iReceptor Platform User Survey - February 2023

iReceptor is a data discovery platform that facilitates the curation, analysis and sharing of antibody/B-cell and T-cell receptor repertoires (Adaptive Immune Receptor Repertoire or AIRR-seq data) and related subject and sample metadata from multiple studies across many labs and institutions. We are committed to providing a platform for researchers to increase the value of their data through sharing with the community. This will greatly increase the amount of data available to answer complex questions about the adaptive immune response, accelerating the development of vaccines, therapeutic antibodies against autoimmune diseases, and cancer immunotherapies.

The iReceptor Gateway integrates large, distributed, AIRR-seq data repositories, following standards for sharing and interoperability developed by the Adaptive Immune Receptor Repertoire (AIRR) Community. The main goal of iReceptor is to connect this distributed network of AIRR-seq repositories into an AIRR Data Commons, allowing queries across multiple projects, labs, and institutions.

SURVEY PART 1: General

As a user of the iReceptor Platform (Science Gateway and Turnkey Repository), the iReceptor team would like to get your input as to the usefulness of the Platform for your research as well as understand key features that might be missing. We appreciate any and all feedback!

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* 1. Your Affiliation

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* 2. What research question(s) are you trying to answer?

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* 3. What were your goals when you requested an account on the Gateway?

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* 4. Did the Gateway meet your expectations?

Yes

Partially

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* 5. Please comment on how the Gateway met, or failed to meet, your expectations?

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* 6. Have you used the Gateway more than once?

Yes

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* 7. If you didn't return, what would bring you back to explore the Gateway?

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* 8. What are the 3 top things that the Gateway does well?

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* 9. What are your 3 main "pain points" with the current Gateway?

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* 10. What are your top "3 wishes for improvements” to the Gateway?

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* 11. Have you reused data from the Gateway and/or the AIRR Data Commons in your research?

Yes

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* 12. If you used the Gateway and/or the AIRR Data Commons and have published the results, please provide a reference to your paper.

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* 13. Have you generated novel AIRR-seq data? (Yes/No)

Yes

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* 14. If yes, have you shared this data in the AIRR Data Commons?

Yes

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* 15. If not, why not (e.g. privacy concerns; don't know how; too much work, etc.)

SURVEY PART 2: Functionality

In December 2022, we released version 4.0 of the iReceptor Platform, which added key functionalities, including the storage and searching of clone data, IG, TR, and MHC genotype, and paired immune receptor chains and gene expression data for single immune cells, as well as integrated analysis capability for these types of data. This section of the survey asks for feedback on previously existing and new features of the iReceptor Platform.

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* 16. On a typical day using the Gateway, which types of data are important in your research? (choose all that apply):

Sequence/Rearrangement data (CDR3, VDJ gene)

Clone data (CDR3, VDJ gene)

Cell/Expression data (Expression level, CDR3 search, VDJ gene search)

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* 17. Indicate which of the pre iReceptor v4.0 functions are critical to your research (choose all that apply):

CDR3 quick search

Antigen specificity links to IEDB

Study/Subject/Sample metadata search

Sample/Repertoire gene usage statistics

Sequence/Rearrangement feature search (CDR3, VDJ gene)

Downloading of Study/Subject/Sample metadata for further analysis

Downloading of Sequence/Rearrangement data for further analysis

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* 18. Indicate which of the new iReceptor v4.0 functions you anticipate will be critical to your research (choose all that apply):

Immune receptor genotype search

MHC genotype search

Clone feature search (CDR3, VDJ gene)

Cell/Expression feature search (Expression level, CDR3 search, VDJ gene search)

Downloading of Clone data for further analysis

Downloading of Cell/Expression data for further analysis

Sequence analysis tools (Statistics, Histogram, Immunarch)

Clone analysis tools (Statistics)

Cell analysis tools (Conga, CellTypist)

Ability to download analysis results (e.g. highly expressed CDR3s) for further analysis (e.g. CDR3 expression comparisons across repertoires)

Analysis for data discovery and visualization

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* 19. Please list any other publicly available databases that you consistently use in your immune repertoire research.

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* 20. How valuable would it be for the Gateway to link to these databases?

Highly Valuable

Valuable

Not Valuable

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* 21. Please list any available tools or capabilities that you would like to see added to the Gateway? (Provide name/documentation link)

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* 22. Select the Turnkey and/or the AIRR Data Commons repository functions that you use (or will use in the future):

Install and run your own repository for internal data management

Install and run your own repository for sharing data in the AIRR Data Commons

Search the AIRR Data Commons using the the AIRR Data Commons web based query API

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* 23. Please list any capabilities that you would like to see added to the iReceptor Turnkey Repository

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* 24. Other comments or any other feedback on the iReceptor Platform?

SURVEY PART 3: Gateway Sustainability

Currently, iReceptor Platform services are free to you, the user. Development and operational costs are paid through academic research grants. This is not a sustainable model and we are unable to continue this level of service at no cost. To help sustain this valuable resource, we are considering other funding sources to support the operation and development of the iReceptor Platform (Gateway and Repositories).

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* 25. Would you be willing to donate (e.g. Wikipedia funding model) to help sustain the operation and development of the iReceptor Platform (Gateway and Repositories)?

Yes

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* 26. Would you be interested in sponsoring the iReceptor Platform in return for a set of sponsorship benefits (e.g. logo placement, website presence)? (Yes/No)

Yes

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* 27. Indicate which of these services you would consider paying for to support your research.

Public Repository Operations (services to operate AIRR compliant repositories to store and share your research data with the community through the AIRR Data Commons)

Private Repository Operations (services to operate AIRR compliant repositories to store and manage your internal, private research data)

Gateway Usage (services to support your use of the iReceptor Gateway platform)

Gateway Operations (services to operate an internal/private iReceptor Gateway that links private, internal data with the public data in the AIRR Data Commons)

Data Curation (services to curate AIRR-seq study data in a public and/or private repository)

Data Discovery (services to help you find data of interest in the AIRR Data Commons)

Data Analysis (services to help you analyze data in the ADC, including the development of analysis pipelines that process data in the AIRR Data Commons and the integration of existing tools into the Gateway)

Other (please specify)

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* 28. If you are interested in learning more about the services offered above please provide your name and email address.

First and Last Name

Company/Affiliation

Email Address

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* 29. Any final comments on sustainability that you would like to share with the iReceptor team?

Thank you for completing the survey and sharing your thoughts. We value your time and are careful to only send surveys when we really need user feedback. Please do let us know if you do not want to receive surveys in the future.