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CMO Cell-Free DNA Informatics (CCI)

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The Team

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The OnBoarding

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The Formal Stuff

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Requesting Time Off

To request time off, just fill in things at MSK TIME, and also please email your manager of the same.

You need to be on the MSK network to access these resources

CMO Cell-Free DNA Informatics (CCI) Wiki

This wiki will help you to get insights into CMO Cell-Free DNA Informatics Team (CCI) at MSKCC

Welcome aboard!

Welcome to CCI wiki! Here you'll find everything you need to know about CCI.

You can read more about the Center for Molecular Oncology (CMO) here:

Meet the Team!

Meet some fabulous people who make things happen

Ronak H Shah

👋 Lead Scientist — 💌 shahr2@mskcc.org — 🇺🇸 New York

Ronak H Shah

Bio

I am responsible for leading a team of Computational Biologists and Bioinformatics Software Engineers who develop, maintain, and operate bioinformatics pipelines and databases in the Center for Molecular Oncology. We also perform collaborative research with other labs and clinicians both within MSKCC and in the broader research community. On a daily basis, we analyze blood samples from patients with tissue-based cancers, using patients’ circulating tumor DNA extracted from blood, avoiding the need for tumor biopsies. More specifically, I lead the team in designing, developing, and implementing software tools for processing and analyzing high throughput, next-generation sequencing data, specifically for liquid biopsy applications (MSK-ACCESS & Clonal Hematopoiesis Panel). Previously in my time as MSK, I helped develop the workflow to analyze MSK-IMACT data for both clinical and research implementation, which is still being used. You can read more about my background here, also here is the link to my google scholar profile

Karthigayini Sivaprakasam

👋 Senior Computational Biologist — 💌 sivaprk@mskcc.org — 🇺🇸 Texas

Bio

Good to know: Encourage employees to write a succinct bio that can help new hires learn about them and how they like to work.

Carmelina Charalambous

👋 Computational Biologist — 💌 charalk@mskcc.org — 🇺🇸 New York

Bio

I am a Computational Biologist as part of the Center of Molecular Oncology Informatics cfDNA group. I am responsible for the development of new and existing tools, maintaining the cfDNA pipeline, and processing samples for both clinical and research work. Previously, I have worked at the NHS trust Cambridge University Hospitals as a Bioinformatician with primary responsibility for the development of the Hemato-Oncology clinical assay. You can read more about my educational background, work experience, and research interests here and you can access my Linkedin profile.

Eric Buehler

👋 Bioinformatics Engineer II — 💌 buehlere@mskcc.org — 🇺🇸 New York

Bio

Good to know: Encourage employees to write a succinct bio that can help new hires learn about them and how they like to work.

Alyssa Vann

👋 Bioinformatics Engineer IV — 💌 vanna1@mskcc.org — 🇺🇸 New York

Bio

Good to know: Encourage employees to write a succinct bio that can help new hires learn about them and how they like to work.

Applications

Applications/Tools the CCI is responsible for at MSKCC in CMO

Application
Location
Description

ACCESS-Pipeline

This has workflows for BAM generation based on , , small variant calling, micro-satellite instabilty calling, copy number variant calling & structural variant calling for Version 1 of MSK-ACCESS assay

ACCESS_SV

This has the core workflow used for structural variant calling in MSK-ACCESS assay

ADMIE

This is the algorithm used for calling MSI status for sample associated with MSK-ACCESS assay

Nucleo

This is the BAM generation workflow for any assay that deals with Unique Molecular Indexs (UMIs) based on

ACCESS Quality Cotrol (For version 1 of the Assay)

This is the version 2 of the ACCESS QC generation and you can read more about it here

ACCESS data analysis

This repos helps with downstream data analysis of MSK-ACCESS data, you can read more about it here:

Biometrics

Python package to calculate various sample contamination metrics.

sequence_qc

Package for doing various ad-hoc quality control steps from MSK-ACCESS generated FASTQ or BAM files

General

What to do first?

CMO onboarding

The first thing to do once you have joined is to visit https://mskcc.github.io/on-boarding/ and finish of task necessary for compliance & initiate the process of getting access to various systems.

