LMU BioDB 2013 - User contributions [en]

Electronic notebook: sinorhizobium meliloti

2013-12-14T00:15:04Z

Mmalefyt: /* Reflection on the Process */

==Week 12==
*Read the paper on the salinity and sucrose stress on gene expression
*Sorted the raw data into an XML file
*started to compile the raw data
**downloaded all raw data and sorted through the information needed
**used the cys5 and cys3 fold change as well as all the IDs
*Uploaded [[Media:Team_Name_NaCl_compiled_raw_Data.xls|300 NaCl compiled data set]]

==Week 13==
*I continued to sort the raw data and began to process the data in an xls file
*this was a very repetitive part because it involved a lot of replications for each time set
*finished my compiled raw data and processed raw data, as well as the data ready for GenMAPP
*Made individual LOG fold change ratios for each time point replicate then averaged all of the LOG fold change ratios for each of the time points
*preformed a Tstat test
*Preformed a Pvalue test
*added a row of N next to the gene ID name in the forGenMAPP tab
*uploaded [[Media:Complete_processed_Data.xls|Processed Data]]
**NOTE:the GenMAPP version of the tab is labeled Complete Processed data_MPM and not forGenMAPP

==week 15==
*I worked on some of the mistakes that I had made in my prior data sets
**removed AVG_LOGFC_ALL row
**added individual Pvalues and TSTAT for each individual replicate of the experiment instead of one Tstat and P value for the whole experiment
*sanity check concluded the number of genes significantly changed at each time point
**T15- 5520
**T30- 7484
**T60- 6711
**T240- 5901
*Removed all of the #DIV/0! from the data that was transferred over to the GenMapp data
*uploaded [[Media:Complete_processed_Data_MPM.xls|XLS Version]] and [[Media:Complete_processed_Data_MPM.txt|TXT version, USE THIS]]

*had to change names of the columns in order to correctly upload to GenMAPP
**system code column was renamed
**Gene ID column was renamed to ID on the Programmers computer to resolve some issues
*it appears that there is something wrong with the actual gene IDs that is not compatible with GenMAPP
*ran the first integration of the data and came up with 5535 errors which is roughly half of the overall genes we loaded.

==Reflection on the Process==
'''What did you learn?'''
*'''With your head?'''
*I learned a lot about gene expression and metabolic pathways and how the cell responds in many ways to a single stimulus. Also I learned a lot about the principles of coding and how to organize a query in language that the computer understands
*'''With you Heart'''
* I learned that people need to keep in contact every few days and need the latest updates on your progression in the work. Also coordinating with your team in order to tackle a broader objective that contains many parts and disciplines, it was really rewarding to see that we all started working on the project at completely different ends but came together in the end with a single final result.
*'''with your Hands? (technical skills)'''
I learned to organize and operate GenMAPP and map finder with enough proficiency that I could probably do it again if I was given the same project but on a different species. I also learned how to format things in a way that the computer could read and understand what I wanted in order to get a desired result
'''What lesson will you take away from this project that you will still use a year from now?'''
*The lessons that I will take away from this project was that you need to understand the gist of where your partners are in their work even if you don't understand what they are doing. This will allow you to get a general idea in mind about when your job and their job will meet and could give you insight if there is a discrepancy between your work and their. In other words a problem that arises when your part of the project meets theirs but cant be found out until both of the pieces of work come together

Electronic notebook: sinorhizobium meliloti

2013-12-14T00:05:56Z

Mmalefyt:

Miles Malefyt deliverables

2013-12-13T23:32:29Z

Mmalefyt: /* week 15 */

==Statement of work==
==Week 12==
*Read the paper on the salinity and sucrose stress on gene expression
*Sorted the raw data into an XML file
*started to compile the raw data
**downloaded all raw data and sorted through the information needed
**used the cys5 and cys3 fold change as well as all the IDs
*Uploaded [[Media:Team_Name_NaCl_compiled_raw_Data.xls|300 NaCl compiled data set]]
==Week 13==
*I continued to sort the raw data and began to process the data in an xls file
*this was a very repetitive part because it involved a lot of replications for each time set
*finished my compiled raw data and processed raw data, as well as the data ready for GenMAPP
*Made individual LOG fold change ratios for each time point replicate then averaged all of the LOG fold change ratios for each of the time points
*preformed a Tstat test
*Preformed a Pvalue test
*added a row of N next to the gene ID name in the forGenMAPP tab
*uploaded [[Media:Complete_processed_Data.xls|Processed Data]]
**NOTE:the GenMAPP version of the tab is labeled Complete Processed data_MPM and not forGenMAPP
==week 15==
*I worked on some of the mistakes that I had made in my prior data sets
**removed AVG_LOGFC_ALL row
**added individual Pvalues and TSTAT for each individual replicate of the experiment instead of one Tstat and P value for the whole experiment
*sanity check concluded the number of genes significantly changed at each time point
**T15- 5520
**T30- 7484
**T60- 6711
**T240- 5901
*Removed all of the #DIV/0! from the data that was transferred over to the GenMapp data
*uploaded [[Media:Complete_processed_Data_MPM.xls|XLS Version]] and [[Media:Complete_processed_Data_MPM.txt|TXT version, USE THIS]]

