[[Media:Leishmania PersonalAssesment 12122013 Hunt.pdf]]
==Links to Works==
:GenMAPP Gene Database for Leishmania: [[Media:LeishmaniaGDB Lena Gabe 20131205.zip[[
:ReadMe: [[Media:ReadMe Leishmania 20131212.pdf]]
:Gene Database Testing Report : [[Media:Leishmania Gene Database Testing Report.pdf]]
:[[Lena Project Notebook]]
:[[Leishmania major]]

Personal Assessment

2013-12-13T03:28:18Z

Lena:

2013-12-13T03:24:13Z

Lena:

User:Lena

2013-12-13T03:23:56Z

Lena: /* Leishmania major */

[[Image:Lena.png|right|]]

==Contact Information==

:Lena Hunt
:1 LMU Drive MSB 4697
:Los Angeles, CA 90045

:lena.m.hunt at gmail dot com

== Education ==

==='''Loyola Marymount University'''===
:[http://www.lmu.edu Loyola Marymount University]
:Bachelor of Art in Biology
:''University Honors Program''
:Class of 2014
:Upper Division Coursework
:*Urban Ecology
:*Plant Physiology
:*Environmental Chemistry
:*Biological Databases

'''Research Projects'''
:#Presence of Wolbachia in Southern California Spiders, with Dr. Ramirez at Loyola Marymount University
:#Crow Predation of Least Tern Eggs on Venice Beach, with Drs. Strauss and Auger at Loyola Marymount University
:#Feral Cats on LMU campus, with Dr. Auger at Loyola Marymount University
:#Mechanisms of Rusty Crayfish Invasion in the Upper Susquehanna River Basin, with Cassie Dresser M.S., at University of Central Michigan and Hartwick College
:#Antimicrobial properties of spices on Salmonella, with Dr. Allen at Hartwick College

=====Scientific Papers=====
[[Media:BIOLAB.pdf|Isolation and Identification of
Plant Growth Promoting
Rhizobacteria on Allium caeruleum]]

==='''Rittner's School of Floral Design'''===
:[http://www.floralschool.com Rittner's School of Floral Design]
:Certificate in Floral Arranging and Business Practices
:Class of 2011
:Studied Floral Designing for weddings, funerals, and novelty occasions, as well as creative and original design practices.

==Work Experience==

:'''Plant Nursery Attendant'''
:Carefree Gardens
:Summer 2011
:Responsibilities: Starting plants from seeds, watering, designing decorative planters, advising customers on which plants best suit their garden conditions
:
:'''Floral Designer'''
:Boston Flower Bouquet
:2010-2011
:Responsibilities: Care of cut flowers, designing window displays, creating bouquets, taking orders, and designing small made-to-order floral arrangements
:
:'''Animal Caretaker and Tour guide'''
:Joseph L Popp Jr Butterfly Conservatory
:2007-2010
:Responsibilities: Providing information about live plants and animals to conservatory visitors, looking after the food and water needs of varied reptiles, birds, mammals, and fish, raising native caterpillars, water plants and performing any needed maintenance on the conservatory grounds

==Personal Interests and Hobbies==

[[Image:BIRD.png|right|]]

:I grew up in the woods of rural upstate New York, and spend most of my life examining moss, following coyote tracks, and tracking the birds that came into our yard. I've been a naturalist as long as I can remember and am interested in just about everything pertaining to nature; from sustainable agriculture, to the paintings of the Hudson River School, to conservation genetics, to the writing of Henry David Thoreau. My hobbies include hiking and camping, photographing wildlife, and reading classical literature and books about science.

==Template==
:[[Template:Lena Hunt]]
{{Template:Lena Hunt}}
: 
:[[Lena's Notes]]
:[[Notes Week 7]]

==Journals and Assignments==
:[[Week 1]]
:[[Class Journal Week 1]]
:[[Week 2]]
:[[Class Journal Week 2]]
:[[Lena Week 2]]
:[[Week 3]]
:[[Class Journal Week 3]]
:[[Lena Week 3]]
:[[Week 4]]
:[[Class Journal Week 4]]
:[[Lena Week 4]]
:[[Week 5]]
:[[Class Journal Week 5]]
:[[Lena Week 5]]
:[[Week 6]]
:[[Class Journal Week 6]]
:[[Lena Week 6]]
:[[Week 7]]
:[[Class Journal Week 7]]
:[[Lena Week 7]]
:[[Week 8]]
:[[Class Journal Week 8]]
:[[Lena Week 8]]
:[[Week 9]]
:[[Class Journal Week 9]]
:[[Lena Week 9]]
:[[Week 10]]
:[[Class Journal Week 10]]
:[[Lena Week 10]]
:[[Week 11]]
:[[Lena Week 11]]
:[[Lena Project Notebook]]
:[[Leishmania major Week 12 Status Report]]
:[[Leishmania major Week 13 Status Report]]
:[[Leishmania Major Group Project Report]]
:[[Lena Week 15]]

==Database==
[[TFClass]]
==Leishmania major==
[[Leishmania major]]
[[Personal Assessment]]
[[category: Individual Homework]] [[category: User Page]] [[category: Journal Entry]]

Final Project Deliverables

2013-12-13T03:17:55Z

Lena:

:GenMAPP Gene Database for assigned species (.gdb): [[Media:LeishmaniaGDB Lena Gabe 20131205.zip]]
:ReadMe file to accompany the Gene Database (.pdf): [[Media:ReadMe Leishmania 20131212.pdf]]
:Gene Database Testing Report for final submitted Gene Database (print from wiki to .pdf file): [[Media:Leishmania Gene Database Testing Report.pdf]]
:Processed and analyzed DNA microarray dataset (.xls): [[File:L.majorStats.xls]],[[Media:L.infantumStats_B.xls]]
:GenMAPP Expression Dataset file (.gex): [[Media:LeishmaniaCompiledStatAnalysisLMJFiltered(B).gex]]
:Filtered MAPPFinder Results (.xls)
:Sample MAPP file of a relevant biological pathway for your species (.mapp)
:Group Report describing the creation of the Gene Database and the biological analysis of the data (.doc or .pdf)
:PowerPoint presentation (.ppt, given on Thursday, December 12): [[Media:Leishmania PowerPoint 12122013.pdf]]

2013-12-05T19:37:35Z

Lena:

#11/5/2013
#*[[Media:A-GEOD-6855.adf_A.txt]] Array Design File
#*[[Media:E-GEOD-10407.idf_A.txt]] Investigation Description File
#*[[Media:E-GEOD-10407.processed.1_A.zip]] Processed Data
#*[[Media:E-GEOD-10407.raw.1_A.zip]] Raw Data
#*[[Media:E-GEOD-10407.sdrf_A.txt]] Sample and Data Relationship File
#11/7/2013
#*[[Media:E-GEOD-10407.sdrf_B.txt]] Leishmania major Chips
#*Completed Import/Export Cycle, conducted a Tally Count, opened .gdb file in Microsoft Access and compared original row counts.
#*Access was missing 2 genes for GeneID and RefSeq, and we had no GO terms in the Tally or in Access.
#11/11/2013
#*[[Media:Leishmania_major_BD.pdf|Leishmania major Genome Reference Article Presentation]]
#11/14/13
#*[[Media:E-GEOD-10407.sdrf_C.txt]] Edited Sample and Data (Ordered based on species and relevant data)
#*[[Media:L.majorCompiledRawData.txt]] L. major raw compiled data
#*[[Media:L.infantumCompliedRawData(A).txt]] L. infantum raw compiled data
#11/19/2013:
#*[[Media:L.majorCompiledRawData_B.txt]] L. major raw compiled data with adjusted dye swap values
#*[[Media:L.infantumCompliedRawData(B).txt]] L. infantum raw compiled data with adjusted dye swap values and sample names
#*[[Media:L.majorCompiledRawData_C.txt]] L. major raw compiled data with adjusted dye swap values and sample names
#11/21/2013
#*[[Media:L.infantumStats.txt]]
#*[[Media:L.infantumStats.xls]]
#*[[File:L.majorStats.xls]]
#*[[File:L.majorStats.txt]]

#*[[File:L.majorStats(A).txt]]
#*[[File:L.infantumStats(A).txt]]
#*[[File:LeishmaniaCompiledStatAnalysis.txt]]
#12/3/2013
#*[[File:LeishmaniaCompiledStatAnalysis(A).txt]]
#*[[File:LeishmaniaCompiledStatAnalysis(A).EX.txt]]
#*[[Media:L.infantumStats_B.xls]] Fixed infantum p-value parenthesis
#*[[Media:LeishmaniaCompiledStatAnalysis(B).txt]]
#*[[Media:LeishmaniaCompiledStatAnalysisLMJFiltered.txt]] Original File That should work in GenMAPP once coding is fixed
#*[[Media:LeishmaniaCompiledStatAnalysisLMJFiltered(B).txt]] Quick fix file with underscores to work in GenMAPP until coding is fixed
#*[[Media:LeishmaniaCompiledStatAnalysisLMJFiltered(B).EX.txt]]
#*[[Media:LeishmaniaCompiledStatAnalysisLMJFiltered(B).gex]]
#*[[Media:ExceptionFileErrorID.txt]]
#*[[Leishmania Major Group Project Report]]
#*[[Media:Dist Leishmania Lena Gabe 05112013.zip]]

File:Dist Leishmania Lena Gabe 05112013.zip

2013-12-05T19:37:08Z

Lena:

Leishmania major

2013-12-05T19:11:39Z

Lena: /* OriginalRowCounts Comparison */

=='''Team Members:'''==
#[[User:kevinmcgee | Kevin McGee]] : GenMAPP User
#[[User:Lena | Lena Hunt]] : Quality Assurance [[Lena Project Notebook]]
#[[User:vkuehn|Viktoria Kuehn]] : GenMAPP User
#[[User:Gleis| Gabriel Leis]] : Coder
[[Gene Database Project]]

=='''Reference Genome Article'''==
:[http://www.sciencemag.org/content/309/5733/436.long ''The Genome of the Kinetoplastid Parasite, Leishmania major'' (Reference Genome)]
* This article was found via the PubMed database and the key terms used were "Leishmania Major [MeSH Terms] AND Genome [Title]"
** This search resulted in 30 articles, about 5 seemed relevant but this one was the first which had the entire genome
:Citation for paper:
:Alasdair C. Ivens, Christopher S. Peacock, Elizabeth A. Worthey, Lee Murphy, Gautam Aggarwa, Matthew Berriman, Ellen Sisk, Marie-Adele Rajandream, Ellen Adlem, Rita Aert, Atashi Anupama, Zina Apostolou, Philip Attipoe, Nathalie Bason, Christopher Bauser, Alfred Beck, Stephen M. Beverley, Gabriella Bianchettin, Katja Borzym, Gordana Bothe, Carlo V. Bruschi, Matt Collins, Eithon Cadag, Laura Ciarloni, Christine Clayton, Richard M. R. Coulson, Ann Cronin, Angela K. Cruz, Robert M. Davies, Javier De Gaudenzi, Deborah E. Dobson, Andreas Duesterhoeft, Gholam Fazelina, Nigel Fosker, Alberto Carlos Frasch, Audrey Fraser, Monika Fuchs, Claudia Gabel, Arlette Goble, André Goffeau, David Harris, Christiane Hertz-Fowler, Helmut Hilbert, David Horn, Yiting Huang, Sven Klages, Andrew Knights, Michael Kube, Natasha Larke, Lyudmila Litvin, Angela Lord, Tin Louie, Marco Marra, David Masuy, Keith Matthews, Shulamit Michaeli, Jeremy C. Mottram, Silke Müller-Auer, Heather Munden, Siri Nelson, Halina Norbertczak, Karen Oliver, Susan O'Neil, Martin Pentony, Thomas M. Poh, Claire Price, Bénédicte Purnelle, Michael A. Quail, Ester Rabbinowitsch, Richard Reinhardt, Michael Rieger, Joel Rinta, Johan Robben, Laura Robertson, Jeronimo C. Ruiz, Simon Rutter, David Saunders, Melanie Schäfer, Jacquie Schein, David C. Schwartz, Kathy Seeger, Amber Seyler, Sarah Sharp, Heesun Shin, Dhileep Sivam, Rob Squares, Steve Squares, Valentina Tosato, Christy Vogt, Guido Volckaert, Rolf Wambutt, Tim Warren, Holger Wedler, John Woodward, Shiguo Zhou, Wolfgang Zimmermann, Deborah F. Smith, Jenefer M. Blackwell, Kenneth D. Stuart, Bart Barrel, Peter J. Myler (2005) The Genome of the Kinetoplastid Parasite, Leishmania major. Science;309(5733):436-42.

