Difference between revisions of "The Plan"
From LMU BioDB 2013
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*Electronic Lab Notebook on updates on the final project | *Electronic Lab Notebook on updates on the final project | ||
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*:[[Week 12]] due 11/15 | *:[[Week 12]] due 11/15 | ||
| + | *:Please link the lab notebooks here: | ||
| + | *::[[Gleis Week 12]] | ||
| + | *::[[Lena Project Notebook]] | ||
| + | *::[[Vkuehn Week 12]] | ||
| + | *::[[Leishmania major Week 12 Status Report]] | ||
*[[Week 13]] due 11/22 | *[[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 | *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 | *[[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 | *'''Final Project Presentations''' 8-10 am on 12/12 | ||
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==='''Important Updates'''=== | ==='''Important Updates'''=== | ||
[[Template:Leishmania Major File Updates]] | [[Template:Leishmania Major File Updates]] | ||
| + | |||
Record names of the files as they are updated and edited with dates. | Record names of the files as they are updated and edited with dates. | ||
Upload any other relevant files here, and document major progress. | Upload any other relevant files here, and document major progress. | ||
Latest revision as of 18:57, 5 December 2013
Contents |
[edit] Leishmania major
Timeline of due dates, helpful links, important updates, etc.
[edit] 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
[edit] 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
[edit] 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:
