LMU BioDB 2015 - User contributions [en]

File:Resume.pdf

2016-10-21T06:55:10Z

Jwoodlee: Jwoodlee uploaded a new version of File:Resume.pdf

User:Jwoodlee

2016-10-21T06:46:17Z

Jwoodlee: removed old resume

==Jake Woodlee==

[[Image:10257442 875082729210542 5054128824308646190 o.jpg]]

[[Image:Snapchat--7945747201980540557.jpg|thumb|right]]

[[Image:10442356 10203022922605747 4101588566629455324 n.jpg|thumb|right]]

==Contact Information==

Email Address: jwoodlee at lion dot lmu dot edu

Mailing Address: Loyola Marymount University, 1 LMU Drive MSB 7090, Los Angeles, CA, 90045

==Education==

#Major: Computer Science
#Expected Graduation Year: 2018
#Calculus 3, Biological Databases

==Career interests and goals==

Interested in all types of programming, I see myself working in security or development in the future.

==Work experience== 

[http://itd.acgov.org/index.page Alameda County ITD:]
*Network Engineering Intern
*Alameda County
*Summer 2015
*Configuration of new network equipment to work with the current network infrastructure.

Lion Express:
*Driver
*Loyola Marymount University
*August 2014-Present
*Driving student and staff to various off campus locations.

==Personal interests/hobbies==

===Soccer===
====Club Soccer @ LMU and played for Heritage FC in Concord====

===Android Customization===
===== Rooting, custom ROMs, and custom recoveries=====

===Investing===
====All kinds of investing, securities, commodities, bonds, etc.====

==What is your favorite aspect of biology and why?==

Biology gives intimate detail on the functioning of earthling species, which is of utmost important to human beings. It is useful to study biology so we can understand what makes us tick.

==What is your favorite aspect of computer science and why?==

Computer science is the best subject (not biased, I swear) because it can be applied to a multitude of disciplines in order to solve problems. Solving complex problems has always been one of the greatest joys in life and computer science lets me do that everyday.

==Biological Databases==

[[Template:Jwoodlee]].

===Jake Woodlee Journal Assignments===

{{Template:Jwoodlee}}

Jwoodlee Individual Reflection

2015-12-18T18:30:46Z

Jwoodlee: /* Statement of Work */ added files that I worked on

===Statement of Work===
*Describe exactly what you did on the project.
Three files, the XML Uniprot file, the GOA file, and the GO-OBO file were all imported into GenMAPP Builder by the QA. These files hold the information to create a gene database (.gdb), where I come in is this second step of exporting the files into a .gdb. I created a custom species profile for Shigella flexneri within the Java code of GenMAPP Builder. In order to do this I had to make my own distribution of GenMAPP Builder, and my own branch to commit to on GitHub. The edits I made to the code were the following:

I created a new subclass of UniProtSpeciesProfile called ShigellaflexneriUniprotSpeciesProfile. Within this new class I created a custom constructor that called the superclass's constructor and passed it information about Shigella flexneri, such as the taxonomy ID, and a custom String. I also overrode a method "getSystemsTableManagerCustomizations()" which, from my understanding, captures genes from the XML file we imported. The code for these initial customizations were provided to us by Dondi. However, as to be expected, the GenMAPP users alerted to us that we were missing 416 genes with these customizations. Trixie discovered that 92 of these genes could be found at unexpected locations in the XML file and so my task was to add another layer of customization. With help from Dondi, we overloaded the getSystemsTableManagerCustomizations method to account for these 92 genes in the XML file. Dondi added a SQL query within the method that captured the 92 missing genes and added them to the .gdb file. This was as many of the missing genes we could add. Throughout all of this I committed and pulled changes as needed.

Another customization that was required was within TallyEngine's gmbuilder.properties file. We added special properties for Shigella flexneri. These changes were pretty standard as they were in our class instructions, however, due to the nature of our GMBuilder java customizations, we need to make sure that TallyEngine could gather both the original genes and the 92 missing ones that were added on later. So, with help from Dondi, we added a SQL query that would be able to do this. The query used the union operation to get both the initial customization genes and the 92 missing genes.

These were the major changes I contributed to complete our project. Step by step and the final product can be seen on [[Jwoodlee Week 12 | Week 12]], [[Jwoodlee Week 14 | Week 14]], and [[Jwoodlee Week 15 | Week 15]]

Final Build of GenMAPP Builder: [[File:GenMAPP Builder 12 14 2015 Number 2.zip | Gene Database .gdb]]

Schema: [[File:ShigellaGeneDatabaseSchema.pdf | Gene Database Schema]]

===Assessment of Project===
*Give an objective assessment of the success of your project workflow and teamwork.
** I think our project workflow and teamwork was overall successful. We got along pretty well and communicated effectively throughout the project. This is a vital part of any team and without it the team cannot improve. I think our workflow could have been improved because we procrastinated a few times, but that is to be expected when we all have a lot of other things going on. In summary I think our workflow and teamwork were very successful, but we could have been a bit more timely.
*What worked and what didn't work?
** The only problems I ran into had to do with my lack of experience navigating the various tools. For Eclipse, several times my code just wouldn't compile because I wasn't organizing imports or because I just typed something incorrectly. Also when it came time to customize GenMAPP Builder for a second time my lack of experience with SQL lead to Dondi essentially writing the queries for us. Other than that I would say most things were successful and went smoothly.
*What would you do differently if you could do it all over again?
** I would definitely try to get everything done as fast as I could to accommodate errors that could come up. On Monday before the presentation we were rushing a bit because I had to make some last minute changes to the source code of GenMAPP Builder which was the result of not figuring out what changes needed to be made in a timely manner.
*Evaluate the Gene Database Project and Group Report in the following areas:
*#Content: I would rate the quality of our work as good; we all tried to complete our tasks the best we could and as a result we have a pretty solid project. I would say that the quality would go up even higher given more time, but for now I am satisfied.
*#Organization: We have all the links and content required on our wiki pages. As far as wiki pages go I think ours are organized well with all the tables we have.
*#Completeness:We have provided all the deliverables that were expected of us, so I would say that yes we did achieve the project objectives, unless there is more that we have to provide that is not in the deliverables section. We completed the presentation and the paper as well.

===Reflection on the Project===
*What did you learn?
**With your head?((biological or computer science principles))
***Computer Science: As far as coding in Java I don't feel like I learned very much, however my SQL knowledge increased 100% because I had never done any SQL before this class. Just basic select queries and the entire way relational databases work were some of the things I will value as I move on to other courses. Also I learned more about GitHub, specifically in how it can work with Eclipse and how different branches can be created for the same project for more advanced version control.
***Biology: I learned the most biology when I had to review the genome paper. I learned about plasmids, pathogenicity, shotgun sequencing, etc. The list goes on. Pretty much every term that was used in that paper I had to look up and know for my presentation.
**With your heart?(personal qualities and teamwork qualities that make things work or not work)
***Definitely the fact that my team got along well and communicated effectively was of the utmost importance. Without that we wouldn't have gotten anything done. We designated tasks that weren't explicitly outlined for us in the wiki and as a result created a project that could actually contribute to the scientific community. The deadlines were always a little bit rough for us I think mainly because we were all so busy, but I think also we could have managed our time better. Other than that I have no criticism for our team and I think we did a great job.
**With your hands?(With your hands (technical skills))
***Navigating eclipse will definitely be the biggest technical takeaway from this project. I learned how I can access GitHub through eclipse as well as miscellaneous functions like "Organize Imports". To add to this list however, I would not skip over the navigation of GenMAPP and excel that I had to do. Excel is always a useful tool and I definitely got more comfortable with that.
*What lesson will you take away from this project that you will still use a year from now?
**Easily I would say my increased proficiency in using GitHub, Eclipse, and Excel will be used a year for now, at least for technical skills. For non-technical skills I would say coordinating with a group on who does what. It was easier because we had designated tasks assigned to us by the professors, however there was still some grey area where we had to designate tasks ourselves. And those grey areas of task designation will be what I take away in a year.

Jwoodlee Week 15

2015-12-18T18:26:47Z

Jwoodlee: /* Individual Reflection(Also on its own individual page here) */ added link to ind. refl.

Jwoodlee Week 15

2015-12-18T18:25:45Z

Jwoodlee: /* Individual Reflection */

== Electronic Lab Notebook ==

Our GenMAPP users were reporting 416 missing genes from the .gdb which was a problem. Trixie found that 92 of these genes were in the XML file in such a way that led to the exporter missing them, the rest of the missing genes simply weren't in the XML file. Specifically, the genes were somewhere else in the file and weren't added to the OrderedLocusNames table by default. To capture these 92 elusive genes we consulted Dondi. Dondi edited the ShigellaflexneriUniProtSpeciesProfile class, which I had previously constructed, by adding a SQL query that captured the 92 missing genes:

This is what the final customized class looks like:
[[Image:FinalCustomizationsPart1.png]]

[[Image:FinalCustomizationsPart2.png]]

A further modification that was required was in the gmbuilder.properties file which we were supposed to edit to assist TallyEngine in its function, the initial customizations to this were the following lines:

[[Image: Gmbuilder.propertiesOriginal.png]]

This customization was insufficient in capturing the 92 missing genes. With the help of Dondi, Trixie and I replaced the insufficient SQL query with one that joined the missing 92 genes in the dbreference tag with the rest of the genes that were found by the default customization. Default customization can be found on [[Jwoodlee Week 12 | Week 12]] and [[Jwoodlee Week 14 | Week 14]]. A sql union was used to execute this task which replaced the original sql query on gmbuilder.properties, as can be seen below:

select count(value) from (select value from genenametype where type = 'ordered locus' and value ~ '(CP|SF?)[0-9][0-9][0-9][0-9](\.[0-9])?' union select extra as value from (select propertytype.value as extra from propertytype inner join dbreferencetype on propertytype.dbreferencetype_property_hjid = dbreferencetype.hjid where dbreferencetype.type = 'EnsemblBacteria' and dbreferencetype.id ~ 'AAN[0-9][0-9][0-9][0-9][0-9]' and propertytype.type = 'gene ID' and propertytype.value ~ 'SF[0-9][0-9][0-9][0-9]') as f left join (select value from genenametype where type = 'ordered locus' and value ~ '(CP|SF?)[0-9][0-9][0-9][0-9](\.[0-9])?') as g on f.extra = g.value where g.value is null) as combined;

== Individual Reflection(Also on its own individual page [[Jwoodlee Individual Reflection | here]]) ==
===Statement of Work===
*Describe exactly what you did on the project.
Three files, the XML Uniprot file, the GOA file, and the GO-OBO file were all imported into GenMAPP Builder by the QA. These files hold the information to create a gene database (.gdb), where I come in is this second step of exporting the files into a .gdb. I created a custom species profile for Shigella flexneri within the Java code of GenMAPP Builder. In order to do this I had to make my own distribution of GenMAPP Builder, and my own branch to commit to on GitHub. The edits I made to the code were the following:

I created a new subclass of UniProtSpeciesProfile called ShigellaflexneriUniprotSpeciesProfile. Within this new class I created a custom constructor that called the superclass's constructor and passed it information about Shigella flexneri, such as the taxonomy ID, and a custom String. I also overrode a method "getSystemsTableManagerCustomizations()" which, from my understanding, captures genes from the XML file we imported. The code for these initial customizations were provided to us by Dondi. However, as to be expected, the GenMAPP users alerted to us that we were missing 416 genes with these customizations. Trixie discovered that 92 of these genes could be found at unexpected locations in the XML file and so my task was to add another layer of customization. With help from Dondi, we overloaded the getSystemsTableManagerCustomizations method to account for these 92 genes in the XML file. Dondi added a SQL query within the method that captured the 92 missing genes and added them to the .gdb file. This was as many of the missing genes we could add. Throughout all of this I committed and pulled changes as needed.

Another customization that was required was within TallyEngine's gmbuilder.properties file. We added special properties for Shigella flexneri. These changes were pretty standard as they were in our class instructions, however, due to the nature of our GMBuilder java customizations, we need to make sure that TallyEngine could gather both the original genes and the 92 missing ones that were added on later. So, with help from Dondi, we added a SQL query that would be able to do this. The query used the union operation to get both the initial customization genes and the 92 missing genes.

These were the major changes I contributed to complete our project. Step by step and the final product can be seen on [[Jwoodlee Week 12 | Week 12]], [[Jwoodlee Week 14 | Week 14]], and [[Jwoodlee Week 15 | Week 15]]

*Provide references or links to artifacts of your work, such as:
**Wiki Pages
**Other files or documents
**Code or scripts

===Assessment of Project===
*Give an objective assessment of the success of your project workflow and teamwork.
** I think our project workflow and teamwork was overall successful. We got along pretty well and communicated effectively throughout the project. This is a vital part of any team and without it the team cannot improve. I think our workflow could have been improved because we procrastinated a few times, but that is to be expected when we all have a lot of other things going on. In summary I think our workflow and teamwork were very successful, but we could have been a bit more timely.
*What worked and what didn't work?
** The only problems I ran into had to do with my lack of experience navigating the various tools. For Eclipse, several times my code just wouldn't compile because I wasn't organizing imports or because I just typed something incorrectly. Also when it came time to customize GenMAPP Builder for a second time my lack of experience with SQL lead to Dondi essentially writing the queries for us. Other than that I would say most things were successful and went smoothly.
*What would you do differently if you could do it all over again?
** I would definitely try to get everything done as fast as I could to accommodate errors that could come up. On Monday before the presentation we were rushing a bit because I had to make some last minute changes to the source code of GenMAPP Builder which was the result of not figuring out what changes needed to be made in a timely manner.
*Evaluate the Gene Database Project and Group Report in the following areas:
*#Content: I would rate the quality of our work as good; we all tried to complete our tasks the best we could and as a result we have a pretty solid project. I would say that the quality would go up even higher given more time, but for now I am satisfied.
*#Organization: We have all the links and content required on our wiki pages. As far as wiki pages go I think ours are organized well with all the tables we have.
*#Completeness:We have provided all the deliverables that were expected of us, so I would say that yes we did achieve the project objectives, unless there is more that we have to provide that is not in the deliverables section. We completed the presentation and the paper as well.

===Reflection on the Project===
*What did you learn?
**With your head?((biological or computer science principles))
***Computer Science: As far as coding in Java I don't feel like I learned very much, however my SQL knowledge increased 100% because I had never done any SQL before this class. Just basic select queries and the entire way relational databases work were some of the things I will value as I move on to other courses. Also I learned more about GitHub, specifically in how it can work with Eclipse and how different branches can be created for the same project for more advanced version control.
***Biology: I learned the most biology when I had to review the genome paper. I learned about plasmids, pathogenicity, shotgun sequencing, etc. The list goes on. Pretty much every term that was used in that paper I had to look up and know for my presentation.
**With your heart?(personal qualities and teamwork qualities that make things work or not work)
***Definitely the fact that my team got along well and communicated effectively was of the utmost importance. Without that we wouldn't have gotten anything done. We designated tasks that weren't explicitly outlined for us in the wiki and as a result created a project that could actually contribute to the scientific community. The deadlines were always a little bit rough for us I think mainly because we were all so busy, but I think also we could have managed our time better. Other than that I have no criticism for our team and I think we did a great job.
**With your hands?(With your hands (technical skills))
***Navigating eclipse will definitely be the biggest technical takeaway from this project. I learned how I can access GitHub through eclipse as well as miscellaneous functions like "Organize Imports". To add to this list however, I would not skip over the navigation of GenMAPP and excel that I had to do. Excel is always a useful tool and I definitely got more comfortable with that.
*What lesson will you take away from this project that you will still use a year from now?
**Easily I would say my increased proficiency in using GitHub, Eclipse, and Excel will be used a year for now, at least for technical skills. For non-technical skills I would say coordinating with a group on who does what. It was easier because we had designated tasks assigned to us by the professors, however there was still some grey area where we had to designate tasks ourselves. And those grey areas of task designation will be what I take away in a year.

{{Template: Jwoodlee}}

Jwoodlee Individual Reflection

2015-12-18T18:24:09Z

Jwoodlee: initial commit

===Statement of Work===
*Describe exactly what you did on the project.
Three files, the XML Uniprot file, the GOA file, and the GO-OBO file were all imported into GenMAPP Builder by the QA. These files hold the information to create a gene database (.gdb), where I come in is this second step of exporting the files into a .gdb. I created a custom species profile for Shigella flexneri within the Java code of GenMAPP Builder. In order to do this I had to make my own distribution of GenMAPP Builder, and my own branch to commit to on GitHub. The edits I made to the code were the following:

I created a new subclass of UniProtSpeciesProfile called ShigellaflexneriUniprotSpeciesProfile. Within this new class I created a custom constructor that called the superclass's constructor and passed it information about Shigella flexneri, such as the taxonomy ID, and a custom String. I also overrode a method "getSystemsTableManagerCustomizations()" which, from my understanding, captures genes from the XML file we imported. The code for these initial customizations were provided to us by Dondi. However, as to be expected, the GenMAPP users alerted to us that we were missing 416 genes with these customizations. Trixie discovered that 92 of these genes could be found at unexpected locations in the XML file and so my task was to add another layer of customization. With help from Dondi, we overloaded the getSystemsTableManagerCustomizations method to account for these 92 genes in the XML file. Dondi added a SQL query within the method that captured the 92 missing genes and added them to the .gdb file. This was as many of the missing genes we could add. Throughout all of this I committed and pulled changes as needed.

Another customization that was required was within TallyEngine's gmbuilder.properties file. We added special properties for Shigella flexneri. These changes were pretty standard as they were in our class instructions, however, due to the nature of our GMBuilder java customizations, we need to make sure that TallyEngine could gather both the original genes and the 92 missing ones that were added on later. So, with help from Dondi, we added a SQL query that would be able to do this. The query used the union operation to get both the initial customization genes and the 92 missing genes.

These were the major changes I contributed to complete our project. Step by step and the final product can be seen on [[Jwoodlee Week 12 | Week 12]], [[Jwoodlee Week 14 | Week 14]], and [[Jwoodlee Week 15 | Week 15]]

*Provide references or links to artifacts of your work, such as:
**Wiki Pages
**Other files or documents
**Code or scripts

===Assessment of Project===
*Give an objective assessment of the success of your project workflow and teamwork.
** I think our project workflow and teamwork was overall successful. We got along pretty well and communicated effectively throughout the project. This is a vital part of any team and without it the team cannot improve. I think our workflow could have been improved because we procrastinated a few times, but that is to be expected when we all have a lot of other things going on. In summary I think our workflow and teamwork were very successful, but we could have been a bit more timely.
*What worked and what didn't work?
** The only problems I ran into had to do with my lack of experience navigating the various tools. For Eclipse, several times my code just wouldn't compile because I wasn't organizing imports or because I just typed something incorrectly. Also when it came time to customize GenMAPP Builder for a second time my lack of experience with SQL lead to Dondi essentially writing the queries for us. Other than that I would say most things were successful and went smoothly.
*What would you do differently if you could do it all over again?
** I would definitely try to get everything done as fast as I could to accommodate errors that could come up. On Monday before the presentation we were rushing a bit because I had to make some last minute changes to the source code of GenMAPP Builder which was the result of not figuring out what changes needed to be made in a timely manner.
*Evaluate the Gene Database Project and Group Report in the following areas:
*#Content: I would rate the quality of our work as good; we all tried to complete our tasks the best we could and as a result we have a pretty solid project. I would say that the quality would go up even higher given more time, but for now I am satisfied.
*#Organization: We have all the links and content required on our wiki pages. As far as wiki pages go I think ours are organized well with all the tables we have.
*#Completeness:We have provided all the deliverables that were expected of us, so I would say that yes we did achieve the project objectives, unless there is more that we have to provide that is not in the deliverables section. We completed the presentation and the paper as well.