Cluster Guide

To learn more about the cluster and its resources visit the MIRO board

CCI specific onboarding

Guides on Confluence

You need to be on the internal network to access msk-confluence, you can request access to it on The Spot

Computational Biologist

Please visit this page once you have done things necessary here: https://mskcc.github.io/on-boarding/

  • The best place to start is to learn more about MSK-ACCESS and for that please read the paper:

    • Brannon, A. R. et al. Enhanced specificity of clinical high-sensitivity tumor mutation profiling in cell- free DNA via paired normal sequencing using MSK-ACCESS. Nat Commun 12, 3770 (2021).

  • Learn more about the current collapsing method Marianas

  • Learn more about the new collapsing (Nucleo) method using Fgbio

  • Learn more about the Quality Control V1

  • Understand the updated version for the above using these Quality Control V2

  • Learn about ACCESS Data analysis scripts that help with downstream analysis

  • Learn about IGV for viewing BAM files to distinguish real variants from artifacts

Below are resources that would be handy for you to learn more about all the tools described in the paper.

Project Management

Assay/Team
Link to the tool

MSK-ACCESS

CMO-CH

CMO Cell-Free Informatics (CCI)

- Request access once you have your msk email id

Functional Resources

Assay/Purpose/Team/Tool
URL

MSK-ACCESS V1 (Marianas)

CCI organization on Github

cBioPortal DMP data

InternalLink:

Quality Control for ACCESS V1

Downstream analysis of ACCESS Data

Fingerpriting using Biometrics

High Performance Computing

Nucleo (Fgbio)

Quality Control for ACCESS V2

Path's to know

CMO-ACCESS

Data on JUNO for CMO-ACCESS samples

Analysis Type
JUNO Location

BAM

/juno/work/access/production/data/bams/{cmo_patient_id}/{cmo_sample_id}/current/

Small Variant (SNV’s/INDEL’s)

/juno/work/access/production/data/small_variants/{cmo_patient_id}/{cmo_sample_id}/current/

Microsatellite Instability(MSI)

/juno/work/access/production/data/microsatellite_instability/{cmo_patient_id}/{cmo_sample_id}/current/

Structural Variant (SV)

/juno/work/access/production/data/structural_variants/{cmo_patient_id}/{cmo_sample_id}/current/

Copy Number Variants (CNV)

/juno/work/access/production/data/copy_number_variants/{cmo_patient_id}/{cmo_sample_id}/current/

Resources

Resource Type
JUNO Location

NYS validation data

/work/access/production/runs/NYS_validation/current

CMO-ACCESS

/work/access/production/

/work/access/production/resources/

CMO-CH

/work/ch/

Berger Lab

/work/bergerm1/bergerlab

Details of CMO ACCESS Resources

  • admie - Files used for microsatellite instability detection tool ADMIE for MSK-ACCESS

  • cosmic - VCF file of cosmic used in MSK-ACCESS workflows

  • dbSNP - VCF file of dbSNP used in MSK-ACCESS workflows

  • exac - VCF file of ExAC used in MSK-ACCESS workflows

  • mills-and-1000g - VCF file of mills-and-1000g used in MSK-ACCESS

  • reference - reference genome file used in MSK-ACCESS workflows

  • tools - general packages used in MSK-ACCESS workflows

  • msk-access - Data-specific resources for MSK-ACCESS workflows. This includes the following:

    • hiseq4000_curated_duplex_bams_dmp - curated DMP duplex BAMS from HiSeq 4000

    • novaseq_curated_simplex_bams_dmp - curated DMP simplex BAM from NovaSeq.

    • hiseq4000_curated_simplex_bams_dmp - curated DMP simplex BAM from HiSeq 4000

    • novaseq_curated_standard_bams_dmp - curated DMP standard BAM from NovaSeq

    • hiseq4000_curated_standard_bams_dmp - curated DMP standard BAM from HiSeq 4000

    • novaseq_curated_unfiltered_bams_dmp - curated DMP unfiltered BAM from NovaSeq

    • hiseq4000_curated_unfiltered_bams_dmp - curated DMP unfiltered BAM from HiSeq 4000

    • novaseq_unmatched_normal_plasma_duplex_bams_dmp - DMP unmatched normal plasma duplex BAM from NovaSeq

    • hiseq4000_unmatched_normal_plasma_duplex_bams_dmp - DMP unmatched normal plasma duplex BAM from HiSeq 4000

    • novaseq_unmatched_normal_plasma_standard_bams_dmp - DMP unmatched normal plasma standard BAM from NovaSeq

    • hiseq4000_unmatched_normal_plasma_standard_bams_dmp - DMP unmatched normal plasma standard BAM from HiSeq 4000

    • novaseq_curated_duplex_bams_dmp - curated DMP duplex BAMS from NovaSeq

    • regions_of_interest - Different interval files describing regions of interest for MSK-ACCESS assay

If we can justify adding data/tools to the above-mentioned location please contact Ronak Shah.

