=== Conclusions ===

−

Write a concluding paragraph that summarizes the overall project and your findings. How closely do your findings correspond to the original study? Are there significant differences? Did you discover anything new?

Write a concluding paragraph that summarizes the overall project and your findings.

* How closely do your findings correspond to the original study?

* Are there significant differences?

* Did you discover anything new?

* What future directions would you take if you were to continue this project?

=== Acknowledgments ===

* List your references in alphabetical order by first author using [https://peerj.com/about/author-instructions/#reference-format PeerJ’s recommended reference format]. This format is very similar to APA style and should feel familiar if you have written research papers before.

* To minimize busy work, the PeerJ website includes links to downloadable style files for [https://www.zotero.org/styles/?q=peerj Zotero] and [http://endnote.com/downloads/style/peerj EndNote], if you use either system for managing and rendering references.

== PowerPoint Presentation ==

Each team of students will prepare and give a 20 minute PowerPoint presentation to report the results of their project on Tuesday, December 18 at 2:00-4:00 PM.

* Please follow the [[Media:PresentationGuidelines.ppt | Presentation Guidelines]] for how to format your slides.

* You will need to prepare ~20 slides (assume 1 slide per minute of presentation) and include the following content:

# Background on your species and your species' genome from the genome paper presentation.

# The results of the Gene Database creation

#* Gene Database Schema figure

#* A table that summarizes how many OrderedLocusNames IDs were found

#** by XMLPipeDB match in the UniProt XML file

#** by TallyEngine in the UniProt XML file

#** by TallyEngine in the PostgreSQL database

#** in the OriginalRowCounts table in the gdb

#** in your external model organism database source

#* Give the command used in match to generate these results

#* Give the query used in PGAdmin III to generate these results

#* Include a screenshot of the TallyEngine results as a figure

#* Report on quantity and identity of gene IDs that did not make it into the database

#*# OrderedLocusNames IDs that were not in the XML source at all

#*# OrderedLocusNames IDs that were in the XML source but did not get imported into Postgres

#*# OrderedLocusNames IDs that were in Postgres but did not get exported to the GenMAPP Gene Database

#* Report on what changes were made to the GenMAPP Builder code in order to to accommodate the second and third type of missing gene IDs and the result of those changes

# Introduce the experiment performed in the microarray paper, including the experimental design flow chart

# Report results of the DNA microarray analysis

#* Include a table that shows the results of your "Sanity Check", i.e., how many genes were significantly increased and decreased at different p value cut-offs in the dataset?

#* Include the criteria you used for a significant increase and decrease in expression for your GenMAPP Expression Dataset

#* Table of filtered MAPPFinder results (from ''.xls'' or ''.xls'')

#** Show a list of 15-20 non-redundant GO terms.

#** Include in your table the GO ID, the name of the GO term, the number changed/number present and the percent (e.g., 10/20 (50%)), the number present/number in GO and the percent, the regular p value and adjusted p value.

#* GenMAPP MAPP of a pathway relevant to your results

* '''''Your PowerPoint slides must be uploaded to the wiki and linked to from your individual journal page and your team page by midnight, Tuesday, December 15.'''''

** You can update your slides before your presentation, but we will be grading the ones you upload by the deadline.

* Your presentation (both the slides and the oral presentation) will be evaluated by the instructors using the [[Presentation Rubric]].

* Your presentation will also be evaluated by your fellow classmates (anonymously) who will answer the following questions:

*# What is the speaker's take-home message (one short sentence)?

*# What are the best points about the presentation's organization, visuals, and delivery? Please give at least 2 specific examples.

*# What points need improvement? Please give at least 2 specific examples.

* We expect that you will take the feedback from your previous presentation into account when doing this presentation.

== Group Files and Datasets ==

* GenMAPP Gene Database for assigned species (''.gdb'')

−

* ReadMe file to accompany the Gene Database (''.pdf'')

* ReadMe file to accompany the Gene Database (''.pdf'')

** Sample ReadMe in Word format: [[Media:ReadMe_Vc-Std_External_20131122.zip | ReadMe_Vc-Std_External_20131122.zip]]

** [https://github.com/lmu-bioinformatics/xmlpipedb/blob/readme/GenMAPP%20Gene%20Databases/V.%20cholerae/V.%20cholerae%2020101022/ReadMe.md Sample ReadMe in markdown (a work in progress)]

** Include Gene Database Schema diagram in ReadMe

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