OpenScPCA: Call for contributions, new grant offerings, and analyses in progress!

July 8, 2024

In April 2024, we announced the Open Single-cell Pediatric Cancer Atlas (OpenScPCA) project. Since then, we’ve been working to build a supportive community while getting started on a few analysis ideas! We’re excited to see growing interest in the project, and we have some big news for prospective collaborators.

Unfamiliar with OpenScPCA? Read all about the open, collaborative project and explore the [.inline-snippet]OpenScPCA-analysis[.inline-snippet] repository and Discussion board on GitHub.

Grants for advancing pediatric cancer research

If you have considered joining the project, now is a great time to start. Contribute your expertise to help us build a valuable pediatric cancer resource, and you may become eligible for a small one-time grant!

Seeking collaborators to help annotate cell types!

We are seeking collaborators with experience analyzing single-cell RNA-seq datasets to help annotate and assign cell types to existing datasets on the Single-cell Pediatric Cancer Atlas (ScPCA) Portal. Small one-time grants are now available for eligible pediatric cancer researchers who annotate cell types for all samples in a given group in the sample table below. 

Please note, this image only shows a partial view of the sample table. View the full sample table here. This table contains a unique group identifier, project identifier, project title, list of diagnoses, total number of samples per group, and the maximum amount that may be awarded. Each group encompasses samples from a single ScPCA project representing either a single diagnosis or a group of related diagnoses. A total of 27 grants are currently available.

Grant eligibility 

To be eligible for a grant:

  • You must complete cell type annotation for all samples assigned to a specified group identifier. Only one grant will be awarded per group of samples.
  • You must complete the cell type annotation analysis openly and collaboratively by contributing your analysis to the OpenScPCA project.
  • ALSF will only award grants with submissions meeting the eligibility requirements and acceptance criteria. All decisions regarding applications and grants, including satisfaction of requirements, are made solely by ALSF, in its sole discretion. 

These are just some of the requirements. Read the full eligibility requirements and acceptance criteria. 

Distribution and Permitted Use of Funds

  • The funds will be distributed to the researcher’s institution and must be used for pediatric cancer research. If the institution is not conducting such research at the time the grant is to be distributed, the grant will be deemed declined. 
  • ALSF does not allow the use of funds for research utilizing human embryonic stem cells or nonhuman primates. Research with human induced pluripotent stem cells is permissible.
  • The institution receiving the grant is responsible for compliance with any governmental reporting requirements and related tax obligations, if any.  

Important Dates

  • Final Table Submission Deadline: November 1, 2024 (5PM EDT)
  • Application Submission Deadline, if eligible: November 15, 2024 (5PM EST) or within ten days of notification of eligibility, whichever is sooner

All participation in this grant opportunity and contributions to the OpenScPCA project are subject to the Terms of Use and all Policies

Getting started 

Are you interested in obtaining a grant for annotating a group of samples? Head over to the OpenScPCAGitHub discussion board and file a discussion in the [.inline-snippet]Propose a new analysis[.inline-snippet] category. The Data Lab will review your idea and respond to help you get started!

Your discussion post must include:

  • The unique group identifier for which you would like to add cell type annotations 
  • The project title, project identifier, and list of diagnoses for that group
  • An outline of the approach you plan to take to complete the cell type annotation, including an explanation of the methods you plan to use to perform cell type annotation
Example of a GitHub discussion post.

All code and results must be reviewed by a Data Lab team member. You can expect multiple rounds of peer review. We encourage you to start as early as possible to avoid missing the submission deadlines.

Explore OpenScPCA analyses in progress

Perhaps these ongoing analyses will spark an idea for you! The Data Lab has started an analysis of Ewing sarcoma samples on the ScPCA Portal, as well as an exploration of doublet detection methodologies for use on ScPCA data. You can follow along and join the discussion on GitHub. 

Annotation of cell types in Ewing sarcoma samples 

This analysis aims to annotate cell types for the existing Ewing sarcoma samples on the ScPCA Portal, which can be found in SCPCP000015. The goal is to provide reliable cell type annotations that can be used for downstream analysis of the Ewing sarcoma samples. In particular, we plan to classify tumor and normal cell types, including any tumor cell states commonly observed in Ewing sarcoma. We welcome feedback from others about how they might approach identifying tumor cells in some of these samples.

Doublet detection

In [.inline-snippet]scpca-nf[.inline-snippet], the data processing pipeline behind the ScPCA Portal, we do not currently analyze or flag potential doublet cells. Adding flagging of potential doublets could improve data quality for cell typing and many other analyses. We are exploring the performance of doublet detection methodologies and their potential use on ScPCA data. 

