.gdb]]
* Time taken to export .gdb: Started at 10:18 AM on 11/21/2013; ended at 1:34 PM

==Important Files 3==

'''From Week 14, December 3-5, 2013'''

NOTE: Forgot that I cannot import data into the same database. I will continue to do an export based on what I have, and will do another import/export cycle on another computer using the same version of gmbuilder that I used here.

Taxon ID: 266834

Version of GenMAPP Builder:

Computer on which export was run: Keck Lab Computer, front computer (closest to the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import: 6.27 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import: 6.07 minutes
* Time taken to process: 12.42 minutes
**NOTE: gmbuilder told me that the GO OBO-XML file was already processed in the database, and wanted to know if I wanted to process the information again. I chose yes.

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import: 0.07 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

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

==Important Files 4==

'''From Week 14, December 3-5, 2013'''

NOTE: Here is the other import/export, using a new database on a different Keck Lab computer

Taxon ID: 266834

Version of GenMAPP Builder:

Computer on which export was run: Keck Lab Computer, front computer (closest to the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import: 6.25 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import: 6.21 minutes
* Time taken to process: 4.50 minutes

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import: 0.07 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file:
* Time taken to export .gdb:

* Upload your file and link to it here.

==Wiki Navigation==
{{Team Name}}
*[[Teamname Week 13 Status Report]]
*[[Laurmagee: Week 13]]

Team Name

2013-12-03T18:24:55Z

Mpetredi: /* Important Files 4 */ added time to process obo-xml

Species: ''Sinorhizobium Meliloti'' (Strain 1021)
==Group Project==
[[media:Sinorhizobium_Meliloti_group_project.pdf|Group Project]]

==Personnel==
===Stephen Louie===
Project Manager, Quality Assurance
:slouie4 at lion.lmu.edu
:1 LMU Drive MSB 5194
:Los Angeles, CA 90045
:[[Stephen Louie Project Notebook|Stephen Louie Project Notebook]]

===Lauren Magee===
GenMAPP Expert
:lmagee1 at lion.lmu.edu
:1 LMU Drive MSB-5258,
:Los Angeles, CA 90045
===Mitchell Petredis===
Coding Supervisor
:mrpetredis at gmail dot com
:mpetredi at lion dot lmu dot edu
:Loyola Marymount University
:1 LMU Drive MSB-5957
:Los Angeles, CA 90045-2659
===Miles Malefyt===
GenMAPP Coordinator
:milesm@malefyt.com
:mmalefyt@lion.lmu.edu
:8416 Campion drive
:Westchester, CA 90045
cell: 831-236-5402

[[User:Mmalefyt|Mmalefyt]] ([[User talk:Mmalefyt|talk]]) 10:31, 31 October 2013 (PDT)

==Micro Array paper==

[[http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-785/?keywords=&organism=Sinorhizobium%20meliloti&array=&exptype Osmotic upshift elicited by salt and sucrose]]
*[[http://jb.asm.org/content/188/21/7617 HTML version]]
*[[http://jb.asm.org/content/188/21/7617.full.pdf+html PDF version]]
*[[Media:A-MEXP-230.adf.txt]]
*[[Media:E-MEXP-785.eSet.r]]
*[[Media:E-MEXP-785.processed.1.zip]]
*[[Media:E-MEXP-785.raw.2.zip]]
*[[Media:E-MEXP-785.idf.txt]]
*[[Media:E-MEXP-785.raw.1.zip]]
*[[Media:E-MEXP-785.sdrf.txt]]
*Raw Data File for 700S (1-3): [[File:Full Raw Data.xls]]
*[[File:Compiled Ratios and Logs.xls]]
*[[File:SinorhizobiumMeliloti_LM_GenMapp_DataSheet.txt]]
*[[File:SinorhizobiumMeliloti_LM_GenMapp_DataSheet.xls]]

Domínguez-Ferreras, A., Pérez-Arnedo, R., Becker, A., Olivares, J., Soto, M.J., Sanjuán, J. (2006) Transcriptome Profiling Reveals the Importance of Plasmid pSymB for Osmoadaptation of Sinorhizobium meliloti ''Journal of Bacteriology'' 188:7617-7625

==Genome Paper==

[http://search.proquest.com/docview/213572450?accountid=7418 The composite genome of the legume symbiont Sinorhizobium meliloti. Science 293, 668–672.]

Galibert, F., Finan, T.M., Long, S., Puhler, A., et al. (2001) The composite genome of the legume symbiont Sinorhizobium meliloti ''Science'' 293:668-672

[[Category: Sinorhizobium meliloti]]
[[Category: Group Projects]]

==Model Organism Database==
Link: http://cmr.jcvi.org/tigr-scripts/CMR/GenomePage.cgi?org=ntsm01

==Compiled raw Data==
[[Media:Team_Name_NaCl_compiled_raw_Data.xls|300 NaCl compiled data set]]
==Compiled processed data==
[[Media:Complete_processed_Data.xls|Processed Data]]

==Data ready for GenMAPP==
[[Media:Data_Sets_ratio2.xls|NaCl 300mm XLS version]]

[[Media:Data_Sets_ratio2.txt|NaCl 300mm TXT Version]]

==Important Files==

Taxon ID: 266834

Version of GenMAPP Builder: [[Media: gmbuilder-2.0b71.zip | gmbuilder-2.0b71.zip]]

Computer on which export was run: Keck Lab Computer, back computer (furthest from the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import:19.17 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import: 17.81 minutes
* Time taken to process: 15.54 minutes

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import: 0.21 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file: [[Media:Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_2013117.gdb | Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_2013117.gdb]]
* Time taken to export .gdb: Started at 2pm on 11-7-2013, finished at 9:47pm
* Upload your file and link to it here.

Note:

replace geneID with ~ when you find MOD link

==Important Files 2==

Info based on export done on 11/21/2013

Taxon ID: 266834

Version of GenMAPP Builder: [[Media:GenMAPP_Builder_2.0b72 S. meliloti.zip|GenMAPP_Builder_2.0b72 S. meliloti.zip]]

Computer on which export was run: Keck Lab Computer, front computer (closest to the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import: 7.34 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import: 6.31 minutes
* Time taken to process: 4.60 minutes

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import: 0.07 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file: [[Media:Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_20131121.gdb|Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_20131121.gdb]]
* Time taken to export .gdb: Started at 10:18 AM on 11/21/2013; ended at 1:34 PM

==Important Files 3==

'''From Week 14, December 3-5, 2013'''

NOTE: Forgot that I cannot import data into the same database. I will continue to do an export based on what I have, and will do another import/export cycle on another computer using the same version of gmbuilder that I used here.

Taxon ID: 266834

Version of GenMAPP Builder:

Computer on which export was run: Keck Lab Computer, front computer (closest to the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import: 6.27 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import: 6.07 minutes
* Time taken to process: 12.42 minutes
**NOTE: gmbuilder told me that the GO OBO-XML file was already processed in the database, and wanted to know if I wanted to process the information again. I chose yes.

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import: 0.07 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

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

==Important Files 4==

'''From Week 14, December 3-5, 2013'''

NOTE: Here is the other import/export, using a new database on a different Keck Lab computer

Taxon ID: 266834

Version of GenMAPP Builder:

Computer on which export was run: Keck Lab Computer, front computer (closest to the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import: 6.25 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import: 6.21 minutes
* Time taken to process: 4.50 minutes

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import:
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file:
* Time taken to export .gdb:

* Upload your file and link to it here.

