Difference between revisions of "Gene Database Project"

Latest revision as of 22:13, 18 December 2015

Deliverables

• You will give a final group PowerPoint presentation in class during the final exam period on Tuesday, December 15, 2:00pm.
• Final due date for all other deliverables is no later than Friday, December 18, 4:30pm (according to official final exam schedule for fall, 2015).
• The deliverables should be uploaded and organized onto one group wiki page, or alternately, delivered on digital media to either Dr. Dahlquist or Dr. Dionisio.
• Each member of the group will be assigned the same grade for the group project.
• Detailed specifications, particularly for the group report and individual assessment and reflection, are given on the Gene Database Project Deliverables page.

Group Deliverables

• GenMAPP Gene Database for assigned species (.gdb)
• ReadMe file to accompany the Gene Database (.pdf)
  • Sample ReadMe in Word format: ReadMe_Vc-Std_External_20131122.zip
  • Sample ReadMe in markdown (a work in progress)
  • Include Gene Database Schema diagram in ReadMe
    • Sample schema in Adobe Illustrator format: GenMAPP_schema_generic_bacteria_20151210.zip
    • Sample schema in jpeg format: GenMAPP_schema_generic_bacteria_20151210.jpg
• Gene Database Testing Report for final submitted Gene Database (print from wiki to .pdf file)
• Processed and analyzed DNA microarray dataset (.xls or .xlsx)
• Data file used for import into GenMAPP (.txt or .csv)
• GenMAPP Expression Dataset file (.gex)
• Exceptions file of data imported into GenMAPP (.EX.txt)
• Raw MAPPFinder results files (-GO.txt)
• .gmf file
• Filtered MAPPFinder Results (.xls or .xlsx)
• Sample MAPP file of a relevant biological pathway for your species (.mapp)
• Group Report describing the creation of the Gene Database and the biological analysis of the data (.doc, .docx, or .pdf)
• PowerPoint presentation (.ppt, .pptx, or .pdf, given on Tuesday, December 15)

Individual Deliverable

The individual deliverable is an assessment and reflection on the process (either wiki or email, depending on your preference; see note in the linked section):

• Statement of work
• Assessment of the work done
• What was learned

Team Journal Entries

• Each team will write a combined journal entry for each week with contributions from all members.
• Week 10 Creation of page and combined annotated bibliography (midnight 11/10)
• Week 11 (midnight 11/17)
• Week 12 (midnight 11/24)
• Week 14 (midnight 12/8)
• Week 15 (midnight 12/15)

Groups

The project groups are:

1. Team 1 - Heavy Metal HaterZ Shewanella oneidensis
   • Coder: Mary Alverson
   • Quality Assurance: Josh Kuroda
   • GenMAPP Users: Ron Legaspi & Emily Simso
   • Project Manager: Ron Legaspi
2. Team 2 - Class Whoopers Bordetella pertussis (Whooping Cough)
   • Coder: Nicole Anguiano
   • Quality Assurance: Brandon Klein
   • GenMAPP Users: Lena Olufson & Mahrad Saeedi
   • Project Manager: Nicole Anguiano
3. Team 3 - GÉNialOMICS - Burkholderia cenocepacia
   • Coder: Anu Varshneya
   • Quality Assurance: Brandon Litvak
   • GenMAPP Users: Veronica Pacheco & Kevin Wyllie
   • Project Manager: Anu Varshneya
4. Team 4 - Oregon Trail Survivors Shigella flexneri
   • Coder: Jake Woodlee
   • Quality Assurance: Trixie Roque
   • GenMAPP Users: Erich Yanoschik & Kristin Zebrowski
   • Project Manager: Kristin Zebrowski

Roles (Guilds)

As the project moves forward, we will use class time for team meetings. In addition, we will also have guild meetings where students sharing the same role can work together on common issues. Each student has been assigned a primary role in the project by the instructors (see above).

Project Manager (PM)

The project manager makes sure that individuals are fulfilling their roles and performing the tasks on time.

GenMAPP User (GU)

The GenMAPP user runs GenMAPP with the microarray dataset (Expression Dataset Manager, MAPPFinder, GenMAPP MAPP). His or her tasks generally correspond to the work done during the DNA microarray analysis exercise (part 1, part 2), as applicable to the team’s chosen bacterium.

Quality Assurance (QA)

The Quality Assurance team member is the resident expert on species ID systems and formats. He or she should be proficient with XMLPipeDB Match, SQL queries in PostgreSQL, Microsoft Excel, and Microsoft Access to navigate through the data and find missing IDs, discrepancies, sanity checks, etc.

Coder (C)

The coder is the resident expert on the technology being used—assorted software, file management, version control, some troubleshooting, some programming. He or she coordinates with Drs. Dahlquist and Dionisio in extending GenMAPP Builder code and making new versions. GenMAPP Builder is written in Java and is built on open source pure-Java libraries. Source code is hosted on GitHub and built using Apache’s ant utility.

Project Milestones

Specific project milestones are found on the individual guild pages.

Overall Flow

A successful project will have the following steps from end to end. Depending on the data and/or other issues that are encountered, one or more of these steps may go through iterations, repetitions, or refinements.

Overall Flow

1. Following the steps shown in the Running GenMAPP Builder instructions, download the UniProt XML proteome set and GOA (GO association) files for your species.
   • Make sure that you are choosing the correct strain/subspecies as the microarray data you have.
   • Note the date of download and the version of the file on your Gene Database Testing Report.
2. Download GO terms from Gene Ontology.
   • You will need the OBO-XML format, the "obo-xml.gz" file.
   • Note the date of download and the version of the file on your Gene Database Testing Report.
3. Create the GenMAPP Builder tables in PostgreSQL.
4. Load files into PostgreSQL database via GenMAPP Builder.
5. Export into a GenMAPP Gene Database.
6. Inspect/vet/validate Gene Database.
   • Create a Gene Database Testing Report each time a new export is run.
   • Compare to the model organism database for your species
7. Find an original journal article describing a DNA microarray experiment performed on your species.
   • Download the microarray data for this article.
   • Consult with Dr. Dahlquist about the proper steps to take to process the data (normalization, statistical analysis) and perform the analysis.
8. Run GenMAPP using the Gene Database.
   • Microarray data (import using Expression Dataset Manager)
   • MAPPFinder
   • Place genes on MAPP and draw pathway

Guild Milestones

These are links to the respective milestone lists in the guild pages:

• Project Manager
• GenMAPP User
• Quality Assurance
• Coder