Mission and Values

Our Mission

The CMO Cell-Free DNA Informatics (CCI) group’s mission is to develop and apply computational methods to organize, analyze and understand genomic data generated from cfDNA assays such as MSK-ACCESS. The group is responsible for all computational infrastructure needed to deploy, run, and deliver results for research cfDNA assays in a production setting for CMO.

CCI's Mission

Our Values

Be Compassionate

We treat everyone we encounter with compassion, seeing the humanity behind their problems and experiences.

Be Mindful

We do not take advantage of our users' attention and adopt mindful working practices so that we can create safe spaces both in our working environment and in our products themselves.

Research First

We challenge our own and others' assumptions through qualitative and quantitative research. Not sure about an idea? Test it.

CMO-CH V1

This wiki explains the CMO-CH V1 assay

What is CMO-CH assay?

CMO-CH is offered by the Center for Molecular Oncology (CMO) to MSK researchers for profiling white blood cell DNA to detect mutations in the most commonly altered (CH) associated genes.

What is the panel design?

  • 596 targets capturing 58% of CH and 90.4% of CH-PD mutations identified in the latest CH dataset from 40K patients

  • Total size = 1,143 probes (0.14 Mb)

  • Full gene coverage for TP53, TET2, ASXL1, DNMT3A, PPM1D, CHEK2, ASXL1, ATM, SF3B1, SRSF2, U2AF1, and U2AF2•Additional targets with hotspot positions from IMPACT heme assay

  • SNP tiling around TP53, CBL, MPL, JAK2, EZH2, TET2, RUNX1, and ATM (+/-10kb) to identify allelic-imbalances

  • 40 fingerprint SNPs that are shared with all other NGS assays (IMPACT, ACCESS, WES etc.) to detect sample mismatches

Glossary

Terms you might encounter

-> information associated with a sample. This is a current work-in-progress written in Java/Neo4J that is supposed to be the one source of truth for metadata associated with samples. Currently, these responsibilities are managed by Beagle.

LIMS -> Laboratory information management system -- when sequencing is complete, metadata and file information on the sequences is first input into this system.

-> triggers and monitors workflows. There's also a part of it that tracks files and metadata associated with those files which may be splintered out in the future. A request typically comes from LIMS which begins the workflow process.

-> a nicer interface for Beagle (sample workflow tracking) and soon the MDB (make updates to metadata)

-> An HTTP API for Toil which Beagle is reliant on for interacting with workflows.

-> A workflow engine that interfaces well with LSF.

Voyager -> The suite of applications built by the Voyager team, including Ridgeback, Beagle, and Hermes.

-> Distributed high-performance computing that's managed in-house. Most data processing and files are housed here.

-> IBM's Platform Computing (Load Sharing Facility) tool for scheduling workflows on HPC. It has a specific to managing workloads.

-> a YAML-like language for defining workflows.

-> Reactive workflow framework and a programming that eases the writing of data-intensive computational pipelines.

-> Sequencing of the Deoxyribonucleic acid ()

-> Sequencing of the Ribonucleic acid ()

-> Cell-Free DNA assay for patients with solid tumors

CMO-CH -> Assay for profiling clonal hematopoiesis mutations from blood

-> Assay for profiling patients tissue DNA for solid tumors

-> Assay for profiling patients blood DNA for Heme malignancies

-> Allele-specific copy number and clonal heterogeneity analysis tool for high-throughput DNA sequencing

-> Whole Exome Sequencing

-> Whole Genome Sequencing

-> Whole Transcriptome Sequencing

-> one of the companies that provides sequencing machine

-> Type of sequencer from Illumina

-> Type of sequencer from Illumina

-> Type of sequencer from Illumina

-> Type of sequencer from Illumina

-> a company that sells instruments for long-read sequencing based on

-> a company that sells instruments for long-read sequencing based on technology

Flagship Projects

(Research)

