Breakout your stretchy pants and have a safe and healthy Thanksgiving!
Data Analysis and Visualization Day: December 14-15
Each funded group is expected to present an update as part of the upcoming December Data Analysis and Visualization Day. Presentations should be approximately 15-20 minutes depending on the group. Additional details including a tentative agenda and the presentation template for TMCs, TTDs and RTIs can be found on the member portal here.
Hacking the Kidney: Identify Glomeruli in Human Kidney Tissue Images
Your challenge is to detect functional tissue units (FTUs) across different tissue preparation pipelines. An FTU is defined as a “three-dimensional block of cells centered around a capillary, such that each cell in this block is within diffusion distance from any other cell in the same block” (de Bono, 2013). The goal of this competition is the implementation of a successful and robust glomeruli FTU detector.
John Marioni and Long Cai have a preprint manuscript describing how to integrate data from scRNA-seq and seqFISH assays. This is in the context of the mouse embryo, but it provides guidelines for similar types of analyses that could be done on HuBMAP tissues.
We have received a few questions about the workgroups what they cover, who should participate and how to sign up.
Our expectation is that all the funded projects are represented in the CP3 and C&E working groups and that for the groups generating data as part of data releases that they also participate in the IDAI and Data Release Teams.
We also strongly encourage participation in the 3 open working groups where they cover topics relevant to your project. The WGs will present an overview of their plans at the December Steering Committee meeting, but in advance of that below are some short descriptions and details of when the groups meet to spark your interest. For full descriptions and scopes of the working groups please see the followingfolder.
Internal Groups (exclusive to HuBMAP members only):
Collaborative Project Planning & Publications
Third Tuesday of the month at 1PM ET.
Communication & Engagement
Last Thursday of the month at 4PM ET.
Integrated Data Analysis & Interpretation
Every other Wednesday at 10:00am ET (day to day concern meetings) or every 6 weeks (big picture meetings)
Data Coordination Team
TBD
Policies
Ad hoc. First Wednesday of the Month, if needed.
External Groups (open to members of any single-cell consortia who would like to work with us):
Affinity Validation
Third Wednesday of the month at 2PM ET.
Common Coordinate Framework + ASCT +B
Next meeting is December 3rd at 1:30 pm.
Beginning in January 2021, first Wednesday of the month at 11 AM ET.
Cell Atlas Curation
Every other Tuesday at 10 AM.
Internal HuBMAP Funding Opportunities
There are two new exciting funding opportunities within HuBMAP:
HuBMAP Jumpstart Program
HuBMAP Underrepresented/Minority Student Internship Program
The Jumpstart program is designed to enable junior investigators, who are already part of HuBMAP, to work on small projects that align with the overall goals of the program. Completed applications will be accepted through December 15. Please return completed applications to jumpstartapply@hubmapconsortium.org.
The Underrepresented/Minority Student Internship Program endeavors to provide underrepresented and minority undergraduate students (as defined by NIH) opportunities to undertake mentored scientific research in an established HuBMAP Lab. For HuBMAP Labs interested in mentoring student(s) in their respective lab please complete the expression of interest form and return it to internshipapply@hubmapconsortium.org by December 1.
Additional information about both of these programs can be found on the Member Portal.
New Assay News
Alex Ropelewski is leading the first new assay data sprint which is slide-seq.
For questions or additional details regarding upcoming data releases, please contact Peter Kant.
Upcoming Meetings
Remaining consortium meetings for this week are cancelled due to the holiday, next week's meetings are:
As we approach the Thanksgiving and winter breaks, please note that the HuBMAP help desk will be operating on reduced hours so our team can celebrate the holidays and have some time to recharge. You can still send in questions and we will respond to them, however our response time will likely be slower than normal.
HHS and the American Society of Nephrology just launched two new KidneyX prize competitions:
Artificial Kidney Prize to radically transform care
COVID-19 Kidney Care Challenge to identify and share frontline solutions
Artificial Kidney Prize to Radically Transform Care
The KidneyX Artificial Kidney Prize is a competition to accelerate the development of artificial kidneys toward human clinical trials. This multiphase competition is KidneyX’s first fully dedicated effort toward artificial kidney advancement, with initial phases offering up to $10 million in prizes.
The Artificial Kidney Prize is open to both U.S. and international entrants, subject to eligibility requirements. The first phase seeks component or integrated prototype solutions that enable and advance the functionality, effectiveness, and/or reliability of artificial kidneys. Phase 1 submissions are due by March 24, 2021. Link to more information here.
COVID-19 Kidney Care Challenge
The KidneyX COVID-19 Kidney Care Challenge seeks solutions that reduce the transmission of coronavirus among people living with kidney disease and/or reduce the risk of kidney damage among people who contract the virus. Winners will receive $20,000 each in recognition of their solutions.
The challenge seeks to identify replicable solutions from providers, staff, patients, and caregivers and share them across healthcare communities. Round 1 of the challenge is now accepting solutions until December 4. Round 2 will be open to eligible entrants from Round 1, as well as new eligible entrants who did not enter the first round; the second round will accept solutions from December 9 to January 20. Link to more information here.
Enter Round 1 by 4:59 p.m. ET on December 4: Submit a frontline solution.
For questions, please contact Anne Rohall at Anne.Rohall@hhs.gov
New Member Orientation
Thank you to all of the new HuBMAP members who joined us for the new member orientation sessions over the past month. These sessions were recorded and are available for reference for all of HuBMAP. We've included the recordings along with a few helpful references for our new and veteran members.
New NCI Innovation Lab: Modeling Emergent Cellular Behavior in Cancer
Are you interested in moving past cataloging cell types to understand how cell states interact to drive tumor behavior?
Join us for a 5-day Innovation Lab to meet new collaborators, ideate new projects, receive real-time feedback and contribute to where this important field is headed.
The virtual lab will be February 25-26 and March 1-2 and 5, 2021; participation via application.
Investigators with independent appointments are encouraged to apply.
Lab mentors: Manu Platt (Georgia Tech), Dana Pe’er (MSKCC), Zev Gartner (UCSF), Deborah Gordon (Stanford), Claire Tomlin (Berkeley)
Developers in need of HIVE infrastructure may request access through the PSC web form, foundhere.
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 found here. Please report any issues or direct any questions to help@hubmapconsortium.org.
Content Suggestions
The IEC is seeking to collect information of general interest from individual members and groups to share with the rest of the Consortium. Please submit content suggestions by emailing admin@hubmapconsortium.org.
Past Newsletters are available on the Collaboration Portal.
For comments, suggestions about how to improve the HuBMAP Happenings, or questions about the consortium, please contact: help@hubmapconsortium.org