*had to change names of the columns in order to correctly upload to GenMAPP
**system code column was renamed
**Gene ID column was renamed to ID on the Programmers computer to resolve some issues
*it appears that there is something wrong with the actual gene IDs that is not compatible with GenMAPP
*ran the first integration of the data and came up with 5535 errors which is roughly half of the overall genes we loaded.
*loaded genMAPP and Mappfinder results

[[Media:MAPPFinder_results_T15-Criterion_Increased-GO.txt|Increased expression at T15]]

[[Media:MAPPFinder_results_T15-Criterion_Decreased-GO.txt|Decreased expression at T15]]

[[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]]

[[Media:MAPPFinder_t60-Criterion_Decreasaed-GO.txt|Decreased expression at t60]]

[[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]]
*analyzed the Gene Ontology report
**found a specific metabolic pathway that was pertinent to the treatment of NaCl

Team Name Deliverables

2013-12-13T23:29:01Z

Mmalefyt: /* Group */

=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)]]

=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

2013-12-13T23:28:33Z

Mmalefyt: /* Group */

=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)]]

=Individual=

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

File:Structural constituent of Ribosome.mapp

2013-12-13T23:27:29Z

Mmalefyt: MAPP for structural constituent of ribosome

MAPP for structural constituent of ribosome

Team Name Deliverables

2013-12-13T23:26:40Z

Mmalefyt: /* Group */

=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]]
: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:T30 MAPP results-Criterion Decreased-GO.txt

2013-12-13T23:25:43Z

Mmalefyt: decreased expression at t30

decreased expression at t30

Team Name Deliverables

2013-12-13T23:24:51Z

Mmalefyt: /* Group */

=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:

=Individual=

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

File:T30 increased-Criterion0-GO.txt

2013-12-13T23:23:59Z

Mmalefyt: increased T30 xpression

increased T30 xpression

Team Name Deliverables

2013-12-13T23:23:05Z

Mmalefyt: /* Group */

=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:[[Media:Complete_processed_Data_MPM.xls|300mm NaCl XLS Version]]
:GenMAPP Expression Dataset file: [[Media:SinorhizobiumMeliloti_LM_GenMapp_FinalFile.txt]]

[[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: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:

=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

2013-12-13T23:22:15Z

Mmalefyt: /* Group */

=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:[[Media:Complete_processed_Data_MPM.xls|300mm NaCl XLS Version]]
:GenMAPP Expression Dataset file: [[Media:SinorhizobiumMeliloti_LM_GenMapp_FinalFile.txt]]

[[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]]

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

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

*[[Media:MAPPFinder_t60-Criterion_Decreasaed-GO.txt|Decreased expression at t60]]
*[[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:

=Individual=

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

File:300N T240 MAPPFINDER-Criterion Decreased-GO.txt

2013-12-13T23:21:28Z

Mmalefyt: Decreased expression at t240

Decreased expression at t240

Team Name Deliverables

2013-12-13T23:20:22Z

Mmalefyt: /* Group */

=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:[[Media:Complete_processed_Data_MPM.xls|300mm NaCl XLS Version]]
:GenMAPP Expression Dataset file: [[Media:SinorhizobiumMeliloti_LM_GenMapp_FinalFile.txt]]

[[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]]

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

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

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

:Sample MAPP file of a relevant biological pathway for your species:[[Media:regulation of transcription, DNA-dependent.mapp]]
:Group Report:
:PowerPoint presentation:

=Individual=

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

File:300N T240 MAPPFINDER-Criterion Increased-GO.txt

2013-12-13T23:18:10Z

Mmalefyt: Increased genes at t240

Increased genes at t240

Team Name Deliverables

2013-12-13T23:17:08Z

Mmalefyt: /* Group */

File:T30.gex

2013-12-13T23:14:46Z

Mmalefyt: MappFinder for T30

MappFinder for T30

Miles Malefyt deliverables

2013-12-13T23:05:43Z

Mmalefyt: /* week 15 */

==Statement of work==
==Week 12==
*Read the paper on the salinity and sucrose stress on gene expression
*Sorted the raw data into an XML file
*started to compile the raw data
**downloaded all raw data and sorted through the information needed
**used the cys5 and cys3 fold change as well as all the IDs
*Uploaded [[Media:Team_Name_NaCl_compiled_raw_Data.xls|300 NaCl compiled data set]]
==Week 13==
*I continued to sort the raw data and began to process the data in an xls file
*this was a very repetitive part because it involved a lot of replications for each time set
*finished my compiled raw data and processed raw data, as well as the data ready for GenMAPP
*Made individual LOG fold change ratios for each time point replicate then averaged all of the LOG fold change ratios for each of the time points
*preformed a Tstat test
*Preformed a Pvalue test
*added a row of N next to the gene ID name in the forGenMAPP tab
*uploaded [[Media:Complete_processed_Data.xls|Processed Data]]
**NOTE:the GenMAPP version of the tab is labeled Complete Processed data_MPM and not forGenMAPP
==week 15==
*I worked on some of the mistakes that I had made in my prior data sets
**removed AVG_LOGFC_ALL row
**added individual Pvalues and TSTAT for each individual replicate of the experiment instead of one Tstat and P value for the whole experiment
*sanity check concluded the number of genes significantly changed at each time point
**T15- 5520
**T30- 7484
**T60- 6711
**T240- 5901
*Removed all of the #DIV/0! from the data that was transferred over to the GenMapp data
*uploaded [[Media:Complete_processed_Data_MPM.xls|XLS Version]] and [[Media:Complete_processed_Data_MPM.txt|TXT version, USE THIS]]

*had to change names of the columns in order to correctly upload to GenMAPP
**system code column was renamed
**Gene ID column was renamed to ID on the Programmers computer to resolve some issues
*it appears that there is something wrong with the actual gene IDs that is not compatible with GenMAPP
*ran the first integration of the data and came up with 5535 errors which is roughly half of the overall genes we loaded.
*loaded genMAPP and Mappfinder results

[[Media:MAPPFinder_results_T15-Criterion_Increased-GO.txt|Increased expression at T15]]
[[Media:MAPPFinder_results_T15-Criterion_Decreased-GO.txt|Decreased expression at T15]]
[[Media:MAPPFinder_t60-Criterion_Increased-GO.txt|Increased expression at t60]]
[[Media:MAPPFinder_t60-Criterion_Decreasaed-GO.txt|Decreased expression at t60]]
*analyzed the Gene Ontology report
**found a specific metabolic pathway that was pertinent to the treatment of NaCl