==Wiki Navigation==
{{Team Name}}
*[[Teamname Week 13 Status Report]]
*[[Laurmagee: Week 13]]

Team Name

2013-12-03T18:18:51Z

Mpetredi: /* Important Files 4 */ added time to import obo-xml

Species: ''Sinorhizobium Meliloti'' (Strain 1021)
==Group Project==
[[media:Sinorhizobium_Meliloti_group_project.pdf|Group Project]]

==Personnel==
===Stephen Louie===
Project Manager, Quality Assurance
:slouie4 at lion.lmu.edu
:1 LMU Drive MSB 5194
:Los Angeles, CA 90045
:[[Stephen Louie Project Notebook|Stephen Louie Project Notebook]]

===Lauren Magee===
GenMAPP Expert
:lmagee1 at lion.lmu.edu
:1 LMU Drive MSB-5258,
:Los Angeles, CA 90045
===Mitchell Petredis===
Coding Supervisor
:mrpetredis at gmail dot com
:mpetredi at lion dot lmu dot edu
:Loyola Marymount University
:1 LMU Drive MSB-5957
:Los Angeles, CA 90045-2659
===Miles Malefyt===
GenMAPP Coordinator
:milesm@malefyt.com
:mmalefyt@lion.lmu.edu
:8416 Campion drive
:Westchester, CA 90045
cell: 831-236-5402

[[User:Mmalefyt|Mmalefyt]] ([[User talk:Mmalefyt|talk]]) 10:31, 31 October 2013 (PDT)

==Micro Array paper==

[[http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-785/?keywords=&organism=Sinorhizobium%20meliloti&array=&exptype Osmotic upshift elicited by salt and sucrose]]
*[[http://jb.asm.org/content/188/21/7617 HTML version]]
*[[http://jb.asm.org/content/188/21/7617.full.pdf+html PDF version]]
*[[Media:A-MEXP-230.adf.txt]]
*[[Media:E-MEXP-785.eSet.r]]
*[[Media:E-MEXP-785.processed.1.zip]]
*[[Media:E-MEXP-785.raw.2.zip]]
*[[Media:E-MEXP-785.idf.txt]]
*[[Media:E-MEXP-785.raw.1.zip]]
*[[Media:E-MEXP-785.sdrf.txt]]
*Raw Data File for 700S (1-3): [[File:Full Raw Data.xls]]
*[[File:Compiled Ratios and Logs.xls]]
*[[File:SinorhizobiumMeliloti_LM_GenMapp_DataSheet.txt]]
*[[File:SinorhizobiumMeliloti_LM_GenMapp_DataSheet.xls]]

Domínguez-Ferreras, A., Pérez-Arnedo, R., Becker, A., Olivares, J., Soto, M.J., Sanjuán, J. (2006) Transcriptome Profiling Reveals the Importance of Plasmid pSymB for Osmoadaptation of Sinorhizobium meliloti ''Journal of Bacteriology'' 188:7617-7625

==Genome Paper==

[http://search.proquest.com/docview/213572450?accountid=7418 The composite genome of the legume symbiont Sinorhizobium meliloti. Science 293, 668–672.]

Galibert, F., Finan, T.M., Long, S., Puhler, A., et al. (2001) The composite genome of the legume symbiont Sinorhizobium meliloti ''Science'' 293:668-672

[[Category: Sinorhizobium meliloti]]
[[Category: Group Projects]]

==Model Organism Database==
Link: http://cmr.jcvi.org/tigr-scripts/CMR/GenomePage.cgi?org=ntsm01

==Compiled raw Data==
[[Media:Team_Name_NaCl_compiled_raw_Data.xls|300 NaCl compiled data set]]
==Compiled processed data==
[[Media:Complete_processed_Data.xls|Processed Data]]

==Data ready for GenMAPP==
[[Media:Data_Sets_ratio2.xls|NaCl 300mm XLS version]]

[[Media:Data_Sets_ratio2.txt|NaCl 300mm TXT Version]]

==Important Files==

Taxon ID: 266834

Version of GenMAPP Builder: [[Media: gmbuilder-2.0b71.zip | gmbuilder-2.0b71.zip]]

Computer on which export was run: Keck Lab Computer, back computer (furthest from the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import:19.17 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import: 17.81 minutes
* Time taken to process: 15.54 minutes

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import: 0.21 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file: [[Media:Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_2013117.gdb | Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_2013117.gdb]]
* Time taken to export .gdb: Started at 2pm on 11-7-2013, finished at 9:47pm
* Upload your file and link to it here.

Note:

replace geneID with ~ when you find MOD link

==Important Files 2==

Info based on export done on 11/21/2013

Taxon ID: 266834

Version of GenMAPP Builder: [[Media:GenMAPP_Builder_2.0b72 S. meliloti.zip|GenMAPP_Builder_2.0b72 S. meliloti.zip]]

Computer on which export was run: Keck Lab Computer, front computer (closest to the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import: 7.34 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import: 6.31 minutes
* Time taken to process: 4.60 minutes

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import: 0.07 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file: [[Media:Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_20131121.gdb|Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_20131121.gdb]]
* Time taken to export .gdb: Started at 10:18 AM on 11/21/2013; ended at 1:34 PM

==Important Files 3==

'''From Week 14, December 3-5, 2013'''

NOTE: Forgot that I cannot import data into the same database. I will continue to do an export based on what I have, and will do another import/export cycle on another computer using the same version of gmbuilder that I used here.

Taxon ID: 266834

Version of GenMAPP Builder:

Computer on which export was run: Keck Lab Computer, front computer (closest to the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import: 6.27 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import: 6.07 minutes
* Time taken to process: 12.42 minutes
**NOTE: gmbuilder told me that the GO OBO-XML file was already processed in the database, and wanted to know if I wanted to process the information again. I chose yes.

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import: 0.07 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

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

==Important Files 4==

'''From Week 14, December 3-5, 2013'''

NOTE: Here is the other import/export, using a new database on a different Keck Lab computer

Taxon ID: 266834

Version of GenMAPP Builder:

Computer on which export was run: Keck Lab Computer, front computer (closest to the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import: 6.25 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import: 6.21 minutes
* Time taken to process:

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import:
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file:
* Time taken to export .gdb:

* Upload your file and link to it here.

==Wiki Navigation==
{{Team Name}}
*[[Teamname Week 13 Status Report]]
*[[Laurmagee: Week 13]]

Team Name

2013-12-03T18:10:31Z

Mpetredi: /* Important Files 4 */ added time to import xml file

Species: ''Sinorhizobium Meliloti'' (Strain 1021)
==Group Project==
[[media:Sinorhizobium_Meliloti_group_project.pdf|Group Project]]

==Personnel==
===Stephen Louie===
Project Manager, Quality Assurance
:slouie4 at lion.lmu.edu
:1 LMU Drive MSB 5194
:Los Angeles, CA 90045
:[[Stephen Louie Project Notebook|Stephen Louie Project Notebook]]

===Lauren Magee===
GenMAPP Expert
:lmagee1 at lion.lmu.edu
:1 LMU Drive MSB-5258,
:Los Angeles, CA 90045
===Mitchell Petredis===
Coding Supervisor
:mrpetredis at gmail dot com
:mpetredi at lion dot lmu dot edu
:Loyola Marymount University
:1 LMU Drive MSB-5957
:Los Angeles, CA 90045-2659
===Miles Malefyt===
GenMAPP Coordinator
:milesm@malefyt.com
:mmalefyt@lion.lmu.edu
:8416 Campion drive
:Westchester, CA 90045
cell: 831-236-5402

[[User:Mmalefyt|Mmalefyt]] ([[User talk:Mmalefyt|talk]]) 10:31, 31 October 2013 (PDT)

==Micro Array paper==

[[http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-785/?keywords=&organism=Sinorhizobium%20meliloti&array=&exptype Osmotic upshift elicited by salt and sucrose]]
*[[http://jb.asm.org/content/188/21/7617 HTML version]]
*[[http://jb.asm.org/content/188/21/7617.full.pdf+html PDF version]]
*[[Media:A-MEXP-230.adf.txt]]
*[[Media:E-MEXP-785.eSet.r]]
*[[Media:E-MEXP-785.processed.1.zip]]
*[[Media:E-MEXP-785.raw.2.zip]]
*[[Media:E-MEXP-785.idf.txt]]
*[[Media:E-MEXP-785.raw.1.zip]]
*[[Media:E-MEXP-785.sdrf.txt]]
*Raw Data File for 700S (1-3): [[File:Full Raw Data.xls]]
*[[File:Compiled Ratios and Logs.xls]]
*[[File:SinorhizobiumMeliloti_LM_GenMapp_DataSheet.txt]]
*[[File:SinorhizobiumMeliloti_LM_GenMapp_DataSheet.xls]]

Domínguez-Ferreras, A., Pérez-Arnedo, R., Becker, A., Olivares, J., Soto, M.J., Sanjuán, J. (2006) Transcriptome Profiling Reveals the Importance of Plasmid pSymB for Osmoadaptation of Sinorhizobium meliloti ''Journal of Bacteriology'' 188:7617-7625

==Genome Paper==

[http://search.proquest.com/docview/213572450?accountid=7418 The composite genome of the legume symbiont Sinorhizobium meliloti. Science 293, 668–672.]

