Thy-mus ask you a question; did you know the thymus is where T cells prepare to defend your body? This week we present imaging mass cytometry of a thymus from the Bodenmiller lab and U. of Florida teams. This image can be found within HuBMAP's Data Portal. Give your immune system a boost and check it out!
Do you have questions about the HuBMAP data submission process? Check our our new data submission guide that outlines the process, in detail.
Suggestions regarding the messaging within this document can be sent to the Help Desk.
NIH Bridge2AI Update
The NIH plans to publish two Funding Opportunity Announcements (FOAs) as part of the NIH Common Fund's Bridge to Artificial Intelligence (Bridge2AI) program. The expected publication date for these future FOAs is June 2021, so now is a good time to start thinking about developing responsive applications. Learn more on our Bridge2AI Funding Opportunities.
Notice of Intent to Publish a Funding Opportunity Announcement for NIH Bridge2AI Integration, Dissemination, and Evaluation (BRIDGE) Center (U54 Clinical Trial Not Allowed). More information.
Notice of Intent to Publish a Funding Opportunity Announcement for Research Opportunity Announcement for the Data Generation Projects of the NIH Bridge to Artificial Intelligence (Bridge2AI) Program (OT2). More information.
Please note that applications are not being solicited at this time. The Bridge2AI program is currently developing teaming activities for potential applicants, and these Notices are being provided to allow potential applicants sufficient time to develop responsive applications and to plan participation in future teaming activities.
You're encouraged to share the Bridge2AI listserv signupwith your contacts and networks so they will receive updates on future funding announcements and the latest news from the Bridge2AI program. You can also keep up to date with the latest information by visiting the Bridge2AI website.
NIH Funding Announcements
Common Fund IDG Program:
Notice of Special Interest (NOSI) for Illuminating the Druggable Genome (IDG) Initiative: Request for Administrative Supplements to Existing Grants for incorporating single cell data into the IDG Knowledgebase. Application Due Date: June 15, 2021. More information.
Cutting Edge Informatics Tools for Illuminating the Druggable Genome (U01 Clinical Trial Not Allowed). Application Due Date: June 15, 2021. More information.
Short-term Mentored Research Career Enhancement Award to Promote Diversity (K18 No Independent Clinical Trials). Application Due Date(s): June 12, 2021; February 12, 2023. More information.
NHGRI Predoctoral to Postdoctoral Transition Award for a Diverse Genomics Workforce (F99/K00). Application Due Date(s): August 8, 2021; December 8, 2021. More information.
NIH Office of Data Science Strategy
Notice of Special Interest: Support for existing data repositories to align with FAIR and TRUST principles and evaluate usage, utility, and impact. Due Date: May 20,2021. More information.
Notice of Special Interest (NOSI): Administrative Supplements to Support Enhancement of Software Tools for Open Science. Due Date: May 15, 2021. More information.
Note: the above funding announcements were added to the RFAs/Competitions column last week and will be available until the due dates pass.
AMP AIM Program Funding
Accelerating Medicines Partnership Autoimmune and Immune-Mediated Diseases: Disease Teams for Rheumatoid Arthritis, Lupus, Psoriatic Spectrum Diseases, and Sjögren’s Syndrome (UC2 Clinical Trial Optional). Letter of intent due: June 15, 2021. More information.
Accelerating Medicines Partnership Autoimmune and Immune-Mediated Diseases: Technology and Analytic Cores (TACs) and Research Management Unit (RMU) (UC2 Clinical Trial Not Allowed). Letter of intent due: June 15, 2021. More information.
Computational biology is undergoing a revolution. Recent advances in microfluidic technology enable high-throughput and high-dimensional of individual cells at unprecedented scale. But there’s a catch. Single-cell analysis is hard.
Check out an effort supported by CZI, openproblems.bio, to learn more and join in the efforts!
HuBMAP Guest Speaker: Integrating single-cell lipidomics and single-cell RNA-seq
Gioele La Mannohas accepted an invitation to present at the next Integrated Data Analysis and Interpretation Working Group meeting on April 14 @ 10 AM. Gioele has done incredible work on collecting single-cell lipidomic profiles (with mass-spec) and integrating them with scRNA-seq profiles. This addresses a key challenge for HuBMAP and it may be of broad interest beyond the members of the WG.
A 1-hour pop-up demo of newly released CFDE Data Portal that allows you to search across data from HuBMAP, Kids First Data Resource Center, Metabolomics, LINCS, exRNA, GTEx, and HMP from a single website is planned for Wednesday, April 14, at 11am PDT / 2pm EDT. Come check out what the portal has to offer and where we'll be taking it next. You can sign up for the event by clicking on the event calendar link.
HuBMAP's own Zhen Chen of TTD-UCSD City of Hope has been asked to guest edit a Method Collection for JoVE that will focus on single-cell protocols for isolating and profiling endothelial cells. If you have a cutting-edge protocol that you would like to submit, please check out this link or contact Zhen by June 15, 2021 for more details.
Cell Atlas Curation WG Call
The next Cell Atlas Curation WG call will be held April 20 @ 10 AM EST and will focus on Workshop Planning Discussion. Zoom link. Running Notes.
The workshop goal:
Define interoperability standards that enable the querying of cell type annotation and expression matrix files.
To Do during this meeting:
Clarify & coordinate dates & a schedule for a summer workshop.
Choose reps ( HCA, HTAN, HuBMAP) 10 or fewer to produce a strawman case and schedule the workshop.
**Attendees are asked to forward your info/suggestions & nominees for contributors to the person who invited you to these biweekly workshop discussions.
HuBMAP Awards Three JumpStart Grants / Eight Summer Internships
HuBMAP has awarded two sets of exciting new awards to well deserving young researchers!
The JumpStart awards are going to three junior investigators who will undertake independent projects in HuBMAP labs. Yang Liu will undertake a project entitled: Spatial multi-omics profiling of human kidney tissue using DBiT-seq as part of the Yale TMC, under the guidance of PI Rong Fan. Angela Kruse will explore: 3D Multimodal Analysis of Eye and Pancreas Blocks Using Light Sheet Microscopy and Imaging Mass Spectrometry in the Vanderbilt TMC with PI Jeffrey Spraggins. Hang Hu will be completing a project titled: Self-supervised Mass Spectrometry Imaging Clustering with Convolutional Neural Network and Contrastive Learning as part of the Purdue TTD with Julia Laskin. Congratulations to these researchers!
The Underrepresented Undergraduate Internship program is a summer internship where students will get to undertake mentored scientific research in a HuBMAP lab. Eight students have been chosen for this inaugural program, out of 60 candidates! They will be hosted at six labs amongst Harvard Medical School, Stanford University and University of Pennsylvania. Thank you to the PI's who have agreed to host these outstanding students: Junhyong Kim, Garry Nolan, John Hickey, Nils Gehlenborg, Alison Pouch, James Gee, Kate O'Neill, and Brian Gregory!
Stay tuned for more information about all of the awardees as their research projects and internships progress.
Reminders, Links to Resources, etc.
How'd the HuBMAP Help Desk know a tree tried to submit data?
Developers in need of HIVE infrastructure may request access through the PSC web form, found here.
Instructions for using HIVE infrastructure can now be found in the "Quick Links" section of the Collaboration Portal. A direct link to this documentation can be foundhere. Please report any issues or direct any questions firstname.lastname@example.org.