===Reflection on the Project===
*What did you learn?
**With your head?((biological or computer science principles))
***Computer Science: As far as coding in Java I don't feel like I learned very much, however my SQL knowledge increased 100% because I had never done any SQL before this class. Just basic select queries and the entire way relational databases work were some of the things I will value as I move on to other courses. Also I learned more about GitHub, specifically in how it can work with Eclipse and how different branches can be created for the same project for more advanced version control.
***Biology: I learned the most biology when I had to review the genome paper. I learned about plasmids, pathogenicity, shotgun sequencing, etc. The list goes on. Pretty much every term that was used in that paper I had to look up and know for my presentation.
**With your heart?(personal qualities and teamwork qualities that make things work or not work)
***Definitely the fact that my team got along well and communicated effectively was of the utmost importance. Without that we wouldn't have gotten anything done. We designated tasks that weren't explicitly outlined for us in the wiki and as a result created a project that could actually contribute to the scientific community. The deadlines were always a little bit rough for us I think mainly because we were all so busy, but I think also we could have managed our time better. Other than that I have no criticism for our team and I think we did a great job.
**With your hands?(With your hands (technical skills))
***Navigating eclipse will definitely be the biggest technical takeaway from this project. I learned how I can access GitHub through eclipse as well as miscellaneous functions like "Organize Imports". To add to this list however, I would not skip over the navigation of GenMAPP and excel that I had to do. Excel is always a useful tool and I definitely got more comfortable with that.
*What lesson will you take away from this project that you will still use a year from now?
**Easily I would say my increased proficiency in using GitHub, Eclipse, and Excel will be used a year for now, at least for technical skills. For non-technical skills I would say coordinating with a group on who does what. It was easier because we had designated tasks assigned to us by the professors, however there was still some grey area where we had to designate tasks ourselves. And those grey areas of task designation will be what I take away in a year.

OTS Deliverables

2015-12-18T18:23:36Z

Jwoodlee: /* Individual Reflections */ formatting

{{Template:Oregon Trail Survivors}}
==OTS Group Files and Datasets==

[[Media:GenMAPP Builder 12 14 2015 Number 2.zip | Gene Database .gdb]]

[[Media:ReadMe Sf-Std External 20151214.pdf | ReadMe]]

[[Media:ShigellaGeneDatabaseSchema.pdf | Gene Database Schema]]

Gene Database Testing Report (.pdf)

[[Media:FINAL CompiledRawData RXRP EYKZ20151210.xlsx | Compiled Raw Microarray Dataset (.xlsx)]]

[[Media:FINAL CompiledRawData RXRP EYKZ20151210.txt | Data Used for Import into GenMAPP (.txt)]]

[[Media:FINAL CompiledRawData RXRP EYKZ20151210 (1).gex | GenMAPP Expression Dataset File (.gex)]]

[[Media:FINAL CompiledRawData RXRP EYKZ20151210.EX.txt | Exceptions file (.EX.txt)]]

[[Media:Criterion.GOfiles.zip | Raw MAPPFinder results files (-GO.txt)]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.gmf | .gmf file]]

[[Media:Filtered MAPPFinder Results.xlsx | Filtered MAPPFinder Results .xlsx]]

[[Media:MAPPFinderResults.zip | Filtered MAPPFinder Results (common GO terms highlighted) .png]]

[[Media:RPRX MAPPs.zip | .zip of .mapp s of relevant genes]]

Group Report (.doc or .pdf)

[[Media:FinalOTSPresentation.pptx | Final PowerPoint Presentation]]

==Individual Reflections==

[[Kzebrows Individual Reflection | Kristin Zebrowski]]

[[Eyanosch Individual Reflection | Erich Yanoschik]]

[[Jwoodlee Individual Reflection | Jake Woodlee]]

OTS Deliverables

2015-12-18T18:23:16Z

Jwoodlee: /* Individual Reflections */ added reflection page

{{Template:Oregon Trail Survivors}}
==OTS Group Files and Datasets==

[[Media:GenMAPP Builder 12 14 2015 Number 2.zip | Gene Database .gdb]]

[[Media:ReadMe Sf-Std External 20151214.pdf | ReadMe]]

[[Media:ShigellaGeneDatabaseSchema.pdf | Gene Database Schema]]

Gene Database Testing Report (.pdf)

[[Media:FINAL CompiledRawData RXRP EYKZ20151210.xlsx | Compiled Raw Microarray Dataset (.xlsx)]]

[[Media:FINAL CompiledRawData RXRP EYKZ20151210.txt | Data Used for Import into GenMAPP (.txt)]]

[[Media:FINAL CompiledRawData RXRP EYKZ20151210 (1).gex | GenMAPP Expression Dataset File (.gex)]]

[[Media:FINAL CompiledRawData RXRP EYKZ20151210.EX.txt | Exceptions file (.EX.txt)]]

[[Media:Criterion.GOfiles.zip | Raw MAPPFinder results files (-GO.txt)]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.gmf | .gmf file]]

[[Media:Filtered MAPPFinder Results.xlsx | Filtered MAPPFinder Results .xlsx]]

[[Media:MAPPFinderResults.zip | Filtered MAPPFinder Results (common GO terms highlighted) .png]]

[[Media:RPRX MAPPs.zip | .zip of .mapp s of relevant genes]]

Group Report (.doc or .pdf)

[[Media:FinalOTSPresentation.pptx | Final PowerPoint Presentation]]

==Individual Reflections==

[[Kzebrows Individual Reflection | Kristin Zebrowski]]

[[Eyanosch Individual Reflection | Erich Yanoschik]]
[[Jwoodlee Individual Reflection | Jake Woodlee]]

Jwoodlee Week 15

2015-12-18T18:22:24Z

Jwoodlee: /* Assessment of Project */ added content for individual reflection

== Electronic Lab Notebook ==

Our GenMAPP users were reporting 416 missing genes from the .gdb which was a problem. Trixie found that 92 of these genes were in the XML file in such a way that led to the exporter missing them, the rest of the missing genes simply weren't in the XML file. Specifically, the genes were somewhere else in the file and weren't added to the OrderedLocusNames table by default. To capture these 92 elusive genes we consulted Dondi. Dondi edited the ShigellaflexneriUniProtSpeciesProfile class, which I had previously constructed, by adding a SQL query that captured the 92 missing genes:

This is what the final customized class looks like:
[[Image:FinalCustomizationsPart1.png]]

[[Image:FinalCustomizationsPart2.png]]

A further modification that was required was in the gmbuilder.properties file which we were supposed to edit to assist TallyEngine in its function, the initial customizations to this were the following lines:

[[Image: Gmbuilder.propertiesOriginal.png]]

This customization was insufficient in capturing the 92 missing genes. With the help of Dondi, Trixie and I replaced the insufficient SQL query with one that joined the missing 92 genes in the dbreference tag with the rest of the genes that were found by the default customization. Default customization can be found on [[Jwoodlee Week 12 | Week 12]] and [[Jwoodlee Week 14 | Week 14]]. A sql union was used to execute this task which replaced the original sql query on gmbuilder.properties, as can be seen below:

select count(value) from (select value from genenametype where type = 'ordered locus' and value ~ '(CP|SF?)[0-9][0-9][0-9][0-9](\.[0-9])?' union select extra as value from (select propertytype.value as extra from propertytype inner join dbreferencetype on propertytype.dbreferencetype_property_hjid = dbreferencetype.hjid where dbreferencetype.type = 'EnsemblBacteria' and dbreferencetype.id ~ 'AAN[0-9][0-9][0-9][0-9][0-9]' and propertytype.type = 'gene ID' and propertytype.value ~ 'SF[0-9][0-9][0-9][0-9]') as f left join (select value from genenametype where type = 'ordered locus' and value ~ '(CP|SF?)[0-9][0-9][0-9][0-9](\.[0-9])?') as g on f.extra = g.value where g.value is null) as combined;

== Individual Reflection ==
===Statement of Work===
*Describe exactly what you did on the project.
Three files, the XML Uniprot file, the GOA file, and the GO-OBO file were all imported into GenMAPP Builder by the QA. These files hold the information to create a gene database (.gdb), where I come in is this second step of exporting the files into a .gdb. I created a custom species profile for Shigella flexneri within the Java code of GenMAPP Builder. In order to do this I had to make my own distribution of GenMAPP Builder, and my own branch to commit to on GitHub. The edits I made to the code were the following:

I created a new subclass of UniProtSpeciesProfile called ShigellaflexneriUniprotSpeciesProfile. Within this new class I created a custom constructor that called the superclass's constructor and passed it information about Shigella flexneri, such as the taxonomy ID, and a custom String. I also overrode a method "getSystemsTableManagerCustomizations()" which, from my understanding, captures genes from the XML file we imported. The code for these initial customizations were provided to us by Dondi. However, as to be expected, the GenMAPP users alerted to us that we were missing 416 genes with these customizations. Trixie discovered that 92 of these genes could be found at unexpected locations in the XML file and so my task was to add another layer of customization. With help from Dondi, we overloaded the getSystemsTableManagerCustomizations method to account for these 92 genes in the XML file. Dondi added a SQL query within the method that captured the 92 missing genes and added them to the .gdb file. This was as many of the missing genes we could add. Throughout all of this I committed and pulled changes as needed.

Another customization that was required was within TallyEngine's gmbuilder.properties file. We added special properties for Shigella flexneri. These changes were pretty standard as they were in our class instructions, however, due to the nature of our GMBuilder java customizations, we need to make sure that TallyEngine could gather both the original genes and the 92 missing ones that were added on later. So, with help from Dondi, we added a SQL query that would be able to do this. The query used the union operation to get both the initial customization genes and the 92 missing genes.

These were the major changes I contributed to complete our project. Step by step and the final product can be seen on [[Jwoodlee Week 12 | Week 12]], [[Jwoodlee Week 14 | Week 14]], and [[Jwoodlee Week 15 | Week 15]]

*Provide references or links to artifacts of your work, such as:
**Wiki Pages
**Other files or documents
**Code or scripts

===Assessment of Project===
*Give an objective assessment of the success of your project workflow and teamwork.
** I think our project workflow and teamwork was overall successful. We got along pretty well and communicated effectively throughout the project. This is a vital part of any team and without it the team cannot improve. I think our workflow could have been improved because we procrastinated a few times, but that is to be expected when we all have a lot of other things going on. In summary I think our workflow and teamwork were very successful, but we could have been a bit more timely.
*What worked and what didn't work?
** The only problems I ran into had to do with my lack of experience navigating the various tools. For Eclipse, several times my code just wouldn't compile because I wasn't organizing imports or because I just typed something incorrectly. Also when it came time to customize GenMAPP Builder for a second time my lack of experience with SQL lead to Dondi essentially writing the queries for us. Other than that I would say most things were successful and went smoothly.
*What would you do differently if you could do it all over again?
** I would definitely try to get everything done as fast as I could to accommodate errors that could come up. On Monday before the presentation we were rushing a bit because I had to make some last minute changes to the source code of GenMAPP Builder which was the result of not figuring out what changes needed to be made in a timely manner.
*Evaluate the Gene Database Project and Group Report in the following areas:
*#Content: I would rate the quality of our work as good; we all tried to complete our tasks the best we could and as a result we have a pretty solid project. I would say that the quality would go up even higher given more time, but for now I am satisfied.
*#Organization: We have all the links and content required on our wiki pages. As far as wiki pages go I think ours are organized well with all the tables we have.
*#Completeness:We have provided all the deliverables that were expected of us, so I would say that yes we did achieve the project objectives, unless there is more that we have to provide that is not in the deliverables section. We completed the presentation and the paper as well.

===Reflection on the Project===
*What did you learn?
**With your head?((biological or computer science principles))
***Computer Science: As far as coding in Java I don't feel like I learned very much, however my SQL knowledge increased 100% because I had never done any SQL before this class. Just basic select queries and the entire way relational databases work were some of the things I will value as I move on to other courses. Also I learned more about GitHub, specifically in how it can work with Eclipse and how different branches can be created for the same project for more advanced version control.
***Biology: I learned the most biology when I had to review the genome paper. I learned about plasmids, pathogenicity, shotgun sequencing, etc. The list goes on. Pretty much every term that was used in that paper I had to look up and know for my presentation.
**With your heart?(personal qualities and teamwork qualities that make things work or not work)
***Definitely the fact that my team got along well and communicated effectively was of the utmost importance. Without that we wouldn't have gotten anything done. We designated tasks that weren't explicitly outlined for us in the wiki and as a result created a project that could actually contribute to the scientific community. The deadlines were always a little bit rough for us I think mainly because we were all so busy, but I think also we could have managed our time better. Other than that I have no criticism for our team and I think we did a great job.
**With your hands?(With your hands (technical skills))
***Navigating eclipse will definitely be the biggest technical takeaway from this project. I learned how I can access GitHub through eclipse as well as miscellaneous functions like "Organize Imports". To add to this list however, I would not skip over the navigation of GenMAPP and excel that I had to do. Excel is always a useful tool and I definitely got more comfortable with that.
*What lesson will you take away from this project that you will still use a year from now?
**Easily I would say my increased proficiency in using GitHub, Eclipse, and Excel will be used a year for now, at least for technical skills. For non-technical skills I would say coordinating with a group on who does what. It was easier because we had designated tasks assigned to us by the professors, however there was still some grey area where we had to designate tasks ourselves. And those grey areas of task designation will be what I take away in a year.

{{Template: Jwoodlee}}

OTS Deliverables

2015-12-18T06:42:49Z

Jwoodlee: /* OTS Group Files and Datasets */ added schema

{{Template:Oregon Trail Survivors}}
==OTS Group Files and Datasets==

[[Media:GenMAPP Builder 12 14 2015 Number 2.zip | Gene Database .gdb]]

[[Media:ReadMe Sf-Std External 20151214.pdf | ReadMe]]

[[Media:ShigellaGeneDatabaseSchema.pdf | Gene Database Schema]]

Gene Database Testing Report (.pdf)

[[Media:FINAL CompiledRawData RXRP EYKZ20151210.xlsx | Compiled Raw Microarray Dataset (.xlsx)]]

[[Media:FINAL CompiledRawData RXRP EYKZ20151210.txt | Data Used for Import into GenMAPP (.txt)]]

[[Media:FINAL CompiledRawData RXRP EYKZ20151210 (1).gex | GenMAPP Expression Dataset File (.gex)]]

[[Media:FINAL CompiledRawData RXRP EYKZ20151210.EX.txt | Exceptions file (.EX.txt)]]

[[Media:Criterion.GOfiles.zip | Raw MAPPFinder results files (-GO.txt)]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.gmf | .gmf file]]

[[Media:Filtered MAPPFinder Results.xlsx | Filtered MAPPFinder Results .xlsx]]

[[Media:MAPPFinderResults.zip | Filtered MAPPFinder Results (common GO terms highlighted) .png]]

Sample MAPP (.mapp)

Group Report (.doc or .pdf)

[[Media:FinalOTSPresentation.pptx | Final PowerPoint Presentation]]

File:ShigellaGeneDatabaseSchema.pdf

2015-12-18T06:41:29Z

Jwoodlee:

Jwoodlee Week 15

2015-12-18T06:35:07Z

Jwoodlee: /* Reflection on the Project */ added more to my individual reflection

== Electronic Lab Notebook ==

Our GenMAPP users were reporting 416 missing genes from the .gdb which was a problem. Trixie found that 92 of these genes were in the XML file in such a way that led to the exporter missing them, the rest of the missing genes simply weren't in the XML file. Specifically, the genes were somewhere else in the file and weren't added to the OrderedLocusNames table by default. To capture these 92 elusive genes we consulted Dondi. Dondi edited the ShigellaflexneriUniProtSpeciesProfile class, which I had previously constructed, by adding a SQL query that captured the 92 missing genes:

This is what the final customized class looks like:
[[Image:FinalCustomizationsPart1.png]]

[[Image:FinalCustomizationsPart2.png]]

A further modification that was required was in the gmbuilder.properties file which we were supposed to edit to assist TallyEngine in its function, the initial customizations to this were the following lines:

[[Image: Gmbuilder.propertiesOriginal.png]]

This customization was insufficient in capturing the 92 missing genes. With the help of Dondi, Trixie and I replaced the insufficient SQL query with one that joined the missing 92 genes in the dbreference tag with the rest of the genes that were found by the default customization. Default customization can be found on [[Jwoodlee Week 12 | Week 12]] and [[Jwoodlee Week 14 | Week 14]]. A sql union was used to execute this task which replaced the original sql query on gmbuilder.properties, as can be seen below:

select count(value) from (select value from genenametype where type = 'ordered locus' and value ~ '(CP|SF?)[0-9][0-9][0-9][0-9](\.[0-9])?' union select extra as value from (select propertytype.value as extra from propertytype inner join dbreferencetype on propertytype.dbreferencetype_property_hjid = dbreferencetype.hjid where dbreferencetype.type = 'EnsemblBacteria' and dbreferencetype.id ~ 'AAN[0-9][0-9][0-9][0-9][0-9]' and propertytype.type = 'gene ID' and propertytype.value ~ 'SF[0-9][0-9][0-9][0-9]') as f left join (select value from genenametype where type = 'ordered locus' and value ~ '(CP|SF?)[0-9][0-9][0-9][0-9](\.[0-9])?') as g on f.extra = g.value where g.value is null) as combined;

== Individual Reflection ==
===Statement of Work===
*Describe exactly what you did on the project.
Three files, the XML Uniprot file, the GOA file, and the GO-OBO file were all imported into GenMAPP Builder by the QA. These files hold the information to create a gene database (.gdb), where I come in is this second step of exporting the files into a .gdb. I created a custom species profile for Shigella flexneri within the Java code of GenMAPP Builder. In order to do this I had to make my own distribution of GenMAPP Builder, and my own branch to commit to on GitHub. The edits I made to the code were the following:

I created a new subclass of UniProtSpeciesProfile called ShigellaflexneriUniprotSpeciesProfile. Within this new class I created a custom constructor that called the superclass's constructor and passed it information about Shigella flexneri, such as the taxonomy ID, and a custom String. I also overrode a method "getSystemsTableManagerCustomizations()" which, from my understanding, captures genes from the XML file we imported. The code for these initial customizations were provided to us by Dondi. However, as to be expected, the GenMAPP users alerted to us that we were missing 416 genes with these customizations. Trixie discovered that 92 of these genes could be found at unexpected locations in the XML file and so my task was to add another layer of customization. With help from Dondi, we overloaded the getSystemsTableManagerCustomizations method to account for these 92 genes in the XML file. Dondi added a SQL query within the method that captured the 92 missing genes and added them to the .gdb file. This was as many of the missing genes we could add. Throughout all of this I committed and pulled changes as needed.

Another customization that was required was within TallyEngine's gmbuilder.properties file. We added special properties for Shigella flexneri. These changes were pretty standard as they were in our class instructions, however, due to the nature of our GMBuilder java customizations, we need to make sure that TallyEngine could gather both the original genes and the 92 missing ones that were added on later. So, with help from Dondi, we added a SQL query that would be able to do this. The query used the union operation to get both the initial customization genes and the 92 missing genes.