Galibert, F., Finan, T.M., Long, S., Puhler, A., et al. (2001) The composite genome of the legume symbiont Sinorhizobium meliloti ''Science'' 293:668-672

[[Category: Sinorhizobium meliloti]]
[[Category: Group Projects]]

==Model Organism Database==
Link: http://cmr.jcvi.org/tigr-scripts/CMR/GenomePage.cgi?org=ntsm01

==Compiled raw Data==
[[Media:Team_Name_NaCl_compiled_raw_Data.xls|300 NaCl compiled data set]]
==Compiled processed data==
[[Media:Complete_processed_Data.xls|Processed Data]]

==Data ready for GenMAPP==
[[Media:Data_Sets_ratio2.xls|NaCl 300mm XLS version]]

[[Media:Data_Sets_ratio2.txt|NaCl 300mm TXT Version]]

==Important Files==

Taxon ID: 266834

Version of GenMAPP Builder: [[Media: gmbuilder-2.0b71.zip | gmbuilder-2.0b71.zip]]

Computer on which export was run: Keck Lab Computer, back computer (furthest from the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import:19.17 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import: 17.81 minutes
* Time taken to process: 15.54 minutes

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import: 0.21 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file: [[Media:Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_2013117.gdb | Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_2013117.gdb]]
* Time taken to export .gdb: Started at 2pm on 11-7-2013, finished at 9:47pm
* Upload your file and link to it here.

Note:

replace geneID with ~ when you find MOD link

==Important Files 2==

Info based on export done on 11/21/2013

Taxon ID: 266834

Version of GenMAPP Builder: [[Media:GenMAPP_Builder_2.0b72 S. meliloti.zip|GenMAPP_Builder_2.0b72 S. meliloti.zip]]

Computer on which export was run: Keck Lab Computer, front computer (closest to the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import: 7.34 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import: 6.31 minutes
* Time taken to process: 4.60 minutes

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import: 0.07 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file: [[Media:Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_20131121.gdb|Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_20131121.gdb]]
* Time taken to export .gdb: Started at 10:18 AM on 11/21/2013; ended at 1:34 PM

==Important Files 3==

'''From Week 14, December 3-5, 2013'''

NOTE: Forgot that I cannot import data into the same database. I will continue to do an export based on what I have, and will do another import/export cycle on another computer using the same version of gmbuilder that I used here.

Taxon ID: 266834

Version of GenMAPP Builder:

Computer on which export was run: Keck Lab Computer, front computer (closest to the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import: 6.27 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import: 6.07 minutes
* Time taken to process: 12.42 minutes
**NOTE: gmbuilder told me that the GO OBO-XML file was already processed in the database, and wanted to know if I wanted to process the information again. I chose yes.

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import: 0.07 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

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

==Important Files 4==

'''From Week 14, December 3-5, 2013'''

NOTE: Here is the other import/export, using a new database on a different Keck Lab computer

Taxon ID: 266834

Version of GenMAPP Builder:

Computer on which export was run: Keck Lab Computer, front computer (closest to the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import: 6.25 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import:
* Time taken to process:

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import:
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file:
* Time taken to export .gdb:

* Upload your file and link to it here.

==Wiki Navigation==
{{Team Name}}
*[[Teamname Week 13 Status Report]]
*[[Laurmagee: Week 13]]

Team Name

2013-12-03T18:04:57Z

Mpetredi: added new entry for important files 4

Species: ''Sinorhizobium Meliloti'' (Strain 1021)
==Group Project==
[[media:Sinorhizobium_Meliloti_group_project.pdf|Group Project]]

==Personnel==
===Stephen Louie===
Project Manager, Quality Assurance
:slouie4 at lion.lmu.edu
:1 LMU Drive MSB 5194
:Los Angeles, CA 90045
:[[Stephen Louie Project Notebook|Stephen Louie Project Notebook]]

===Lauren Magee===
GenMAPP Expert
:lmagee1 at lion.lmu.edu
:1 LMU Drive MSB-5258,
:Los Angeles, CA 90045
===Mitchell Petredis===
Coding Supervisor
:mrpetredis at gmail dot com
:mpetredi at lion dot lmu dot edu
:Loyola Marymount University
:1 LMU Drive MSB-5957
:Los Angeles, CA 90045-2659
===Miles Malefyt===
GenMAPP Coordinator
:milesm@malefyt.com
:mmalefyt@lion.lmu.edu
:8416 Campion drive
:Westchester, CA 90045
cell: 831-236-5402

[[User:Mmalefyt|Mmalefyt]] ([[User talk:Mmalefyt|talk]]) 10:31, 31 October 2013 (PDT)

==Micro Array paper==

[[http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-785/?keywords=&organism=Sinorhizobium%20meliloti&array=&exptype Osmotic upshift elicited by salt and sucrose]]
*[[http://jb.asm.org/content/188/21/7617 HTML version]]
*[[http://jb.asm.org/content/188/21/7617.full.pdf+html PDF version]]
*[[Media:A-MEXP-230.adf.txt]]
*[[Media:E-MEXP-785.eSet.r]]
*[[Media:E-MEXP-785.processed.1.zip]]
*[[Media:E-MEXP-785.raw.2.zip]]
*[[Media:E-MEXP-785.idf.txt]]
*[[Media:E-MEXP-785.raw.1.zip]]
*[[Media:E-MEXP-785.sdrf.txt]]
*Raw Data File for 700S (1-3): [[File:Full Raw Data.xls]]
*[[File:Compiled Ratios and Logs.xls]]
*[[File:SinorhizobiumMeliloti_LM_GenMapp_DataSheet.txt]]
*[[File:SinorhizobiumMeliloti_LM_GenMapp_DataSheet.xls]]

Domínguez-Ferreras, A., Pérez-Arnedo, R., Becker, A., Olivares, J., Soto, M.J., Sanjuán, J. (2006) Transcriptome Profiling Reveals the Importance of Plasmid pSymB for Osmoadaptation of Sinorhizobium meliloti ''Journal of Bacteriology'' 188:7617-7625

==Genome Paper==

[http://search.proquest.com/docview/213572450?accountid=7418 The composite genome of the legume symbiont Sinorhizobium meliloti. Science 293, 668–672.]

Galibert, F., Finan, T.M., Long, S., Puhler, A., et al. (2001) The composite genome of the legume symbiont Sinorhizobium meliloti ''Science'' 293:668-672

[[Category: Sinorhizobium meliloti]]
[[Category: Group Projects]]

==Model Organism Database==
Link: http://cmr.jcvi.org/tigr-scripts/CMR/GenomePage.cgi?org=ntsm01

==Compiled raw Data==
[[Media:Team_Name_NaCl_compiled_raw_Data.xls|300 NaCl compiled data set]]
==Compiled processed data==
[[Media:Complete_processed_Data.xls|Processed Data]]

==Data ready for GenMAPP==
[[Media:Data_Sets_ratio2.xls|NaCl 300mm XLS version]]

[[Media:Data_Sets_ratio2.txt|NaCl 300mm TXT Version]]

==Important Files==

Taxon ID: 266834

Version of GenMAPP Builder: [[Media: gmbuilder-2.0b71.zip | gmbuilder-2.0b71.zip]]

Computer on which export was run: Keck Lab Computer, back computer (furthest from the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import:19.17 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import: 17.81 minutes
* Time taken to process: 15.54 minutes

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import: 0.21 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file: [[Media:Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_2013117.gdb | Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_2013117.gdb]]
* Time taken to export .gdb: Started at 2pm on 11-7-2013, finished at 9:47pm
* Upload your file and link to it here.

Note:

replace geneID with ~ when you find MOD link

==Important Files 2==

Info based on export done on 11/21/2013

Taxon ID: 266834

Version of GenMAPP Builder: [[Media:GenMAPP_Builder_2.0b72 S. meliloti.zip|GenMAPP_Builder_2.0b72 S. meliloti.zip]]

Computer on which export was run: Keck Lab Computer, front computer (closest to the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import: 7.34 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import: 6.31 minutes
* Time taken to process: 4.60 minutes

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import: 0.07 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file: [[Media:Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_20131121.gdb|Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_20131121.gdb]]
* Time taken to export .gdb: Started at 10:18 AM on 11/21/2013; ended at 1:34 PM

==Important Files 3==

'''From Week 14, December 3-5, 2013'''

NOTE: Forgot that I cannot import data into the same database. I will continue to do an export based on what I have, and will do another import/export cycle on another computer using the same version of gmbuilder that I used here.

Taxon ID: 266834

Version of GenMAPP Builder:

Computer on which export was run: Keck Lab Computer, front computer (closest to the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import: 6.27 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import: 6.07 minutes
* Time taken to process: 12.42 minutes
**NOTE: gmbuilder told me that the GO OBO-XML file was already processed in the database, and wanted to know if I wanted to process the information again. I chose yes.

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import: 0.07 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

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

==Important Files 4==

'''From Week 14, December 3-5, 2013'''

NOTE: Here is the other import/export, using a new database on a different Keck Lab computer

Taxon ID: 266834

Version of GenMAPP Builder:

Computer on which export was run: Keck Lab Computer, front computer (closest to the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import:

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import:
* Time taken to process:

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import:
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file:
* Time taken to export .gdb:

* Upload your file and link to it here.

==Wiki Navigation==
{{Team Name}}
*[[Teamname Week 13 Status Report]]
*[[Laurmagee: Week 13]]

Team Name

2013-12-03T17:41:46Z

Mpetredi: /* Important Files 3 */ added time to import goa file and note about new database

Species: ''Sinorhizobium Meliloti'' (Strain 1021)
==Group Project==
[[media:Sinorhizobium_Meliloti_group_project.pdf|Group Project]]

==Personnel==
===Stephen Louie===
Project Manager, Quality Assurance
:slouie4 at lion.lmu.edu
:1 LMU Drive MSB 5194
:Los Angeles, CA 90045
:[[Stephen Louie Project Notebook|Stephen Louie Project Notebook]]

===Lauren Magee===
GenMAPP Expert
:lmagee1 at lion.lmu.edu
:1 LMU Drive MSB-5258,
:Los Angeles, CA 90045
===Mitchell Petredis===
Coding Supervisor
:mrpetredis at gmail dot com
:mpetredi at lion dot lmu dot edu
:Loyola Marymount University
:1 LMU Drive MSB-5957
:Los Angeles, CA 90045-2659
===Miles Malefyt===
GenMAPP Coordinator
:milesm@malefyt.com
:mmalefyt@lion.lmu.edu
:8416 Campion drive
:Westchester, CA 90045
cell: 831-236-5402

[[User:Mmalefyt|Mmalefyt]] ([[User talk:Mmalefyt|talk]]) 10:31, 31 October 2013 (PDT)

==Micro Array paper==

[[http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-785/?keywords=&organism=Sinorhizobium%20meliloti&array=&exptype Osmotic upshift elicited by salt and sucrose]]
*[[http://jb.asm.org/content/188/21/7617 HTML version]]
*[[http://jb.asm.org/content/188/21/7617.full.pdf+html PDF version]]
*[[Media:A-MEXP-230.adf.txt]]
*[[Media:E-MEXP-785.eSet.r]]
*[[Media:E-MEXP-785.processed.1.zip]]
*[[Media:E-MEXP-785.raw.2.zip]]
*[[Media:E-MEXP-785.idf.txt]]
*[[Media:E-MEXP-785.raw.1.zip]]
*[[Media:E-MEXP-785.sdrf.txt]]
*Raw Data File for 700S (1-3): [[File:Full Raw Data.xls]]
*[[File:Compiled Ratios and Logs.xls]]
*[[File:GenMapp Sinorhizobium Meliloti.txt]]
*[[File:Final Gene Mapp Spreadsheet.xls]]

Domínguez-Ferreras, A., Pérez-Arnedo, R., Becker, A., Olivares, J., Soto, M.J., Sanjuán, J. (2006) Transcriptome Profiling Reveals the Importance of Plasmid pSymB for Osmoadaptation of Sinorhizobium meliloti ''Journal of Bacteriology'' 188:7617-7625

==Genome Paper==

[http://search.proquest.com/docview/213572450?accountid=7418 The composite genome of the legume symbiont Sinorhizobium meliloti. Science 293, 668–672.]

Galibert, F., Finan, T.M., Long, S., Puhler, A., et al. (2001) The composite genome of the legume symbiont Sinorhizobium meliloti ''Science'' 293:668-672

[[Category: Sinorhizobium meliloti]]
[[Category: Group Projects]]

==Model Organism Database==
Link: http://cmr.jcvi.org/tigr-scripts/CMR/GenomePage.cgi?org=ntsm01

==Compiled raw Data==
[[Media:Team_Name_NaCl_compiled_raw_Data.xls|300 NaCl compiled data set]]
==Compiled processed data==
[[Media:Complete_processed_Data.xls|Processed Data]]

==Data ready for GenMAPP==
[[Media:Data_Sets_ratio2.xls|NaCl 300mm XLS version]]

[[Media:Data_Sets_ratio2.txt|NaCl 300mm TXT Version]]

==Important Files==

Taxon ID: 266834

Version of GenMAPP Builder: [[Media: gmbuilder-2.0b71.zip | gmbuilder-2.0b71.zip]]

Computer on which export was run: Keck Lab Computer, back computer (furthest from the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import:19.17 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import: 17.81 minutes
* Time taken to process: 15.54 minutes

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import: 0.21 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file: [[Media:Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_2013117.gdb | Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_2013117.gdb]]
* Time taken to export .gdb: Started at 2pm on 11-7-2013, finished at 9:47pm
* Upload your file and link to it here.

Note:

replace geneID with ~ when you find MOD link

==Important Files 2==

Info based on export done on 11/21/2013

Taxon ID: 266834

Version of GenMAPP Builder: [[Media:GenMAPP_Builder_2.0b72 S. meliloti.zip|GenMAPP_Builder_2.0b72 S. meliloti.zip]]

Computer on which export was run: Keck Lab Computer, front computer (closest to the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import: 7.34 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import: 6.31 minutes
* Time taken to process: 4.60 minutes

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import: 0.07 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file: [[Media:Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_20131121.gdb|Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_20131121.gdb]]
* Time taken to export .gdb: Started at 10:18 AM on 11/21/2013; ended at 1:34 PM

==Important Files 3==

'''From Week 14, December 3-5, 2013'''

NOTE: Forgot that I cannot import data into the same database. I will continue to do an export based on what I have, and will do another import/export cycle on another computer using the same version of gmbuilder that I used here.

Taxon ID: 266834

Version of GenMAPP Builder:

Computer on which export was run: Keck Lab Computer, front computer (closest to the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import: 6.27 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import: 6.07 minutes
* Time taken to process: 12.42 minutes
**NOTE: gmbuilder told me that the GO OBO-XML file was already processed in the database, and wanted to know if I wanted to process the information again. I chose yes.

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import: 0.07 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file:
* Time taken to export .gdb:

* Upload your file and link to it here.

==Wiki Navigation==
{{Team Name}}
*[[Teamname Week 13 Status Report]]
*[[Laurmagee: Week 13]]

Team Name

2013-12-03T17:27:02Z

Mpetredi: /* Important Files 3 */ added time to process obo-xml

Species: ''Sinorhizobium Meliloti'' (Strain 1021)
==Group Project==
[[media:Sinorhizobium_Meliloti_group_project.pdf|Group Project]]

==Personnel==
===Stephen Louie===
Project Manager, Quality Assurance
:slouie4 at lion.lmu.edu
:1 LMU Drive MSB 5194
:Los Angeles, CA 90045
:[[Stephen Louie Project Notebook|Stephen Louie Project Notebook]]

===Lauren Magee===
GenMAPP Expert
:lmagee1 at lion.lmu.edu
:1 LMU Drive MSB-5258,
:Los Angeles, CA 90045
===Mitchell Petredis===
Coding Supervisor
:mrpetredis at gmail dot com
:mpetredi at lion dot lmu dot edu
:Loyola Marymount University
:1 LMU Drive MSB-5957
:Los Angeles, CA 90045-2659
===Miles Malefyt===
GenMAPP Coordinator
:milesm@malefyt.com
:mmalefyt@lion.lmu.edu
:8416 Campion drive
:Westchester, CA 90045
cell: 831-236-5402

[[User:Mmalefyt|Mmalefyt]] ([[User talk:Mmalefyt|talk]]) 10:31, 31 October 2013 (PDT)

==Micro Array paper==

[[http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-785/?keywords=&organism=Sinorhizobium%20meliloti&array=&exptype Osmotic upshift elicited by salt and sucrose]]
*[[http://jb.asm.org/content/188/21/7617 HTML version]]
*[[http://jb.asm.org/content/188/21/7617.full.pdf+html PDF version]]
*[[Media:A-MEXP-230.adf.txt]]
*[[Media:E-MEXP-785.eSet.r]]
*[[Media:E-MEXP-785.processed.1.zip]]
*[[Media:E-MEXP-785.raw.2.zip]]
*[[Media:E-MEXP-785.idf.txt]]
*[[Media:E-MEXP-785.raw.1.zip]]
*[[Media:E-MEXP-785.sdrf.txt]]
*Raw Data File for 700S (1-3): [[File:Full Raw Data.xls]]
*[[File:Compiled Ratios and Logs.xls]]
*[[File:GenMapp Sinorhizobium Meliloti.txt]]
*[[File:Final Gene Mapp Spreadsheet.xls]]

Domínguez-Ferreras, A., Pérez-Arnedo, R., Becker, A., Olivares, J., Soto, M.J., Sanjuán, J. (2006) Transcriptome Profiling Reveals the Importance of Plasmid pSymB for Osmoadaptation of Sinorhizobium meliloti ''Journal of Bacteriology'' 188:7617-7625

==Genome Paper==

[http://search.proquest.com/docview/213572450?accountid=7418 The composite genome of the legume symbiont Sinorhizobium meliloti. Science 293, 668–672.]

Galibert, F., Finan, T.M., Long, S., Puhler, A., et al. (2001) The composite genome of the legume symbiont Sinorhizobium meliloti ''Science'' 293:668-672

[[Category: Sinorhizobium meliloti]]
[[Category: Group Projects]]

==Model Organism Database==
Link: http://cmr.jcvi.org/tigr-scripts/CMR/GenomePage.cgi?org=ntsm01

==Compiled raw Data==
[[Media:Team_Name_NaCl_compiled_raw_Data.xls|300 NaCl compiled data set]]
==Compiled processed data==
[[Media:Complete_processed_Data.xls|Processed Data]]

==Data ready for GenMAPP==
[[Media:Data_Sets_ratio2.xls|NaCl 300mm XLS version]]

[[Media:Data_Sets_ratio2.txt|NaCl 300mm TXT Version]]

==Important Files==

Taxon ID: 266834

Version of GenMAPP Builder: [[Media: gmbuilder-2.0b71.zip | gmbuilder-2.0b71.zip]]

Computer on which export was run: Keck Lab Computer, back computer (furthest from the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import:19.17 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import: 17.81 minutes
* Time taken to process: 15.54 minutes

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import: 0.21 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file: [[Media:Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_2013117.gdb | Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_2013117.gdb]]
* Time taken to export .gdb: Started at 2pm on 11-7-2013, finished at 9:47pm
* Upload your file and link to it here.

Note:

replace geneID with ~ when you find MOD link

==Important Files 2==

Info based on export done on 11/21/2013

Taxon ID: 266834

Version of GenMAPP Builder: [[Media:GenMAPP_Builder_2.0b72 S. meliloti.zip|GenMAPP_Builder_2.0b72 S. meliloti.zip]]

Computer on which export was run: Keck Lab Computer, front computer (closest to the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import: 7.34 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import: 6.31 minutes
* Time taken to process: 4.60 minutes

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import: 0.07 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file: [[Media:Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_20131121.gdb|Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_20131121.gdb]]
* Time taken to export .gdb: Started at 10:18 AM on 11/21/2013; ended at 1:34 PM

==Important Files 3==

'''From Week 14, December 3-5, 2013'''

Taxon ID: 266834

Version of GenMAPP Builder:

Computer on which export was run: Keck Lab Computer, front computer (closest to the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import: 6.27 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import: 6.07 minutes
* Time taken to process: 12.42 minutes
**NOTE: gmbuilder told me that the GO OBO-XML file was already processed in the database, and wanted to know if I wanted to process the information again. I chose yes.

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import: minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file:
* Time taken to export .gdb:

* Upload your file and link to it here.

==Wiki Navigation==
{{Team Name}}
*[[Teamname Week 13 Status Report]]
*[[Laurmagee: Week 13]]

Team Name

2013-12-03T17:15:23Z

Mpetredi: /* Important Files 3 */ note about processing obo-xml

Species: ''Sinorhizobium Meliloti'' (Strain 1021)
==Group Project==
[[media:Sinorhizobium_Meliloti_group_project.pdf|Group Project]]

==Personnel==
===Stephen Louie===
Project Manager, Quality Assurance
:slouie4 at lion.lmu.edu
:1 LMU Drive MSB 5194
:Los Angeles, CA 90045
:[[Stephen Louie Project Notebook|Stephen Louie Project Notebook]]

===Lauren Magee===
GenMAPP Expert
:lmagee1 at lion.lmu.edu
:1 LMU Drive MSB-5258,
:Los Angeles, CA 90045
===Mitchell Petredis===
Coding Supervisor
:mrpetredis at gmail dot com
:mpetredi at lion dot lmu dot edu
:Loyola Marymount University
:1 LMU Drive MSB-5957
:Los Angeles, CA 90045-2659
===Miles Malefyt===
GenMAPP Coordinator
:milesm@malefyt.com
:mmalefyt@lion.lmu.edu
:8416 Campion drive
:Westchester, CA 90045
cell: 831-236-5402

[[User:Mmalefyt|Mmalefyt]] ([[User talk:Mmalefyt|talk]]) 10:31, 31 October 2013 (PDT)

==Micro Array paper==

[[http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-785/?keywords=&organism=Sinorhizobium%20meliloti&array=&exptype Osmotic upshift elicited by salt and sucrose]]
*[[http://jb.asm.org/content/188/21/7617 HTML version]]
*[[http://jb.asm.org/content/188/21/7617.full.pdf+html PDF version]]
*[[Media:A-MEXP-230.adf.txt]]
*[[Media:E-MEXP-785.eSet.r]]
*[[Media:E-MEXP-785.processed.1.zip]]
*[[Media:E-MEXP-785.raw.2.zip]]
*[[Media:E-MEXP-785.idf.txt]]
*[[Media:E-MEXP-785.raw.1.zip]]
*[[Media:E-MEXP-785.sdrf.txt]]
*Raw Data File for 700S (1-3): [[File:Full Raw Data.xls]]
*[[File:Compiled Ratios and Logs.xls]]
*[[File:GenMapp Sinorhizobium Meliloti.txt]]
*[[File:Final Gene Mapp Spreadsheet.xls]]

Domínguez-Ferreras, A., Pérez-Arnedo, R., Becker, A., Olivares, J., Soto, M.J., Sanjuán, J. (2006) Transcriptome Profiling Reveals the Importance of Plasmid pSymB for Osmoadaptation of Sinorhizobium meliloti ''Journal of Bacteriology'' 188:7617-7625

==Genome Paper==

[http://search.proquest.com/docview/213572450?accountid=7418 The composite genome of the legume symbiont Sinorhizobium meliloti. Science 293, 668–672.]