Developed by scientists in the CMO Technology Innovation Lab and Department of Pathology, this high-sensitivity assay is offered by the CMO to MSK researchers for profiling circulating tumor DNA derived from blood plasma. The inclusion of matched buffy coat DNA enables the identification and elimination of germline variants and mutations associated with clonal hematopoiesis, a significant confounder of most commercial assays. The assay is available for clinical use in the Molecular Diagnostics Service and for research projects in the Integrated Genomics Operations (IGO). CCI supports the data processing and analysis of research projects utilizing MSK-ACCESS in IGO and leads the ongoing development of the MSK-ACCESS pipeline for all applications. The current version of the pipeline is available here: , and more details about the assay and analysis are described in this paper below as well as :

CMO-CH

Developed by scientists in the CMO Technology Innovation Lab in collaboration with CCI and Clonal Hematopoiesis (CH) program, Diagnostic Molecular Pathology, Precision Interception, and Prevention Initiative & CCI, this assay utilizes the same barcoding and ultra-deep sequencing technology as MSK-ACCESS to detect CH mutations in white blood cells at high sensitivity. CMO-CH is offered by the CMO to MSK researchers for profiling white blood cell DNA to detect mutations in the most commonly altered CH-associated genes. The assay is run in IGO, and CCI supports the data processing and analysis. You can learn more about it

For both projects, additional analysis packages and development versions of the workflows can be found here:

MSK-ACCESS V1

Things to know for MSK-ACCESS V1 for Research

What is MSK-ACCESS?

It is a hybrid capture panel designed for Analysis of Circulating to Evaluate Somatic Status using the Unique Molecular Index (UMIs) for high sensitivity. MSK-ACCESS is 13% as large, captures 47% of all mutations detected by MSK-IMPACT.

What is the panel design?

Selected exons of 129 genes for mutation detection

  • Level 1-4

  • High rates of mutations

SNPs of & of 12 genes

Common for

Introns for of 10 genes

genes

What are the Design Implications?

  • Matched cfDNA-WBC (”tumor-normal”) assay to detect somatic alterations

  • Sensitivity for mutation calling depends on ‘duplex’ collapsed coverage

  • Different sensitivities for different classes of alterations

    • Genotyping +++++

    • De novo mutations, indels ++++

    • MSI +++

    • Rearrangements +++

    • Copy number ++

    • Tumor mutation burden ○

+ -> sensitivity for that event type

○ -> cannot be calculated

Workflows V1

Workflows associated with version 1 of the Assay

BAM Generation & Quality Control

Github Location ->

Tools Used:

Variant Calling

Small Variants

Github Location ->

Tools Used:

Copy Number Variant (CNV)

Github Location ->

Refer to Bioinformatics Pipeline to Detect CNA's section in this paper for details:

Structural Variant (SV)

Github Location ->

Tool Used:

Microsatellite Instability Status (MSI)

Github Location ->

Tool Used:

Configurations

Voyager has all our configurations in the jinja template, it includes all the paths for various files and tools associated with the workflows, all location are on JUNO:

snps_indels:

CNV:

Fastq_to_bam:

MSI:

SV :

clonal hematopoiesis
SMILE
Beagle
Hermes
Ridgeback
Toil
HPC
LSF
suite of commands
Common workflow language
Nextflow
DSL
DNA-SEQ
DNA
RNA-SEQ
RNA
MSK-ACCESS
MSK-IMPACT
MSK-IMPACT Heme
Facets
WES
WGS
WTS
Illumina
Novaseq
Nextseq
Miseq
Hiseq
PacBio
zero-mode waveguide
Oxford Nanopore
Nanopore