Team Name Deliverables

2013-12-13T23:03:43Z

Mmalefyt: /* Group */

Team Name Deliverables

2013-12-13T22:56:25Z

Mmalefyt: /* Group */

File:MAPPFinder t60-Criterion Decreasaed-GO.txt

2013-12-13T22:55:48Z

Mmalefyt: decreased expression at t60

decreased expression at t60

Team Name Deliverables

2013-12-13T22:55:13Z

Mmalefyt: /* Group */

File:MAPPFinder t60-Criterion Increased-GO.txt

2013-12-13T22:54:19Z

Mmalefyt: increased at t60

increased at t60

Team Name Deliverables

2013-12-13T22:53:18Z

Mmalefyt: /* Group */

File:MAPPFinder results T15-Criterion Decreased-GO.txt

2013-12-13T22:52:49Z

Mmalefyt: Decreased gene expression at T15

Decreased gene expression at T15

Team Name Deliverables

2013-12-13T22:51:14Z

Mmalefyt: /* Group */

File:MAPPFinder results T15-Criterion Increased-GO.txt

2013-12-13T22:50:07Z

Mmalefyt: increased genes and T15

increased genes and T15

Miles Malefyt deliverables

2013-12-13T21:52:30Z

Mmalefyt: /* Statement of work */

==Statement of work==
==Week 12==
*Read the paper on the salinity and sucrose stress on gene expression
*Sorted the raw data into an XML file
*started to compile the raw data
**downloaded all raw data and sorted through the information needed
**used the cys5 and cys3 fold change as well as all the IDs
*Uploaded [[Media:Team_Name_NaCl_compiled_raw_Data.xls|300 NaCl compiled data set]]
==Week 13==
*I continued to sort the raw data and began to process the data in an xls file
*this was a very repetitive part because it involved a lot of replications for each time set
*finished my compiled raw data and processed raw data, as well as the data ready for GenMAPP
*Made individual LOG fold change ratios for each time point replicate then averaged all of the LOG fold change ratios for each of the time points
*preformed a Tstat test
*Preformed a Pvalue test
*added a row of N next to the gene ID name in the forGenMAPP tab
*uploaded [[Media:Complete_processed_Data.xls|Processed Data]]
**NOTE:the GenMAPP version of the tab is labeled Complete Processed data_MPM and not forGenMAPP
==week 15==
*I worked on some of the mistakes that I had made in my prior data sets
**removed AVG_LOGFC_ALL row
**added individual Pvalues and TSTAT for each individual replicate of the experiment instead of one Tstat and P value for the whole experiment
*sanity check concluded the number of genes significantly changed at each time point
**T15- 5520
**T30- 7484
**T60- 6711
**T240- 5901
*Removed all of the #DIV/0! from the data that was transferred over to the GenMapp data
*uploaded [[Media:Complete_processed_Data_MPM.xls|XLS Version]] and [[Media:Complete_processed_Data_MPM.txt|TXT version, USE THIS]]

*had to change names of the columns in order to correctly upload to GenMAPP
**system code column was renamed
**Gene ID column was renamed to ID on the Programmers computer to resolve some issues
*it appears that there is something wrong with the actual gene IDs that is not compatible with GenMAPP
*ran the first integration of the data and came up with 5535 errors which is roughly half of the overall genes we loaded.
*loaded genMAPP and Mappfinder results
*analyzed the Gene Ontology report
**found a specific metabolic pathway that was pertinent to the treatment of NaCl

Miles Malefyt deliverables

2013-12-13T21:48:43Z

Mmalefyt: Created page with "==Statement of work=="

==Statement of work==

Team Name Deliverables

2013-12-13T21:48:06Z

Mmalefyt: /* Individual */

Team Name Deliverables

2013-12-13T21:47:53Z

Mmalefyt: /* Individual */

Team Name Deliverables

2013-12-13T21:45:11Z

Mmalefyt: /* Group */

Team Name Deliverables

2013-12-13T21:42:12Z

Mmalefyt: /* Group */

Teamname Week 15 Status Report

2013-12-06T04:37:03Z

Mmalefyt: /* Miles Malefyt */

=='''[[Team Name]]'''==

=='''[[user:mmalefyt|Miles Malefyt]]'''==
What worked?
*This week I finally began to see the fruits of my labor over the past couple weeks. I successfully uploaded some data to GenMAPP even though some of it didnt work, it turns out that a lot of the gene IDs went through. The test file I used was the t15 log fold change. I also went through and re-did some of the original title heading in the xls file before I converted it into a text file and compiled in on GenMAPP
What didn't work?
*There was an issue with a lot of the gene IDs that GenMAPP didnt recognize their format. Also, before I corrected it the names of the columns weren't importing into GenMAPP
What will I do next to fix what didn't work?
*Well first we need to isolate the problem. There seems to be 3 sets of IDs for each replicate and 3 replicates. I suspect that it has something to do with the labeling they gave the genes to distinguish the two megaplasmids and the chromosome. If I am correct then I will have to talk to the coder to see what we can do about it. If its another error then we will have to get to the bottom of that.

=='''[[user:laurmagee|Lauren Magee]]''': Reflection Questions==
#What worked?
#*A lot has been accomplished since the last status report and I now have a file that is ready for the GenMapp protocol. I have been going through an intense editing process of this file for sometime now with Dr. Dahlquist and my fellow group members, so that the file I currently have will hopefully produce error free results during GenMapp analysis.
#What didn't work?
#*In my original data file for GenMapp, I had accidentally copied over an entire column, but had labeled it as something else. This made the rest of my calculations, that had been based off of this data, invalid so I had to carefully correct my mistakes. If this error hadn't been pointed out by Dr. Dahlquis during the editing process, the results for my entire GenMapp analysis would have been incorrect. That is why professor and peer review is so important, because they are able to catch mistakes you may have glazed over in your own editing.
#What will I do next to fix what didn't work?
#*I have already fixed the incorrect column in my original data set, so I know have an error free document to run in GenMapp. There may be new errors that are shown while I am following the GenMapp protocol, but for now, everything appears correct.