* Pdf of the reference article: [http://www.sciencemag.org/content/309/5733/436.full.pdf''PDF Reference Article'']
**The genome sequencing article was used to do a prospective search on the Web of Knowledge database.
***There were 696 results found that referenced this article, the most recent one was in October 2013.
***Many of the most recent articles that cited this paper were involved in studying drug resistance of Leishmania major and studied related pathogenic parasites using sequence comparative analysis, for example.
*Link to the results page for our reference genome article
Website: http://apps.webofknowledge.com/CitingArticles.do?product=WOS&SID=4BN9U1ila7MPj92Jjlp&search_mode=CitingArticles&parentProduct=WOS&parentQid=3&parentDoc=1&REFID=518694
:
:Below is a screen shot of the results.
[[File:WebOfKnowledge.png]]

=='''[[Leishmania Major Articles| Leishmania Major Articles]]'''==

===Leishmania Major Data Updates===
To update this list edit the following template page: [[Template:Leishmania Major File Updates]]
{{Leishmania Major File Updates}}

====Data Links====
*[http://www.ebi.ac.uk/arrayexpress/ ''Array Express'']
*[http://www.ncbi.nlm.nih.gov/pubmed?holding=calmulib ''PubMed'']
*[http://apps.webofknowledge.com/WOS_GeneralSearch_input.do?product=WOS&search_mode=GeneralSearch&SID=3EzLbnixsjRACypZYp3&preferencesSaved= ''Web of Knowledge'']

{{Leishmania Major Navigation}}

==Group Projects==

:[[Leishmania major Week 12 Status Report]]
:[[Leishmania major Week 13 Status Report]]
:[[Leishmania major Week 15 Status Report]]

[[Media:Leishmania_major_BD.pdf|Leishmania major Genome Reference Article Presentation]]

==Import/Export==
===Export Information===
:Uniprot: 7.12 minutes
:[[Media:UniprotXML Leishmania 05112013 Gabe Lena.xml]]
:GO OBO: 6.32 minutes
:[[Media:Leishmania 05112013 Gabe Lena.obo-xml.gz]]
:GOA: 4.54 minutes
:[[Media:LeishmaniaGOA 05112013 GabeLena.goa]]

===Tally Engine===
[[Image:Screen_shot_2013-11-07_at_10.49.17_AM.png]]

===Original Row Counts Comparison===
*Uniprot has 8041 which is the same the tallycount.
*There were 0 ordered locus, which is the same as the tallycount.
*There were 8315 hits for RefSeq, which is 2 fewer than was seen in the tallycount.
*There were 8315 hits for GeneID, which is 2 fewer than was seen in the tallycount.

==Gene Database Testing Report==
==Export Information==

Version of GenMAPP Builder: gmbuilder2.0-b72

Computer on which export was run: Front row , second computer from the left

Postgres Database name:Leishmania_major_11262013

UniProt XML filename: UniprotXML Leishmania 05112013 Gabe Lena.xml
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10 - October 16, 2013
* Time taken to import: 7.12 minutes

GO OBO-XML filename: Leishmania 05112013 Gabe Lena.obo-xml.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): Monday, ‎November ‎04, ‎2013, ‏‎2:03:38 AM
* Time taken to import:6.32 minutes
* Time taken to process: 0.4 minutes

GOA filename:LeishmaniaGOA 19112013 Lena Gabe.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]): 14 November, 2013
12-Nov-2013 11:47 3.0M
* Time taken to import: 4.54 minutes

Name of .gdb file: [[Media:LeishmaniaGDB Lena Gabe 20131203.gdb]]
* Upload your file and link to it here.

Note:

==TallyEngine==

[[Image:Leishmania TallyResults 05122013.PNG]]

== Using XMLPipeDB match to Validate the XML Results from the TallyEngine==

[[Image:Leishmania Match Results 05122013 2.PNG]]

Are your results the same as you got for the TallyEngine? Why or why not?
:*We found 8353, we are missing 2 ORFs, but cannot reach the stragglers via coding.

== Using SQL Queries to Validate the PostgreSQL Database Results from the TallyEngine==
:'''select value from genenametype where type='ORF' and not value ~ 'L[Mm][Jj]F([\. _]|)[0-9][0-9][\. _][0-9][0-9][0-9][0-9]';'''
:[[Image:Leishmania postgres.PNG]]
:'''select count(*) from genenametype where type='ORF' and value ~ 'L[Mm][Jj]F(.|)[0-9][0-9].[0-9][0-9][0-9][0-9]';'''
:[[Image:Leishmania Postrges2.PNG]]
:
:8350 that match original pattern, 5 stragglers. There is an inconsistancy in patterns where some have underscores, some have periods, some have spaces. We were unable to capture all IDs at once.

==OriginalRowCounts Comparison==

Within the .gdb file, look at the OriginalRowCounts table to see if the database has the expected tables with the expected number of records. Compare the tables and records with a benchmark .gdb file.

