Campaign: Data Priorities

Access to level 1 & 2 TCGA DNA methylation data

Provide access to level 1 and 2 data for TCGA DNA methylation data for analysis

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Campaign: Data Priorities

Make it so we can still download the raw files

For those of us who don't want to use the cloud workflow, please make it so we still have access to all the raw data. Please don't lock us into your analytic approaches!

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10 votes
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Campaign: Data Priorities

Access to level 1 & 2 data TCGA copy number array data

Provide access to level 1 and 2 data for TCGA copy number array data for analysis

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9 votes
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Campaign: Analysis Priorities

Track data permissions, including consent

Track data provenance and permissions, including IRB approvals and patient consent and be able to support different levels of permissions rather than insisting on uniform consent

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8 votes
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Campaign: Data Priorities

Access to BAM files for TCGA miRNA sequencing data

Provide access to BAM files for TCGA miRNA sequencing data for analysis

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8 votes
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Campaign: Analysis Priorities

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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7 votes
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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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5 votes
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Campaign: Analysis Priorities

Correlate subjects’ expression & genotyping data

Correlate expression data from multiple reporters from multiple subjects with genotyping data

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3 votes
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Campaign: Data Priorities

ENCODE datasets

Include ENCODE datasets from both normal and cancer cell lines

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3 votes
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Campaign: Data Priorities

Connect data with available specimens for follow-up studies

Mining cancer data in the cloud is great, but to enable ongoing research there should be a connection to specimens so researchers can pursue followup studies. This will require storing data about specimens from studies such as TCGA - where they are, how they can be accessed and what consent they are governed by. Just as the data from publications should be made available to allow reproduction of results, so should samples ...more »

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3 votes
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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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3 votes
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