Mazumder - QC paper draft

[steph-sing]

QC Paper Items

Materials and Methods sections draft due: Friday Aug 11th COB. Please note that I am still editing my sections, and will also add to or edit every section after you've had a chance to draft.

Link: QC Paper
Draft

• All citations should be in this format: [PMID: xxxxxxx; xxxxxxx]
• Please add to the draft in suggestion mode or as comments. The entire document is open to your review and input. If you have figure ideas please let me know.
• Sections have been assigned with a lead/assist. It's up to the lead and assist to work out the level of contribution (which can vary throughout the paper), but generally the lead has the right to the first pass. If you are close to a deadline and the lead has not get generated content, the assist should discuss with the lead and step in as needed. Please be communicative and respectful of everyone's time given the tight timeline. Each person has an opportunity to lead a section. If you do not agree with your section please discuss with me asap.

MATERIALS AND METHODS
Data Selection
Current FDA BioProject Data
NCBI-derived datasets: ngs, assembly, biosample [Hadley]
Supplementary Data Table 1-3: ngsQC_NCBI, assemblyQC_NCBI, biosampleMeta_NCBI

External Data
5 selected Orgs at the start of the project [Steph/Emily]
Viruses, Fungi [Sergei/Stephen, Jingyue/Joe/Steph]
Bacteria [Keith/Crandall Group, Emily ]
Refer to data selection protocols
Protocols as Supplementary material? [Raja please confirm?]
Quality Control Protocols and Pipelines
HIVE QC
ngsQC [Joe/Jingyue]
assemblyQC [Emily/Jingyue]
siteQC [Joe/Emily]
BiosampleMeta [Dan/Hadley]

Galaxy QC [Stephen]
Galaxy should be framed as an orthogonal method to assess critical quality control attributes (CQAs) + providing optional workflows for publicly available tools
Observable figure related to QC? [Raja please confirm?]

BioCompute Objects [Jonathon, Hadley, Steph]
Description, use, structure and function + tie into the DB

Data Dictionary
Curation and Maintenance [Steph/Hadley]
Terms and description of Dictionary, requirements

Error Testing Protocols [Hadley/Steph]
Supplementary Table 4: Current data dictionary + links to GitHub
Data.ArgosDB
Data Model [Robel/Raja/Pat/Jonathon]
Figure 1: Data Model (Steph to update)

Description of Database [Jingyue/Steph]
SupplementaryTables 5-8: Core QC datasets

[rykahsay]

https://docs.google.com/document/d/1AC3BDI4f34h8LHBPxQHvmR6EdSSP4BQ_CcPwXM0lEMs/edit

[steph-sing]

Week of 9/4 Items:

• Reviewing other Bioinformatics QC tools; cross check more info from 1stiteration of the project and adding info to the introduction (roughly 1 more page of material)
• Review methods and materials section and collaborators input: leave comments/additional writing assignments + add own material
• Finish drafting figures and get approval
  If more time this week:
• draft use case for results and discussion section

Nearly submission ready before FDA works on paper. Add their names in all Caps as needed. Raja needs two days to review, be available between 7-12pm on the appropriate review day.

• Send to Raja by 9/12 COB to review

[cwoodside1278]

As of Monday Nov 20, it is still in progress. Update needs to be provided by Stephanie

[cwoodside1278]

As of Jan 16 it is in Raja's hands and he would like to cut down on some more information before sending it out again.