These were the major changes I contributed to complete our project. Step by step and the final product can be seen on [[Jwoodlee Week 12 | Week 12]], [[Jwoodlee Week 14 | Week 14]], and [[Jwoodlee Week 15 | Week 15]]

*Provide references or links to artifacts of your work, such as:
**Wiki Pages
**Other files or documents
**Code or scripts

===Assessment of Project===
*Give an objective assessment of the success of your project workflow and teamwork.
** I think our project workflow and teamwork was overall successful. We got along pretty well and communicated effectively throughout the project. This is a vital part of any team and without it the team cannot improve. I think our workflow could have been improved because we procrastinated a few times, but that is to be expected when we all have a lot of other things going on. In summary I think our workflow and teamwork were very successful, but we could have been a bit more timely.
*What worked and what didn't work?
** The only problems I ran into had to do with my lack of experience navigating the various tools. For Eclipse, several times my code just wouldn't compile because I wasn't organizing imports or because I just typed something incorrectly. Also when it came time to customize GenMAPP Builder for a second time my lack of experience with SQL lead to Dondi essentially writing the queries for us. Other than that I would say most things were successful and went smoothly.
*What would you do differently if you could do it all over again?
** I would definitely try to get everything done as fast as I could to accommodate errors that could come up. On Monday before the presentation we were rushing a bit because I had to make some last minute changes to the source code of GenMAPP Builder which was the result of not figuring out what changes needed to be made in a timely manner.
*Evaluate the Gene Database Project and Group Report in the following areas:
*#Content: What is the quality of the work?
*#Organization: Comment on the organization of the project and of your group's wiki pages.
*#Completeness: Did your team achieve all of the project objectives? Why or why not?

===Reflection on the Project===
*What did you learn?
**With your head?((biological or computer science principles))
***Computer Science: As far as coding in Java I don't feel like I learned very much, however my SQL knowledge increased 100% because I had never done any SQL before this class. Just basic select queries and the entire way relational databases work were some of the things I will value as I move on to other courses. Also I learned more about GitHub, specifically in how it can work with Eclipse and how different branches can be created for the same project for more advanced version control.
***Biology: I learned the most biology when I had to review the genome paper. I learned about plasmids, pathogenicity, shotgun sequencing, etc. The list goes on. Pretty much every term that was used in that paper I had to look up and know for my presentation.
**With your heart?(personal qualities and teamwork qualities that make things work or not work)
***Definitely the fact that my team got along well and communicated effectively was of the utmost importance. Without that we wouldn't have gotten anything done. We designated tasks that weren't explicitly outlined for us in the wiki and as a result created a project that could actually contribute to the scientific community. The deadlines were always a little bit rough for us I think mainly because we were all so busy, but I think also we could have managed our time better. Other than that I have no criticism for our team and I think we did a great job.
**With your hands?(With your hands (technical skills))
***Navigating eclipse will definitely be the biggest technical takeaway from this project. I learned how I can access GitHub through eclipse as well as miscellaneous functions like "Organize Imports". To add to this list however, I would not skip over the navigation of GenMAPP and excel that I had to do. Excel is always a useful tool and I definitely got more comfortable with that.
*What lesson will you take away from this project that you will still use a year from now?
**Easily I would say my increased proficiency in using GitHub, Eclipse, and Excel will be used a year for now, at least for technical skills. For non-technical skills I would say coordinating with a group on who does what. It was easier because we had designated tasks assigned to us by the professors, however there was still some grey area where we had to designate tasks ourselves. And those grey areas of task designation will be what I take away in a year.

{{Template: Jwoodlee}}

Jwoodlee Week 15

2015-12-18T06:30:54Z

Jwoodlee: /* Assessment of Project */ added more to individual reflection

== Electronic Lab Notebook ==

Our GenMAPP users were reporting 416 missing genes from the .gdb which was a problem. Trixie found that 92 of these genes were in the XML file in such a way that led to the exporter missing them, the rest of the missing genes simply weren't in the XML file. Specifically, the genes were somewhere else in the file and weren't added to the OrderedLocusNames table by default. To capture these 92 elusive genes we consulted Dondi. Dondi edited the ShigellaflexneriUniProtSpeciesProfile class, which I had previously constructed, by adding a SQL query that captured the 92 missing genes:

This is what the final customized class looks like:
[[Image:FinalCustomizationsPart1.png]]

[[Image:FinalCustomizationsPart2.png]]

A further modification that was required was in the gmbuilder.properties file which we were supposed to edit to assist TallyEngine in its function, the initial customizations to this were the following lines:

[[Image: Gmbuilder.propertiesOriginal.png]]

This customization was insufficient in capturing the 92 missing genes. With the help of Dondi, Trixie and I replaced the insufficient SQL query with one that joined the missing 92 genes in the dbreference tag with the rest of the genes that were found by the default customization. Default customization can be found on [[Jwoodlee Week 12 | Week 12]] and [[Jwoodlee Week 14 | Week 14]]. A sql union was used to execute this task which replaced the original sql query on gmbuilder.properties, as can be seen below:

select count(value) from (select value from genenametype where type = 'ordered locus' and value ~ '(CP|SF?)[0-9][0-9][0-9][0-9](\.[0-9])?' union select extra as value from (select propertytype.value as extra from propertytype inner join dbreferencetype on propertytype.dbreferencetype_property_hjid = dbreferencetype.hjid where dbreferencetype.type = 'EnsemblBacteria' and dbreferencetype.id ~ 'AAN[0-9][0-9][0-9][0-9][0-9]' and propertytype.type = 'gene ID' and propertytype.value ~ 'SF[0-9][0-9][0-9][0-9]') as f left join (select value from genenametype where type = 'ordered locus' and value ~ '(CP|SF?)[0-9][0-9][0-9][0-9](\.[0-9])?') as g on f.extra = g.value where g.value is null) as combined;

== Individual Reflection ==
===Statement of Work===
*Describe exactly what you did on the project.
Three files, the XML Uniprot file, the GOA file, and the GO-OBO file were all imported into GenMAPP Builder by the QA. These files hold the information to create a gene database (.gdb), where I come in is this second step of exporting the files into a .gdb. I created a custom species profile for Shigella flexneri within the Java code of GenMAPP Builder. In order to do this I had to make my own distribution of GenMAPP Builder, and my own branch to commit to on GitHub. The edits I made to the code were the following:

I created a new subclass of UniProtSpeciesProfile called ShigellaflexneriUniprotSpeciesProfile. Within this new class I created a custom constructor that called the superclass's constructor and passed it information about Shigella flexneri, such as the taxonomy ID, and a custom String. I also overrode a method "getSystemsTableManagerCustomizations()" which, from my understanding, captures genes from the XML file we imported. The code for these initial customizations were provided to us by Dondi. However, as to be expected, the GenMAPP users alerted to us that we were missing 416 genes with these customizations. Trixie discovered that 92 of these genes could be found at unexpected locations in the XML file and so my task was to add another layer of customization. With help from Dondi, we overloaded the getSystemsTableManagerCustomizations method to account for these 92 genes in the XML file. Dondi added a SQL query within the method that captured the 92 missing genes and added them to the .gdb file. This was as many of the missing genes we could add. Throughout all of this I committed and pulled changes as needed.

Another customization that was required was within TallyEngine's gmbuilder.properties file. We added special properties for Shigella flexneri. These changes were pretty standard as they were in our class instructions, however, due to the nature of our GMBuilder java customizations, we need to make sure that TallyEngine could gather both the original genes and the 92 missing ones that were added on later. So, with help from Dondi, we added a SQL query that would be able to do this. The query used the union operation to get both the initial customization genes and the 92 missing genes.

These were the major changes I contributed to complete our project. Step by step and the final product can be seen on [[Jwoodlee Week 12 | Week 12]], [[Jwoodlee Week 14 | Week 14]], and [[Jwoodlee Week 15 | Week 15]]

*Provide references or links to artifacts of your work, such as:
**Wiki Pages
**Other files or documents
**Code or scripts

===Assessment of Project===
*Give an objective assessment of the success of your project workflow and teamwork.
** I think our project workflow and teamwork was overall successful. We got along pretty well and communicated effectively throughout the project. This is a vital part of any team and without it the team cannot improve. I think our workflow could have been improved because we procrastinated a few times, but that is to be expected when we all have a lot of other things going on. In summary I think our workflow and teamwork were very successful, but we could have been a bit more timely.
*What worked and what didn't work?
** The only problems I ran into had to do with my lack of experience navigating the various tools. For Eclipse, several times my code just wouldn't compile because I wasn't organizing imports or because I just typed something incorrectly. Also when it came time to customize GenMAPP Builder for a second time my lack of experience with SQL lead to Dondi essentially writing the queries for us. Other than that I would say most things were successful and went smoothly.
*What would you do differently if you could do it all over again?
** I would definitely try to get everything done as fast as I could to accommodate errors that could come up. On Monday before the presentation we were rushing a bit because I had to make some last minute changes to the source code of GenMAPP Builder which was the result of not figuring out what changes needed to be made in a timely manner.
*Evaluate the Gene Database Project and Group Report in the following areas:
*#Content: What is the quality of the work?
*#Organization: Comment on the organization of the project and of your group's wiki pages.
*#Completeness: Did your team achieve all of the project objectives? Why or why not?

===Reflection on the Project===
*What did you learn?
**With your head?((biological or computer science principles))
***Computer Science: As far as coding in Java I don't feel like I learned very much, however my SQL knowledge increased 100% because I had never done any SQL before this class. Just basic select queries and the entire way relational databases work were some of the things I will value as I move on to other courses. Also I learned more about GitHub, specifically in how it can work with Eclipse and how different branches can be created for the same project for more advanced version control.
***Biology: I learned the most biology when I had to review the genome paper. I learned about plasmids, pathogenicity, shotgun sequencing, etc. The list goes on. Pretty much every term that was used in that paper I had to look up and know for my presentation.
**With your heart?(personal qualities and teamwork qualities that make things work or not work)
**With your hands?(With your hands (technical skills))
***Navigating eclipse will definitely be the biggest technical takeaway from this project. I learned how I can access GitHub through eclipse as well as miscellaneous functions like "Organize Imports". To add to this list however, I would not skip over the navigation of GenMAPP and excel that I had to do. Excel is always a useful tool and I definitely got more comfortable with that.
*What lesson will you take away from this project that you will still use a year from now?
**Easily I would say my increased proficiency in using GitHub, Eclipse, and Excel will be used a year for now, at least for technical skills. For non-technical skills I would say coordinating with a group on who does what. It was easier because we had designated tasks assigned to us by the professors, however there was still some grey area where we had to designate tasks ourselves. And those grey areas of task designation will be what I take away in a year.

{{Template: Jwoodlee}}

Jwoodlee Week 15

2015-12-18T06:07:01Z

Jwoodlee: /* Assessment of Project */ added more to individual reflection

== Electronic Lab Notebook ==

Our GenMAPP users were reporting 416 missing genes from the .gdb which was a problem. Trixie found that 92 of these genes were in the XML file in such a way that led to the exporter missing them, the rest of the missing genes simply weren't in the XML file. Specifically, the genes were somewhere else in the file and weren't added to the OrderedLocusNames table by default. To capture these 92 elusive genes we consulted Dondi. Dondi edited the ShigellaflexneriUniProtSpeciesProfile class, which I had previously constructed, by adding a SQL query that captured the 92 missing genes:

This is what the final customized class looks like:
[[Image:FinalCustomizationsPart1.png]]

[[Image:FinalCustomizationsPart2.png]]

A further modification that was required was in the gmbuilder.properties file which we were supposed to edit to assist TallyEngine in its function, the initial customizations to this were the following lines:

[[Image: Gmbuilder.propertiesOriginal.png]]

This customization was insufficient in capturing the 92 missing genes. With the help of Dondi, Trixie and I replaced the insufficient SQL query with one that joined the missing 92 genes in the dbreference tag with the rest of the genes that were found by the default customization. Default customization can be found on [[Jwoodlee Week 12 | Week 12]] and [[Jwoodlee Week 14 | Week 14]]. A sql union was used to execute this task which replaced the original sql query on gmbuilder.properties, as can be seen below:

select count(value) from (select value from genenametype where type = 'ordered locus' and value ~ '(CP|SF?)[0-9][0-9][0-9][0-9](\.[0-9])?' union select extra as value from (select propertytype.value as extra from propertytype inner join dbreferencetype on propertytype.dbreferencetype_property_hjid = dbreferencetype.hjid where dbreferencetype.type = 'EnsemblBacteria' and dbreferencetype.id ~ 'AAN[0-9][0-9][0-9][0-9][0-9]' and propertytype.type = 'gene ID' and propertytype.value ~ 'SF[0-9][0-9][0-9][0-9]') as f left join (select value from genenametype where type = 'ordered locus' and value ~ '(CP|SF?)[0-9][0-9][0-9][0-9](\.[0-9])?') as g on f.extra = g.value where g.value is null) as combined;

== Individual Reflection ==
===Statement of Work===
*Describe exactly what you did on the project.
Three files, the XML Uniprot file, the GOA file, and the GO-OBO file were all imported into GenMAPP Builder by the QA. These files hold the information to create a gene database (.gdb), where I come in is this second step of exporting the files into a .gdb. I created a custom species profile for Shigella flexneri within the Java code of GenMAPP Builder. In order to do this I had to make my own distribution of GenMAPP Builder, and my own branch to commit to on GitHub. The edits I made to the code were the following:

I created a new subclass of UniProtSpeciesProfile called ShigellaflexneriUniprotSpeciesProfile. Within this new class I created a custom constructor that called the superclass's constructor and passed it information about Shigella flexneri, such as the taxonomy ID, and a custom String. I also overrode a method "getSystemsTableManagerCustomizations()" which, from my understanding, captures genes from the XML file we imported. The code for these initial customizations were provided to us by Dondi. However, as to be expected, the GenMAPP users alerted to us that we were missing 416 genes with these customizations. Trixie discovered that 92 of these genes could be found at unexpected locations in the XML file and so my task was to add another layer of customization. With help from Dondi, we overloaded the getSystemsTableManagerCustomizations method to account for these 92 genes in the XML file. Dondi added a SQL query within the method that captured the 92 missing genes and added them to the .gdb file. This was as many of the missing genes we could add. Throughout all of this I committed and pulled changes as needed.

Another customization that was required was within TallyEngine's gmbuilder.properties file. We added special properties for Shigella flexneri. These changes were pretty standard as they were in our class instructions, however, due to the nature of our GMBuilder java customizations, we need to make sure that TallyEngine could gather both the original genes and the 92 missing ones that were added on later. So, with help from Dondi, we added a SQL query that would be able to do this. The query used the union operation to get both the initial customization genes and the 92 missing genes.

These were the major changes I contributed to complete our project. Step by step and the final product can be seen on [[Jwoodlee Week 12 | Week 12]], [[Jwoodlee Week 14 | Week 14]], and [[Jwoodlee Week 15 | Week 15]]

*Provide references or links to artifacts of your work, such as:
**Wiki Pages
**Other files or documents
**Code or scripts

===Assessment of Project===
*Give an objective assessment of the success of your project workflow and teamwork.
** I think our project workflow and teamwork was overall successful. We got along pretty well and communicated effectively throughout the project. This is a vital part of any team and without it the team cannot improve. I think our workflow could have been improved because we procrastinated a few times, but that is to be expected when we all have a lot of other things going on. In summary I think our workflow and teamwork were very successful, but we could have been a bit more timely.
*What worked and what didn't work?
**
*What would you do differently if you could do it all over again?
** I would definitely try to get everything done as fast as I could to accommodate errors that could come up. On Monday before the presentation we were rushing a bit because I had to make some last minute changes to the source code of GenMAPP Builder which was the result of not figuring out what changes needed to be made in a timely manner.
*Evaluate the Gene Database Project and Group Report in the following areas:
*#Content: What is the quality of the work?
*#Organization: Comment on the organization of the project and of your group's wiki pages.
*#Completeness: Did your team achieve all of the project objectives? Why or why not?

===Reflection on the Project===
*What did you learn?
**With your head?((biological or computer science principles))
***Computer Science: As far as coding in Java I don't feel like I learned very much, however my SQL knowledge increased 100% because I had never done any SQL before this class. Just basic select queries and the entire way relational databases work were some of the things I will value as I move on to other courses. Also I learned more about GitHub, specifically in how it can work with Eclipse and how different branches can be created for the same project for more advanced version control.
***Biology: I learned the most biology when I had to review the genome paper. I learned about plasmids, pathogenicity, shotgun sequencing, etc. The list goes on. Pretty much every term that was used in that paper I had to look up and know for my presentation.
**With your heart?(personal qualities and teamwork qualities that make things work or not work)
**With your hands?(With your hands (technical skills))
***Navigating eclipse will definitely be the biggest technical takeaway from this project. I learned how I can access GitHub through eclipse as well as miscellaneous functions like "Organize Imports". To add to this list however, I would not skip over the navigation of GenMAPP and excel that I had to do. Excel is always a useful tool and I definitely got more comfortable with that.
*What lesson will you take away from this project that you will still use a year from now?
**Easily I would say my increased proficiency in using GitHub, Eclipse, and Excel will be used a year for now, at least for technical skills. For non-technical skills I would say coordinating with a group on who does what. It was easier because we had designated tasks assigned to us by the professors, however there was still some grey area where we had to designate tasks ourselves. And those grey areas of task designation will be what I take away in a year.

{{Template: Jwoodlee}}

Jwoodlee Week 15

2015-12-18T05:57:19Z

Jwoodlee: /* Assessment of Project */ added more to individual reflection

== Electronic Lab Notebook ==

Our GenMAPP users were reporting 416 missing genes from the .gdb which was a problem. Trixie found that 92 of these genes were in the XML file in such a way that led to the exporter missing them, the rest of the missing genes simply weren't in the XML file. Specifically, the genes were somewhere else in the file and weren't added to the OrderedLocusNames table by default. To capture these 92 elusive genes we consulted Dondi. Dondi edited the ShigellaflexneriUniProtSpeciesProfile class, which I had previously constructed, by adding a SQL query that captured the 92 missing genes:

This is what the final customized class looks like:
[[Image:FinalCustomizationsPart1.png]]

[[Image:FinalCustomizationsPart2.png]]

A further modification that was required was in the gmbuilder.properties file which we were supposed to edit to assist TallyEngine in its function, the initial customizations to this were the following lines:

[[Image: Gmbuilder.propertiesOriginal.png]]

This customization was insufficient in capturing the 92 missing genes. With the help of Dondi, Trixie and I replaced the insufficient SQL query with one that joined the missing 92 genes in the dbreference tag with the rest of the genes that were found by the default customization. Default customization can be found on [[Jwoodlee Week 12 | Week 12]] and [[Jwoodlee Week 14 | Week 14]]. A sql union was used to execute this task which replaced the original sql query on gmbuilder.properties, as can be seen below:

select count(value) from (select value from genenametype where type = 'ordered locus' and value ~ '(CP|SF?)[0-9][0-9][0-9][0-9](\.[0-9])?' union select extra as value from (select propertytype.value as extra from propertytype inner join dbreferencetype on propertytype.dbreferencetype_property_hjid = dbreferencetype.hjid where dbreferencetype.type = 'EnsemblBacteria' and dbreferencetype.id ~ 'AAN[0-9][0-9][0-9][0-9][0-9]' and propertytype.type = 'gene ID' and propertytype.value ~ 'SF[0-9][0-9][0-9][0-9]') as f left join (select value from genenametype where type = 'ordered locus' and value ~ '(CP|SF?)[0-9][0-9][0-9][0-9](\.[0-9])?') as g on f.extra = g.value where g.value is null) as combined;

== Individual Reflection ==
===Statement of Work===
*Describe exactly what you did on the project.
Three files, the XML Uniprot file, the GOA file, and the GO-OBO file were all imported into GenMAPP Builder by the QA. These files hold the information to create a gene database (.gdb), where I come in is this second step of exporting the files into a .gdb. I created a custom species profile for Shigella flexneri within the Java code of GenMAPP Builder. In order to do this I had to make my own distribution of GenMAPP Builder, and my own branch to commit to on GitHub. The edits I made to the code were the following:

I created a new subclass of UniProtSpeciesProfile called ShigellaflexneriUniprotSpeciesProfile. Within this new class I created a custom constructor that called the superclass's constructor and passed it information about Shigella flexneri, such as the taxonomy ID, and a custom String. I also overrode a method "getSystemsTableManagerCustomizations()" which, from my understanding, captures genes from the XML file we imported. The code for these initial customizations were provided to us by Dondi. However, as to be expected, the GenMAPP users alerted to us that we were missing 416 genes with these customizations. Trixie discovered that 92 of these genes could be found at unexpected locations in the XML file and so my task was to add another layer of customization. With help from Dondi, we overloaded the getSystemsTableManagerCustomizations method to account for these 92 genes in the XML file. Dondi added a SQL query within the method that captured the 92 missing genes and added them to the .gdb file. This was as many of the missing genes we could add. Throughout all of this I committed and pulled changes as needed.

