Difference between revisions of "Team Name"
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==Group Project== | ==Group Project== | ||
[[media:Sinorhizobium_Meliloti_group_project.pdf|Group Project]] | [[media:Sinorhizobium_Meliloti_group_project.pdf|Group Project]] | ||
| − | + | ==Project Deliverables== | |
| + | [[Team Name Deliverables]] | ||
==Personnel== | ==Personnel== | ||
===Stephen Louie=== | ===Stephen Louie=== | ||
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===Mitchell Petredis=== | ===Mitchell Petredis=== | ||
Coding Supervisor | Coding Supervisor | ||
| − | |||
: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 | ||
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*[[http://jb.asm.org/content/188/21/7617.full.pdf+html PDF version]] | *[[http://jb.asm.org/content/188/21/7617.full.pdf+html PDF version]] | ||
*[[Media:A-MEXP-230.adf.txt]] | *[[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.eSet.r]]-unable to download, because the file is too big |
*[[Media:E-MEXP-785.processed.1.zip]] | *[[Media:E-MEXP-785.processed.1.zip]] | ||
| − | *[[Media:E-MEXP-785.raw.2.zip]] | + | *[[Media:E-MEXP-785.raw.2.zip]] |
*[[Media:E-MEXP-785.idf.txt]] | *[[Media:E-MEXP-785.idf.txt]] | ||
| − | *[[Media:E-MEXP-785.raw.1.zip]] | + | *[[Media:E-MEXP-785.raw.1.zip]]-unable to download, because the file is too big |
*[[Media:E-MEXP-785.sdrf.txt]] | *[[Media:E-MEXP-785.sdrf.txt]] | ||
*Raw Data File for 700S (1-3): [[File:Full Raw Data.xls]] | *Raw Data File for 700S (1-3): [[File:Full Raw Data.xls]] | ||
Latest revision as of 23:56, 13 December 2013
Species: Sinorhizobium Meliloti (Strain 1021)
Contents |
[edit] Group Project
[edit] Project Deliverables
[edit] Personnel
[edit] Stephen Louie
Project Manager, Quality Assurance
- slouie4 at lion.lmu.edu
- 1 LMU Drive MSB 5194
- Los Angeles, CA 90045
- Stephen Louie Project Notebook
[edit] Lauren Magee
GenMAPP Expert
- lmagee1 at lion.lmu.edu
- 1 LMU Drive MSB-5258,
- Los Angeles, CA 90045
[edit] Mitchell Petredis
Coding Supervisor
- mpetredi at lion dot lmu dot edu
- Loyola Marymount University
- 1 LMU Drive MSB-5957
- Los Angeles, CA 90045-2659
[edit] 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)
[edit] Micro Array paper
[Osmotic upshift elicited by salt and sucrose]
- [HTML version]
- [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
[edit] 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
[edit] Model Organism Database
Link: http://cmr.jcvi.org/tigr-scripts/CMR/GenomePage.cgi?org=ntsm01
[edit] Compiled raw Data
[edit] Compiled processed data
[edit] Data ready for GenMAPP
[edit] 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
[edit] 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
[edit] 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.
[edit] 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
[edit]
- Stephen Louie
- Mitchell Petredis
- Lauren Magee
- Miles Malefyt
- Gene Database Project
- Gene Database Project Report Guidelines
- Project Manager
- Coder
- Quality Assurance
- GenMAPP User
- Teamname Week 12 Status Report
- Laurmagee: Week 12
- [Sinorhizobium meliloti 1021 Genome Page]
- Team Name Deliverables
- Teamname Week 13 Status Report
- Laurmagee: Week 13
- Teamname Week 15 Status Report
- Laurmagee: Week 15
- Miles Malefyt electronic notebook
