NCI Cancer Genomics Cloud Pilots

User Feedback Survey

OMB No.: 0925-0743

Expiration Date: June 30, 2019
Collection of this information is authorized by The Public Health Service Act, Section 413 [285a-2]. Rights of study participants are protected by The Privacy Act of 1974. Participation is voluntary, and there are no penalties for not participating or withdrawing from the study at any time. Refusal to participate will not affect your benefits in any way. The information collected in this study will be kept private to the extent provided by law. Names and other identifiers will not appear in any report of the study. Information provided will be combined for all study participants and reported as summaries. You are being contacted by email, on-line, during live presentations to complete this instrument so that we can understand the utility and usefulness of the Cancer Genomics Cloud Pilots and determine how to proceed with these platforms in future.

Public reporting burden for this collection of information is estimated to average 15 minutes per response, including the time for reviewing instructions, searching existing data sources, gathering and maintaining the data needed, and completing and reviewing the collection of information. An agency may not conduct or sponsor, and a person is not required to respond to, a collection of information unless it displays a currently valid OMB control number. Send comments regarding this burden estimate or any other aspect of this collection of information, including suggestions for reducing this burden to: NIH, Project Clearance Branch, 6705 Rockledge Drive, MSC 7974, Bethesda, MD 20892-7974, ATTN: PRA (0925-XXXX). Do not return the completed form to this address.

Question Title

* 1. Please provide your institutional affiliation.

Question Title

* 2. What is your role at your institution?

Principal Investigator

Investigator

Post-doc / Fellow

Student

Other (please specify)

Question Title

* 3. How would you describe your primary expertise?

Clinical care / clinical research

Bench / basic biology

Bioinformatics / genomics – analysis, integration of data using existing tools, scripting languages

Computational biology / systems biology– development of novel algorithms

Other (please specify)

Question Title

* 4. Please describe your familiarity with the following (with 1 being least familiar/ 10 being most familiar)

	1 - Not Familiar	2	3	4	5	6	7	8	9	10 - Expert	N/A
Bioinformatics tools – DNA-Seq	Bioinformatics tools – DNA-Seq 1 - Not Familiar	Bioinformatics tools – DNA-Seq 2	Bioinformatics tools – DNA-Seq 3	Bioinformatics tools – DNA-Seq 4	Bioinformatics tools – DNA-Seq 5	Bioinformatics tools – DNA-Seq 6	Bioinformatics tools – DNA-Seq 7	Bioinformatics tools – DNA-Seq 8	Bioinformatics tools – DNA-Seq 9	Bioinformatics tools – DNA-Seq 10 - Expert	Bioinformatics tools – DNA-Seq N/A
Bioinformatics tools – RNA-Seq	Bioinformatics tools – RNA-Seq 1 - Not Familiar	Bioinformatics tools – RNA-Seq 2	Bioinformatics tools – RNA-Seq 3	Bioinformatics tools – RNA-Seq 4	Bioinformatics tools – RNA-Seq 5	Bioinformatics tools – RNA-Seq 6	Bioinformatics tools – RNA-Seq 7	Bioinformatics tools – RNA-Seq 8	Bioinformatics tools – RNA-Seq 9	Bioinformatics tools – RNA-Seq 10 - Expert	Bioinformatics tools – RNA-Seq N/A
Bioinformatics tools – Arrays	Bioinformatics tools – Arrays 1 - Not Familiar	Bioinformatics tools – Arrays 2	Bioinformatics tools – Arrays 3	Bioinformatics tools – Arrays 4	Bioinformatics tools – Arrays 5	Bioinformatics tools – Arrays 6	Bioinformatics tools – Arrays 7	Bioinformatics tools – Arrays 8	Bioinformatics tools – Arrays 9	Bioinformatics tools – Arrays 10 - Expert	Bioinformatics tools – Arrays N/A
TCGA data – Clinical	TCGA data – Clinical 1 - Not Familiar	TCGA data – Clinical 2	TCGA data – Clinical 3	TCGA data – Clinical 4	TCGA data – Clinical 5	TCGA data – Clinical 6	TCGA data – Clinical 7	TCGA data – Clinical 8	TCGA data – Clinical 9	TCGA data – Clinical 10 - Expert	TCGA data – Clinical N/A
TCGA data – Variants (MAF/VCF)	TCGA data – Variants (MAF/VCF) 1 - Not Familiar	TCGA data – Variants (MAF/VCF) 2	TCGA data – Variants (MAF/VCF) 3	TCGA data – Variants (MAF/VCF) 4	TCGA data – Variants (MAF/VCF) 5	TCGA data – Variants (MAF/VCF) 6	TCGA data – Variants (MAF/VCF) 7	TCGA data – Variants (MAF/VCF) 8	TCGA data – Variants (MAF/VCF) 9	TCGA data – Variants (MAF/VCF) 10 - Expert	TCGA data – Variants (MAF/VCF) N/A
TCGA data – DNA Sequence (e.g., BAM)	TCGA data – DNA Sequence (e.g., BAM) 1 - Not Familiar	TCGA data – DNA Sequence (e.g., BAM) 2	TCGA data – DNA Sequence (e.g., BAM) 3	TCGA data – DNA Sequence (e.g., BAM) 4	TCGA data – DNA Sequence (e.g., BAM) 5	TCGA data – DNA Sequence (e.g., BAM) 6	TCGA data – DNA Sequence (e.g., BAM) 7	TCGA data – DNA Sequence (e.g., BAM) 8	TCGA data – DNA Sequence (e.g., BAM) 9	TCGA data – DNA Sequence (e.g., BAM) 10 - Expert	TCGA data – DNA Sequence (e.g., BAM) N/A
TCGA data – mRNA Sequence (e.g., FASTQ)	TCGA data – mRNA Sequence (e.g., FASTQ) 1 - Not Familiar	TCGA data – mRNA Sequence (e.g., FASTQ) 2	TCGA data – mRNA Sequence (e.g., FASTQ) 3	TCGA data – mRNA Sequence (e.g., FASTQ) 4	TCGA data – mRNA Sequence (e.g., FASTQ) 5	TCGA data – mRNA Sequence (e.g., FASTQ) 6	TCGA data – mRNA Sequence (e.g., FASTQ) 7	TCGA data – mRNA Sequence (e.g., FASTQ) 8	TCGA data – mRNA Sequence (e.g., FASTQ) 9	TCGA data – mRNA Sequence (e.g., FASTQ) 10 - Expert	TCGA data – mRNA Sequence (e.g., FASTQ) N/A
TCGA data – miRNA Sequence (e.g., BAM)	TCGA data – miRNA Sequence (e.g., BAM) 1 - Not Familiar	TCGA data – miRNA Sequence (e.g., BAM) 2	TCGA data – miRNA Sequence (e.g., BAM) 3	TCGA data – miRNA Sequence (e.g., BAM) 4	TCGA data – miRNA Sequence (e.g., BAM) 5	TCGA data – miRNA Sequence (e.g., BAM) 6	TCGA data – miRNA Sequence (e.g., BAM) 7	TCGA data – miRNA Sequence (e.g., BAM) 8	TCGA data – miRNA Sequence (e.g., BAM) 9	TCGA data – miRNA Sequence (e.g., BAM) 10 - Expert	TCGA data – miRNA Sequence (e.g., BAM) N/A
TCGA data – Copy Number Array	TCGA data – Copy Number Array 1 - Not Familiar	TCGA data – Copy Number Array 2	TCGA data – Copy Number Array 3	TCGA data – Copy Number Array 4	TCGA data – Copy Number Array 5	TCGA data – Copy Number Array 6	TCGA data – Copy Number Array 7	TCGA data – Copy Number Array 8	TCGA data – Copy Number Array 9	TCGA data – Copy Number Array 10 - Expert	TCGA data – Copy Number Array N/A
TCGA data – Gene Expression Array	TCGA data – Gene Expression Array 1 - Not Familiar	TCGA data – Gene Expression Array 2	TCGA data – Gene Expression Array 3	TCGA data – Gene Expression Array 4	TCGA data – Gene Expression Array 5	TCGA data – Gene Expression Array 6	TCGA data – Gene Expression Array 7	TCGA data – Gene Expression Array 8	TCGA data – Gene Expression Array 9	TCGA data – Gene Expression Array 10 - Expert	TCGA data – Gene Expression Array N/A
TCGA data – Protein Expression	TCGA data – Protein Expression 1 - Not Familiar	TCGA data – Protein Expression 2	TCGA data – Protein Expression 3	TCGA data – Protein Expression 4	TCGA data – Protein Expression 5	TCGA data – Protein Expression 6	TCGA data – Protein Expression 7	TCGA data – Protein Expression 8	TCGA data – Protein Expression 9	TCGA data – Protein Expression 10 - Expert	TCGA data – Protein Expression N/A
TCGA data – Methylation	TCGA data – Methylation 1 - Not Familiar	TCGA data – Methylation 2	TCGA data – Methylation 3	TCGA data – Methylation 4	TCGA data – Methylation 5	TCGA data – Methylation 6	TCGA data – Methylation 7	TCGA data – Methylation 8	TCGA data – Methylation 9	TCGA data – Methylation 10 - Expert	TCGA data – Methylation N/A
TCGA data – Images (Diagnostic, Tissue, Radiological)	TCGA data – Images (Diagnostic, Tissue, Radiological) 1 - Not Familiar	TCGA data – Images (Diagnostic, Tissue, Radiological) 2	TCGA data – Images (Diagnostic, Tissue, Radiological) 3	TCGA data – Images (Diagnostic, Tissue, Radiological) 4	TCGA data – Images (Diagnostic, Tissue, Radiological) 5	TCGA data – Images (Diagnostic, Tissue, Radiological) 6	TCGA data – Images (Diagnostic, Tissue, Radiological) 7	TCGA data – Images (Diagnostic, Tissue, Radiological) 8	TCGA data – Images (Diagnostic, Tissue, Radiological) 9	TCGA data – Images (Diagnostic, Tissue, Radiological) 10 - Expert	TCGA data – Images (Diagnostic, Tissue, Radiological) N/A
Command Line Utilities	Command Line Utilities 1 - Not Familiar	Command Line Utilities 2	Command Line Utilities 3	Command Line Utilities 4	Command Line Utilities 5	Command Line Utilities 6	Command Line Utilities 7	Command Line Utilities 8	Command Line Utilities 9	Command Line Utilities 10 - Expert	Command Line Utilities N/A
Docker or other software portability tool	Docker or other software portability tool 1 - Not Familiar	Docker or other software portability tool 2	Docker or other software portability tool 3	Docker or other software portability tool 4	Docker or other software portability tool 5	Docker or other software portability tool 6	Docker or other software portability tool 7	Docker or other software portability tool 8	Docker or other software portability tool 9	Docker or other software portability tool 10 - Expert	Docker or other software portability tool N/A
Local Compute Clusters	Local Compute Clusters 1 - Not Familiar	Local Compute Clusters 2	Local Compute Clusters 3	Local Compute Clusters 4	Local Compute Clusters 5	Local Compute Clusters 6	Local Compute Clusters 7	Local Compute Clusters 8	Local Compute Clusters 9	Local Compute Clusters 10 - Expert	Local Compute Clusters N/A
REST-based APIs	REST-based APIs 1 - Not Familiar	REST-based APIs 2	REST-based APIs 3	REST-based APIs 4	REST-based APIs 5	REST-based APIs 6	REST-based APIs 7	REST-based APIs 8	REST-based APIs 9	REST-based APIs 10 - Expert	REST-based APIs N/A

Question Title

* 5. This survey is in response to work you performed on which Cancer Genomics Cloud (CGC) platform?
(Select only one - please complete a separate survey for each CGC platform you used)

Broad Institute (FireCloud)

Institute for Systems Biology

Seven Bridges Genomics

Question Title

* 6. What kinds of tasks did you perform?

Query TCGA Data

Upload locally-generated genomic data to analyze in conjunction with TCGA data

Perform TCGA data processing or analyses using CGC-provided or user-uploaded tools

Install new analysis tool(s) to test tools performance on large-scale genomic data set and/or to conduct novel research

Store and share analyses with collaborators

Other (please describe)

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* 7. Approximately how much time have you spent using the platform before completing this evaluation?

Question Title

* 8. Please rate the Cloud platform you used on the following functions.
(With 1 being the lowest / poorest rating and 10 being the highest / best)

	1 - Poor	2	3	4	5	6	7	8	9	10 - Excellent	N/A
Overall Usability	Overall Usability 1 - Poor	Overall Usability 2	Overall Usability 3	Overall Usability 4	Overall Usability 5	Overall Usability 6	Overall Usability 7	Overall Usability 8	Overall Usability 9	Overall Usability 10 - Excellent	Overall Usability N/A
Analysis Framework	Analysis Framework 1 - Poor	Analysis Framework 2	Analysis Framework 3	Analysis Framework 4	Analysis Framework 5	Analysis Framework 6	Analysis Framework 7	Analysis Framework 8	Analysis Framework 9	Analysis Framework 10 - Excellent	Analysis Framework N/A
Cohort Selection	Cohort Selection 1 - Poor	Cohort Selection 2	Cohort Selection 3	Cohort Selection 4	Cohort Selection 5	Cohort Selection 6	Cohort Selection 7	Cohort Selection 8	Cohort Selection 9	Cohort Selection 10 - Excellent	Cohort Selection N/A
Data Upload	Data Upload 1 - Poor	Data Upload 2	Data Upload 3	Data Upload 4	Data Upload 5	Data Upload 6	Data Upload 7	Data Upload 8	Data Upload 9	Data Upload 10 - Excellent	Data Upload N/A
Tool Integration	Tool Integration 1 - Poor	Tool Integration 2	Tool Integration 3	Tool Integration 4	Tool Integration 5	Tool Integration 6	Tool Integration 7	Tool Integration 8	Tool Integration 9	Tool Integration 10 - Excellent	Tool Integration N/A
Overall Performance	Overall Performance 1 - Poor	Overall Performance 2	Overall Performance 3	Overall Performance 4	Overall Performance 5	Overall Performance 6	Overall Performance 7	Overall Performance 8	Overall Performance 9	Overall Performance 10 - Excellent	Overall Performance N/A
Tool Selection	Tool Selection 1 - Poor	Tool Selection 2	Tool Selection 3	Tool Selection 4	Tool Selection 5	Tool Selection 6	Tool Selection 7	Tool Selection 8	Tool Selection 9	Tool Selection 10 - Excellent	Tool Selection N/A
Workflow Construction	Workflow Construction 1 - Poor	Workflow Construction 2	Workflow Construction 3	Workflow Construction 4	Workflow Construction 5	Workflow Construction 6	Workflow Construction 7	Workflow Construction 8	Workflow Construction 9	Workflow Construction 10 - Excellent	Workflow Construction N/A
Ease of Collaboration	Ease of Collaboration 1 - Poor	Ease of Collaboration 2	Ease of Collaboration 3	Ease of Collaboration 4	Ease of Collaboration 5	Ease of Collaboration 6	Ease of Collaboration 7	Ease of Collaboration 8	Ease of Collaboration 9	Ease of Collaboration 10 - Excellent	Ease of Collaboration N/A

Question Title

* 9. Please indicate if you agree or disagree with the following statements.

	Strongly Agree	Agree	Neutral	Disagree	Strongly Disagree
The system improved my ability to store my analysis results/provenance in a reproducible manner so that the same method could be used with other data.	The system improved my ability to store my analysis results/provenance in a reproducible manner so that the same method could be used with other data. Strongly Agree	The system improved my ability to store my analysis results/provenance in a reproducible manner so that the same method could be used with other data. Agree	The system improved my ability to store my analysis results/provenance in a reproducible manner so that the same method could be used with other data. Neutral	The system improved my ability to store my analysis results/provenance in a reproducible manner so that the same method could be used with other data. Disagree	The system improved my ability to store my analysis results/provenance in a reproducible manner so that the same method could be used with other data. Strongly Disagree
The system improved my ability to correlate patient’s molecular data with clinical data.	The system improved my ability to correlate patient’s molecular data with clinical data. Strongly Agree	The system improved my ability to correlate patient’s molecular data with clinical data. Agree	The system improved my ability to correlate patient’s molecular data with clinical data. Neutral	The system improved my ability to correlate patient’s molecular data with clinical data. Disagree	The system improved my ability to correlate patient’s molecular data with clinical data. Strongly Disagree
The system made it possible for me to run analyses which would have been difficult or time consuming otherwise.	The system made it possible for me to run analyses which would have been difficult or time consuming otherwise. Strongly Agree	The system made it possible for me to run analyses which would have been difficult or time consuming otherwise. Agree	The system made it possible for me to run analyses which would have been difficult or time consuming otherwise. Neutral	The system made it possible for me to run analyses which would have been difficult or time consuming otherwise. Disagree	The system made it possible for me to run analyses which would have been difficult or time consuming otherwise. Strongly Disagree
My research benefited from insights I gained while using the system.	My research benefited from insights I gained while using the system. Strongly Agree	My research benefited from insights I gained while using the system. Agree	My research benefited from insights I gained while using the system. Neutral	My research benefited from insights I gained while using the system. Disagree	My research benefited from insights I gained while using the system. Strongly Disagree

Question Title

* 10. Which of these TCGA data sets did you use? (Select all that apply)

Gene Expression Array

Copy Number Array

Whole Genome Sequence (WGS)

Whole Exome Sequence (WXS)

Methylation

RNA-Seq

I did not use any TCGA data

Other (please specify)

Question Title

* 11. Which additional TCGA data sets would you like to access through this platform? (Select all that apply)

Radiololgy

Pathology

Proteomics

Other (please specify)

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* 12. Did you upload local data?

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* 13. Did you use an Application Programming Interface (API) to access data in the system?

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* 14. Did you use APIs to access analysis tools or pipelines?

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* 15. Which of the following analyses did you perform? (Select all that apply)

RNA-Seq Analysis

Exome Analysis

Whole Genome Analysis

Transcription Analysis / Assembly

Other (please specify)

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* 16. Did you upload local pipelines/tools to the CGC?

If yes, please describe.

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* 17. Are you willing to share pipelines/tools you have developed to the CGC?

Yes, willing to share

Not sure

At a later date

Yes, already shared as open source (please provide the URLs to GitHub or other repositories)

NCI Cancer Genomics Cloud Pilots

User Feedback Survey

Question Title

* 1. Please provide your institutional affiliation.

Question Title

* 2. What is your role at your institution?

Question Title

* 3. How would you describe your primary expertise?

Question Title

* 4. Please describe your familiarity with the following (with 1 being least familiar/ 10 being most familiar)

Question Title

* 5. This survey is in response to work you performed on which Cancer Genomics Cloud (CGC) platform?
(Select only one - please complete a separate survey for each CGC platform you used)

Question Title

* 6. What kinds of tasks did you perform?

Question Title

* 7. Approximately how much time have you spent using the platform before completing this evaluation?

Question Title

* 8. Please rate the Cloud platform you used on the following functions.
(With 1 being the lowest / poorest rating and 10 being the highest / best)

Question Title

* 9. Please indicate if you agree or disagree with the following statements.

Question Title

* 10. Which of these TCGA data sets did you use? (Select all that apply)

Question Title

* 11. Which additional TCGA data sets would you like to access through this platform? (Select all that apply)

Question Title

* 12. Did you upload local data?

Question Title

* 13. Did you use an Application Programming Interface (API) to access data in the system?

Question Title

* 14. Did you use APIs to access analysis tools or pipelines?

Question Title

* 15. Which of the following analyses did you perform? (Select all that apply)

Question Title

* 16. Did you upload local pipelines/tools to the CGC?

Question Title

* 17. Are you willing to share pipelines/tools you have developed to the CGC?

Question Title

* 18. What additional open source bioinformatics pipelines/tools would you like incorporated in the CGC?

Question Title

* 19. Please add your comments about whether you would you use this platform again, and what tools and functions you found most useful.

Question Title

* 1. Please provide your institutional affiliation.

Question Title

* 2. What is your role at your institution?

Question Title

* 3. How would you describe your primary expertise?

Question Title

* 4. Please describe your familiarity with the following (with 1 being least familiar/ 10 being most familiar)

Question Title

* 5. This survey is in response to work you performed on which Cancer Genomics Cloud (CGC) platform? (Select only one - please complete a separate survey for each CGC platform you used)

Question Title

* 6. What kinds of tasks did you perform?

Question Title

* 7. Approximately how much time have you spent using the platform before completing this evaluation?

Question Title

* 8. Please rate the Cloud platform you used on the following functions. (With 1 being the lowest / poorest rating and 10 being the highest / best)

Question Title

* 9. Please indicate if you agree or disagree with the following statements.

Question Title

* 10. Which of these TCGA data sets did you use? (Select all that apply)

Question Title

* 11. Which additional TCGA data sets would you like to access through this platform? (Select all that apply)

Question Title

* 12. Did you upload local data?

Question Title

* 13. Did you use an Application Programming Interface (API) to access data in the system?

Question Title

* 14. Did you use APIs to access analysis tools or pipelines?

Question Title

* 15. Which of the following analyses did you perform? (Select all that apply)

Question Title

* 16. Did you upload local pipelines/tools to the CGC?

Question Title

* 17. Are you willing to share pipelines/tools you have developed to the CGC?

Question Title

* 18. What additional open source bioinformatics pipelines/tools would you like incorporated in the CGC?

Question Title

* 19. Please add your comments about whether you would you use this platform again, and what tools and functions you found most useful.

* 5. This survey is in response to work you performed on which Cancer Genomics Cloud (CGC) platform?
(Select only one - please complete a separate survey for each CGC platform you used)

* 8. Please rate the Cloud platform you used on the following functions.
(With 1 being the lowest / poorest rating and 10 being the highest / best)