Analysis

This is a wiki for analysis of MSK-ACCESS data

This pages

https://github.com/mskcc/ACCESS-Pipeline
https://github.com/mskcc/ACCESS_SV
https://github.com/mskcc/ADMIE
https://github.com/msk-access/nucleo
Fgbio
https://github.com/msk-access/access_qc_generation
https://github.com/msk-access/access_data_analysis
https://github.com/msk-access/biometrics
https://github.com/msk-access/sequence_qc
Link to AirTable
Link to AirTable
https://clickup.com/
https://github.com/mskcc/ACCESS-Pipeline
https://github.com/msk-access
https://github.mskcc.org/knowledgesystems/dmp-2022
https://cmo-ci.gitbook.io/cmo-access-data-analysis/
https://cmo-ci.gitbook.io/biometrics/
https://mskcchpc.org/
https://github.com/msk-access/nucleo
https://cmo-ci.gitbook.io/access-quality-control-v2/
CMO-ACCESS Resources
MSK-ACCESS
mskcc/ACCESS-Pipeline: cfDNA Sequencing Pipeline with UMI (github.com)
here
Brannon, A. R. et al. Enhanced specificity of clinical high-sensitivity tumor mutation profiling in cell- free DNA via paired normal sequencing using MSK-ACCESS. Nat Commun 12, 3770 (2021).
here
CMO Cell-Free DNA (cfDNA) Informatics Team (github.com)
MSK-ACCESS Version 1 assay overview
cfDNA
Brannon, A. R. et al. Enhanced specificity of clinical high-sensitivity tumor mutation profiling in cell- free DNA via paired normal sequencing using MSK-ACCESS. Nat Commun 12, 3770 (2021).
OncoKB
Hotspot sites
Protein kinase domains
Tumor suppressor genes
Microsatellite regions
zygosity
copy number
SNPs
genome-wide copy number
structural variants
Clonal hematopoiesis
Duplex UMIs for Error Correction
https://github.com/mskcc/ACCESS-Pipeline/blob/master/workflows/ACCESS_pipeline.cwl
BWA
Trimgalore
GATK
Picard Tools
ABRA2
Marianas
https://github.com/mskcc/ACCESS-Pipeline/blob/master/workflows/subworkflows/snps_and_indels.cwl
VardictJava
MuTect
VCF2MAF
https://github.com/mskcc/ACCESS-Pipeline/blob/master/workflows/subworkflows/call_cnv.cwl
Dara S. Ross, Ahmet Zehir, Donavan T. Cheng, Ryma Benayed, Khedoudja Nafa, Jaclyn F. Hechtman, Yelena Y. Janjigian, Britta Weigelt, Pedram Razavi, David M. Hyman, José Baselga, Michael F. Berger, Marc Ladanyi, Maria E. Arcila, Next-Generation Assessment of Human Epidermal Growth Factor Receptor 2 (ERBB2) Amplification Status: Clinical Validation in the Context of a Hybrid Capture-Based, Comprehensive Solid Tumor Genomic Profiling Assay, The Journal of Molecular Diagnostics, Volume 19, Issue 2, 2017, Pages 244-254, ISSN 1525-1578, https://doi.org/10.1016/j.jmoldx.2016.09.010.
https://github.com/mskcc/ACCESS-Pipeline/blob/master/workflows/subworkflows/manta.cwl
Manta
iAnnotateSV
https://github.com/mskcc/ACCESS-Pipeline/blob/master/workflows/subworkflows/msi.cwl
ADMIE
beagle/input_template.json.jinja2 at master · mskcc/beagle (github.com)
beagle/input_template.json.jinja2 at master · mskcc/beagle (github.com)
beagle/input_template.json.jinja2 at master · mskcc/beagle (github.com)
beagle/input_template.json.jinja2 at master · mskcc/beagle (github.com)
beagle/input_template.json.jinja2 at master · mskcc/beagle (github.com)
Overview of the BAM Generation and Quality Control workflow
BAM files used for the workflows

Software Engineers

Please visit this page once you have done things necessary here: https://mskcc.github.io/on-boarding/

  • The best place to start would be to understand the data flow:

    • LIMS/SMILE -> Voyager -> JUNO

  • Learn more about the codebases listed below that form Voyager

  • Learn about the codebases the form mPATH

Sites

Code/Project Management

Resource
URL

ACCESS/Voyager team uses this to manage sprints/stories. In addition, ACCESS uses this to keep track of the statuses of samples.

Auto Track Sample Status

Internal Gitlab where MPath and other software is hosted.

(forked from mpath repositories)

Code specific to ACCESS team pipelines.

Code for other CMO/MSK teams

Information on HPC/LSF

Beagle

Hermes

Ridgeback

Applications

Application
URL

LIMS

For Authentication ask your Manager:

Beagle API

  • http://silo:4001 (Staging)

  • http://voyager:5001 (Production)

Ridgeback API

  • http://silo:4003 (Staging)

  • http://voyager:5003 (Production)

Flower (Celery Task UI) for Voyager, for Production only

http://voyager:4001

ELK for Voyager

MPath (for Clinical)

MPath (for Research)

http://access01:7331/api/ui/

CVR (to be replaced by MPath)

cvr.mskcc.org:8083/

People

Projects, who to speak with, slack channel

  • MPath & CVR (Aijazuddin Syed/Anoop Balakrishnan Rema)

