Difference between revisions of "Team Name"

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===Mitchell Petredis===  
 
===Mitchell Petredis===  
 
Coding Supervisor
 
Coding Supervisor
−
:mrpetredis at gmail dot com
 
 
:mpetredi at lion dot lmu dot edu
 
:mpetredi at lion dot lmu dot edu
 
:Loyola Marymount University
 
:Loyola Marymount University
 
:1 LMU Drive MSB-5957
 
:1 LMU Drive MSB-5957
 
:Los Angeles, CA 90045-2659
 
:Los Angeles, CA 90045-2659
 +
 
===Miles Malefyt===  
 
===Miles Malefyt===  
 
GenMAPP Coordinator
 
GenMAPP Coordinator

Revision as of 22:11, 13 December 2013

Species: Sinorhizobium Meliloti (Strain 1021)

Contents

Group Project

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

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

Mmalefyt (talk) 10:31, 31 October 2013 (PDT)

Micro Array paper

[Osmotic upshift elicited by salt and sucrose]

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

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

Model Organism Database

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

Compiled raw Data

300 NaCl compiled data set

Compiled processed data

Processed Data

Data ready for GenMAPP

XLS Version

TXT version, USE THIS

Important Files

Taxon ID: 266834

Version of GenMAPP Builder: 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:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml

  • UniProt XML version (The version information can be found at the UniProt News Page): UniProt release 2013_10
  • Time taken to import:19.17 minutes

GO OBO-XML filename: 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 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:R meliloti.goa

  • GOA version (News on this page records past releases; current information can be found in the Last modified field on the 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: 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: 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:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml

  • UniProt XML version (The version information can be found at the UniProt News Page): UniProt release 2013_10
  • Time taken to import: 7.34 minutes

GO OBO-XML filename: 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 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:R meliloti.goa

  • GOA version (News on this page records past releases; current information can be found in the Last modified field on the 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: 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:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml

  • UniProt XML version (The version information can be found at the UniProt News Page): UniProt release 2013_10
  • Time taken to import: 6.27 minutes

GO OBO-XML filename: 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 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:R meliloti.goa

  • GOA version (News on this page records past releases; current information can be found in the Last modified field on the 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:Sinorhizobium meliloti 1021 mpetredi 2013115 UniProt XML.xml

  • UniProt XML version (The version information can be found at the UniProt News Page): UniProt release 2013_10
  • Time taken to import: 6.25 minutes

GO OBO-XML filename: 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 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:R meliloti.goa

  • GOA version (News on this page records past releases; current information can be found in the Last modified field on the 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

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