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 (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

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