Copy the OriginalRowCounts table and paste it here: 8354

Note: [[Image:Leishmania OriginalRowCounts 05122013.PNG]]

==Visual Inspection==

Perform visual inspection of individual tables to see if there are any problems.

* Look at the Systems table. Is there a date in the Date field for all gene ID systems present in the database? There are 1820 errors in the exceptions file.

* Open the UniProt, RefSeq, and OrderedLocusNames tables. Scroll down through the table. Do all of the IDs look like they take the correct form for that type of ID?

Note:

==.gdb Use in GenMAPP==

Note:

===Putting a gene on the MAPP using the GeneFinder window===

* Try a sample ID from each of the gene ID systems. Open the Backpage and see if all of the cross-referenced IDs that are supposed to be there are there.

Note:

===Creating an Expression Dataset in the Expression Dataset Manager===

* How many of the IDs were imported out of the total IDs in the microarray dataset? How many exceptions were there? Look in the EX.txt file and look at the error codes for the records that were not imported into the Expression Dataset. Do these represent IDs that were present in the UniProt XML, but were somehow not imported? or were they not present in the UniProt XML?

Note:

===Coloring a MAPP with expression data===

Note:

===Running MAPPFinder===

Note:

Leishmania major

2013-12-05T19:11:10Z

Lena: /* Visual Inspection */

=='''Team Members:'''==
#[[User:kevinmcgee | Kevin McGee]] : GenMAPP User
#[[User:Lena | Lena Hunt]] : Quality Assurance [[Lena Project Notebook]]
#[[User:vkuehn|Viktoria Kuehn]] : GenMAPP User
#[[User:Gleis| Gabriel Leis]] : Coder
[[Gene Database Project]]

=='''Reference Genome Article'''==
:[http://www.sciencemag.org/content/309/5733/436.long ''The Genome of the Kinetoplastid Parasite, Leishmania major'' (Reference Genome)]
* This article was found via the PubMed database and the key terms used were "Leishmania Major [MeSH Terms] AND Genome [Title]"
** This search resulted in 30 articles, about 5 seemed relevant but this one was the first which had the entire genome
:Citation for paper:
:Alasdair C. Ivens, Christopher S. Peacock, Elizabeth A. Worthey, Lee Murphy, Gautam Aggarwa, Matthew Berriman, Ellen Sisk, Marie-Adele Rajandream, Ellen Adlem, Rita Aert, Atashi Anupama, Zina Apostolou, Philip Attipoe, Nathalie Bason, Christopher Bauser, Alfred Beck, Stephen M. Beverley, Gabriella Bianchettin, Katja Borzym, Gordana Bothe, Carlo V. Bruschi, Matt Collins, Eithon Cadag, Laura Ciarloni, Christine Clayton, Richard M. R. Coulson, Ann Cronin, Angela K. Cruz, Robert M. Davies, Javier De Gaudenzi, Deborah E. Dobson, Andreas Duesterhoeft, Gholam Fazelina, Nigel Fosker, Alberto Carlos Frasch, Audrey Fraser, Monika Fuchs, Claudia Gabel, Arlette Goble, André Goffeau, David Harris, Christiane Hertz-Fowler, Helmut Hilbert, David Horn, Yiting Huang, Sven Klages, Andrew Knights, Michael Kube, Natasha Larke, Lyudmila Litvin, Angela Lord, Tin Louie, Marco Marra, David Masuy, Keith Matthews, Shulamit Michaeli, Jeremy C. Mottram, Silke Müller-Auer, Heather Munden, Siri Nelson, Halina Norbertczak, Karen Oliver, Susan O'Neil, Martin Pentony, Thomas M. Poh, Claire Price, Bénédicte Purnelle, Michael A. Quail, Ester Rabbinowitsch, Richard Reinhardt, Michael Rieger, Joel Rinta, Johan Robben, Laura Robertson, Jeronimo C. Ruiz, Simon Rutter, David Saunders, Melanie Schäfer, Jacquie Schein, David C. Schwartz, Kathy Seeger, Amber Seyler, Sarah Sharp, Heesun Shin, Dhileep Sivam, Rob Squares, Steve Squares, Valentina Tosato, Christy Vogt, Guido Volckaert, Rolf Wambutt, Tim Warren, Holger Wedler, John Woodward, Shiguo Zhou, Wolfgang Zimmermann, Deborah F. Smith, Jenefer M. Blackwell, Kenneth D. Stuart, Bart Barrel, Peter J. Myler (2005) The Genome of the Kinetoplastid Parasite, Leishmania major. Science;309(5733):436-42.

* Pdf of the reference article: [http://www.sciencemag.org/content/309/5733/436.full.pdf''PDF Reference Article'']
**The genome sequencing article was used to do a prospective search on the Web of Knowledge database.
***There were 696 results found that referenced this article, the most recent one was in October 2013.
***Many of the most recent articles that cited this paper were involved in studying drug resistance of Leishmania major and studied related pathogenic parasites using sequence comparative analysis, for example.
*Link to the results page for our reference genome article
Website: http://apps.webofknowledge.com/CitingArticles.do?product=WOS&SID=4BN9U1ila7MPj92Jjlp&search_mode=CitingArticles&parentProduct=WOS&parentQid=3&parentDoc=1&REFID=518694
:
:Below is a screen shot of the results.
[[File:WebOfKnowledge.png]]

=='''[[Leishmania Major Articles| Leishmania Major Articles]]'''==

===Leishmania Major Data Updates===
To update this list edit the following template page: [[Template:Leishmania Major File Updates]]
{{Leishmania Major File Updates}}

====Data Links====
*[http://www.ebi.ac.uk/arrayexpress/ ''Array Express'']
*[http://www.ncbi.nlm.nih.gov/pubmed?holding=calmulib ''PubMed'']
*[http://apps.webofknowledge.com/WOS_GeneralSearch_input.do?product=WOS&search_mode=GeneralSearch&SID=3EzLbnixsjRACypZYp3&preferencesSaved= ''Web of Knowledge'']

