Page Comparison

Oct 29, 2018:

1. Just a reminder that PDC has issued an alpha of it's MVP release.  Would be nice to have more Broadies take a look.  Presently supports only CPTAC2 data.

2. iCoMut:
   1. undergoing update for UCEC AWG
      1. FYI:  HG38 mutation calls underway by WashU (slated for 11/8 V2 freeze)
   2. waiting for Broad example data to add new proteomics tracks
3. HG38:  progress, GDCtools config file needed
   1. CN data:  

      /xchip/gdac_data/cptac3/genomic_data_mirror/CPTAC3_WashU_hg38/UCEC/WXS_CNV_hg38_v1.0_20180809

   2. But what is more biologically important:  WGS for CN or HG38?

      1. Because at present only VCFs available for WGS CN data

      2. Feedback:  Mani says WES is fine for Broad PG pipeline

      3. Karl needs WGS for some of his investigatory work (non-canonical ORFs, from HLA), but that's not ready for prime time sharing with other PGDACs yet, so it doesn't impact our G-CDAP

4. LUAD: new proteomic data "in progress," but in "new location" @ DCC:
   1. per this email exchange

   2. Changed from/to:

   1. 8_CPTAC3_Lung_Adeno_Carcinoma/LUAD_mzML/

   2. 8_CPTAC3_Lung_Adeno_Carcinoma/A_CPTAC3_hg38_CDAP/LUAD_mzML/

   3. Per Nathan: "The files under A_CPTAC3_hg38_CDAP represent the re-run of the CDAP
      analysis for files analyzed before the release of Broad's new
      RefSeq/hg38 protein sequence database and any new ones going forward."

...

1. Recap of last week's F2F: 

   1. Good FireCloud workshop attendance & feedback

   2. Proteomic:

   3. Genomic: 

      1. GDC has made progress automating their pipelines

      2. CPTAC genomic data will be HG38 going forward; 

   4. Phased delivery CCRC & UCEC first, to allow publications to be in pipeline by next funding cycle (Gantt chart)

2. Two special journals in Fall 2018:
   1. Special issue Mol. Cell Proteomics:tools, algorithms & computational methods
      1. Submission deadline will be in November, 2018
         
   2. Journal of Proteome Research: Software Tools and Resources
      
      1. Submission deadline September 14, 2018
3. FOA: Sustained Support for Informatics Resources for Cancer Research and Management (U24)
   
   1. Due June 14
   2. Submit LOI by May 14
   3. Letters of support: gathering now
4. Time Permitting:  genomic pathway analyses
   1. GDAN Lung pathifier analyses
   2. iCluster: Hailei

...