Galibert, F., Finan, T.M., Long, S., Puhler, A., et al. (2001) The composite genome of the legume symbiont Sinorhizobium meliloti ''Science'' 293:668-672

[[Category: Sinorhizobium meliloti]]
[[Category: Group Projects]]

==Model Organism Database==
Link: http://cmr.jcvi.org/tigr-scripts/CMR/GenomePage.cgi?org=ntsm01

==Compiled raw Data==
[[Media:Team_Name_NaCl_compiled_raw_Data.xls|300 NaCl compiled data set]]
==Compiled processed data==
[[Media:Complete_processed_Data.xls|Processed Data]]

==Data ready for GenMAPP==
[[Media:Data_Sets_ratio2.xls|NaCl 300mm XLS version]]

[[Media:Data_Sets_ratio2.txt|NaCl 300mm TXT Version]]

==Important Files==

Taxon ID: 266834

Version of GenMAPP Builder: [[Media: gmbuilder-2.0b71.zip | gmbuilder-2.0b71.zip]]

Computer on which export was run: Keck Lab Computer, back computer (furthest from the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import:19.17 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import: 17.81 minutes
* Time taken to process: 15.54 minutes

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import: 0.21 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file: [[Media:Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_2013117.gdb | Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_2013117.gdb]]
* Time taken to export .gdb: Started at 2pm on 11-7-2013, finished at 9:47pm
* Upload your file and link to it here.

Note:

replace geneID with ~ when you find MOD link

==Important Files 2==

Info based on export done on 11/21/2013

Taxon ID: 266834

Version of GenMAPP Builder: [[Media:GenMAPP_Builder_2.0b72 S. meliloti.zip|GenMAPP_Builder_2.0b72 S. meliloti.zip]]

Computer on which export was run: Keck Lab Computer, front computer (closest to the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import: 7.34 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import: 6.31 minutes
* Time taken to process: 4.60 minutes

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import: 0.07 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file: [[Media:Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_20131121.gdb|Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_20131121.gdb]]
* Time taken to export .gdb: Started at 10:18 AM on 11/21/2013; ended at 1:34 PM

==Important Files 3==

'''From Week 14, December 3-5, 2013'''

Taxon ID: 266834

Version of GenMAPP Builder:

Computer on which export was run: Keck Lab Computer, front computer (closest to the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import: 6.27 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import: 6.07 minutes
* Time taken to process: minutes
**NOTE: gmbuilder told me that the GO OBO-XML file was already processed in the database, and wanted to know if I wanted to process the information again. I chose yes.

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import: minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file:
* Time taken to export .gdb:

* Upload your file and link to it here.

==Wiki Navigation==
{{Team Name}}
*[[Teamname Week 13 Status Report]]
*[[Laurmagee: Week 13]]

Team Name

2013-12-03T17:11:06Z

Mpetredi: /* Important Files 3 */ added time to import obo-xml file

Species: ''Sinorhizobium Meliloti'' (Strain 1021)
==Group Project==
[[media:Sinorhizobium_Meliloti_group_project.pdf|Group Project]]

==Personnel==
===Stephen Louie===
Project Manager, Quality Assurance
:slouie4 at lion.lmu.edu
:1 LMU Drive MSB 5194
:Los Angeles, CA 90045
:[[Stephen Louie Project Notebook|Stephen Louie Project Notebook]]

===Lauren Magee===
GenMAPP Expert
:lmagee1 at lion.lmu.edu
:1 LMU Drive MSB-5258,
:Los Angeles, CA 90045
===Mitchell Petredis===
Coding Supervisor
:mrpetredis at gmail dot com
:mpetredi at lion dot lmu dot edu
:Loyola Marymount University
:1 LMU Drive MSB-5957
:Los Angeles, CA 90045-2659
===Miles Malefyt===
GenMAPP Coordinator
:milesm@malefyt.com
:mmalefyt@lion.lmu.edu
:8416 Campion drive
:Westchester, CA 90045
cell: 831-236-5402

[[User:Mmalefyt|Mmalefyt]] ([[User talk:Mmalefyt|talk]]) 10:31, 31 October 2013 (PDT)

==Micro Array paper==

[[http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-785/?keywords=&organism=Sinorhizobium%20meliloti&array=&exptype Osmotic upshift elicited by salt and sucrose]]
*[[http://jb.asm.org/content/188/21/7617 HTML version]]
*[[http://jb.asm.org/content/188/21/7617.full.pdf+html PDF version]]
*[[Media:A-MEXP-230.adf.txt]]
*[[Media:E-MEXP-785.eSet.r]]
*[[Media:E-MEXP-785.processed.1.zip]]
*[[Media:E-MEXP-785.raw.2.zip]]
*[[Media:E-MEXP-785.idf.txt]]
*[[Media:E-MEXP-785.raw.1.zip]]
*[[Media:E-MEXP-785.sdrf.txt]]
*Raw Data File for 700S (1-3): [[File:Full Raw Data.xls]]
*[[File:Compiled Ratios and Logs.xls]]
*[[File:GenMapp Sinorhizobium Meliloti.txt]]
*[[File:Final Gene Mapp Spreadsheet.xls]]

Domínguez-Ferreras, A., Pérez-Arnedo, R., Becker, A., Olivares, J., Soto, M.J., Sanjuán, J. (2006) Transcriptome Profiling Reveals the Importance of Plasmid pSymB for Osmoadaptation of Sinorhizobium meliloti ''Journal of Bacteriology'' 188:7617-7625

==Genome Paper==

[http://search.proquest.com/docview/213572450?accountid=7418 The composite genome of the legume symbiont Sinorhizobium meliloti. Science 293, 668–672.]

Galibert, F., Finan, T.M., Long, S., Puhler, A., et al. (2001) The composite genome of the legume symbiont Sinorhizobium meliloti ''Science'' 293:668-672

[[Category: Sinorhizobium meliloti]]
[[Category: Group Projects]]

==Model Organism Database==
Link: http://cmr.jcvi.org/tigr-scripts/CMR/GenomePage.cgi?org=ntsm01

==Compiled raw Data==
[[Media:Team_Name_NaCl_compiled_raw_Data.xls|300 NaCl compiled data set]]
==Compiled processed data==
[[Media:Complete_processed_Data.xls|Processed Data]]

==Data ready for GenMAPP==
[[Media:Data_Sets_ratio2.xls|NaCl 300mm XLS version]]

[[Media:Data_Sets_ratio2.txt|NaCl 300mm TXT Version]]

==Important Files==

Taxon ID: 266834

Version of GenMAPP Builder: [[Media: gmbuilder-2.0b71.zip | gmbuilder-2.0b71.zip]]

Computer on which export was run: Keck Lab Computer, back computer (furthest from the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import:19.17 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import: 17.81 minutes
* Time taken to process: 15.54 minutes

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import: 0.21 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file: [[Media:Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_2013117.gdb | Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_2013117.gdb]]
* Time taken to export .gdb: Started at 2pm on 11-7-2013, finished at 9:47pm
* Upload your file and link to it here.

Note:

replace geneID with ~ when you find MOD link

==Important Files 2==

Info based on export done on 11/21/2013

Taxon ID: 266834

Version of GenMAPP Builder: [[Media:GenMAPP_Builder_2.0b72 S. meliloti.zip|GenMAPP_Builder_2.0b72 S. meliloti.zip]]

Computer on which export was run: Keck Lab Computer, front computer (closest to the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import: 7.34 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import: 6.31 minutes
* Time taken to process: 4.60 minutes

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import: 0.07 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file: [[Media:Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_20131121.gdb|Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_20131121.gdb]]
* Time taken to export .gdb: Started at 10:18 AM on 11/21/2013; ended at 1:34 PM

==Important Files 3==

'''From Week 14, December 3-5, 2013'''

Taxon ID: 266834

Version of GenMAPP Builder:

Computer on which export was run: Keck Lab Computer, front computer (closest to the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import: 6.27 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import: 6.07 minutes
* Time taken to process: minutes

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import: minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file:
* Time taken to export .gdb:

* Upload your file and link to it here.