{{Leishmania Major Navigation}}

==Group Projects==

:[[Leishmania major Week 12 Status Report]]
:[[Leishmania major Week 13 Status Report]]
:[[Leishmania major Week 15 Status Report]]

[[Media:Leishmania_major_BD.pdf|Leishmania major Genome Reference Article Presentation]]

==Import/Export==
===Export Information===
:Uniprot: 7.12 minutes
:[[Media:UniprotXML Leishmania 05112013 Gabe Lena.xml]]
:GO OBO: 6.32 minutes
:[[Media:Leishmania 05112013 Gabe Lena.obo-xml.gz]]
:GOA: 4.54 minutes
:[[Media:LeishmaniaGOA 05112013 GabeLena.goa]]

===Tally Engine===
[[Image:Screen_shot_2013-11-07_at_10.49.17_AM.png]]

===Original Row Counts Comparison===
*Uniprot has 8041 which is the same the tallycount.
*There were 0 ordered locus, which is the same as the tallycount.
*There were 8315 hits for RefSeq, which is 2 fewer than was seen in the tallycount.
*There were 8315 hits for GeneID, which is 2 fewer than was seen in the tallycount.

==Gene Database Testing Report==
==Export Information==

Version of GenMAPP Builder: gmbuilder2.0-b72

Computer on which export was run: Front row , second computer from the left

Postgres Database name:Leishmania_major_11262013

UniProt XML filename: UniprotXML Leishmania 05112013 Gabe Lena.xml
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10 - October 16, 2013
* Time taken to import: 7.12 minutes

GO OBO-XML filename: Leishmania 05112013 Gabe Lena.obo-xml.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): Monday, ‎November ‎04, ‎2013, ‏‎2:03:38 AM
* Time taken to import:6.32 minutes
* Time taken to process: 0.4 minutes

GOA filename:LeishmaniaGOA 19112013 Lena Gabe.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]): 14 November, 2013
12-Nov-2013 11:47 3.0M
* Time taken to import: 4.54 minutes

Name of .gdb file: [[Media:LeishmaniaGDB Lena Gabe 20131203.gdb]]
* Upload your file and link to it here.

Note:

==TallyEngine==

[[Image:Leishmania TallyResults 05122013.PNG]]

== Using XMLPipeDB match to Validate the XML Results from the TallyEngine==

[[Image:Leishmania Match Results 05122013 2.PNG]]

Are your results the same as you got for the TallyEngine? Why or why not?
:*We found 8353, we are missing 2 ORFs, but cannot reach the stragglers via coding.

== Using SQL Queries to Validate the PostgreSQL Database Results from the TallyEngine==
:'''select value from genenametype where type='ORF' and not value ~ 'L[Mm][Jj]F([\. _]|)[0-9][0-9][\. _][0-9][0-9][0-9][0-9]';'''
:[[Image:Leishmania postgres.PNG]]
:'''select count(*) from genenametype where type='ORF' and value ~ 'L[Mm][Jj]F(.|)[0-9][0-9].[0-9][0-9][0-9][0-9]';'''
:[[Image:Leishmania Postrges2.PNG]]
:
:8350 that match original pattern, 5 stragglers. There is an inconsistancy in patterns where some have underscores, some have periods, some have spaces. We were unable to capture all IDs at once.

==OriginalRowCounts Comparison==

Within the .gdb file, look at the OriginalRowCounts table to see if the database has the expected tables with the expected number of records. Compare the tables and records with a benchmark .gdb file.

Benchmark .gdb file: (for the [[Week 9]] Assignment, use the "Vc-Std_External_20101022.gdb" as your benchmark, downloadable from [http://sourceforge.net/projects/xmlpipedb/files/V.%20cholerae%20Gene%20Database/V.%20cholerae%2020101022/Vc-Std_External_20101022.zip/download here].

Copy the OriginalRowCounts table and paste it here: 8354

Note:

==Visual Inspection==

Perform visual inspection of individual tables to see if there are any problems.

* Look at the Systems table. Is there a date in the Date field for all gene ID systems present in the database? There are 1820 errors in the exceptions file.

* Open the UniProt, RefSeq, and OrderedLocusNames tables. Scroll down through the table. Do all of the IDs look like they take the correct form for that type of ID?

Note:

==.gdb Use in GenMAPP==

Note:

===Putting a gene on the MAPP using the GeneFinder window===

* Try a sample ID from each of the gene ID systems. Open the Backpage and see if all of the cross-referenced IDs that are supposed to be there are there.

Note:

===Creating an Expression Dataset in the Expression Dataset Manager===

* How many of the IDs were imported out of the total IDs in the microarray dataset? How many exceptions were there? Look in the EX.txt file and look at the error codes for the records that were not imported into the Expression Dataset. Do these represent IDs that were present in the UniProt XML, but were somehow not imported? or were they not present in the UniProt XML?

Note:

===Coloring a MAPP with expression data===

Note:

===Running MAPPFinder===

Note:

2013-12-05T18:51:39Z

Lena:

File:Leishmania postgres.PNG

2013-12-05T18:51:07Z

Lena:

Leishmania major

2013-12-05T18:48:38Z

Lena: /* Using XMLPipeDB match to Validate the XML Results from the TallyEngine */

=='''Team Members:'''==
#[[User:kevinmcgee | Kevin McGee]] : GenMAPP User
#[[User:Lena | Lena Hunt]] : Quality Assurance [[Lena Project Notebook]]
#[[User:vkuehn|Viktoria Kuehn]] : GenMAPP User
#[[User:Gleis| Gabriel Leis]] : Coder
[[Gene Database Project]]

=='''Reference Genome Article'''==
:[http://www.sciencemag.org/content/309/5733/436.long ''The Genome of the Kinetoplastid Parasite, Leishmania major'' (Reference Genome)]
* This article was found via the PubMed database and the key terms used were "Leishmania Major [MeSH Terms] AND Genome [Title]"
** This search resulted in 30 articles, about 5 seemed relevant but this one was the first which had the entire genome
:Citation for paper:
:Alasdair C. Ivens, Christopher S. Peacock, Elizabeth A. Worthey, Lee Murphy, Gautam Aggarwa, Matthew Berriman, Ellen Sisk, Marie-Adele Rajandream, Ellen Adlem, Rita Aert, Atashi Anupama, Zina Apostolou, Philip Attipoe, Nathalie Bason, Christopher Bauser, Alfred Beck, Stephen M. Beverley, Gabriella Bianchettin, Katja Borzym, Gordana Bothe, Carlo V. Bruschi, Matt Collins, Eithon Cadag, Laura Ciarloni, Christine Clayton, Richard M. R. Coulson, Ann Cronin, Angela K. Cruz, Robert M. Davies, Javier De Gaudenzi, Deborah E. Dobson, Andreas Duesterhoeft, Gholam Fazelina, Nigel Fosker, Alberto Carlos Frasch, Audrey Fraser, Monika Fuchs, Claudia Gabel, Arlette Goble, André Goffeau, David Harris, Christiane Hertz-Fowler, Helmut Hilbert, David Horn, Yiting Huang, Sven Klages, Andrew Knights, Michael Kube, Natasha Larke, Lyudmila Litvin, Angela Lord, Tin Louie, Marco Marra, David Masuy, Keith Matthews, Shulamit Michaeli, Jeremy C. Mottram, Silke Müller-Auer, Heather Munden, Siri Nelson, Halina Norbertczak, Karen Oliver, Susan O'Neil, Martin Pentony, Thomas M. Poh, Claire Price, Bénédicte Purnelle, Michael A. Quail, Ester Rabbinowitsch, Richard Reinhardt, Michael Rieger, Joel Rinta, Johan Robben, Laura Robertson, Jeronimo C. Ruiz, Simon Rutter, David Saunders, Melanie Schäfer, Jacquie Schein, David C. Schwartz, Kathy Seeger, Amber Seyler, Sarah Sharp, Heesun Shin, Dhileep Sivam, Rob Squares, Steve Squares, Valentina Tosato, Christy Vogt, Guido Volckaert, Rolf Wambutt, Tim Warren, Holger Wedler, John Woodward, Shiguo Zhou, Wolfgang Zimmermann, Deborah F. Smith, Jenefer M. Blackwell, Kenneth D. Stuart, Bart Barrel, Peter J. Myler (2005) The Genome of the Kinetoplastid Parasite, Leishmania major. Science;309(5733):436-42.

* Pdf of the reference article: [http://www.sciencemag.org/content/309/5733/436.full.pdf''PDF Reference Article'']
**The genome sequencing article was used to do a prospective search on the Web of Knowledge database.
***There were 696 results found that referenced this article, the most recent one was in October 2013.
***Many of the most recent articles that cited this paper were involved in studying drug resistance of Leishmania major and studied related pathogenic parasites using sequence comparative analysis, for example.
*Link to the results page for our reference genome article
Website: http://apps.webofknowledge.com/CitingArticles.do?product=WOS&SID=4BN9U1ila7MPj92Jjlp&search_mode=CitingArticles&parentProduct=WOS&parentQid=3&parentDoc=1&REFID=518694
:
:Below is a screen shot of the results.
[[File:WebOfKnowledge.png]]

=='''[[Leishmania Major Articles| Leishmania Major Articles]]'''==

===Leishmania Major Data Updates===
To update this list edit the following template page: [[Template:Leishmania Major File Updates]]
{{Leishmania Major File Updates}}

====Data Links====
*[http://www.ebi.ac.uk/arrayexpress/ ''Array Express'']
*[http://www.ncbi.nlm.nih.gov/pubmed?holding=calmulib ''PubMed'']
*[http://apps.webofknowledge.com/WOS_GeneralSearch_input.do?product=WOS&search_mode=GeneralSearch&SID=3EzLbnixsjRACypZYp3&preferencesSaved= ''Web of Knowledge'']

{{Leishmania Major Navigation}}

==Group Projects==

:[[Leishmania major Week 12 Status Report]]
:[[Leishmania major Week 13 Status Report]]

[[Media:Leishmania_major_BD.pdf|Leishmania major Genome Reference Article Presentation]]

==Import/Export==
===Export Information===
:Uniprot: 7.12 minutes
:[[Media:UniprotXML Leishmania 05112013 Gabe Lena.xml]]
:GO OBO: 6.32 minutes
:[[Media:Leishmania 05112013 Gabe Lena.obo-xml.gz]]
:GOA: 4.54 minutes
:[[Media:LeishmaniaGOA 05112013 GabeLena.goa]]

===Tally Engine===
[[Image:Screen_shot_2013-11-07_at_10.49.17_AM.png]]

===Original Row Counts Comparison===
*Uniprot has 8041 which is the same the tallycount.
*There were 0 ordered locus, which is the same as the tallycount.
*There were 8315 hits for RefSeq, which is 2 fewer than was seen in the tallycount.
*There were 8315 hits for GeneID, which is 2 fewer than was seen in the tallycount.

==Gene Database Testing Report==
==Export Information==

Version of GenMAPP Builder: gmbuilder2.0-b72

Computer on which export was run: Front row , second computer from the left

Postgres Database name:Leishmania_major_11262013

UniProt XML filename: UniprotXML Leishmania 05112013 Gabe Lena.xml
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10 - October 16, 2013
* Time taken to import: 7.12 minutes

GO OBO-XML filename: Leishmania 05112013 Gabe Lena.obo-xml.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): Monday, ‎November ‎04, ‎2013, ‏‎2:03:38 AM
* Time taken to import:6.32 minutes
* Time taken to process: 0.4 minutes

GOA filename:LeishmaniaGOA 19112013 Lena Gabe.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]): 14 November, 2013
12-Nov-2013 11:47 3.0M
* Time taken to import: 4.54 minutes

Name of .gdb file: [[Media:LeishmaniaGDB Lena Gabe 20131203.gdb]]
* Upload your file and link to it here.

Note:

==TallyEngine==

[[Image:Leishmania TallyResults 05122013.PNG]]

== Using XMLPipeDB match to Validate the XML Results from the TallyEngine==

[[Image:Leishmania Match Results 05122013 2.PNG]]

Are your results the same as you got for the TallyEngine? Why or why not?
:*We found 8353, we are missing 2 ORFs, but cannot reach the stragglers via coding.

== Using SQL Queries to Validate the PostgreSQL Database Results from the TallyEngine==

[[How_Do_I_Count_Thee%3F_Let_Me_Count_The_Ways#SQL | Follow the instructions on this page to query the PostgreSQL Database.]]

8350 that match original pattern, 5 stragglers. There is an inconsistancy in patterns where some have underscores, some have periods, some have spaces. We were unable to capture all IDs at once.

==OriginalRowCounts Comparison==

Within the .gdb file, look at the OriginalRowCounts table to see if the database has the expected tables with the expected number of records. Compare the tables and records with a benchmark .gdb file.

Benchmark .gdb file: (for the [[Week 9]] Assignment, use the "Vc-Std_External_20101022.gdb" as your benchmark, downloadable from [http://sourceforge.net/projects/xmlpipedb/files/V.%20cholerae%20Gene%20Database/V.%20cholerae%2020101022/Vc-Std_External_20101022.zip/download here].

Copy the OriginalRowCounts table and paste it here:

Note:

==Visual Inspection==

Perform visual inspection of individual tables to see if there are any problems.

* Look at the Systems table. Is there a date in the Date field for all gene ID systems present in the database?
* Open the UniProt, RefSeq, and OrderedLocusNames tables. Scroll down through the table. Do all of the IDs look like they take the correct form for that type of ID?

Note:

==.gdb Use in GenMAPP==

Note:

===Putting a gene on the MAPP using the GeneFinder window===

* Try a sample ID from each of the gene ID systems. Open the Backpage and see if all of the cross-referenced IDs that are supposed to be there are there.

Note:

===Creating an Expression Dataset in the Expression Dataset Manager===

* How many of the IDs were imported out of the total IDs in the microarray dataset? How many exceptions were there? Look in the EX.txt file and look at the error codes for the records that were not imported into the Expression Dataset. Do these represent IDs that were present in the UniProt XML, but were somehow not imported? or were they not present in the UniProt XML?

Note:

===Coloring a MAPP with expression data===

Note:

===Running MAPPFinder===

Note:

2013-12-05T18:30:08Z

Lena: /* Using XMLPipeDB match to Validate the XML Results from the TallyEngine */

=='''Team Members:'''==
#[[User:kevinmcgee | Kevin McGee]] : GenMAPP User
#[[User:Lena | Lena Hunt]] : Quality Assurance [[Lena Project Notebook]]
#[[User:vkuehn|Viktoria Kuehn]] : GenMAPP User
#[[User:Gleis| Gabriel Leis]] : Coder
[[Gene Database Project]]

=='''Reference Genome Article'''==
:[http://www.sciencemag.org/content/309/5733/436.long ''The Genome of the Kinetoplastid Parasite, Leishmania major'' (Reference Genome)]
* This article was found via the PubMed database and the key terms used were "Leishmania Major [MeSH Terms] AND Genome [Title]"
** This search resulted in 30 articles, about 5 seemed relevant but this one was the first which had the entire genome
:Citation for paper:
:Alasdair C. Ivens, Christopher S. Peacock, Elizabeth A. Worthey, Lee Murphy, Gautam Aggarwa, Matthew Berriman, Ellen Sisk, Marie-Adele Rajandream, Ellen Adlem, Rita Aert, Atashi Anupama, Zina Apostolou, Philip Attipoe, Nathalie Bason, Christopher Bauser, Alfred Beck, Stephen M. Beverley, Gabriella Bianchettin, Katja Borzym, Gordana Bothe, Carlo V. Bruschi, Matt Collins, Eithon Cadag, Laura Ciarloni, Christine Clayton, Richard M. R. Coulson, Ann Cronin, Angela K. Cruz, Robert M. Davies, Javier De Gaudenzi, Deborah E. Dobson, Andreas Duesterhoeft, Gholam Fazelina, Nigel Fosker, Alberto Carlos Frasch, Audrey Fraser, Monika Fuchs, Claudia Gabel, Arlette Goble, André Goffeau, David Harris, Christiane Hertz-Fowler, Helmut Hilbert, David Horn, Yiting Huang, Sven Klages, Andrew Knights, Michael Kube, Natasha Larke, Lyudmila Litvin, Angela Lord, Tin Louie, Marco Marra, David Masuy, Keith Matthews, Shulamit Michaeli, Jeremy C. Mottram, Silke Müller-Auer, Heather Munden, Siri Nelson, Halina Norbertczak, Karen Oliver, Susan O'Neil, Martin Pentony, Thomas M. Poh, Claire Price, Bénédicte Purnelle, Michael A. Quail, Ester Rabbinowitsch, Richard Reinhardt, Michael Rieger, Joel Rinta, Johan Robben, Laura Robertson, Jeronimo C. Ruiz, Simon Rutter, David Saunders, Melanie Schäfer, Jacquie Schein, David C. Schwartz, Kathy Seeger, Amber Seyler, Sarah Sharp, Heesun Shin, Dhileep Sivam, Rob Squares, Steve Squares, Valentina Tosato, Christy Vogt, Guido Volckaert, Rolf Wambutt, Tim Warren, Holger Wedler, John Woodward, Shiguo Zhou, Wolfgang Zimmermann, Deborah F. Smith, Jenefer M. Blackwell, Kenneth D. Stuart, Bart Barrel, Peter J. Myler (2005) The Genome of the Kinetoplastid Parasite, Leishmania major. Science;309(5733):436-42.

