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Sage Bionetworks: Scientific Computing Survey
We're currently investigating the development of new tools to support the scientific community. Participants will be entered into a drawing to receive a $50 Amazon Gift card.
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* Indicates required question
What is your role?
*
Student
Postdoc
Research scientist
Data or software engineer
Principal Investigator
Other:
What type of organization do you work for?
*
Academic institution
Pharmaceutical or biotech company
Non-profit organization
Start-up company
Other:
What types of research computing do you routinely do? (check all that apply)
*
Processing data prior to analysis (e.g. fastq files to gene counts)
Statistical analysis (e.g. differential expression, GWAS)
Machine learning
None of these
Other:
Required
Which of the following data processing procedures do you perform?
*
Currently perform
Not yet, but plan to perform
Have no plans to perform
RNA sequencing (bulk)
Single cell RNA sequencing
Germline variant calling
Somatic variant calling
Proteomics
Other omics
Currently perform
Not yet, but plan to perform
Have no plans to perform
RNA sequencing (bulk)
Single cell RNA sequencing
Germline variant calling
Somatic variant calling
Proteomics
Other omics
Which data types do you use or have plans to use? (check all that apply)
*
Protected health information
Genomic/transcriptomic data from human samples
Genomic/transcriptomic data from non-human samples
Required
What data sources do you use in your research? (check all that apply)
*
Data generated by my group or collaborators
Public data generated by other researchers
Required
Where do you obtain your analysis pipelines/software for your current work? (check all that apply)
*
I write them myself
I get them from a colleague or collaborator
I customize available community tools
I use off the shelf packages
Required
What is your current computing environment? (check all that apply)
*
Laptop/desktop computer
Server physically located at workspace (e.g. in your lab group)
Local computing cluster
Amazon Web Services Cloud
Google Cloud Platform
Azure
Computing platform such as Seven Bridges, DNA Nexus, Galaxy
Other:
Required
Have you previously used a workflow management system (e.g. Nextflow, CWL, Snakemake)?
*
Yes
No
Which of the following present bottlenecks or challenges in your current research? (check all that apply)
*
Data storage/transfer is expensive
Data transfer is too time consuming
Don’t have access to sufficient computing power
Challenging to evaluate and select specific software tools (e.g. Bowtie vs STAR)
Difficult to develop reproducible analysis pipelines
Difficult to customize existing pipelines or tools
Other:
Required
When running your current analysis pipelines, which of the following challenges do you commonly face? (check all that apply)
Difficult to manage execution of steps in a pipeline (i.e. automation)
Jobs frequently fail and have to be diagnosed and restarted
Concerned about computational efficiency
Difficult to monitor progress of pipeline while it’s running
Other:
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Would you be interested in a participating in a follow up 1-hour user research study on next generation scientific computing and workflows?
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