Teamname Week 15 Status Report

2013-12-06T04:36:41Z

Mmalefyt:

=='''[[Team Name]]'''==

=='''[[user:mmalefyt|Miles Malefyt]]'''==
#What worked?
*This week I finally began to see the fruits of my labor over the past couple weeks. I successfully uploaded some data to GenMAPP even though some of it didnt work, it turns out that a lot of the gene IDs went through. The test file I used was the t15 log fold change. I also went through and re-did some of the original title heading in the xls file before I converted it into a text file and compiled in on GenMAPP
#What didn't work?
*There was an issue with a lot of the gene IDs that GenMAPP didnt recognize their format. Also, before I corrected it the names of the columns weren't importing into GenMAPP
#What will I do next to fix what didn't work?
*Well first we need to isolate the problem. There seems to be 3 sets of IDs for each replicate and 3 replicates. I suspect that it has something to do with the labeling they gave the genes to distinguish the two megaplasmids and the chromosome. If I am correct then I will have to talk to the coder to see what we can do about it. If its another error then we will have to get to the bottom of that.

=='''[[user:laurmagee|Lauren Magee]]''': Reflection Questions==
#What worked?
#*A lot has been accomplished since the last status report and I now have a file that is ready for the GenMapp protocol. I have been going through an intense editing process of this file for sometime now with Dr. Dahlquist and my fellow group members, so that the file I currently have will hopefully produce error free results during GenMapp analysis.
#What didn't work?
#*In my original data file for GenMapp, I had accidentally copied over an entire column, but had labeled it as something else. This made the rest of my calculations, that had been based off of this data, invalid so I had to carefully correct my mistakes. If this error hadn't been pointed out by Dr. Dahlquis during the editing process, the results for my entire GenMapp analysis would have been incorrect. That is why professor and peer review is so important, because they are able to catch mistakes you may have glazed over in your own editing.
#What will I do next to fix what didn't work?
#*I have already fixed the incorrect column in my original data set, so I know have an error free document to run in GenMapp. There may be new errors that are shown while I am following the GenMapp protocol, but for now, everything appears correct.

Team Name

2013-12-06T04:28:02Z

Mmalefyt: /* Wiki Navigation */

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]]
*[[Teamname Week 15 Status Report]]
*[[Laurmagee: Week 15]]
*[[Electronic notebook: sinorhizobium meliloti|Miles Malefyt electronic notebook]]

User:Mmalefyt

2013-12-06T04:26:05Z

Mmalefyt: /* class assignments */

=== '''Miles Malefyt''' ===

=== '''Contact Information''' ===

*milesm@malefyt.com
*mmalefyt@lion.lmu.edu

==='''Snail Mail'''===
8416 Campion drive, 90045, Westchester, CA

=== Education ===

==Major==
*Biology
==Graduation Year==
*2014
==Upper Division courses==
*Study Of Mammals
*Vertebrate field Biology
*Endocrinology
*Microbiology
*Genetics
*Vertebrate Physiology
*Urban ecology

== Work Experience ==
*Large animal consultant
**self employed
**2009-2012
**Taking care of goats [[File:photo.JPG]]

*Veterinary assistant
[http://www.cvvethosp.com Carmel Valley veterinary clinic]
**Carmel Valley Veterinary Clinic
**Summer 2013
**Cleaning animals, helping in surgery,walking dogs, taking care of well being

== Hobbies ==
*Taking care of animals
*Gardening and plants in general

== class assignments ==
{{mmalefyt}}

[[TFClass]]

[[Genetic Code]]

[[Individual hw week 4]]

[[individual HW week 5]]

[[individual hw week 6]]

[[Individual hw week 7]]

[[individual hw week 8]]

[[individual hw week 9]]

[[individual hw week 10]]

[[Sinorhizobium meliloti]]

[[Genome paper Sinorhizonium Meliloti]]

[[Team Name Week 12]]

[[Teamname Week 13 Status Report]]

[[Teamname week 15]]

[[[[Team Name]]]]

[[electronic notebook: sinorhizobium meliloti]]

User:Mmalefyt

2013-12-06T04:25:38Z

Mmalefyt: /* class assignments */

=== '''Miles Malefyt''' ===

=== '''Contact Information''' ===

*milesm@malefyt.com
*mmalefyt@lion.lmu.edu

==='''Snail Mail'''===
8416 Campion drive, 90045, Westchester, CA

=== Education ===

==Major==
*Biology
==Graduation Year==
*2014
==Upper Division courses==
*Study Of Mammals
*Vertebrate field Biology
*Endocrinology
*Microbiology
*Genetics
*Vertebrate Physiology
*Urban ecology