==Wiki Navigation==
{{Team Name}}
*[[Teamname Week 13 Status Report]]
*[[Laurmagee: Week 13]]

Mpetredi Week 14

2013-12-03T17:10:19Z

Mpetredi: fixed formatting (sorta)

==[[user:mpetredi|'''Mitchell Petredis''']]==

'''Lab Progression'''

==December 3, 2013==
*Added the following string of code in Eclipse (line is highlighted)
**[Insert New String of Code Picture Here]
**String of code also available below as text:

@Override
public TableManager getSystemTableManagerCustomizations(TableManager tableManager, TableManager primarySystemTableManager, Date version) throws SQLException, InvalidParameterException {
List<String> comparisonList = new ArrayList<String>();
comparisonList.add("ordered locus");
comparisonList.add("ORF");

return systemTableManagerCustomizationsHelper(tableManager, primarySystemTableManager, version, "OrderedLocusNames", comparisonList);
}
*Used all files except for the .gdb to run another import/export, using the latest version of gmbuilder
*All information pertaining to import/export 3 can be found under [[[[Team Name]]]] in "Important Files 3".

[[[[Team Name]]]]

Mpetredi Week 14

2013-12-03T17:08:09Z

Mpetredi: notes about new string of code and start of new import/export process

==[[user:mpetredi|'''Mitchell Petredis''']]==

'''Lab Progression'''

==December 3, 2013==
#Added the following string of code in Eclipse (line is highlighted)
#*[Insert New String of Code Picture Here]
#*String of code also available below as text:
#* @Override
public TableManager getSystemTableManagerCustomizations(TableManager tableManager, TableManager primarySystemTableManager, Date version) throws SQLException, InvalidParameterException {
List<String> comparisonList = new ArrayList<String>();
comparisonList.add("ordered locus");
comparisonList.add("ORF");

return systemTableManagerCustomizationsHelper(tableManager, primarySystemTableManager, version, "OrderedLocusNames", comparisonList);
}
#Used all files except for the .gdb to run another import/export, using the latest version of gmbuilder
#All information pertaining to import/export 3 can be found under [[[[Team Name]]]] in "Important Files 3".

[[[[Team Name]]]]

Team Name

2013-12-03T17:02:27Z

Mpetredi: added import/export 3 info

Species: ''Sinorhizobium Meliloti'' (Strain 1021)
==Group Project==
[[media:Sinorhizobium_Meliloti_group_project.pdf|Group Project]]

==Personnel==
===Stephen Louie===
Project Manager, Quality Assurance
:slouie4 at lion.lmu.edu
:1 LMU Drive MSB 5194
:Los Angeles, CA 90045
:[[Stephen Louie Project Notebook|Stephen Louie Project Notebook]]

===Lauren Magee===
GenMAPP Expert
:lmagee1 at lion.lmu.edu
:1 LMU Drive MSB-5258,
:Los Angeles, CA 90045
===Mitchell Petredis===
Coding Supervisor
:mrpetredis at gmail dot com
:mpetredi at lion dot lmu dot edu
:Loyola Marymount University
:1 LMU Drive MSB-5957
:Los Angeles, CA 90045-2659
===Miles Malefyt===
GenMAPP Coordinator
:milesm@malefyt.com
:mmalefyt@lion.lmu.edu
:8416 Campion drive
:Westchester, CA 90045
cell: 831-236-5402

[[User:Mmalefyt|Mmalefyt]] ([[User talk:Mmalefyt|talk]]) 10:31, 31 October 2013 (PDT)

==Micro Array paper==

[[http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-785/?keywords=&organism=Sinorhizobium%20meliloti&array=&exptype Osmotic upshift elicited by salt and sucrose]]
*[[http://jb.asm.org/content/188/21/7617 HTML version]]
*[[http://jb.asm.org/content/188/21/7617.full.pdf+html PDF version]]
*[[Media:A-MEXP-230.adf.txt]]
*[[Media:E-MEXP-785.eSet.r]]
*[[Media:E-MEXP-785.processed.1.zip]]
*[[Media:E-MEXP-785.raw.2.zip]]
*[[Media:E-MEXP-785.idf.txt]]
*[[Media:E-MEXP-785.raw.1.zip]]
*[[Media:E-MEXP-785.sdrf.txt]]
*Raw Data File for 700S (1-3): [[File:Full Raw Data.xls]]
*[[File:Compiled Ratios and Logs.xls]]
*[[File:GenMapp Sinorhizobium Meliloti.txt]]
*[[File:Final Gene Mapp Spreadsheet.xls]]

Domínguez-Ferreras, A., Pérez-Arnedo, R., Becker, A., Olivares, J., Soto, M.J., Sanjuán, J. (2006) Transcriptome Profiling Reveals the Importance of Plasmid pSymB for Osmoadaptation of Sinorhizobium meliloti ''Journal of Bacteriology'' 188:7617-7625

==Genome Paper==

[http://search.proquest.com/docview/213572450?accountid=7418 The composite genome of the legume symbiont Sinorhizobium meliloti. Science 293, 668–672.]

Galibert, F., Finan, T.M., Long, S., Puhler, A., et al. (2001) The composite genome of the legume symbiont Sinorhizobium meliloti ''Science'' 293:668-672

[[Category: Sinorhizobium meliloti]]
[[Category: Group Projects]]

==Model Organism Database==
Link: http://cmr.jcvi.org/tigr-scripts/CMR/GenomePage.cgi?org=ntsm01

==Compiled raw Data==
[[Media:Team_Name_NaCl_compiled_raw_Data.xls|300 NaCl compiled data set]]
==Compiled processed data==
[[Media:Complete_processed_Data.xls|Processed Data]]

==Data ready for GenMAPP==
[[Media:Data_Sets_ratio2.xls|NaCl 300mm XLS version]]

[[Media:Data_Sets_ratio2.txt|NaCl 300mm TXT Version]]

==Important Files==

Taxon ID: 266834

Version of GenMAPP Builder: [[Media: gmbuilder-2.0b71.zip | gmbuilder-2.0b71.zip]]

Computer on which export was run: Keck Lab Computer, back computer (furthest from the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import:19.17 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import: 17.81 minutes
* Time taken to process: 15.54 minutes

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import: 0.21 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file: [[Media:Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_2013117.gdb | Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_2013117.gdb]]
* Time taken to export .gdb: Started at 2pm on 11-7-2013, finished at 9:47pm
* Upload your file and link to it here.

Note:

replace geneID with ~ when you find MOD link

==Important Files 2==

Info based on export done on 11/21/2013

Taxon ID: 266834

Version of GenMAPP Builder: [[Media:GenMAPP_Builder_2.0b72 S. meliloti.zip|GenMAPP_Builder_2.0b72 S. meliloti.zip]]

Computer on which export was run: Keck Lab Computer, front computer (closest to the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import: 7.34 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import: 6.31 minutes
* Time taken to process: 4.60 minutes

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import: 0.07 minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file: [[Media:Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_20131121.gdb|Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_20131121.gdb]]
* Time taken to export .gdb: Started at 10:18 AM on 11/21/2013; ended at 1:34 PM

==Important Files 3==

'''From Week 14, December 3-5, 2013'''

Taxon ID: 266834

Version of GenMAPP Builder:

Computer on which export was run: Keck Lab Computer, front computer (closest to the whiteboard)

Postgres Database name: Sinorhizobium meliloti

UniProt XML filename:[[Media:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml|Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml]]
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10
* Time taken to import: 6.27 minutes

GO OBO-XML filename:[[Media:Go daily-termdb.obo-xml mpetredi 2013116.gz| Go daily-termdb.obo-xml mpetredi 2013116.gz]]
* 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): from 11/4/2013
* Time taken to import: minutes
* Time taken to process: minutes

GOA filename:[[Media:R meliloti.goa|R meliloti.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]): from 11/7/2013
* Time taken to import: minutes
*Note about GOA file
**From Running GenMAPP Builder page, clicked on the UniProt-GOA Downloads link.
**Was given an error message. Changed url from "ftp" to "http" at beginning.
**Was entered, was taken to Index of/pub/database/GO/goa
**Clicked on "proteomes" folder
**Directed to Index of /pub/databases/GO/goa/proteomes. Downloaded 58.R_meliloti.goa
***Note: R. meliloti is an alternative name to S. Melitoti.

Name of .gdb file:
* Time taken to export .gdb:

* Upload your file and link to it here.

==Wiki Navigation==
{{Team Name}}
*[[Teamname Week 13 Status Report]]
*[[Laurmagee: Week 13]]

User:Mpetredi

2013-12-03T16:52:55Z

Mpetredi: /* Individual Class Journals */ added week 14 journal notes

{{mpetredi}}

==Contact Information==
:Loyola Marymount University
:1 LMU Drive MSB-5957
:Los Angeles, CA 90045-2659

*mrpetredis at gmail dot com
*mpetredi at lion dot lmu dot edu

==Weekly Assignments==
*[[Week 1]]
*[[Week 2]]
*[[Week 3]]
*[[Week 4]]
*[[Week 5]]
*[[Week 6]]
*[[Week 7]]
*[[Week 8]]
*[[Week 9]]
*[[Week 10]]
*[[Week 11]]
*[[Week 12]]
*[[Week 13]]
*[[Week 14]]
*[[Week 15]]

==Journals==

===Class 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]]

====My Class Journal Entries====
#[[Class_Journal_Week_1#Mitchell Petredis|Response to Class Journal 1]]
#[[Class_Journal_Week_2#Mitchell Petredis|Response to Class Journal 2]]
#[[Class_Journal_Week_3#Mitchell Petredis|Response to Class Journal 3]]
#[[Class_Journal_Week_4#Mitchell Petredis|Response to Class Journal 4]]
#[[Class_Journal_Week_5#Mitchell Petredis|Response to Class Journal 5]]
#*[[Protegen]]
#[[Class_Journal_Week_6#Mitchell Petredis|Response to Class Journal 6]]
#[[Class_Journal_Week_7#Mitchell Petredis|Response to Class Journal 7]]
#[[Class_Journal_Week_8#Mitchell Petredis|Response to Class Journal 8]]
#[[Class_Journal_Week_9#Mitchell Petredis|Response to Class Journal 9]]

===Individual Class Journals===
*[[mpetredi Week 2]]
*[[mpetredi Week 3]]
*[[mpetredi Week 4]]
*[[mpetredi Week 5]]
*[[mpetredi Week 6]]
*[[mpetredi Week 7]]
*[[mpetredi Week 8]]
*[[mpetredi Week 9]]
*[[mpetredi Week 10]]
*[[mpetredi Week 11]]
*[[mpetredi Week 12]]
*[[mpetredi Week 13]]
*[[mpetredi Week 14]]

==Education==

===Loyola Marymount University===

:Major: Biology
:Expected Graduation: 2015

*Started taking upper division classes this year.

===Research Projects===
:*[http://phagesdb.org/phages/MePac/ MePac Bacteriophage]
[[Image:MePac EMPic (1).jpg | thumb | border | right]] 
:**Mentors
:***Dr. Yiwen Fang
:***Dr. Carl Urbinati
:***Dr. Gary Kuleck
:**Presentations
:***2012 LMU Undergraduate Research Symposium
:***[[Media:WCBSURC+Proceedings+2012.pdf|37th Annual West Coast Biological Sciences Undergraduate Research Conference]]

==Work Experience==

===Loyola Marymount University===
:'''Information Technology Services'''
:*2011-2012
:#Lab Assistant: Diagnose and troubleshoot issues in computer labs.
:*2012-2013
:#Foley 220 Lab Manager: Maintain logs of supply usage and assist with computer issues.
:#Student Innovation Center Technician: Diagnose and troubleshoot student and teacher technology issues.

===Withers Dental===
:'''Dental Technician'''
:*Summer 2013
:**Stocked and sanitized operating rooms
:**Sterilized and bagged dental instruments according to function.
:**Assisted in creating 40 sport guards for the entire Mira Costa High School Varsity football team.

==Personal Interests and Hobbies==
*Technology
*Gaming
*Photography
*Art
*Swimming
*Gardening



==Templates==

*[[Template:mpetredi]]
*[[Template: mpetredi Week 2 Journal Entry]]
*[[Template: mpetredi Week 4 Journal Entry]]
*[[Template: Hilda and Mitchell Week 5 Journal Entry]]
*[[Template: Individual Assignment Categories]]
*[[Template: User Page Link]]

==Wiki Pages==
*[[Week 1 Journal Entry]]
*[[Week 2 Journal Entry]]
*[[Week 3 Journal Entry]]
*[[mpetredi Week 2]]
*[[mpetredi Week 3]]
*[[Class Notes]]
*[[Class Notes 2]]
*[[Class Notes 3]]

==Useful Links==
[[http://libguides.lmu.edu/BIOL367 BIOL 367 LibGuide]]

[[Category: Individual Homework]]
[[Category: User Page]]

Team Name

2013-11-26T17:16:39Z

Mpetredi: /* Important Files 2 */ found out time to finish export

Team Name

2013-11-21T22:22:15Z

Mpetredi: /* Important Files 2 */ added second export file to team page

File:Sinorhizobium meliloti 1021 GenMAPP database mpetredi 20131121.gdb

2013-11-21T22:21:11Z

Mpetredi: second export, using custom gmbuilder for the first time

second export, using custom gmbuilder for the first time

Team Name

2013-11-21T22:17:26Z

Mpetredi: /* Important Files 2 */ added time to finish export of gdb

Mpetredi Week 13

2013-11-21T18:33:54Z

Mpetredi: /* Lab Progression */ added export settings image

{{User Page Link}}

11/19/2013

==Lab Progression==
#Attempting to find URL pattern of S. meliloti
##Navigated to model organism database (link: http://cmr.jcvi.org/tigr-scripts/CMR/GenomePage.cgi?org=ntsm01)
##Clicked on all 3 GenBank Accession.Versions and looked for locus ID formatting
##*[[http://www.ncbi.nlm.nih.gov/nucleotide/AL591688 Complete Chromosome]]
##**SMc#####
##*[[http://www.ncbi.nlm.nih.gov/nucleotide/AL591985 plasmid pSymB]]
##**SMb#####
##***NOTE: in the XML file (from [[[[Team Name]]]]) appears as SM_b for gene ID; uses SMb for ORF name
##*[[http://www.ncbi.nlm.nih.gov/nucleotide/AE006469 plasmid pSymA]]
##**SMa####
##Copy any locus ID that follows the format of the options above
##After many trials, the general link looks like this: http://cmr.jcvi.org/tigr-scripts/CMR/shared/GenePage.cgi?locus=~
#Copied link to Eclipse
#Opened the .gdb file (from [[[[Team Name]]]]) in Microsoft Access to determine how GeneIDs look like
##Open OrderedLocusNames and look at how IDs are named (R.####, where "." is either a letter or a number) and how many records are displayed
##*4712 records

11/21/2013

==Lab Progression==
#Started a new export based on latest, custom build of gmbuilder (GenMAPP Builder 2.0b72).
#* Except for gmbuilder, I used all files posted on [[[[Team Name]]]] under "Important Files" section.
#Name of export file is Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_20131121.gdb
#*Settings used for export: [[Image:Export_Information_20131121.PNG]]
{{Individual Assignment Categories}}
[[Category: Sinorhizobium meliloti]]
[[Category: Group Projects]]

File:Export Information 20131121.PNG

2013-11-21T18:32:15Z

Mpetredi: describes the export file using the custom gmbuilder 72

describes the export file using the custom gmbuilder 72

Team Name

2013-11-21T18:27:59Z

Mpetredi: /* Important Files */ added GO OBO XML version

Team Name

2013-11-21T18:27:25Z

Mpetredi: added versions for GOA file