  • Voyager Projects [Beagle/Seqosystem/Ridgeback] (Sinisa Ivkovic/Nikhil Kumar/Allan Bolipata)

    • #voyager

  • LIMS (David Mcmanamon)

  • MDB (Angelica Ochoa/Benjamin Gross/Allan Bolipata)

    • #metadb-informatics

  • Toil/CWL (Nikhil Kumar)

  • ACCESS (Ronak Shah)

    • #msk-access

  • ACCESS Servers (HPC Request/Neeraj Paramasivam)

Collaborations

This will help you to find correct people to connect with from the subgroups.

In all the groups there are multiple amazing individuals involved, but listing just a few

Confluence knowledgebase across collabrators

CMO Project Managers

CCI works closely with CMO project managers to track the progress of cfDNA projects submitted to CMO by MSK researchers. CMO project managers support CCI by facilitating and coordinating project initiation, sample collection, and metadata collection.

People to connect

  • Kirsten Fuller

  • Casey Savin

  • Jennifer Milbank

Integrated Genomics Operations (IGO)

CCI works with to make sure that the data generated for the cfDNA assays is of the highest standards.

People to connect

  • Neeman Mohibullah

  • Ruchi Patel

  • Marisa Dunigan

  • David Mcmanamon

CMO Informatics (CI)

CCI works closely with CMO Software Engineering (CSE) team within CI to support the development of Voyager & Hermes. The CSE/CAS team supports the development, integration, processing of CCI’s workflows implemented in Voyager.

People to connect

CMO Software Engineers (CSE)

  • Christopher Allan Bolipata

  • Sinisa Ivkovic

  • Nikhil Kumar

CMO Analysis Systems (CAS)

  • Timothy Song

  • Stephen Kelly

  • Suleman Vural

Berger Lab/Technology Innovation Lab/CMO Computational Science (CCS)

CCI collaborates with scientists in various CMO groups to improve the existing workflows and to analyze the data in a consistent manner.

People to connect

Berger Lab

  • Kanika Arora

  • Shalabh Suman

  • Chaitanya Bandlamundi

Technology Innovation Lab

  • Brian Loomis

  • David Brown

CMO Computational Sciences (CCS)

  • Mark Donoghue

  • Yixiao Gong

Clinical Bioinformatics (ClinBx)

CCI works closely with the ClinBx group in the Molecular Diagnostics Service to deploy core workflows and maintain consistency among analyses performed on research and clinical cfDNA samples. We work together to improve the workflows in sync and to learn from one another about how to identify artifacts and interpret the data. CCI is also working with the ClinBx Software group to port an instance of the mPATH system used by the ClinBx team to sign-out cases for research.

People to know

Rose Brannon

Aijazuddin Syed

Ryan Ptashkin

Anoop Balakrishnan

High Performance Computing (HPC)

CCI works with HPC to request resources and support w.r.t JUNO cluster and virtual machines that enable various aspects of our goals.

Neeraj Girija

Lohit Valleru

Slack Channel

hpc-request@cbio.mskcc.org

clickup.com
jira.mskcc.org:8090
http://crux.mskcc.org:8929/mpath
http://crux.mskcc.org:8929/access
github.com/mskcc-access
github.com/mskcc
https://mskcchpc.org/
https://github.com/mskcc/beagle
https://github.com/mskcc/hermes
https://github.com/mskcc/ridgeback
https://igolims.mskcc.org:8443/LimsRest/swagger-ui.html
bic-dockerapp01.mskcc.org:5601/
https://mpath.mskcc.org/

Filing Expenses

To get reimbursed for your expenses, just fill in the expense report online.

You need to be on the MSK network to access these resources

Marie-Josée and Henry R. Kravis Center for Molecular OncologyMemorial Sloan Kettering Cancer Center
External CMO Website
Marianas
https://mskconfluence.mskcc.org/x/9zZ2Bmskconfluence.mskcc.org
Link to CCI Knowledgebase for internal process
MSK-ACCESS QC generation V2
Access Quality Control (v1)
Quality control generation
https://cmo.mskcc.orgcmo.mskcc.org
Internal CMO Website
Logo
space
Biometrics
https://mskconfluence.mskcc.org/x/vzV2Bmskconfluence.mskcc.org
Link to Knowledgebase for information across groups
sequence_qc