== Work Experience ==
*Large animal consultant
**self employed
**2009-2012
**Taking care of goats [[File:photo.JPG]]

*Veterinary assistant
[http://www.cvvethosp.com Carmel Valley veterinary clinic]
**Carmel Valley Veterinary Clinic
**Summer 2013
**Cleaning animals, helping in surgery,walking dogs, taking care of well being

== Hobbies ==
*Taking care of animals
*Gardening and plants in general

== class assignments ==
{{mmalefyt}}

[[TFClass]]

[[Genetic Code]]

[[Individual hw week 4]]

[[individual HW week 5]]

[[individual hw week 6]]

[[Individual hw week 7]]

[[individual hw week 8]]

[[individual hw week 9]]

[[individual hw week 10]]

[[Sinorhizobium meliloti]]

[[Genome paper Sinorhizonium Meliloti]]

[[Team Name Week 12]]

[[Teamname Week 13 Status Report]]

[[Teamname week 15]]

[[[[Team name]]]]

[[electronic notebook: sinorhizobium meliloti]]

Electronic notebook: sinorhizobium meliloti

2013-12-05T18:03:37Z

Mmalefyt: /* Week 13 */

Electronic notebook: sinorhizobium meliloti

2013-12-05T18:00:58Z

Mmalefyt: /* Week 13 */

Electronic notebook: sinorhizobium meliloti

2013-12-05T17:59:58Z

Mmalefyt: /* Week 12 */

Electronic notebook: sinorhizobium meliloti

2013-12-05T17:58:51Z

Mmalefyt: /* week 15 */

Electronic notebook: sinorhizobium meliloti

2013-12-05T17:57:44Z

Mmalefyt: /* week 15 */

Electronic notebook: sinorhizobium meliloti

2013-12-05T17:47:32Z

Mmalefyt: /* Week 12 */

Electronic notebook: sinorhizobium meliloti

2013-12-05T17:46:00Z

Mmalefyt: /* week 15 */

==Week 12==
*Read the paper on the salinity and sucrose stress on gene expression
*Sorted the raw data into an XML file
*started to compile the raw data

==Week 13==
*I continued to sort the raw data and began to process the data in an xls file
*this was a very repetitive part because it involved a lot of replications for each time set
*finished my compiled raw data and processed raw data, as well as the data ready for GenMAPP
*Made individual LOG fold change ratios for each time point replicate then averaged all of the LOG fold change ratios for each of the time points
*preformed a Tstat test
*Preformed a Pvalue test
*added a row of N next to the gene ID name in the forGenMAPP tab
*uploaded all the files to the wiki at the team page

==week 15==
*I worked on some of the mistakes that I had made in my prior data sets
**removed AVG_LOGFC_ALL row
**added individual Pvalues and TSTAT for each individual replicate of the experiment instead of one Tstat and P value for the whole experiment
*sanity check concluded the number of genes significantly changed at each time point
**T15- 5520
**T30- 7484
**T60- 6711
**T240- 5901
*Removed all of the #DIV/0! from the data that was transferred over to the GenMapp data
*had to change names of the columns in order to correctly upload to GenMAPP
**system code column was renamed
**Gene ID column was renamed to ID
*it appears that there is something wrong with the actual gene IDs that is not compatible with GenMAPP

File:UPLOAD FOR GENMAPP.txt

2013-12-05T17:41:14Z

Mmalefyt: NEW FILE, MAYBE THIS ONE WORKS

NEW FILE, MAYBE THIS ONE WORKS

Team Name

2013-12-05T17:37:30Z

Mmalefyt: /* Data ready for GenMAPP */

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.

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

File:Complete processed Data MPM.txt

2013-12-05T17:36:33Z

Mmalefyt: TXT processed data

TXT processed data

Team Name

2013-12-05T17:33:17Z

Mmalefyt: /* Data ready for GenMAPP */

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|Upload me to GenMAPP]]

==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]]

File:Complete processed Data MPM.xls

2013-12-05T17:32:03Z

Mmalefyt: Processed data ready for gen MAPP

Processed data ready for gen MAPP

Electronic notebook: sinorhizobium meliloti

2013-12-03T18:33:25Z

Mmalefyt: /* Week 12 */