Campaign: Analysis Priorities

Construct background mutation rate

Construct background mutation rate (noise) based on the correlation of mutation frequency and expression levels or replication time. It has been shown that longer replication time and lower expression levels imply higher mutation rates among the genome (http://www.nature.com/nature/journal/v499/n7457/full/nature12213.html). Transcription-coupled DNA repair results in high expression levels and low mutation rate. So I ...more »

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Campaign: Analysis Priorities

Education and usability

Provide a series of online short videos and short courses that will help users adopt the new tools and instructors to incorporate into courses. (Maybe this is obvious, but high-quality tutorials and case studies take significant time to develop.)

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Campaign: Analysis Priorities

Provide GPU computational resources

GPU technologies are rapidly becoming useful for speeding up some workflows by orders of magnitude. It would be useful to have some GPU resources available for cloud computing.

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Campaign: Analysis Priorities

Deployment of databases and web applications

Please provide a process for the deployment of databases and web applications such as MSKCC cBio, or ISB's Regulome Explorer or GeneSpot.

 

(You could use Github as a platform for accepting contributions.)

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Campaign: Analysis Priorities

CANCER whole genomes codon populations analysis

In this main open access article

http://fr.scribd.com/doc/169323556/7401586of18september2013

published in october 2013 by APPLIED MATHEMATICS (BIOMATHEMATICS issue http://www.scirp.org/journal/am/ ) we show how our human genome MUST be considedred as a NUMERICAL WHOLE. The idea is now to run this kind of analysis on complete genomes DNA from CANCER CELLS (LOH) at individual chromosomes and whole genome scales.

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Campaign: Analysis Priorities

Support multiple workflow tools and data access mechanisms

Galaxy and GenePattern are examples of systems that could provide access to data sets, pipelines, and publishable, shareable, and reproducible workflows. Ideally, existing familiar and popular platforms such as these would be supported. In addition to improving or enabling interactions between these tools, effort should be directed towards facilitating programmatic access to the underlying data in order to support custom ...more »

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Campaign: Analysis Priorities

Integrative Analysis of molecular datatypes for a given sample

A sample could be analyzed for DNA sequence variations, structural variations, CNVs, Gene or transcript isoform expression, genome-wide methylation patterns, ChIP-seq for specific transcription factors, metabolomic or proteomic analysis, and other molecular profiles. A framework that allows a researcher to readily identify all molecular data types associated with a particular sample and integrate the results of such analyses ...more »

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Campaign: Analysis Priorities

large scale computation time

Provide CPU time for the community with allocations set by NCI to users AND on a pay per node model.

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Actively support crowd-sourcing challenges

To stimulate learning as much as possible, as quickly as possible, the data cloud could have a utility where interested parties could pose "crowd-sourcing" challenges, e,g, Kaggle. Indeed, Harold Varmus, NCI & leaders in cancer & genomics could pose the leading questions they would like bright people to take a run at answering, e.g. Hilbert's 23 problems

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dissect tumors into clones and store the information for reuse

each tumor contains multiple clones, genomic alterations are linked to these clones. clinical factors such as survival, drug response should be correlated with patients at the clonal level but not whole tumor level

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Common framework for all kind of analysis

One backend framework for custom analysis tools that can be developed by the community.

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Link genomic analysis results with “external” annotations

Link genomic analysis results with “external” data such as molecular interaction networks, drug-target associations, or semantic associations extracted from the literature

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