Another customization that was required was within TallyEngine's gmbuilder.properties file. We added special properties for Shigella flexneri. These changes were pretty standard as they were in our class instructions, however, due to the nature of our GMBuilder java customizations, we need to make sure that TallyEngine could gather both the original genes and the 92 missing ones that were added on later. So, with help from Dondi, we added a SQL query that would be able to do this. The query used the union operation to get both the initial customization genes and the 92 missing genes.

These were the major changes I contributed to complete our project. Step by step and the final product can be seen on [[Jwoodlee Week 12 | Week 12]], [[Jwoodlee Week 14 | Week 14]], and [[Jwoodlee Week 15 | Week 15]]

*Provide references or links to artifacts of your work, such as:
**Wiki Pages
**Other files or documents
**Code or scripts

===Assessment of Project===
*Give an objective assessment of the success of your project workflow and teamwork.
*What worked and what didn't work?
*What would you do differently if you could do it all over again?
** I would definitely try to get everything done as fast as I could to accommodate errors that could come up. On Monday before the presentation we were rushing a bit because I had to make some last minute changes to the source code of GenMAPP Builder which was the result of not figuring out what changes needed to be made in a timely manner.
*Evaluate the Gene Database Project and Group Report in the following areas:
*#Content: What is the quality of the work?
*#Organization: Comment on the organization of the project and of your group's wiki pages.
*#Completeness: Did your team achieve all of the project objectives? Why or why not?

===Reflection on the Project===
*What did you learn?
**With your head?((biological or computer science principles))
***Computer Science: As far as coding in Java I don't feel like I learned very much, however my SQL knowledge increased 100% because I had never done any SQL before this class. Just basic select queries and the entire way relational databases work were some of the things I will value as I move on to other courses. Also I learned more about GitHub, specifically in how it can work with Eclipse and how different branches can be created for the same project for more advanced version control.
***Biology: I learned the most biology when I had to review the genome paper. I learned about plasmids, pathogenicity, shotgun sequencing, etc. The list goes on. Pretty much every term that was used in that paper I had to look up and know for my presentation.
**With your heart?(personal qualities and teamwork qualities that make things work or not work)
**With your hands?(With your hands (technical skills))
***Navigating eclipse will definitely be the biggest technical takeaway from this project. I learned how I can access GitHub through eclipse as well as miscellaneous functions like "Organize Imports". To add to this list however, I would not skip over the navigation of GenMAPP and excel that I had to do. Excel is always a useful tool and I definitely got more comfortable with that.
*What lesson will you take away from this project that you will still use a year from now?
**Easily I would say my increased proficiency in using GitHub, Eclipse, and Excel will be used a year for now, at least for technical skills. For non-technical skills I would say coordinating with a group on who does what. It was easier because we had designated tasks assigned to us by the professors, however there was still some grey area where we had to designate tasks ourselves. And those grey areas of task designation will be what I take away in a year.

{{Template: Jwoodlee}}

Jwoodlee Week 15

2015-12-18T05:24:54Z

Jwoodlee: /* Reflection on the Project */ filled out more individual reflection

== Electronic Lab Notebook ==

Our GenMAPP users were reporting 416 missing genes from the .gdb which was a problem. Trixie found that 92 of these genes were in the XML file in such a way that led to the exporter missing them, the rest of the missing genes simply weren't in the XML file. Specifically, the genes were somewhere else in the file and weren't added to the OrderedLocusNames table by default. To capture these 92 elusive genes we consulted Dondi. Dondi edited the ShigellaflexneriUniProtSpeciesProfile class, which I had previously constructed, by adding a SQL query that captured the 92 missing genes:

This is what the final customized class looks like:
[[Image:FinalCustomizationsPart1.png]]

[[Image:FinalCustomizationsPart2.png]]

A further modification that was required was in the gmbuilder.properties file which we were supposed to edit to assist TallyEngine in its function, the initial customizations to this were the following lines:

[[Image: Gmbuilder.propertiesOriginal.png]]

This customization was insufficient in capturing the 92 missing genes. With the help of Dondi, Trixie and I replaced the insufficient SQL query with one that joined the missing 92 genes in the dbreference tag with the rest of the genes that were found by the default customization. Default customization can be found on [[Jwoodlee Week 12 | Week 12]] and [[Jwoodlee Week 14 | Week 14]]. A sql union was used to execute this task which replaced the original sql query on gmbuilder.properties, as can be seen below:

select count(value) from (select value from genenametype where type = 'ordered locus' and value ~ '(CP|SF?)[0-9][0-9][0-9][0-9](\.[0-9])?' union select extra as value from (select propertytype.value as extra from propertytype inner join dbreferencetype on propertytype.dbreferencetype_property_hjid = dbreferencetype.hjid where dbreferencetype.type = 'EnsemblBacteria' and dbreferencetype.id ~ 'AAN[0-9][0-9][0-9][0-9][0-9]' and propertytype.type = 'gene ID' and propertytype.value ~ 'SF[0-9][0-9][0-9][0-9]') as f left join (select value from genenametype where type = 'ordered locus' and value ~ '(CP|SF?)[0-9][0-9][0-9][0-9](\.[0-9])?') as g on f.extra = g.value where g.value is null) as combined;

== Individual Reflection ==
===Statement of Work===
*Describe exactly what you did on the project.
Three files, the XML Uniprot file, the GOA file, and the GO-OBO file were all imported into GenMAPP Builder by the QA. These files hold the information to create a gene database (.gdb), where I come in is this second step of exporting the files into a .gdb. I created a custom species profile for Shigella flexneri within the Java code of GenMAPP Builder. In order to do this I had to make my own distribution of GenMAPP Builder, and my own branch to commit to on GitHub. The edits I made to the code were the following:

I created a new subclass of UniProtSpeciesProfile called ShigellaflexneriUniprotSpeciesProfile. Within this new class I created a custom constructor that called the superclass's constructor and passed it information about Shigella flexneri, such as the taxonomy ID, and a custom String. I also overrode a method "getSystemsTableManagerCustomizations()" which, from my understanding, captures genes from the XML file we imported. The code for these initial customizations were provided to us by Dondi. However, as to be expected, the GenMAPP users alerted to us that we were missing 416 genes with these customizations. Trixie discovered that 92 of these genes could be found at unexpected locations in the XML file and so my task was to add another layer of customization. With help from Dondi, we overloaded the getSystemsTableManagerCustomizations method to account for these 92 genes in the XML file. Dondi added a SQL query within the method that captured the 92 missing genes and added them to the .gdb file. This was as many of the missing genes we could add. Throughout all of this I committed and pulled changes as needed.

Another customization that was required was within TallyEngine's gmbuilder.properties file. We added special properties for Shigella flexneri. These changes were pretty standard as they were in our class instructions, however, due to the nature of our GMBuilder java customizations, we need to make sure that TallyEngine could gather both the original genes and the 92 missing ones that were added on later. So, with help from Dondi, we added a SQL query that would be able to do this. The query used the union operation to get both the initial customization genes and the 92 missing genes.

These were the major changes I contributed to complete our project. Step by step and the final product can be seen on [[Jwoodlee Week 12 | Week 12]], [[Jwoodlee Week 14 | Week 14]], and [[Jwoodlee Week 15 | Week 15]]

*Provide references or links to artifacts of your work, such as:
**Wiki Pages
**Other files or documents
**Code or scripts

===Assessment of Project===
*Give an objective assessment of the success of your project workflow and teamwork.
*What worked and what didn't work?
*What would you do differently if you could do it all over again?
*Evaluate the Gene Database Project and Group Report in the following areas:
*#Content: What is the quality of the work?
*#Organization: Comment on the organization of the project and of your group's wiki pages.
*#Completeness: Did your team achieve all of the project objectives? Why or why not?
===Reflection on the Project===
*What did you learn?
**With your head?((biological or computer science principles))
***Computer Science: As far as coding in Java I don't feel like I learned very much, however my SQL knowledge increased 100% because I had never done any SQL before this class. Just basic select queries and the entire way relational databases work were some of the things I will value as I move on to other courses. Also I learned more about GitHub, specifically in how it can work with Eclipse and how different branches can be created for the same project for more advanced version control.
***Biology: I learned the most biology when I had to review the genome paper. I learned about plasmids, pathogenicity, shotgun sequencing, etc. The list goes on. Pretty much every term that was used in that paper I had to look up and know for my presentation.
**With your heart?(personal qualities and teamwork qualities that make things work or not work)
**With your hands?(With your hands (technical skills))
***Navigating eclipse will definitely be the biggest technical takeaway from this project. I learned how I can access GitHub through eclipse as well as miscellaneous functions like "Organize Imports". To add to this list however, I would not skip over the navigation of GenMAPP and excel that I had to do. Excel is always a useful tool and I definitely got more comfortable with that.
*What lesson will you take away from this project that you will still use a year from now?
**Easily I would say my increased proficiency in using GitHub, Eclipse, and Excel will be used a year for now, at least for technical skills. For non-technical skills I would say coordinating with a group on who does what. It was easier because we had designated tasks assigned to us by the professors, however there was still some grey area where we had to designate tasks ourselves. And those grey areas of task designation will be what I take away in a year.

{{Template: Jwoodlee}}

Jwoodlee Week 15

2015-12-18T04:51:49Z

Jwoodlee: /* Statement of Work */ added week 12

Jwoodlee Week 15

2015-12-17T22:25:16Z

Jwoodlee: /* Individual Reflection */ added clarification

Jwoodlee Week 15

2015-12-16T21:05:11Z

Jwoodlee: /* Electronic Lab Notebook */ clarification

Jwoodlee Week 14

2015-12-16T21:04:46Z

Jwoodlee: Added template

*What worked?
**Almost every procedural action I took from Dondi worked. The only hiccup I had was in regard to Eclipse and navigating the directories.

*What didn't work?
**In Eclipse, my edits to the GenMAPP builder source code were causing red error marks, but after selecting "Organize Imports" from the source menu the errors were fixed easily and the proper classes were imported. Also I had difficulty navigating to the dist file in my Temp drive, however I traced this back within Eclipse and was able to make a zip that I could hand off to Trixie for export.

*What will I do next week to fix what didn't work?
**It seems to me that there wasn't a whole lot that went wrong with my procedure. What wasn't working I already fixed. Currently Trixie and I are running an export that will take 4 hours with the new additions in the property files, so there may be some new hiccups when that export is finished but we will have to wait and see.

The following is what I did this week.
=== Milestone 3: Species Profile Creation ===
Majority of the procedure was from [[Coder | here]].
==== Adding a Species Profile to GenMAPP Builder ====

In the Java perspective within Eclipse(change perspective on the top right), the following was executed.

====== Create the Species Profile ======

# I exposed the contents of the ''src'' folder in my gmbuilder project.
# Right-clicked on the ''edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles'' package and chose '''New > Class''' from the popup menu.
# In the dialog that appears, I entered the following:
#* '''Name:''' <code>ShigellaflexneriUniProtSpeciesProfile</code>
#* '''Superclass:''' <code>edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles.UniProtSpeciesProfile</code>
# Clicked ''Finish''. A new ''.java'' file within the ''edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles'' package was created.

====== Customize the Species Profile ======

* I opened the file that I just created.
* I added the following constructor block right below the ''public class'' line in the new file.
public ShigellaflexneriUniProtSpeciesProfile() {
super("Shigella flexneri",
623,
"This profile customizes the GenMAPP Builder export for " +
"Shigella flexneri" +
" data loaded from a UniProt XML file.");
}
* I added the following method block right below the constructor block that I added above.
@Override
public TableManager getSystemsTableManagerCustomizations(TableManager tableManager, DatabaseProfile dbProfile) {
super.getSystemsTableManagerCustomizations(tableManager, dbProfile);
tableManager.submit("Systems", QueryType.update, new String[][] {
{ "SystemCode", "N" },
{ "Species", "|" + getSpeciesName() + "|" }
});

tableManager.submit("Systems", QueryType.update, new String[][] {
{ "SystemCode", "N" },
{ "Link", "http://www.mgc.ac.cn/cgi-bin/ShiBASE/ShiBASE_query.cgi?synonym=~" }
});

return tableManager;
}
* I chose ''Organize Imports'' from the ''Source'' menu to make sure I had everything imported.

====== Add the Species Profile to the Catalog of Known Species Profiles ======

* Under ''edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles'', I opened ''UniProtDatabaseProfile.java''.
* Near the top of the file is a block that looks like this:
super("org.uniprot.uniprot.Uniprot",
"This profile defines the requirements "
+ "for any UniProt centric gene database.",
new SpeciesProfile[] {
new EscherichiaColiUniProtSpeciesProfile(),
new ArabidopsisThalianaUniProtSpeciesProfile(),
new PlasmodiumFalciparumUniProtSpeciesProfile(),
new VibrioCholeraeUniprotSpeciesProfile() });
* I added the species profile that I created to the block.
super("org.uniprot.uniprot.Uniprot",
"This profile defines the requirements "
+ "for any UniProt centric gene database.",
new SpeciesProfile[] {
new EscherichiaColiUniProtSpeciesProfile(),
new ArabidopsisThalianaUniProtSpeciesProfile(),
new PlasmodiumFalciparumUniProtSpeciesProfile(),
new VibrioCholeraeUniprotSpeciesProfile(),
new ShigellaflexneriUniProtSpeciesProfile() });

* I saved changes and selected ''Organize Imports''.

====== Build, Test, and Possibly Commit ======

# I created a new distribution of GenMAPP Builder.
#*Expanded the custom project, scrolled down the build.xml and right clicked it. In the menu that appeared I clicked on Ant Build... (with ellipses). Now in the menu that appeared I deselected dist, and selected clean, dist in that order. The build order was now clean, dist so it will wipe the current version of genmappbuilder and create a new distribution. I clicked run.
# With Trixie, we performed a new export run with this custom version of GenMAPP Builder. A new .gdb was created.
# I checked the ''Systems'' table in the resulting ''.gdb'' with Microsoft Access and verified that it contained the custom information:
#* The record ''OrderedLocusNames'' was there with the species name under the ''Species'' column and our link URL under the ''Link'' column.
#Opened up a gene in GenMAPP with the custom .gdb created to make sure the link that I inserted was working properly.
# I then committed the custom version of GenMAPP builder to our GitHub branch.

=== Milestone 4: Species Export Customization ===
#Trixie noticed that the microarray data has IDs that have CP#### and SF####.# not the typical SF####, which will need to accounted for.
#This week, we edited the gmbuilder.properties file in eclipse as found in the Quality Assurance guild page. We added lines for our species.

{{Template: Jwoodlee}}

Jwoodlee Week 15

2015-12-16T21:03:44Z

Jwoodlee: /* Electronic Lab Notebook */ fixed image

Jwoodlee Week 15

2015-12-16T21:03:06Z

Jwoodlee: /* Electronic Lab Notebook */ added clarification

File:Gmbuilder.propertiesOriginal.png

2015-12-16T21:01:18Z

Jwoodlee:

Jwoodlee Week 15

2015-12-16T20:52:43Z

Jwoodlee: /* Electronic Lab Notebook */ added sql query

Jwoodlee Week 15

2015-12-16T20:50:13Z

Jwoodlee: /* Electronic Lab Notebook */ added photos

File:FinalCustomizationsPart2.png

2015-12-16T20:49:34Z

Jwoodlee: code for custom Shigella flexneri class

code for custom Shigella flexneri class

File:FinalCustomizationsPart1.png

2015-12-16T20:49:14Z

Jwoodlee: Code for customized Shigella flexneri class

Code for customized Shigella flexneri class

Jwoodlee Week 15

2015-12-16T20:44:52Z

Jwoodlee: /* Electronic Lab Notebook */ added code

== Electronic Lab Notebook ==

Our GenMAPP users were reporting 416 missing genes from the .gdb which was a problem. Trixie found that 92 of these genes were in the XML file in such a way that led to the exporter missing them, the rest of the missing genes simply weren't in the XML file. Specifically, the genes were somewhere else in the file and weren't added to the OrderedLocusNames table by default. To capture these 92 elusive genes we consulted Dondi. Dondi edited the ShigellaflexneriUniProtSpeciesProfile class, which I had previously constructed, by adding a SQL query that captured the 92 missing genes:

This is what the final customized class looks like:

<code>
package edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles;

import java.sql.Connection;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.util.Date;

import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;

import edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.ConnectionManager;
import edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.TableManager;
import edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.TableManager.QueryType;
import edu.lmu.xmlpipedb.util.exceptions.InvalidParameterException;

public class ShigellaflexneriUniProtSpeciesProfile extends UniProtSpeciesProfile {
public ShigellaflexneriUniProtSpeciesProfile() {
super("Shigella flexneri",
623,
"This profile customizes the GenMAPP Builder export for " +
"Shigella flexneri" +
" data loaded from a UniProt XML file.");
}

@Override
public TableManager getSystemsTableManagerCustomizations(TableManager tableManager, DatabaseProfile dbProfile) {
super.getSystemsTableManagerCustomizations(tableManager, dbProfile);
tableManager.submit("Systems", QueryType.update, new String[][] {
{ "SystemCode", "N" },
{ "Species", "|" + getSpeciesName() + "|" }
});

tableManager.submit("Systems", QueryType.update, new String[][] {
{ "SystemCode", "N" },
{ "Link", "http://www.mgc.ac.cn/cgi-bin/ShiBASE/ShiBASE_query.cgi?synonym=~" }
});

return tableManager;
}

@Override
public TableManager getSystemTableManagerCustomizations(TableManager tableManager,
TableManager primarySystemTableManager, Date version) throws SQLException, InvalidParameterException {
// Start with the default OrderedLocusNames behavior.
TableManager result = super.getSystemTableManagerCustomizations(tableManager, primarySystemTableManager,
version);

String sqlQuery = "select dbreferencetype.entrytype_dbreference_hjid as hjid, " +
"propertytype.value from propertytype inner join dbreferencetype on " +
"propertytype.dbreferencetype_property_hjid = dbreferencetype.hjid " +
"where dbreferencetype.type = 'EnsemblBacteria' and " +
"dbreferencetype.id ~ 'AAN[0-9][0-9][0-9][0-9][0-9]' and " +
"propertytype.type = 'gene ID' and " +
"propertytype.value ~ 'SF[0-9][0-9][0-9][0-9]' order by propertytype.value";

Connection c = ConnectionManager.getRelationalDBConnection();
PreparedStatement ps;
ResultSet rs;
try {
// Query, iterate, add to table manager.
ps = c.prepareStatement(sqlQuery);
rs = ps.executeQuery();
while (rs.next()) {
String hjid = Long.valueOf(rs.getLong("hjid")).toString();
String id = rs.getString("value");
String[] substrings = id.split("/");
for (int i = 0; i < substrings.length; i++) {
result.submit("OrderedLocusNames", QueryType.insert, new Object[][] {
{ "ID", id },
{ "Species", "|" + getSpeciesName() + "|" },
{ "Date", version },
{ "UID", hjid }
});
}
}
} catch(SQLException sqlexc) {
logSQLException(sqlexc, sqlQuery);
}

return result;
}

private void logSQLException(SQLException sqlexc, String sqlQuery) {
LOG.error("Exception trying to execute query: " + sqlQuery);
while (sqlexc != null) {
LOG.error("Error code: [" + sqlexc.getErrorCode() + "]");
LOG.error("Error message: [" + sqlexc.getMessage() + "]");
LOG.error("Error SQL State: [" + sqlexc.getSQLState() + "]");
sqlexc = sqlexc.getNextException();
}
}

private static final Log LOG = LogFactory.getLog(ShigellaflexneriUniProtSpeciesProfile.class);
}
</code>

A further modification that was required was in the gmbuilder.properties file which we were supposed to edit to assist TallyEngine in its function. With the help of Dondi, Trixie and I inserted a SQL query that joined the missing 92 genes in the dbreference tag with the rest of the genes that were found by the default customization as found on [[Jwoodlee Week 14 | Week 14]].

== Individual Reflection ==
===Statement of Work===
*Describe exactly what you did on the project.
Three files, the XML Uniprot file, the GOA file, and the GO-OBO file were all imported into GenMAPP Builder by the QA. These files hold the information to create a gene database (.gdb), where I come in is this second step of exporting the files into a .gdb. I created a custom species profile for Shigella flexneri within the Java code of GenMAPP Builder. In order to do this I had to make my own distribution of GenMAPP Builder, and my own branch to commit to on GitHub. The edits I made to the code were the following:

I created a new subclass of UniProtSpeciesProfile called ShigellaflexneriUniprotSpeciesProfile. Within this new class I created a custom constructor that called the superclass's constructor and passed it information about Shigella flexneri, such as the taxonomy ID, and a custom String. I also overrode a method "getSystemsTableManagerCustomizations()" which, from my understanding, captures genes from the XML file we imported. The code for these initial customizations were provided to us by Dondi. However, as to be expected, the GenMAPP users alerted to us that we were missing 416 genes with these customizations. Trixie discovered that 92 of these genes could be found at unexpected locations in the XML file and so my task was to add another layer of customization. With help from Dondi, we overloaded the getSystemsTableManagerCustomizations method to account for these 92 genes in the XML file. Dondi added a SQL query within the method that captured the 92 missing genes and added them to the .gdb file. This was as many of the missing genes we could add. Throughout all of this I committed and pulled changes as needed.

Another customization that was required was within TallyEngine's gmbuilder.properties file. We added special properties for Shigella flexneri. These changes were pretty standard as they were in our class instructions, however, due to the nature of our GMBuilder java customizations, we need to make sure that TallyEngine could gather both the original genes and the 92 missing ones that were added on later. So, with help from Dondi, we added a SQL query that would be able to do this. The query used the union operation to get both the initial customization genes and the 92 missing genes.

These were the major changes I contributed to complete our project. Step by step can be seen on [[Jwoodlee Week 14 | Week 14]] and [[Jwoodlee Week 15 | Week 15]]

*Provide references or links to artifacts of your work, such as:
**Wiki Pages
**Other files or documents
**Code or scripts

===Assessment of Project===
*Give an objective assessment of the success of your project workflow and teamwork.
*What worked and what didn't work?
*What would you do differently if you could do it all over again?
*Evaluate the Gene Database Project and Group Report in the following areas:
*#Content: What is the quality of the work?
*#Organization: Comment on the organization of the project and of your group's wiki pages.
*#Completeness: Did your team achieve all of the project objectives? Why or why not?
===Reflection on the Project===
*What did you learn?
**With your head?((biological or computer science principles))
**With your heart?(personal qualities and teamwork qualities that make things work or not work)
**With your hands?(With your hands (technical skills))
*What lesson will you take away from this project that you will still use a year from now?

{{Template: Jwoodlee}}

Jwoodlee Week 15

2015-12-16T20:43:24Z

Jwoodlee: /* Statement of Work */ added links to week 14 and 15

Jwoodlee Week 15

2015-12-16T20:42:13Z

Jwoodlee: /* Individual Reflection */ formatting

Jwoodlee Week 15

2015-12-16T20:41:54Z

Jwoodlee: /* Individual Reflection */ added what I did

Template:Oregon Trail Survivors

2015-12-16T19:43:58Z

Jwoodlee: /* Helpful Links */ Added deliverable page link

== Helpful Links ==

[[OTS Deliverables | Deliverables]]
{| class="wikitable" style="width: 100%; text-align: center"
! colspan="6"| Team Links
|-
! Files
! Team Members
! [[Week 11 | Week 11 Assignment]]
! [[Week 12 | Week 12 Assignment]]
! [[Week 14 | Week 14 Assignment]]
! [[Week 15 | Week 15 Assignment]]
|-
| rowspan="2" | [[OTS Files | OTS Files]]
| [[User:Troque | Trixie]]
| [[Troque_Week_11 | Week 11]]
| [[Troque_Week_12 | Week 12]]
| [[Troque_Week_14 | Week 14]]
| [[Troque_Week_15 | Week 15]]
|-
| [[User:Jwoodlee | Jake]]
| [[Jwoodlee_Week_11|Week 11]]
| [[Jwoodlee_Week_12|Week 12]]
| [[Jwoodlee_Week_14|Week 14]]
| [[Jwoodlee_Week_15|Week 15]]
|-
| rowspan="2" | [[Gene_Database_Testing_Report_-_Oregon_Trail_Survivors | Gene Database Testing Report]]
| [[User:Eyanosch | Erich]]
| [[Eyanosch Week 11|Week 11]]
| [[Eyanosch Week 12|Week 12]]
| [[Eyanosch Week 14|Week 14]]
| [[Eyanosch Week 15|Week 15]]
|-
| [[User:Kzebrows | Kristin]]
| [[Kzebrows Week 11| Week 11]]
| [[Kzebrows Week 12| Week 12]]
| [[Kzebrows Week 14| Week 14]]
| [[Kzebrows Week 15| Week 15]]
|-
|}

[[Category:Group Projects]]
[[Category:Oregon Trail Survivors]]

{{Gene Database Project Links}}

Jwoodlee Week 15

2015-12-16T19:38:17Z

Jwoodlee: /* Electronic Lab Notebook */ added some more of what i did

Jwoodlee Week 15

2015-12-16T19:24:58Z

Jwoodlee: /* Electronic Lab Notebook */ added outline for individual reflection

Jwoodlee Week 15

2015-12-15T04:34:44Z

Jwoodlee: Added some ELN for the week.

OTS Deliverables

2015-12-15T04:15:11Z

Jwoodlee: /* OTS Files */ added new file

==OTS Files==

[[Media:Micro Array Shigella Flexneri 20151011.pdf | Shigella Flexneri Microarray Paper (PDF)]]

[[Media:Shigellamicroarray.pptx | Microarray Journal Club Power Point]]

[[Media:CompiledRaw data RPRX IDLR EYKZ20152211.xlsx | Microarray Compiled Raw Data RP/RX IDLR]]

[[Media:SamplesFilesCorrespondanceTable SF301a EYKZ201522111.xls | Microarray Corresponding Files Table]]

[[Media: GMBuilder Shigella flexneri.zip]]

[[Media: QA Files.zip | Download QA files]]

[[File:GMBuilder December7 2015 build 2.zip]]

[[File:GenMAPP Builder 12 14 2015.zip]]

[[File:GenMAPP Builder 12 14 2015 Number 2.zip]]

==GenMAPP User Files==
[[Media:CompiledRaw data RPRX IDLR EYKZ2015121.xlsx | ScalingCentering file from 12/1]]

[[Media:FINAL CompiledRawData RXRP EYKZ20151210.xlsx | Final Compiled Raw Data 12/10 Excel format]]

[[Media:FINAL CompiledRawData RXRP EYKZ20151210.txt | Final Compiled Raw Data 12/10 .txt format]]

[[Media:FINAL CompiledRawData RXRP EYKZ20151210 (1).gex | Final Compiled Raw Data 12/12 .gex]]

[[Media:Filtered MAPPFinder Results.xlsx | Filtered MAPPFinder Results]]

[[Media:Flagellum Ribosomal Mapp 1 60min 20151012.jpg | RP vs RX 1 MIC @ 60 minutes MAPP 12/12 .jpg]]

[[Media:Flagellum Ribosomal Mapp 0pt5 10min 20151012.jpg | RP vs RX 0.5 MIC @ 10 minutes MAPP 12/12 .jpg]]

====RP (Erich)====
[[Media:CompiledRaw data GenMAPP Final RP IDLR EYKZ2015126.xlsx | RP Compiled Raw Data Final 12/10]]

[[Media:CompiledRaw data GenMAPP ready RP IDLR EYKZ2015126.txt | RP .txt format GenMAPP ready 12/6]]

[[Media:CompiledRaw data Errors RP EYKZ2015126.EX.xlsx | RP Exceptions file in Excel format (filtered)]]

[[Media:CompiledRaw data Errors RP EYKZ2015126.EX.txt | RP Exceptions (txt)]]

[[Media:CompiledRaw data GenMAPP ready RP IDLR EYKZ2015126.gex | RP .gex file]]

====RX (Kristin)====
[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.xlsx | RX Compiled Raw Data 12/6]]

[[Media:CompiledRaw data statistics BonferroniPvalue RP IDLR EYKZ2015126.txt | RX .txt format GenMAPP ready 12/6]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.xlsx | RX Compiled Raw Data as of 12/6]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.txt | RX .txt format updated as of 12/6]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.EX.txt | RX Exceptions file]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.gex | RX .gex file]]

[[Media:CompiledRaw data RX IDLR KZ2015126.EX.xlsx | RX Exceptions file in Excel format (filtered)]]

{{Template:Oregon Trail Survivors}}

File:GenMAPP Builder 12 14 2015 Number 2.zip

2015-12-15T04:14:45Z

Jwoodlee:

Jwoodlee Week 15

2015-12-15T03:42:19Z

Jwoodlee: added template

Oregon Trail Survivors

2015-12-15T03:41:57Z

Jwoodlee: /* Week 15 */ edited formatting

<div style="text-align: center; font-size: 250%; line-height: 1.25em">'''Oregon Trail Survivors'''</div>

<div class="center">
[[Image:Oregon-trail-dysentery 5 biodb.jpg | thumb | right | 350px | The third leading cause of death in the Oregon Trail.]]
</div>

== Group Members ==
*Coder: [[User:Jwoodlee | Jake Woodlee]]
*Quality Assurance: [[User:Troque | Trixie Roque]]
*GenMAPP Users: [[User:Eyanosch | Erich Yanoschik]] & [[User:Kzebrows | Kristin Zebrowski]]
* Project Manager: [[User:Kzebrows | Kristin Zebrowski]]

{{Template:Oregon Trail Survivors}}

=== Presentation (QA/Coder) ===
* PDF can be seen [[Media: Genome Paper Presentation BioDB.pdf | here]]

===Group Meeting Times===
*Thursday, November 5th at 8:00 pm
*Met most Sundays and Monday evenings in the Biol DB lab to check in with one another.

== Goals ==
Over the upcoming weeks our group will be investigating ''Shigella flexneri''.

===Week 10===

# Find genome sequence paper
# Find 4-8 microarray data and paper that goes with the genome paper
# Compile team page to and create a ranked annotated bibliography

===Week 11===

#Prepare for journal club presentations in Weeks 12 and 13
#Begin initial tasks on research project

Click on username links for more information regarding each team member's contributions for Week 11.

[[Jwoodlee Week 11 | Jake]]: Read through the genome paper and tried to get through the accessible things I had the ability to understand. Made an outline for the genome paper. Worked on the presentation with Trixie and found a database. And of course I answered the assigned questions.

[[Troque Week 11 | Trixie]]: Mainly focused on the Genome paper presentation with Jake. This includes searching for a viable database that we will be using for the rest of the group assignment and actually creating the presentation we will be doing for October 17th, 2015. I've also updated our group page to reflect what Dr. Dahlquist suggested would improve our team page.

[[Eyanosch Week 11 | Erich]]: Analyzed the microarray paper in order to describe the experimental design of the microarray data, treatments, number of replicates, and dye swaps. Worked with Kristin to produce the power point for the GennMAP users presentation at Journal Club. Worked on the individual journal entry and created an outline of the microarray paper.

[[Kzebrows Week 11 | Kristin]]: Using the team's selected microarray paper I developed an outline including background information, experimental outline/methods and how samples corresponded to the data, a brief description of the results, and a discussion including the implications of the research and its results in comparison to previous studies. Using this outline, I created a flow chart corresponding to the research. I also worked with Erich in order to create a PowerPoint for the Journal Club presentation on Nov. 24.

=== Week 12 ===
#QA will be doing an initial database export.
#Coder will be setting up version control.
#GenMAPP users will compile the raw data from the micorarray file to prepare for normalization and statistic analysis (will begin if time permits after consultation with Dr. Dahlquist). Additionally, the GenMAPP users will be determining the number of biological or technical replicates and how samples were labeled.
#Coder and QA will present on genome paper in class Tuesday, Nov. 24.

Click on username links for more information regarding each team member's contributions for Week 12.
* [[Jwoodlee Week 12 | Jake]]:Setup my environment in eclipse, created the s-flexneri branch, created my own copy of GenMAPP that I can modify for later use and I cloned the repository with the Git commands.
* [[Troque Week 12 | Trixie]]: Finished the preliminary export of the XML and GOA files and the corresponding Gene Testing Report. Also started identifying the gene id's for the specie. Decided on file management system with Jake.
* [[Eyanosch Week 12 | Erich]]: Worked with Kristin in determining the total number of biological and technical replicates. Compiled the raw data for RP samples, specifically the ID and Log ratio columns. Incorporated the RP and RX data into one spreadsheet with Kristins data. We created a table of the sample data and file each corresponds with, also figured out there were no dye swaps in the experiment(The control was the Cy3 dye and the treatment the Cy5 dye).
* [[Kzebrows Week 12 | Kristin]]: Determined that there were 3 biological replicates per treatment for 6 treatments total. Compiled raw data for RX samples by re-naming columns for ID and Log Ratio and putting into same worksheet, which was later combined with Erich's worksheet for RP samples. Erich and I met and worked together to create a table of which samples correspond to which file.

===Week 14===
#QA will be documenting the IDs using MATCH, Postgres, Microsoft Access, and Excel and get a head start of Milestone 3, which is customizing the TallyEngine.
#Coder will determine and document any modified export behavior that the GenMAPP Builder will have and resolve bugs. Coder will also work with QA by uploading GM Builder for additional export.
#GenMAPP Users will perform statistical analysis on Excel (normalization, tests) and format for import into GenMAPP. Users will also import data into GenMAPP and run MAPPFinder, and then document these test runs.

Click on username links for more information regarding each team member's contributions for Week 14.
* [[Jwoodlee Week 14 | Jake]]: Finished custom GenMAPP builder, committed to GitHub, and ran the export with the custom software. This created a custom .gdb which was opened in Microsoft Access and GenMAPP to check for accuracy.
* [[Troque Week 14 | Trixie]]: Trixie has finished identifying the gene IDs using MATCH, Postgres, Microsoft Access, and Excel. It was discovered that some IDs are in "dbReference/property&type&gene ID", and so another export was done on 12/7/15 to add the newly discovered gene IDs.
* [[Eyanosch Week 14 | Erich]]: Kristin and I completed the corrections provided via Dr. Dhalquist on Kristins talk page. We split the work into two halves and I worked on the RP data. We completed the statistics, Bonferroni p value correction, and the sanity check. I downloaded the database and formatted/exported the file for GenMAPP, and tried to create a GO tree for one of the trail points with RX.
* [[Kzebrows Week 14 | Kristin]]: This week Erich and I made corrections from the talk page and normalized log ratios for the slides in the experiment. I completed the statistical analysis for RX samples and calculated the Bonferroni p value correction. I also performed a sanity check for the RX samples and, going off of that, I calculated the Benjamini & Hochberg p value correction for RX-1-30, which had the most statistically significant changes in gene expression. I also formatted and exported the file for GenMAPP, downloaded the database, and attempted to create color sets to run the data set through MappFINDER.

==== Reflection ====

Each team member should reflect on the team's progress:
# What worked?
# What didn't work?
# What will I do next to fix what didn't work?

''Kristin'':
#What worked?
#*In terms of communication is having a group text. We also meet at least once a week outside of class in order to work together on the assignments and make sure we are all on the same page. So far, this has allowed us to troubleshoot and address bugs together as a team quickly. It also worked for Erich and I to divide up the samples so that I did all RX and Erich did all RP. Then, we could work at the same time and double-check procedures with each other but we were still getting the work done twice as quickly.
#What didn't work?
#*After creating the initial compiled raw data file, I had to make several corrections before the file could be run through GenMAPP. First of all, I had to get rid of the ".", and I also had to change all #DIV/0! with a space character for the file to be read at all. Also, although we were unable to find all of the b#### and CP#### gene ID's in UniProt or ShiBASE. Also, after creating my color set and trying to run MAPPFinder, I tried three computers and all of them crashed with the "not responding" message.
#What will I do next to fix what didn't work?
#*I will communicate with the QA and Coder in order to create a database with a minimal number of "Gene ID not found's" and then communicate with Erich when we try to run our dataset through MappFinder. Once the gene database is re-customized and the export is complete I can try and re-run my dataset to see if that makes a difference.

'' Trixie '':
# What worked?
#* What worked in identifying the gene IDs is to look export .gdb file into Excel and compare with what the OrderedLocusNames table had (from Microsoft Access). From doing this, it was easier to find which genes were not found in the .gdb file and made it easier to look through them in the UniProt XML file. With the Excel file comparing the lists of gene IDs and using the CTRL+F shortcut, I was also able to discern which tags to include into the new builds for the databases. Because of this, I was able to confirm that some genes indeed do not exist in the XML file, while only a couple exist within the "dbReference" tag. In terms of group work, what worked is posting all our files into a single page as we progress through the assignment. Night meetings were also helpful in order to better communicate with the rest of my group.
# What didn't work?
#* What didn't work is using Match multiple times without thinking. Even when I was trying to match the number of gene IDs with what Tally Engine gives me, Match didn't really help me in identifying where to find the genes in the XML file. Waiting for the database to finish didn't help much at all since our builds would take more than 4 hours to finish.
# What will I do next to fix what didn't work?
#* What I would do next to fix what didn't work is to actually use Match in conjunction to the XML file, or just use the Excel method completely since that was actually more helpful in finding the necessary tags than the Match method. I would probably have to time myself to check the lab after about 4.5 hours since one of our builds lasted that long.

''Jake'':
#What worked?
#*Almost every procedural action I took from Dondi worked. The only hiccup I had was in regard to Eclipse and navigating the directories.
#What didn't work?
#*In Eclipse, my edits to the GenMAPP builder source code were causing red error marks, but after selecting "Organize Imports" from the source menu the errors were fixed easily and the proper classes were imported. Also I had difficulty navigating to the dist file in my Temp drive, however I traced this back within Eclipse and was able to make a zip that I could hand off to Trixie for export.
#What will I do next week to fix what didn't work?
#*It seems to me that there wasn't a whole lot that went wrong with my procedure. What wasn't working I already fixed. Currently Trixie and I are running an export that will take 4 hours with the new additions in the property files, so there may be some new hiccups when that export is finished but we will have to wait and see.

''Erich'':
# What worked?
#*Having a GenMAPP user meeting with Dr. Dhalquist helped focus on what goals we wanted to achieve by the time of our next meeting. A group text helped organize meeting times of both the coders and GenMAPP users helped keep us on schedule.
# What didn't work?
#*The GenMapp Gene Ontology Tree was unable to pull files for each GO selection. We need to work on and make sure the GO files can be found. We also had to remove and edit our compiled raw data files so that they are able to be read by GenMAPP.
# What will I do next to fix what didn't work?
#*A new .gex was created, so this might help with the problems experienced in the MappBuilder. Also communicating with the QA and coder to make sure we finish up the GO tree smoothly in order to assess the results of the Publication we chose for Shigella Flexneri.

===Week 15===
#Coder: Work with QA to fix bugs.
#QA: Work with coder to fix bugs in the .gdb.
#GenMAPP Users: Finish Milestone 3. Run tests with GenMAPP. Do a journal club outline of the paper to use in the Discussion section of group report and presentation. Create a .mapp file showing one changed pathway from the data.
#All team members will be working together to put together deliverables including the final report and presentation for next Tuesday.

Click on username links for more information regarding each team member's contributions for Week 14.
* [[Jwoodlee Week 15 | Jake]]: Pulled Dondi's changes, and then created a new clean distribution. I then uploaded that distribution to our OTS Files page. Edited properties file for TallyEngine.
* [[Troque Week 15 | Trixie]]:
* [[Eyanosch Week 15 | Erich]]:
* [[Kzebrows Week 15 | Kristin]]: I created color sets with Increased/Decreased criteria for all of the 12 treatment/time point combos. Then, based on the criterion.go files, I created tables by filtering the results comparing the most commonly induced or repressed genes for the 1 x MIC at 60 minutes and 0.5 x MIC at 10 minutes between RX and RP. Strikingly, we found that between RX and RP the effects were very similar. I then compared them with the .mapp files that Erich created and put my portion of the project (compiled sanity check, color set, comparison tables) in the power point.

==Overview of Genome Paper==
*Used the genome sequencing article to perform a prospective search in the [https://apps.webofknowledge.com/UA_GeneralSearch_input.do?product=UA&search_mode=GeneralSearch&SID=1FRKcNxUgxiGX6spITI&preferencesSaved= Web of Science] database.
*Overview of the search:
**How many articles does this article cite? 37
**How many articles cite this article? 303
**Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced?
***Now that the genome has been sequenced, a majority of research has been done on discovering which genes are responsible for virulence and pathogenesis as well as potential antibiotics. Genomic research is also focused on how ''S. flexneri'' has been able to develop resistance to multiple drugs. Furthermore, ''Shigella'' is suspected to have evolved from ''Escherichia coli'' so a lot of research has been done in how and when pathogenic ''Shigella'' split from ''E. coli'' on the evolutionary tree.

==Annotated Bibliography==
=== Genome Paper ===
Jin, Q., Yuan, Z., Xu, J., Wang, Y., Shen, Y., Lu, W., … Yu, J. (2002). Genome sequence of ''Shigella flexneri'' 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157. Nucleic Acids Research, 30(20), 4432–4441.
* PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/?term=Genome+sequence+of+Shigella+flexneri+2a%3A+insights+into+pathogenicity+through+comparison+with+genomes+of+Escherichia+coli+K12+and+O157
* PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC137130/
* Publisher Full Text (HTML): http://nar.oxfordjournals.org/content/30/20/4432.full
* Publisher Full Text (PDF): http://nar.oxfordjournals.org/content/30/20/4432.full.pdf+html
* Copyright: 2002 Oxford University Press
* Publisher: Oxford University Press
* Availability: in print and online
* Did LMU pay a fee for this article: no

===Microarray Paper===





Fu H, Liu L, Zhang X, Zhu Y, Zhao L, Peng J, et al. (2012) Common Changes in Global Gene Expression Induced by RNA Polymerase Inhibitors in ''shigella flexneri''. PLoS ONE 7(3): e33240. doi:10.1371/journal.pone.0033240

*The link to the [http://www.ncbi.nlm.nih.gov/pubmed/22428000 abstract]
*The link to the [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3299763/ full text of the article] in PubMed Central
*The link to the [http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0033240 full text of the article] (HTML format) from the publisher web site.
*The link to the [http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0033240&representation=PDF full PDF version] of the article from the publisher web site.
*Copyright: © 2012 Fu et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
*Does the journal own the copyright? NO
*Do the authors own the copyright? Yes
*Do the authors own the rights under a Creative Commons license? Yes
*Is the article available “Open Access”? Yes
*What organization is the publisher of the article? What type of organization is it? PLoS One is the publisher/Journal. It hosts open access research articles. (Public Library of Science)
*Is this article available in print or online only? Online only
*Has LMU paid a subscription or other fee for your access to this article? No LMU has not paid a subscription or other fee because it is open access on the Public Library of Science.
*Use the genome sequencing article you found to perform a prospective search in the ISI Web of Science/Knowledge database.
**How many articles does this article cite? 25 cited references
**How many articles cite this article? 0 articles cite this article
**Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced?
*Well given that there are no papers that cite this paper there hasn't been anything done to build on this specific topic. In regards to the genome I think this paper has built on the work of the people who sequenced the first genome of Shigella flexneri as well as the other micro array papers.
*State which database you used to find the data and article: ArrayExpress
*State what you used as search terms and what type of search terms they were: "shigella flexneri" filtered by organism, experiment type: "rna assay", experiment type: "array assay"
*Give an overview of the results of the search.
**How many results did you get? 7 results returned with 6 viable options due to the number assays.
**Give an assessment of how relevant the results were: Very relevant, 6/7 results were viable.
*Link to [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-32978/?keywords=shigella+flexneri&organism=Shigella+flexneri&exptype%5B%5D=%22rna+assay%22&exptype%5B%5D=%22array+assay%22&array= microarray data]
*What experiment was performed? What was the "treatment" and what was the "control" in the experiment?
**Antibiotics (RNA Polymerase Inhibitors) were added to ''Shigella flexneri'' in order to see if bacteria became less active. The control was a group of bacteria with no drugs added to them, and the treatment was a group of bacteria with drugs added to them.
*Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each?
**There are two drugs RX and RP with 6 samples per drug. The experiment was run 3 times which yielded 36 assays. I believe that means 3 biological replicates and 12 technical replicates within each experiment, but I am not 100 percent sure.

Oregon Trail Survivors

2015-12-15T03:41:31Z

Jwoodlee: /* Week 15 */ added summary of changes

<div style="text-align: center; font-size: 250%; line-height: 1.25em">'''Oregon Trail Survivors'''</div>

<div class="center">
[[Image:Oregon-trail-dysentery 5 biodb.jpg | thumb | right | 350px | The third leading cause of death in the Oregon Trail.]]
</div>

== Group Members ==
*Coder: [[User:Jwoodlee | Jake Woodlee]]
*Quality Assurance: [[User:Troque | Trixie Roque]]
*GenMAPP Users: [[User:Eyanosch | Erich Yanoschik]] & [[User:Kzebrows | Kristin Zebrowski]]
* Project Manager: [[User:Kzebrows | Kristin Zebrowski]]

{{Template:Oregon Trail Survivors}}

=== Presentation (QA/Coder) ===
* PDF can be seen [[Media: Genome Paper Presentation BioDB.pdf | here]]

===Group Meeting Times===
*Thursday, November 5th at 8:00 pm
*Met most Sundays and Monday evenings in the Biol DB lab to check in with one another.

== Goals ==
Over the upcoming weeks our group will be investigating ''Shigella flexneri''.

===Week 10===

# Find genome sequence paper
# Find 4-8 microarray data and paper that goes with the genome paper
# Compile team page to and create a ranked annotated bibliography

===Week 11===

#Prepare for journal club presentations in Weeks 12 and 13
#Begin initial tasks on research project

Click on username links for more information regarding each team member's contributions for Week 11.

[[Jwoodlee Week 11 | Jake]]: Read through the genome paper and tried to get through the accessible things I had the ability to understand. Made an outline for the genome paper. Worked on the presentation with Trixie and found a database. And of course I answered the assigned questions.

[[Troque Week 11 | Trixie]]: Mainly focused on the Genome paper presentation with Jake. This includes searching for a viable database that we will be using for the rest of the group assignment and actually creating the presentation we will be doing for October 17th, 2015. I've also updated our group page to reflect what Dr. Dahlquist suggested would improve our team page.

[[Eyanosch Week 11 | Erich]]: Analyzed the microarray paper in order to describe the experimental design of the microarray data, treatments, number of replicates, and dye swaps. Worked with Kristin to produce the power point for the GennMAP users presentation at Journal Club. Worked on the individual journal entry and created an outline of the microarray paper.

[[Kzebrows Week 11 | Kristin]]: Using the team's selected microarray paper I developed an outline including background information, experimental outline/methods and how samples corresponded to the data, a brief description of the results, and a discussion including the implications of the research and its results in comparison to previous studies. Using this outline, I created a flow chart corresponding to the research. I also worked with Erich in order to create a PowerPoint for the Journal Club presentation on Nov. 24.

=== Week 12 ===
#QA will be doing an initial database export.
#Coder will be setting up version control.
#GenMAPP users will compile the raw data from the micorarray file to prepare for normalization and statistic analysis (will begin if time permits after consultation with Dr. Dahlquist). Additionally, the GenMAPP users will be determining the number of biological or technical replicates and how samples were labeled.
#Coder and QA will present on genome paper in class Tuesday, Nov. 24.

Click on username links for more information regarding each team member's contributions for Week 12.
* [[Jwoodlee Week 12 | Jake]]:Setup my environment in eclipse, created the s-flexneri branch, created my own copy of GenMAPP that I can modify for later use and I cloned the repository with the Git commands.
* [[Troque Week 12 | Trixie]]: Finished the preliminary export of the XML and GOA files and the corresponding Gene Testing Report. Also started identifying the gene id's for the specie. Decided on file management system with Jake.
* [[Eyanosch Week 12 | Erich]]: Worked with Kristin in determining the total number of biological and technical replicates. Compiled the raw data for RP samples, specifically the ID and Log ratio columns. Incorporated the RP and RX data into one spreadsheet with Kristins data. We created a table of the sample data and file each corresponds with, also figured out there were no dye swaps in the experiment(The control was the Cy3 dye and the treatment the Cy5 dye).
* [[Kzebrows Week 12 | Kristin]]: Determined that there were 3 biological replicates per treatment for 6 treatments total. Compiled raw data for RX samples by re-naming columns for ID and Log Ratio and putting into same worksheet, which was later combined with Erich's worksheet for RP samples. Erich and I met and worked together to create a table of which samples correspond to which file.

===Week 14===
#QA will be documenting the IDs using MATCH, Postgres, Microsoft Access, and Excel and get a head start of Milestone 3, which is customizing the TallyEngine.
#Coder will determine and document any modified export behavior that the GenMAPP Builder will have and resolve bugs. Coder will also work with QA by uploading GM Builder for additional export.
#GenMAPP Users will perform statistical analysis on Excel (normalization, tests) and format for import into GenMAPP. Users will also import data into GenMAPP and run MAPPFinder, and then document these test runs.

Click on username links for more information regarding each team member's contributions for Week 14.
* [[Jwoodlee Week 14 | Jake]]: Finished custom GenMAPP builder, committed to GitHub, and ran the export with the custom software. This created a custom .gdb which was opened in Microsoft Access and GenMAPP to check for accuracy.
* [[Troque Week 14 | Trixie]]: Trixie has finished identifying the gene IDs using MATCH, Postgres, Microsoft Access, and Excel. It was discovered that some IDs are in "dbReference/property&type&gene ID", and so another export was done on 12/7/15 to add the newly discovered gene IDs.
* [[Eyanosch Week 14 | Erich]]: Kristin and I completed the corrections provided via Dr. Dhalquist on Kristins talk page. We split the work into two halves and I worked on the RP data. We completed the statistics, Bonferroni p value correction, and the sanity check. I downloaded the database and formatted/exported the file for GenMAPP, and tried to create a GO tree for one of the trail points with RX.
* [[Kzebrows Week 14 | Kristin]]: This week Erich and I made corrections from the talk page and normalized log ratios for the slides in the experiment. I completed the statistical analysis for RX samples and calculated the Bonferroni p value correction. I also performed a sanity check for the RX samples and, going off of that, I calculated the Benjamini & Hochberg p value correction for RX-1-30, which had the most statistically significant changes in gene expression. I also formatted and exported the file for GenMAPP, downloaded the database, and attempted to create color sets to run the data set through MappFINDER.

==== Reflection ====

Each team member should reflect on the team's progress:
# What worked?
# What didn't work?
# What will I do next to fix what didn't work?

''Kristin'':
#What worked?
#*In terms of communication is having a group text. We also meet at least once a week outside of class in order to work together on the assignments and make sure we are all on the same page. So far, this has allowed us to troubleshoot and address bugs together as a team quickly. It also worked for Erich and I to divide up the samples so that I did all RX and Erich did all RP. Then, we could work at the same time and double-check procedures with each other but we were still getting the work done twice as quickly.
#What didn't work?
#*After creating the initial compiled raw data file, I had to make several corrections before the file could be run through GenMAPP. First of all, I had to get rid of the ".", and I also had to change all #DIV/0! with a space character for the file to be read at all. Also, although we were unable to find all of the b#### and CP#### gene ID's in UniProt or ShiBASE. Also, after creating my color set and trying to run MAPPFinder, I tried three computers and all of them crashed with the "not responding" message.
#What will I do next to fix what didn't work?
#*I will communicate with the QA and Coder in order to create a database with a minimal number of "Gene ID not found's" and then communicate with Erich when we try to run our dataset through MappFinder. Once the gene database is re-customized and the export is complete I can try and re-run my dataset to see if that makes a difference.

'' Trixie '':
# What worked?
#* What worked in identifying the gene IDs is to look export .gdb file into Excel and compare with what the OrderedLocusNames table had (from Microsoft Access). From doing this, it was easier to find which genes were not found in the .gdb file and made it easier to look through them in the UniProt XML file. With the Excel file comparing the lists of gene IDs and using the CTRL+F shortcut, I was also able to discern which tags to include into the new builds for the databases. Because of this, I was able to confirm that some genes indeed do not exist in the XML file, while only a couple exist within the "dbReference" tag. In terms of group work, what worked is posting all our files into a single page as we progress through the assignment. Night meetings were also helpful in order to better communicate with the rest of my group.
# What didn't work?
#* What didn't work is using Match multiple times without thinking. Even when I was trying to match the number of gene IDs with what Tally Engine gives me, Match didn't really help me in identifying where to find the genes in the XML file. Waiting for the database to finish didn't help much at all since our builds would take more than 4 hours to finish.
# What will I do next to fix what didn't work?
#* What I would do next to fix what didn't work is to actually use Match in conjunction to the XML file, or just use the Excel method completely since that was actually more helpful in finding the necessary tags than the Match method. I would probably have to time myself to check the lab after about 4.5 hours since one of our builds lasted that long.

''Jake'':
#What worked?
#*Almost every procedural action I took from Dondi worked. The only hiccup I had was in regard to Eclipse and navigating the directories.
#What didn't work?
#*In Eclipse, my edits to the GenMAPP builder source code were causing red error marks, but after selecting "Organize Imports" from the source menu the errors were fixed easily and the proper classes were imported. Also I had difficulty navigating to the dist file in my Temp drive, however I traced this back within Eclipse and was able to make a zip that I could hand off to Trixie for export.
#What will I do next week to fix what didn't work?
#*It seems to me that there wasn't a whole lot that went wrong with my procedure. What wasn't working I already fixed. Currently Trixie and I are running an export that will take 4 hours with the new additions in the property files, so there may be some new hiccups when that export is finished but we will have to wait and see.

''Erich'':
# What worked?
#*Having a GenMAPP user meeting with Dr. Dhalquist helped focus on what goals we wanted to achieve by the time of our next meeting. A group text helped organize meeting times of both the coders and GenMAPP users helped keep us on schedule.
# What didn't work?
#*The GenMapp Gene Ontology Tree was unable to pull files for each GO selection. We need to work on and make sure the GO files can be found. We also had to remove and edit our compiled raw data files so that they are able to be read by GenMAPP.
# What will I do next to fix what didn't work?
#*A new .gex was created, so this might help with the problems experienced in the MappBuilder. Also communicating with the QA and coder to make sure we finish up the GO tree smoothly in order to assess the results of the Publication we chose for Shigella Flexneri.

===Week 15===
#Coder: Work with QA to fix bugs.
#QA: Work with coder to fix bugs in the .gdb.
#GenMAPP Users: Finish Milestone 3. Run tests with GenMAPP. Do a journal club outline of the paper to use in the Discussion section of group report and presentation. Create a .mapp file showing one changed pathway from the data.
#All team members will be working together to put together deliverables including the final report and presentation for next Tuesday.

Click on username links for more information regarding each team member's contributions for Week 14.
* [[Jwoodlee Week 15 | Jake]]:Pulled Dondi's changes, and then created a new clean distribution. I then uploaded that distribution to our OTS Files page. Edited properties file for TallyEngine.
* [[Troque Week 15 | Trixie]]:
* [[Eyanosch Week 15 | Erich]]:
* [[Kzebrows Week 15 | Kristin]]: I created color sets with Increased/Decreased criteria for all of the 12 treatment/time point combos. Then, based on the criterion.go files, I created tables by filtering the results comparing the most commonly induced or repressed genes for the 1 x MIC at 60 minutes and 0.5 x MIC at 10 minutes between RX and RP. Strikingly, we found that between RX and RP the effects were very similar. I then compared them with the .mapp files that Erich created and put my portion of the project (compiled sanity check, color set, comparison tables) in the power point.

==Overview of Genome Paper==
*Used the genome sequencing article to perform a prospective search in the [https://apps.webofknowledge.com/UA_GeneralSearch_input.do?product=UA&search_mode=GeneralSearch&SID=1FRKcNxUgxiGX6spITI&preferencesSaved= Web of Science] database.
*Overview of the search:
**How many articles does this article cite? 37
**How many articles cite this article? 303
**Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced?
***Now that the genome has been sequenced, a majority of research has been done on discovering which genes are responsible for virulence and pathogenesis as well as potential antibiotics. Genomic research is also focused on how ''S. flexneri'' has been able to develop resistance to multiple drugs. Furthermore, ''Shigella'' is suspected to have evolved from ''Escherichia coli'' so a lot of research has been done in how and when pathogenic ''Shigella'' split from ''E. coli'' on the evolutionary tree.

==Annotated Bibliography==
=== Genome Paper ===
Jin, Q., Yuan, Z., Xu, J., Wang, Y., Shen, Y., Lu, W., … Yu, J. (2002). Genome sequence of ''Shigella flexneri'' 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157. Nucleic Acids Research, 30(20), 4432–4441.
* PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/?term=Genome+sequence+of+Shigella+flexneri+2a%3A+insights+into+pathogenicity+through+comparison+with+genomes+of+Escherichia+coli+K12+and+O157
* PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC137130/
* Publisher Full Text (HTML): http://nar.oxfordjournals.org/content/30/20/4432.full
* Publisher Full Text (PDF): http://nar.oxfordjournals.org/content/30/20/4432.full.pdf+html
* Copyright: 2002 Oxford University Press
* Publisher: Oxford University Press
* Availability: in print and online
* Did LMU pay a fee for this article: no

===Microarray Paper===





Fu H, Liu L, Zhang X, Zhu Y, Zhao L, Peng J, et al. (2012) Common Changes in Global Gene Expression Induced by RNA Polymerase Inhibitors in ''shigella flexneri''. PLoS ONE 7(3): e33240. doi:10.1371/journal.pone.0033240

*The link to the [http://www.ncbi.nlm.nih.gov/pubmed/22428000 abstract]
*The link to the [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3299763/ full text of the article] in PubMed Central
*The link to the [http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0033240 full text of the article] (HTML format) from the publisher web site.
*The link to the [http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0033240&representation=PDF full PDF version] of the article from the publisher web site.
*Copyright: © 2012 Fu et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
*Does the journal own the copyright? NO
*Do the authors own the copyright? Yes
*Do the authors own the rights under a Creative Commons license? Yes
*Is the article available “Open Access”? Yes
*What organization is the publisher of the article? What type of organization is it? PLoS One is the publisher/Journal. It hosts open access research articles. (Public Library of Science)
*Is this article available in print or online only? Online only
*Has LMU paid a subscription or other fee for your access to this article? No LMU has not paid a subscription or other fee because it is open access on the Public Library of Science.
*Use the genome sequencing article you found to perform a prospective search in the ISI Web of Science/Knowledge database.
**How many articles does this article cite? 25 cited references
**How many articles cite this article? 0 articles cite this article
**Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced?
*Well given that there are no papers that cite this paper there hasn't been anything done to build on this specific topic. In regards to the genome I think this paper has built on the work of the people who sequenced the first genome of Shigella flexneri as well as the other micro array papers.
*State which database you used to find the data and article: ArrayExpress
*State what you used as search terms and what type of search terms they were: "shigella flexneri" filtered by organism, experiment type: "rna assay", experiment type: "array assay"
*Give an overview of the results of the search.
**How many results did you get? 7 results returned with 6 viable options due to the number assays.
**Give an assessment of how relevant the results were: Very relevant, 6/7 results were viable.
*Link to [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-32978/?keywords=shigella+flexneri&organism=Shigella+flexneri&exptype%5B%5D=%22rna+assay%22&exptype%5B%5D=%22array+assay%22&array= microarray data]
*What experiment was performed? What was the "treatment" and what was the "control" in the experiment?
**Antibiotics (RNA Polymerase Inhibitors) were added to ''Shigella flexneri'' in order to see if bacteria became less active. The control was a group of bacteria with no drugs added to them, and the treatment was a group of bacteria with drugs added to them.
*Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each?
**There are two drugs RX and RP with 6 samples per drug. The experiment was run 3 times which yielded 36 assays. I believe that means 3 biological replicates and 12 technical replicates within each experiment, but I am not 100 percent sure.

OTS Deliverables

2015-12-14T19:30:21Z

Jwoodlee: /* OTS Files */ added new dist

==OTS Files==

[[Media:Micro Array Shigella Flexneri 20151011.pdf | Shigella Flexneri Microarray Paper (PDF)]]

[[Media:Shigellamicroarray.pptx | Microarray Journal Club Power Point]]

[[Media:CompiledRaw data RPRX IDLR EYKZ20152211.xlsx | Microarray Compiled Raw Data RP/RX IDLR]]

[[Media:SamplesFilesCorrespondanceTable SF301a EYKZ201522111.xls | Microarray Corresponding Files Table]]

[[Media: GMBuilder Shigella flexneri.zip]]

[[Media: QA Files.zip | Download QA files]]

[[File:GMBuilder December7 2015 build 2.zip]]

[[File:GenMAPP Builder 12 14 2015.zip]]

==GenMAPP User Files==
[[Media:CompiledRaw data RPRX IDLR EYKZ2015121.xlsx | ScalingCentering file from 12/1]]

[[Media:FINAL CompiledRawData RXRP EYKZ20151210.xlsx | Final Compiled Raw Data 12/10 Excel format]]

[[Media:FINAL CompiledRawData RXRP EYKZ20151210.txt | Final Compiled Raw Data 12/10 .txt format]]

[[Media:FINAL CompiledRawData RXRP EYKZ20151210 (1).gex | Final Compiled Raw Data 12/12 .gex]]

[[Media:Filtered MAPPFinder Results.xlsx | Filtered MAPPFinder Results]]

[[Media:Flagellum Ribosomal Mapp 1 60min 20151012.jpg | RP vs RX 1 MIC @ 60 minutes MAPP 12/12 .jpg]]

[[Media:Flagellum Ribosomal Mapp 0pt5 10min 20151012.jpg | RP vs RX 0.5 MIC @ 10 minutes MAPP 12/12 .jpg]]

====RP (Erich)====
[[Media:CompiledRaw data GenMAPP Final RP IDLR EYKZ2015126.xlsx | RP Compiled Raw Data Final 12/10]]

[[Media:CompiledRaw data GenMAPP ready RP IDLR EYKZ2015126.txt | RP .txt format GenMAPP ready 12/6]]

[[Media:CompiledRaw data Errors RP EYKZ2015126.EX.xlsx | RP Exceptions file in Excel format (filtered)]]

[[Media:CompiledRaw data Errors RP EYKZ2015126.EX.txt | RP Exceptions (txt)]]

[[Media:CompiledRaw data GenMAPP ready RP IDLR EYKZ2015126.gex | RP .gex file]]

====RX (Kristin)====
[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.xlsx | RX Compiled Raw Data 12/6]]

[[Media:CompiledRaw data statistics BonferroniPvalue RP IDLR EYKZ2015126.txt | RX .txt format GenMAPP ready 12/6]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.xlsx | RX Compiled Raw Data as of 12/6]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.txt | RX .txt format updated as of 12/6]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.EX.txt | RX Exceptions file]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.gex | RX .gex file]]

[[Media:CompiledRaw data RX IDLR KZ2015126.EX.xlsx | RX Exceptions file in Excel format (filtered)]]

{{Template:Oregon Trail Survivors}}

File:GenMAPP Builder 12 14 2015.zip

2015-12-14T19:29:57Z

Jwoodlee:

Oregon Trail Survivors

2015-12-08T06:09:05Z

Jwoodlee: /* Reflection */ added jake reflection

<div style="text-align: center; font-size: 250%; line-height: 1.25em">'''Oregon Trail Survivors'''</div>

<div class="center">
[[Image:Oregon-trail-dysentery 5 biodb.jpg | thumb | right | 350px | The third leading cause of death in the Oregon Trail.]]
</div>

== Group Members ==
*Coder: [[User:Jwoodlee | Jake Woodlee]]
*Quality Assurance: [[User:Troque | Trixie Roque]]
*GenMAPP Users: [[User:Eyanosch | Erich Yanoschik]] & [[User:Kzebrows | Kristin Zebrowski]]
* Project Manager: [[User:Kzebrows | Kristin Zebrowski]]

{{Template:Oregon Trail Survivors}}

=== Presentation (QA/Coder) ===
* PDF can be seen [[Media: Genome Paper Presentation BioDB.pdf | here]]

===Group Meeting Times===
Thursday, November 5th at 8:00 pm

== Goals ==
Over the upcoming weeks our group will be investigating ''Shigella flexneri''.

====Week 10====

# Find genome sequence paper
# Find 4-8 microarray data and paper that goes with the genome paper
# Compile team page to and create a ranked annotated bibliography

====Week 11====

#Prepare for journal club presentations in Weeks 12 and 13
#Begin initial tasks on research project

Click on username links for more information regarding each team member's contributions for Week 11.

[[Jwoodlee Week 11 | Jake]]: Read through the genome paper and tried to get through the accessible things I had the ability to understand. Made an outline for the genome paper. Worked on the presentation with Trixie and found a database. And of course I answered the assigned questions.

[[Troque Week 11 | Trixie]]: Mainly focused on the Genome paper presentation with Jake. This includes searching for a viable database that we will be using for the rest of the group assignment and actually creating the presentation we will be doing for October 17th, 2015. I've also updated our group page to reflect what Dr. Dahlquist suggested would improve our team page.

[[Eyanosch Week 11 | Erich]]: Analyzed the microarray paper in order to describe the experimental design of the microarray data, treatments, number of replicates, and dye swaps. Worked with Kristin to produce the power point for the GennMAP users presentation at Journal Club. Worked on the individual journal entry and created an outline of the microarray paper.

[[Kzebrows Week 11 | Kristin]]: Using the team's selected microarray paper I developed an outline including background information, experimental outline/methods and how samples corresponded to the data, a brief description of the results, and a discussion including the implications of the research and its results in comparison to previous studies. Using this outline, I created a flow chart corresponding to the research. I also worked with Erich in order to create a PowerPoint for the Journal Club presentation on Nov. 24.

==== Week 12 ====
#QA will be doing an initial database export.
#Coder will be setting up version control.
#GenMAPP users will compile the raw data from the micorarray file to prepare for normalization and statistic analysis (will begin if time permits after consultation with Dr. Dahlquist). Additionally, the GenMAPP users will be determining the number of biological or technical replicates and how samples were labeled.
#Coder and QA will present on genome paper in class Tuesday, Nov. 24.

Click on username links for more information regarding each team member's contributions for Week 12.
* [[Jwoodlee Week 12 | Jake]]:Setup my environment in eclipse, created the s-flexneri branch, created my own copy of GenMAPP that I can modify for later use and I cloned the repository with the Git commands.
* [[Troque Week 12 | Trixie]]: Finished the preliminary export of the XML and GOA files and the corresponding Gene Testing Report. Also started identifying the gene id's for the specie. Decided on file management system with Jake.
* [[Eyanosch Week 12 | Erich]]: Worked with Kristin in determining the total number of biological and technical replicates. Compiled the raw data for RP samples, specifically the ID and Log ratio columns. Incorporated the RP and RX data into one spreadsheet with Kristins data. We created a table of the sample data and file each corresponds with, also figured out there were no dye swaps in the experiment(The control was the Cy3 dye and the treatment the Cy5 dye).
* [[Kzebrows Week 12 | Kristin]]: Determined that there were 3 biological replicates per treatment for 6 treatments total. Compiled raw data for RX samples by re-naming columns for ID and Log Ratio and putting into same worksheet, which was later combined with Erich's worksheet for RP samples. Erich and I met and worked together to create a table of which samples correspond to which file.

===Week 14===
#QA will be documenting the IDs using MATCH, Postgres, Microsoft Access, and Excel and get a head start of Milestone 3, which is customizing the TallyEngine.
#Coder will determine and document any modified export behavior that the GenMAPP Builder will have and resolve bugs. Coder will also work with QA by uploading GM Builder for additional export.
#GenMAPP Users will perform statistical analysis on Excel (normalization, tests) and format for import into GenMAPP. Users will also import data into GenMAPP and run MAPPFinder, and then document these test runs.

Click on username links for more information regarding each team member's contributions for Week 14.
* [[Jwoodlee Week 14 | Jake]]: Finished custom GenMAPP builder, committed to GitHub, and ran the export with the custom software. This created a custom .gdb which was opened in Microsoft Access and GenMAPP to check for accuracy.
* [[Troque Week 14 | Trixie]]: Trixie has finished identifying the gene IDs using MATCH, Postgres, Microsoft Access, and Excel. It was discovered that some IDs are in "dbReference/property&type&gene ID", and so another export was done on 12/7/15 to add the newly discovered gene IDs.
* [[Eyanosch Week 14 | Erich]]:
* [[Kzebrows Week 14 | Kristin]]: This week Erich and I made corrections from the talk page and normalized log ratios for the slides in the experiment. I completed the statistical analysis for RX samples and calculated the Bonferroni p value correction. I also performed a sanity check for the RX samples and, going off of that, I calculated the Benjamini & Hochberg p value correction for RX-1-30, which had the most statistically significant changes in gene expression. I also formatted and exported the file for GenMAPP, downloaded the database, and attempted to create color sets to run the data set through MappFINDER.

==== Reflection ====

Each team member should reflect on the team's progress:
# What worked?
# What didn't work?
# What will I do next to fix what didn't work?

''Kristin'':
#What worked in terms of communication is having a group text. We also meet at least once a week outside of class in order to work together on the assignments and make sure we are all on the same page. So far, this has allowed us to troubleshoot and address bugs together as a team quickly.
#After creating the initial compiled raw data file, I had to make several corrections before the file could be run through GenMAPP. First of all, I had to get rid of the ".", and I also had to change all #DIV/0! with a space character for the file to be read at all. Also, although we were unable to find all of the b#### and CP#### gene ID's in UniProt or ShiBASE. Also, after creating my color set and trying to run MAPPFinder, I tried three computers and all of them crashed with the "not responding" message.
#I will communicate with the QA and Coder in order to create a database with a minimal number of "Gene ID not found's" and then communicate with Erich when we try to run our dataset through MappFinder. Once the gene database is re-customized and the export is complete I can try and re-run my dataset to see if that makes a difference.

'' Trixie '':
# What worked?
#* What worked in identifying the gene IDs is to look export .gdb file into Excel and compare with what the OrderedLocusNames table had (from Microsoft Access). From doing this, it was easier to find which genes were not found in the .gdb file and made it easier to look through them in the UniProt XML file. With the Excel file comparing the lists of gene IDs and using the CTRL+F shortcut, I was also able to discern which tags to include into the new builds for the databases. Because of this, I was able to confirm that some genes indeed do not exist in the XML file, while only a couple exist within the "dbReference" tag. In terms of group work, what worked is posting all our files into a single page as we progress through the assignment. Night meetings were also helpful in order to better communicate with the rest of my group.
# What didn't work?
#* What didn't work is using Match multiple times without thinking. Even when I was trying to match the number of gene IDs with what Tally Engine gives me, Match didn't really help me in identifying where to find the genes in the XML file. Waiting for the database to finish didn't help much at all since our builds would take more than 4 hours to finish.
# What will I do next to fix what didn't work?
#* What I would do next to fix what didn't work is to actually use Match in conjunction to the XML file, or just use the Excel method completely since that was actually more helpful in finding the necessary tags than the Match method. I would probably have to time myself to check the lab after about 4.5 hours since one of our builds lasted that long.

''Jake'':
#What worked?
#*Almost every procedural action I took from Dondi worked. The only hiccup I had was in regard to Eclipse and navigating the directories.
#What didn't work?
#*In Eclipse, my edits to the GenMAPP builder source code were causing red error marks, but after selecting "Organize Imports" from the source menu the errors were fixed easily and the proper classes were imported. Also I had difficulty navigating to the dist file in my Temp drive, however I traced this back within Eclipse and was able to make a zip that I could hand off to Trixie for export.
#What will I do next week to fix what didn't work?
#*It seems to me that there wasn't a whole lot that went wrong with my procedure. What wasn't working I already fixed. Currently Trixie and I are running an export that will take 4 hours with the new additions in the property files, so there may be some new hiccups when that export is finished but we will have to wait and see.

==Overview of Genome Paper==
*Used the genome sequencing article to perform a prospective search in the [https://apps.webofknowledge.com/UA_GeneralSearch_input.do?product=UA&search_mode=GeneralSearch&SID=1FRKcNxUgxiGX6spITI&preferencesSaved= Web of Science] database.
*Overview of the search:
**How many articles does this article cite? 37
**How many articles cite this article? 303
**Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced?
***Now that the genome has been sequenced, a majority of research has been done on discovering which genes are responsible for virulence and pathogenesis as well as potential antibiotics. Genomic research is also focused on how ''S. flexneri'' has been able to develop resistance to multiple drugs. Furthermore, ''Shigella'' is suspected to have evolved from ''Escherichia coli'' so a lot of research has been done in how and when pathogenic ''Shigella'' split from ''E. coli'' on the evolutionary tree.

==Annotated Bibliography==
=== Genome Paper ===
Jin, Q., Yuan, Z., Xu, J., Wang, Y., Shen, Y., Lu, W., … Yu, J. (2002). Genome sequence of ''Shigella flexneri'' 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157. Nucleic Acids Research, 30(20), 4432–4441.
* PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/?term=Genome+sequence+of+Shigella+flexneri+2a%3A+insights+into+pathogenicity+through+comparison+with+genomes+of+Escherichia+coli+K12+and+O157
* PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC137130/
* Publisher Full Text (HTML): http://nar.oxfordjournals.org/content/30/20/4432.full
* Publisher Full Text (PDF): http://nar.oxfordjournals.org/content/30/20/4432.full.pdf+html
* Copyright: 2002 Oxford University Press
* Publisher: Oxford University Press
* Availability: in print and online
* Did LMU pay a fee for this article: no

===Microarray Paper===





Fu H, Liu L, Zhang X, Zhu Y, Zhao L, Peng J, et al. (2012) Common Changes in Global Gene Expression Induced by RNA Polymerase Inhibitors in ''shigella flexneri''. PLoS ONE 7(3): e33240. doi:10.1371/journal.pone.0033240

*The link to the [http://www.ncbi.nlm.nih.gov/pubmed/22428000 abstract]
*The link to the [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3299763/ full text of the article] in PubMed Central
*The link to the [http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0033240 full text of the article] (HTML format) from the publisher web site.
*The link to the [http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0033240&representation=PDF full PDF version] of the article from the publisher web site.
*Copyright: © 2012 Fu et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
*Does the journal own the copyright? NO
*Do the authors own the copyright? Yes
*Do the authors own the rights under a Creative Commons license? Yes
*Is the article available “Open Access”? Yes
*What organization is the publisher of the article? What type of organization is it? PLoS One is the publisher/Journal. It hosts open access research articles. (Public Library of Science)
*Is this article available in print or online only? Online only
*Has LMU paid a subscription or other fee for your access to this article? No LMU has not paid a subscription or other fee because it is open access on the Public Library of Science.
*Use the genome sequencing article you found to perform a prospective search in the ISI Web of Science/Knowledge database.
**How many articles does this article cite? 25 cited references
**How many articles cite this article? 0 articles cite this article
**Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced?
*Well given that there are no papers that cite this paper there hasn't been anything done to build on this specific topic. In regards to the genome I think this paper has built on the work of the people who sequenced the first genome of Shigella flexneri as well as the other micro array papers.
*State which database you used to find the data and article: ArrayExpress
*State what you used as search terms and what type of search terms they were: "shigella flexneri" filtered by organism, experiment type: "rna assay", experiment type: "array assay"
*Give an overview of the results of the search.
**How many results did you get? 7 results returned with 6 viable options due to the number assays.
**Give an assessment of how relevant the results were: Very relevant, 6/7 results were viable.
*Link to [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-32978/?keywords=shigella+flexneri&organism=Shigella+flexneri&exptype%5B%5D=%22rna+assay%22&exptype%5B%5D=%22array+assay%22&array= microarray data]
*What experiment was performed? What was the "treatment" and what was the "control" in the experiment?
**Antibiotics (RNA Polymerase Inhibitors) were added to ''Shigella flexneri'' in order to see if bacteria became less active. The control was a group of bacteria with no drugs added to them, and the treatment was a group of bacteria with drugs added to them.
*Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each?
**There are two drugs RX and RP with 6 samples per drug. The experiment was run 3 times which yielded 36 assays. I believe that means 3 biological replicates and 12 technical replicates within each experiment, but I am not 100 percent sure.

Jwoodlee Week 14

2015-12-08T05:29:26Z

Jwoodlee: added what worked/didn't work

Jwoodlee Week 14

2015-12-08T05:21:51Z

Jwoodlee: /* Milestone 4: Species Export Customization */ added more of what we did

=== Milestone 3: Species Profile Creation ===
Majority of the procedure was from [[Coder | here]].
==== Adding a Species Profile to GenMAPP Builder ====

In the Java perspective within Eclipse(change perspective on the top right), the following was executed.

====== Create the Species Profile ======

# I exposed the contents of the ''src'' folder in my gmbuilder project.
# Right-clicked on the ''edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles'' package and chose '''New > Class''' from the popup menu.
# In the dialog that appears, I entered the following:
#* '''Name:''' <code>ShigellaflexneriUniProtSpeciesProfile</code>
#* '''Superclass:''' <code>edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles.UniProtSpeciesProfile</code>
# Clicked ''Finish''. A new ''.java'' file within the ''edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles'' package was created.

====== Customize the Species Profile ======

* I opened the file that I just created.
* I added the following constructor block right below the ''public class'' line in the new file.
public ShigellaflexneriUniProtSpeciesProfile() {
super("Shigella flexneri",
623,
"This profile customizes the GenMAPP Builder export for " +
"Shigella flexneri" +
" data loaded from a UniProt XML file.");
}
* I added the following method block right below the constructor block that I added above.
@Override
public TableManager getSystemsTableManagerCustomizations(TableManager tableManager, DatabaseProfile dbProfile) {
super.getSystemsTableManagerCustomizations(tableManager, dbProfile);
tableManager.submit("Systems", QueryType.update, new String[][] {
{ "SystemCode", "N" },
{ "Species", "|" + getSpeciesName() + "|" }
});

tableManager.submit("Systems", QueryType.update, new String[][] {
{ "SystemCode", "N" },
{ "Link", "http://www.mgc.ac.cn/cgi-bin/ShiBASE/ShiBASE_query.cgi?synonym=~" }
});

return tableManager;
}
* I chose ''Organize Imports'' from the ''Source'' menu to make sure I had everything imported.

====== Add the Species Profile to the Catalog of Known Species Profiles ======

* Under ''edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles'', I opened ''UniProtDatabaseProfile.java''.
* Near the top of the file is a block that looks like this:
super("org.uniprot.uniprot.Uniprot",
"This profile defines the requirements "
+ "for any UniProt centric gene database.",
new SpeciesProfile[] {
new EscherichiaColiUniProtSpeciesProfile(),
new ArabidopsisThalianaUniProtSpeciesProfile(),
new PlasmodiumFalciparumUniProtSpeciesProfile(),
new VibrioCholeraeUniprotSpeciesProfile() });
* I added the species profile that I created to the block.
super("org.uniprot.uniprot.Uniprot",
"This profile defines the requirements "
+ "for any UniProt centric gene database.",
new SpeciesProfile[] {
new EscherichiaColiUniProtSpeciesProfile(),
new ArabidopsisThalianaUniProtSpeciesProfile(),
new PlasmodiumFalciparumUniProtSpeciesProfile(),
new VibrioCholeraeUniprotSpeciesProfile(),
new ShigellaflexneriUniProtSpeciesProfile() });

* I saved changes and selected ''Organize Imports''.

====== Build, Test, and Possibly Commit ======

# I created a new distribution of GenMAPP Builder.
#*Expanded the custom project, scrolled down the build.xml and right clicked it. In the menu that appeared I clicked on Ant Build... (with ellipses). Now in the menu that appeared I deselected dist, and selected clean, dist in that order. The build order was now clean, dist so it will wipe the current version of genmappbuilder and create a new distribution. I clicked run.
# With Trixie, we performed a new export run with this custom version of GenMAPP Builder. A new .gdb was created.
# I checked the ''Systems'' table in the resulting ''.gdb'' with Microsoft Access and verified that it contained the custom information:
#* The record ''OrderedLocusNames'' was there with the species name under the ''Species'' column and our link URL under the ''Link'' column.
#Opened up a gene in GenMAPP with the custom .gdb created to make sure the link that I inserted was working properly.
# I then committed the custom version of GenMAPP builder to our GitHub branch.

=== Milestone 4: Species Export Customization ===
#Trixie noticed that the microarray data has IDs that have CP#### and SF####.# not the typical SF####, which will need to accounted for.
#This week, we edited the gmbuilder.properties file in eclipse as found in the Quality Assurance guild page. We added lines for our species.

OTS Deliverables

2015-12-08T05:16:28Z

Jwoodlee: /* OTS Files */ added new file

==OTS Files==

[[Media:Micro Array Shigella Flexneri 20151011.pdf | Shigella Flexneri Microarray Paper (PDF)]]

[[Media:Shigellamicroarray.pptx | Microarray Journal Club Power Point]]

[[Media:CompiledRaw data RPRX IDLR EYKZ20152211.xlsx | Microarray Compiled Raw Data RP/RX IDLR]]

[[Media:SamplesFilesCorrespondanceTable SF301a EYKZ201522111.xls | Microarray Corresponding Files Table]]

[[Media: GMBuilder Shigella flexneri.zip]]

[[Media: QA Files.zip | Download QA files]]

[[File:GMBuilder December7 2015 build 2.zip]]

==GenMAPP User Files==
[[Media:CompiledRaw data RPRX IDLR EYKZ2015121.xlsx | ScalingCentering file from 12/1]]

====RP (Erich)====
[[Media:CompiledRaw data statistics BonferroniPvalue RP IDLR EYKZ2015123.xlsx | RP Compiled Raw Data 12/6]]

[[Media:CompiledRaw data GenMAPP ready RP IDLR EYKZ2015126.txt | RP .txt format GenMAPP ready 12/6]]

[[Media:CompiledRaw data Errors RP EYKZ2015126.EX.xlsx | RP Exceptions file in Excel format (filtered)]]

[[Media:CompiledRaw data Errors RP EYKZ2015126.EX.txt | RP Exceptions (txt)]]

[[Media:CompiledRaw data GenMAPP ready RP IDLR EYKZ2015126.gex | RP .gex file]]

====RX (Kristin)====
[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.xlsx | RX Compiled Raw Data 12/6]]

[[Media:CompiledRaw data statistics BonferroniPvalue RP IDLR EYKZ2015126.txt | RX .txt format GenMAPP ready 12/6]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.xlsx | RX Compiled Raw Data as of 12/6]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.txt | RX .txt format updated as of 12/6]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.EX.txt | RX Exceptions file]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.gex | RX .gex file]]

[[Media:CompiledRaw data RX IDLR KZ2015126.EX.xlsx | RX Exceptions file in Excel format (filtered)]]

{{Template:Oregon Trail Survivors}}

File:GMBuilder December7 2015 build 2.zip

2015-12-08T05:15:58Z

Jwoodlee:

Jwoodlee Week 14

2015-12-08T04:09:55Z

Jwoodlee: /* Build, Test, and Possibly Commit */ added one line to the procedure

Oregon Trail Survivors

2015-12-08T04:07:23Z

Jwoodlee: /* Week 14 */ added Jake's summary for the week

<div style="text-align: center; font-size: 250%; line-height: 1.25em">'''Oregon Trail Survivors'''</div>

<div class="center">
[[Image:Oregon-trail-dysentery 5 biodb.jpg | thumb | right | 350px | The third leading cause of death in the Oregon Trail.]]
</div>

== Group Members ==
*Coder: [[User:Jwoodlee | Jake Woodlee]]
*Quality Assurance: [[User:Troque | Trixie Roque]]
*GenMAPP Users: [[User:Eyanosch | Erich Yanoschik]] & [[User:Kzebrows | Kristin Zebrowski]]
* Project Manager: [[User:Kzebrows | Kristin Zebrowski]]

{{Template:Oregon Trail Survivors}}

=== Presentation (QA/Coder) ===
* PDF can be seen [[Media: Genome Paper Presentation BioDB.pdf | here]]

===Group Meeting Times===
Thursday, November 5th at 8:00 pm

== Goals ==
Over the upcoming weeks our group will be investigating ''Shigella flexneri''.

====Week 10====

# Find genome sequence paper
# Find 4-8 microarray data and paper that goes with the genome paper
# Compile team page to and create a ranked annotated bibliography

====Week 11====

#Prepare for journal club presentations in Weeks 12 and 13
#Begin initial tasks on research project

Click on username links for more information regarding each team member's contributions for Week 11.

[[Jwoodlee Week 11 | Jake]]: Read through the genome paper and tried to get through the accessible things I had the ability to understand. Made an outline for the genome paper. Worked on the presentation with Trixie and found a database. And of course I answered the assigned questions.

[[Troque Week 11 | Trixie]]: Mainly focused on the Genome paper presentation with Jake. This includes searching for a viable database that we will be using for the rest of the group assignment and actually creating the presentation we will be doing for October 17th, 2015. I've also updated our group page to reflect what Dr. Dahlquist suggested would improve our team page.

[[Eyanosch Week 11 | Erich]]: Analyzed the microarray paper in order to describe the experimental design of the microarray data, treatments, number of replicates, and dye swaps. Worked with Kristin to produce the power point for the GennMAP users presentation at Journal Club. Worked on the individual journal entry and created an outline of the microarray paper.

[[Kzebrows Week 11 | Kristin]]: Using the team's selected microarray paper I developed an outline including background information, experimental outline/methods and how samples corresponded to the data, a brief description of the results, and a discussion including the implications of the research and its results in comparison to previous studies. Using this outline, I created a flow chart corresponding to the research. I also worked with Erich in order to create a PowerPoint for the Journal Club presentation on Nov. 24.

==== Week 12 ====
#QA will be doing an initial database export.
#Coder will be setting up version control.
#GenMAPP users will compile the raw data from the micorarray file to prepare for normalization and statistic analysis (will begin if time permits after consultation with Dr. Dahlquist). Additionally, the GenMAPP users will be determining the number of biological or technical replicates and how samples were labeled.
#Coder and QA will present on genome paper in class Tuesday, Nov. 24.

Click on username links for more information regarding each team member's contributions for Week 12.
* [[Jwoodlee Week 12 | Jake]]:Setup my environment in eclipse, created the s-flexneri branch, created my own copy of GenMAPP that I can modify for later use and I cloned the repository with the Git commands.
* [[Troque Week 12 | Trixie]]: Finished the preliminary export of the XML and GOA files and the corresponding Gene Testing Report. Also started identifying the gene id's for the specie. Decided on file management system with Jake.
* [[Eyanosch Week 12 | Erich]]: Worked with Kristin in determining the total number of biological and technical replicates. Compiled the raw data for RP samples, specifically the ID and Log ratio columns. Incorporated the RP and RX data into one spreadsheet with Kristins data. We created a table of the sample data and file each corresponds with, also figured out there were no dye swaps in the experiment(The control was the Cy3 dye and the treatment the Cy5 dye).
* [[Kzebrows Week 12 | Kristin]]: Determined that there were 3 biological replicates per treatment for 6 treatments total. Compiled raw data for RX samples by re-naming columns for ID and Log Ratio and putting into same worksheet, which was later combined with Erich's worksheet for RP samples. Erich and I met and worked together to create a table of which samples correspond to which file.

===Week 14===
#QA will be documenting the IDs using MATCH, Postgres, Microsoft Access, and Excel and get a head start of Milestone 3, which is customizing the TallyEngine.
#Coder will determine and document any modified export behavior that the GenMAPP Builder will have and resolve bugs. Coder will also work with QA by uploading GM Builder for additional export.
#GenMAPP Users will perform statistical analysis on Excel (normalization, tests) and format for import into GenMAPP. Users will also import data into GenMAPP and run MAPPFinder, and then document these test runs.

Click on username links for more information regarding each team member's contributions for Week 14.
* [[Jwoodlee Week 14 | Jake]]: Finished custom GenMAPP builder, committed to GitHub, and ran the export with the custom software. This created a custom .gdb which was opened in Microsoft Access and GenMAPP to check for accuracy.
* [[Troque Week 14 | Trixie]]: Trixie has finished identifying the gene IDs using MATCH, Postgres, Microsoft Access, and Excel.
* [[Eyanosch Week 14 | Erich]]:
* [[Kzebrows Week 14 | Kristin]]:

==== Reflection ====

Each team member should reflect on the team's progress:
# What worked?
# What didn't work?
# What will I do next to fix what didn't work?

==Overview of Genome Paper==
*Used the genome sequencing article to perform a prospective search in the [https://apps.webofknowledge.com/UA_GeneralSearch_input.do?product=UA&search_mode=GeneralSearch&SID=1FRKcNxUgxiGX6spITI&preferencesSaved= Web of Science] database.
*Overview of the search:
**How many articles does this article cite? 37
**How many articles cite this article? 303
**Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced?
***Now that the genome has been sequenced, a majority of research has been done on discovering which genes are responsible for virulence and pathogenesis as well as potential antibiotics. Genomic research is also focused on how ''S. flexneri'' has been able to develop resistance to multiple drugs. Furthermore, ''Shigella'' is suspected to have evolved from ''Escherichia coli'' so a lot of research has been done in how and when pathogenic ''Shigella'' split from ''E. coli'' on the evolutionary tree.

==Annotated Bibliography==
=== Genome Paper ===
Jin, Q., Yuan, Z., Xu, J., Wang, Y., Shen, Y., Lu, W., … Yu, J. (2002). Genome sequence of ''Shigella flexneri'' 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157. Nucleic Acids Research, 30(20), 4432–4441.
* PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/?term=Genome+sequence+of+Shigella+flexneri+2a%3A+insights+into+pathogenicity+through+comparison+with+genomes+of+Escherichia+coli+K12+and+O157
* PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC137130/
* Publisher Full Text (HTML): http://nar.oxfordjournals.org/content/30/20/4432.full
* Publisher Full Text (PDF): http://nar.oxfordjournals.org/content/30/20/4432.full.pdf+html
* Copyright: 2002 Oxford University Press
* Publisher: Oxford University Press
* Availability: in print and online
* Did LMU pay a fee for this article: no

===Microarray Paper===





Fu H, Liu L, Zhang X, Zhu Y, Zhao L, Peng J, et al. (2012) Common Changes in Global Gene Expression Induced by RNA Polymerase Inhibitors in ''shigella flexneri''. PLoS ONE 7(3): e33240. doi:10.1371/journal.pone.0033240

*The link to the [http://www.ncbi.nlm.nih.gov/pubmed/22428000 abstract]
*The link to the [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3299763/ full text of the article] in PubMed Central
*The link to the [http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0033240 full text of the article] (HTML format) from the publisher web site.
*The link to the [http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0033240&representation=PDF full PDF version] of the article from the publisher web site.
*Copyright: © 2012 Fu et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
*Does the journal own the copyright? NO
*Do the authors own the copyright? Yes
*Do the authors own the rights under a Creative Commons license? Yes
*Is the article available “Open Access”? Yes
*What organization is the publisher of the article? What type of organization is it? PLoS One is the publisher/Journal. It hosts open access research articles. (Public Library of Science)
*Is this article available in print or online only? Online only
*Has LMU paid a subscription or other fee for your access to this article? No LMU has not paid a subscription or other fee because it is open access on the Public Library of Science.
*Use the genome sequencing article you found to perform a prospective search in the ISI Web of Science/Knowledge database.
**How many articles does this article cite? 25 cited references
**How many articles cite this article? 0 articles cite this article
**Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced?
*Well given that there are no papers that cite this paper there hasn't been anything done to build on this specific topic. In regards to the genome I think this paper has built on the work of the people who sequenced the first genome of Shigella flexneri as well as the other micro array papers.
*State which database you used to find the data and article: ArrayExpress
*State what you used as search terms and what type of search terms they were: "shigella flexneri" filtered by organism, experiment type: "rna assay", experiment type: "array assay"
*Give an overview of the results of the search.
**How many results did you get? 7 results returned with 6 viable options due to the number assays.
**Give an assessment of how relevant the results were: Very relevant, 6/7 results were viable.
*Link to [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-32978/?keywords=shigella+flexneri&organism=Shigella+flexneri&exptype%5B%5D=%22rna+assay%22&exptype%5B%5D=%22array+assay%22&array= microarray data]
*What experiment was performed? What was the "treatment" and what was the "control" in the experiment?
**Antibiotics (RNA Polymerase Inhibitors) were added to ''Shigella flexneri'' in order to see if bacteria became less active. The control was a group of bacteria with no drugs added to them, and the treatment was a group of bacteria with drugs added to them.
*Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each?
**There are two drugs RX and RP with 6 samples per drug. The experiment was run 3 times which yielded 36 assays. I believe that means 3 biological replicates and 12 technical replicates within each experiment, but I am not 100 percent sure.

Jwoodlee Week 14

2015-12-08T04:01:58Z

Jwoodlee: /* Milestone 4: Species Export Customization */ added some notes

=== Milestone 3: Species Profile Creation ===
Majority of the procedure was from [[Coder | here]].
==== Adding a Species Profile to GenMAPP Builder ====

In the Java perspective within Eclipse(change perspective on the top right), the following was executed.

====== Create the Species Profile ======

# I exposed the contents of the ''src'' folder in my gmbuilder project.
# Right-clicked on the ''edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles'' package and chose '''New > Class''' from the popup menu.
# In the dialog that appears, I entered the following:
#* '''Name:''' <code>ShigellaflexneriUniProtSpeciesProfile</code>
#* '''Superclass:''' <code>edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles.UniProtSpeciesProfile</code>
# Clicked ''Finish''. A new ''.java'' file within the ''edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles'' package was created.

====== Customize the Species Profile ======

* I opened the file that I just created.
* I added the following constructor block right below the ''public class'' line in the new file.
public ShigellaflexneriUniProtSpeciesProfile() {
super("Shigella flexneri",
623,
"This profile customizes the GenMAPP Builder export for " +
"Shigella flexneri" +
" data loaded from a UniProt XML file.");
}
* I added the following method block right below the constructor block that I added above.
@Override
public TableManager getSystemsTableManagerCustomizations(TableManager tableManager, DatabaseProfile dbProfile) {
super.getSystemsTableManagerCustomizations(tableManager, dbProfile);
tableManager.submit("Systems", QueryType.update, new String[][] {
{ "SystemCode", "N" },
{ "Species", "|" + getSpeciesName() + "|" }
});

tableManager.submit("Systems", QueryType.update, new String[][] {
{ "SystemCode", "N" },
{ "Link", "http://www.mgc.ac.cn/cgi-bin/ShiBASE/ShiBASE_query.cgi?synonym=~" }
});

return tableManager;
}
* I chose ''Organize Imports'' from the ''Source'' menu to make sure I had everything imported.

====== Add the Species Profile to the Catalog of Known Species Profiles ======

* Under ''edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles'', I opened ''UniProtDatabaseProfile.java''.
* Near the top of the file is a block that looks like this:
super("org.uniprot.uniprot.Uniprot",
"This profile defines the requirements "
+ "for any UniProt centric gene database.",
new SpeciesProfile[] {
new EscherichiaColiUniProtSpeciesProfile(),
new ArabidopsisThalianaUniProtSpeciesProfile(),
new PlasmodiumFalciparumUniProtSpeciesProfile(),
new VibrioCholeraeUniprotSpeciesProfile() });
* I added the species profile that I created to the block.
super("org.uniprot.uniprot.Uniprot",
"This profile defines the requirements "
+ "for any UniProt centric gene database.",
new SpeciesProfile[] {
new EscherichiaColiUniProtSpeciesProfile(),
new ArabidopsisThalianaUniProtSpeciesProfile(),
new PlasmodiumFalciparumUniProtSpeciesProfile(),
new VibrioCholeraeUniprotSpeciesProfile(),
new ShigellaflexneriUniProtSpeciesProfile() });

* I saved changes and selected ''Organize Imports''.

====== Build, Test, and Possibly Commit ======

# I created a new distribution of GenMAPP Builder.
#*Expanded the custom project, scrolled down the build.xml and right clicked it. In the menu that appeared I clicked on Ant Build... (with ellipses). Now in the menu that appeared I deselected dist, and selected clean, dist in that order. The build order was now clean, dist so it will wipe the current version of genmappbuilder and create a new distribution. I clicked run.
# With Trixie, we performed a new export run with this custom version of GenMAPP Builder. A new .gdb was created.
# I checked the ''Systems'' table in the resulting ''.gdb'' with Microsoft Access and verified that it contained the custom information:
#* The record ''OrderedLocusNames'' was there with the species name under the ''Species'' column and our link URL under the ''Link'' column.
# I then committed the custom version of GenMAPP builder to our GitHub branch.

=== Milestone 4: Species Export Customization ===
#Trixie noticed that the microarray data has IDs that have CP#### and SF####.# not the typical SF####, which will need to accounted for.