Do you need assistance getting set up, have an analysis idea that you are unsure about, or just have questions about where to begin? We can help! Our team can provide guidance and meet with interested collaborators as needed. Post in the [.inline-snippet]Questions[.inline-snippet] category on discussions, email us at scpca@ccdatalab.org or send a message on our #open-scpca Slack channel

In April 2024, we announced the Open Single-cell Pediatric Cancer Atlas (OpenScPCA) project. Since then, we’ve been working to build a supportive community while getting started on a few analysis ideas! We’re excited to see growing interest in the project, and we have some big news for prospective collaborators.

Unfamiliar with OpenScPCA? Read all about the open, collaborative project and explore the [.inline-snippet]OpenScPCA-analysis[.inline-snippet] repository and Discussion board on GitHub.

Grants for advancing pediatric cancer research

If you have considered joining the project, now is a great time to start. Contribute your expertise to help us build a valuable pediatric cancer resource, and you may become eligible for a small one-time grant!

Seeking collaborators to help annotate cell types!

We are seeking collaborators with experience analyzing single-cell RNA-seq datasets to help annotate and assign cell types to existing datasets on the Single-cell Pediatric Cancer Atlas (ScPCA) Portal. Small one-time grants are now available for eligible pediatric cancer researchers who annotate cell types for all samples in a given group in the sample table below. 

Please note, this image only shows a partial view of the sample table. View the full sample table here. This table contains a unique group identifier, project identifier, project title, list of diagnoses, total number of samples per group, and the maximum amount that may be awarded. Each group encompasses samples from a single ScPCA project representing either a single diagnosis or a group of related diagnoses. A total of 27 grants are currently available.

Grant eligibility 

To be eligible for a grant:

  • You must complete cell type annotation for all samples assigned to a specified group identifier. Only one grant will be awarded per group of samples.
  • You must complete the cell type annotation analysis openly and collaboratively by contributing your analysis to the OpenScPCA project.
  • ALSF will only award grants with submissions meeting the eligibility requirements and acceptance criteria. All decisions regarding applications and grants, including satisfaction of requirements, are made solely by ALSF, in its sole discretion. 

These are just some of the requirements. Read the full eligibility requirements and acceptance criteria. 

Distribution and Permitted Use of Funds

  • The funds will be distributed to the researcher’s institution and must be used for pediatric cancer research. If the institution is not conducting such research at the time the grant is to be distributed, the grant will be deemed declined. 
  • ALSF does not allow the use of funds for research utilizing human embryonic stem cells or nonhuman primates. Research with human induced pluripotent stem cells is permissible.
  • The institution receiving the grant is responsible for compliance with any governmental reporting requirements and related tax obligations, if any.  

Important Dates

  • Final Table Submission Deadline: November 1, 2024 (5PM EDT)
  • Application Submission Deadline, if eligible: November 15, 2024 (5PM EST) or within ten days of notification of eligibility, whichever is sooner

All participation in this grant opportunity and contributions to the OpenScPCA project are subject to the Terms of Use and all Policies

Getting started 

Are you interested in obtaining a grant for annotating a group of samples? Head over to the OpenScPCAGitHub discussion board and file a discussion in the [.inline-snippet]Propose a new analysis[.inline-snippet] category. The Data Lab will review your idea and respond to help you get started!

Your discussion post must include:

  • The unique group identifier for which you would like to add cell type annotations 
  • The project title, project identifier, and list of diagnoses for that group
  • An outline of the approach you plan to take to complete the cell type annotation, including an explanation of the methods you plan to use to perform cell type annotation
Example of a GitHub discussion post.

All code and results must be reviewed by a Data Lab team member. You can expect multiple rounds of peer review. We encourage you to start as early as possible to avoid missing the submission deadlines.

Explore OpenScPCA analyses in progress

Perhaps these ongoing analyses will spark an idea for you! The Data Lab has started an analysis of Ewing sarcoma samples on the ScPCA Portal, as well as an exploration of doublet detection methodologies for use on ScPCA data. You can follow along and join the discussion on GitHub. 

Annotation of cell types in Ewing sarcoma samples 

This analysis aims to annotate cell types for the existing Ewing sarcoma samples on the ScPCA Portal, which can be found in SCPCP000015. The goal is to provide reliable cell type annotations that can be used for downstream analysis of the Ewing sarcoma samples. In particular, we plan to classify tumor and normal cell types, including any tumor cell states commonly observed in Ewing sarcoma. We welcome feedback from others about how they might approach identifying tumor cells in some of these samples.

Doublet detection

In [.inline-snippet]scpca-nf[.inline-snippet], the data processing pipeline behind the ScPCA Portal, we do not currently analyze or flag potential doublet cells. Adding flagging of potential doublets could improve data quality for cell typing and many other analyses. We are exploring the performance of doublet detection methodologies and their potential use on ScPCA data. 

Do you need assistance getting set up, have an analysis idea that you are unsure about, or just have questions about where to begin? We can help! Our team can provide guidance and meet with interested collaborators as needed. Post in the [.inline-snippet]Questions[.inline-snippet] category on discussions, email us at scpca@ccdatalab.org or send a message on our #open-scpca Slack channel

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