The Plan
From LMU BioDB 2013
Contents |
Leishmania major
Timeline of due dates, helpful links, important updates, etc.
Timeline
- Preparation for Journal Club Individual Journal-- 11/12
- Journal Club Presentation-- 11/12
- 15 min ppt presentation on genome reference article
- Finish individual journal by 11/8
- Meet for work on ppt 11/8-11/10
- Practice and final touches on ppt, and upload to wiki 11/11
- Week 11
- Electronic Lab Notebook on updates on the final project
- Week 12 due 11/15
- Please link the lab notebooks here:
- Week 13 due 11/22
- GenMAPP users: Perform Statistical Analysis and get ready for Import in to GenMAPP 11/22
- QA: Get to know System IDs, Characterize regular expression patterns to detect the IDs 11/22
- Week 14
- GenMAPP users: Run GenMAPP and generate all of the relevant files begin analysis 11/28
- QA: customize the tally engine setup, add ordered locus IDs 11/28
- Week 15 due 12/6
- GenMAPP users: Analyze data 12/6
- QA: Document the relational database schema for the gene database and create the ReadMe with comparisons to MOD for Leishmania 12/6
- Leishmania major Week 15 Status Report
- Final Project Presentations 8-10 am on 12/12
- Project Deliverables due at 4:30 on 12/13
Important Updates
Template:Leishmania Major File Updates
Record names of the files as they are updated and edited with dates. Upload any other relevant files here, and document major progress.
- 11/5/2013
- Media:A-GEOD-6855.adf_A.txt Array Design File
- Media:E-GEOD-10407.idf_A.txt Investigation Description File
- Media:E-GEOD-10407.processed.1_A.zip Processed Data
- Media:E-GEOD-10407.raw.1_A.zip Raw Data
- Media:E-GEOD-10407.sdrf_A.txt Sample and Data Relationship File
- 11/7/2013
- Media:E-GEOD-10407.sdrf_B.txt Leishmania major Chips
- Completed Import/Export Cycle, conducted a Tally Count, opened .gdb file in Microsoft Access and compared original row counts.
- Access was missing 2 genes for GeneID and RefSeq, and we had no GO terms in the Tally or in Access.
- 11/11/2013
- 11/14/13
- Media:E-GEOD-10407.sdrf_C.txt Edited Sample and Data (Ordered based on species and relevant data)
- Media:L.majorCompiledRawData.txt L. major raw compiled data
- Media:L.infantumCompliedRawData(A).txt L. infantum raw compiled data
- 11/19/2013:
- Media:L.majorCompiledRawData_B.txt L. major raw compiled data with adjusted dye swap values
- Media:L.infantumCompliedRawData(B).txt L. infantum raw compiled data with adjusted dye swap values and sample names
- Media:L.majorCompiledRawData_C.txt L. major raw compiled data with adjusted dye swap values and sample names
- 11/21/2013
- 12/3/2013
- File:LeishmaniaCompiledStatAnalysis(A).txt
- File:LeishmaniaCompiledStatAnalysis(A).EX.txt
- Media:L.infantumStats_B.xls Fixed infantum p-value parenthesis
- Media:LeishmaniaCompiledStatAnalysis(B).txt
- Media:LeishmaniaCompiledStatAnalysisLMJFiltered.txt Original File That should work in GenMAPP once coding is fixed
- Media:LeishmaniaCompiledStatAnalysisLMJFiltered(B).txt Quick fix file with underscores to work in GenMAPP until coding is fixed
- Media:LeishmaniaCompiledStatAnalysisLMJFiltered(B).EX.txt
- Media:LeishmaniaCompiledStatAnalysisLMJFiltered(B).gex
- Media:ExceptionFileErrorID.txt
- Leishmania Major Group Project Report
- Media:Dist Leishmania Lena Gabe 05112013.zip
- 12/5/2013
- 12/7/2013
- 12/11/2013
- 12/12/13
- File:LeishmaniaCompiledStatAnalysis(C).txt The data from L. major only for analyzing statistics
Leishmania Major Helpful Links
- Leishmania Major Articles
- Template:Leishmania Major Navigation
- Template:Leishmania Major File Updates
- The Plan
Team Members:
- Viktoria (GenMAPP User, Project Manager)
- Gabriel (Coder)
- Lena (Quality Assurance)
- Kevin (GenMAPP User)
Status Reports:
Relevant Project Links:
