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

2015-12-18T18:26:47Z

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

Jwoodlee: /* Individual Reflection */

2015-12-18T18:25:45Z

‎Individual Reflection

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   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]]) ==
+== Individual Reflection(Found [[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}}

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   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 ==
+== Individual Reflection(Also on its own individual page [[Jwoodlee Individual Reflection | here]]) ==
 ===Statement of Work===
 *Describe exactly what you did on the project.

Jwoodlee Week 15 - Revision history

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

Jwoodlee: /* Individual Reflection */