* Pdf of the reference article: [http://www.sciencemag.org/content/309/5733/436.full.pdf''PDF Reference Article'']
**The genome sequencing article was used to do a prospective search on the Web of Knowledge database.
***There were 696 results found that referenced this article, the most recent one was in October 2013.
***Many of the most recent articles that cited this paper were involved in studying drug resistance of Leishmania major and studied related pathogenic parasites using sequence comparative analysis, for example.
*Link to the results page for our reference genome article
Website: http://apps.webofknowledge.com/CitingArticles.do?product=WOS&SID=4BN9U1ila7MPj92Jjlp&search_mode=CitingArticles&parentProduct=WOS&parentQid=3&parentDoc=1&REFID=518694
:
:Below is a screen shot of the results.
[[File:WebOfKnowledge.png]]

=='''[[Leishmania Major Articles| Leishmania Major Articles]]'''==

===Leishmania Major Data Updates===
To update this list edit the following template page: [[Template:Leishmania Major File Updates]]
{{Leishmania Major File Updates}}

====Data Links====
*[http://www.ebi.ac.uk/arrayexpress/ ''Array Express'']
*[http://www.ncbi.nlm.nih.gov/pubmed?holding=calmulib ''PubMed'']
*[http://apps.webofknowledge.com/WOS_GeneralSearch_input.do?product=WOS&search_mode=GeneralSearch&SID=3EzLbnixsjRACypZYp3&preferencesSaved= ''Web of Knowledge'']

{{Leishmania Major Navigation}}

==Group Projects==

:[[Leishmania major Week 12 Status Report]]
:[[Leishmania major Week 13 Status Report]]

[[Media:Leishmania_major_BD.pdf|Leishmania major Genome Reference Article Presentation]]

==Import/Export==
===Export Information===
:Uniprot: 7.12 minutes
:[[Media:UniprotXML Leishmania 05112013 Gabe Lena.xml]]
:GO OBO: 6.32 minutes
:[[Media:Leishmania 05112013 Gabe Lena.obo-xml.gz]]
:GOA: 4.54 minutes
:[[Media:LeishmaniaGOA 05112013 GabeLena.goa]]

===Tally Engine===
[[Image:Screen_shot_2013-11-07_at_10.49.17_AM.png]]

===Original Row Counts Comparison===
*Uniprot has 8041 which is the same the tallycount.
*There were 0 ordered locus, which is the same as the tallycount.
*There were 8315 hits for RefSeq, which is 2 fewer than was seen in the tallycount.
*There were 8315 hits for GeneID, which is 2 fewer than was seen in the tallycount.

==Gene Database Testing Report==
==Export Information==

Version of GenMAPP Builder: gmbuilder2.0-b72

Computer on which export was run: Front row , second computer from the left

Postgres Database name:Leishmania_major_11262013

UniProt XML filename: UniprotXML Leishmania 05112013 Gabe Lena.xml
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10 - October 16, 2013
* Time taken to import: 7.12 minutes

GO OBO-XML filename: Leishmania 05112013 Gabe Lena.obo-xml.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): Monday, ‎November ‎04, ‎2013, ‏‎2:03:38 AM
* Time taken to import:6.32 minutes
* Time taken to process: 0.4 minutes

GOA filename:LeishmaniaGOA 19112013 Lena Gabe.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]): 14 November, 2013
12-Nov-2013 11:47 3.0M
* Time taken to import: 4.54 minutes

Name of .gdb file: [[Media:LeishmaniaGDB Lena Gabe 20131203.gdb]]
* Upload your file and link to it here.

Note:

==TallyEngine==

[[Image:Leishmania TallyResults 05122013.PNG]]

== Using XMLPipeDB match to Validate the XML Results from the TallyEngine==

[[Image:Leishmania Match Results 05122013.PNG]]

Are your results the same as you got for the TallyEngine? Why or why not?
:*We are missing two ORFs, but we will try to find them in Postgres Query.

== Using SQL Queries to Validate the PostgreSQL Database Results from the TallyEngine==

[[How_Do_I_Count_Thee%3F_Let_Me_Count_The_Ways#SQL | Follow the instructions on this page to query the PostgreSQL Database.]]

==OriginalRowCounts Comparison==

Within the .gdb file, look at the OriginalRowCounts table to see if the database has the expected tables with the expected number of records. Compare the tables and records with a benchmark .gdb file.

Benchmark .gdb file: (for the [[Week 9]] Assignment, use the "Vc-Std_External_20101022.gdb" as your benchmark, downloadable from [http://sourceforge.net/projects/xmlpipedb/files/V.%20cholerae%20Gene%20Database/V.%20cholerae%2020101022/Vc-Std_External_20101022.zip/download here].

Copy the OriginalRowCounts table and paste it here:

Note:

==Visual Inspection==

Perform visual inspection of individual tables to see if there are any problems.

* Look at the Systems table. Is there a date in the Date field for all gene ID systems present in the database?
* Open the UniProt, RefSeq, and OrderedLocusNames tables. Scroll down through the table. Do all of the IDs look like they take the correct form for that type of ID?

Note:

==.gdb Use in GenMAPP==

Note:

===Putting a gene on the MAPP using the GeneFinder window===

* Try a sample ID from each of the gene ID systems. Open the Backpage and see if all of the cross-referenced IDs that are supposed to be there are there.

Note:

===Creating an Expression Dataset in the Expression Dataset Manager===

* How many of the IDs were imported out of the total IDs in the microarray dataset? How many exceptions were there? Look in the EX.txt file and look at the error codes for the records that were not imported into the Expression Dataset. Do these represent IDs that were present in the UniProt XML, but were somehow not imported? or were they not present in the UniProt XML?

Note:

===Coloring a MAPP with expression data===

Note:

===Running MAPPFinder===

Note: