HuBMAP Happenings 11/17/2020

 
HuBMAP Happenings 11/17/2020
November 17, 2020
Image of the Week

This lightsheet microscopy video (still pictured above) of a thymus from a one-year old human male was sent to us by Seth Currlin at the TMC-University of Florida. The neural network within the thymus is in green, and the tyrosine hydroxylase elements are magenta, and the external capsule appears as a semi-transparent white curved wall. After clearing the tissue of light scattering lipids a Zeiss Z.1 light sheet microscope was used to acquire sequential images through the specimen. Arivis4D software was used for 3D rendering.

If you are right now thinking “Hey! I have cool images and videos! Why can’t I have mine as an Image of the Week?”, fret not my dear ones! You can! Just send Dena an image or a video and we will make it happen. 
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.

Link to more information here.
ACMI Fellowship Recipient
 
Congratulations to HuBMAP member Griffin Weber, MD (of HIVE TC - IU) on being elected!

Link to more information here.
Guidelines for reporting single-cell RNA-seq experiments (Publication)
 
Congratulations are also in order to Nils Gehlenborg, Sarah Teichmann, Laura Clarke, John Maroni, and other colleagues (including HCA members), on their publication in Nature Biotechnology.

Direct link to the pdf, here.
Working Groups & Meeting Dates/Times:
 
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.

The signup sheet can be found here.

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 following folder.

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 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)

Applications due December 7. Apply here.
Follow @NCISysBio for updates
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. Further details, including a template, will be sent out via email.
Upcoming Meetings

Wednesday, November 18 @ 10 AM -
DRT Portal

Monday, November 23 @ 2 PM -
DRT Sequencing

All times are Eastern
RFAs

Developmental Genotype-Tissue Expression 

Link to additional information here.

HeartShare: Next-Generation Phenomics to Define Heart Failure Subtypes and Treatment Targets

Clinical Centers

Link to additional information here.

Data Translation Center

Link to additional information here.  

RFA-MH-21-140 BRAIN Initiative Cell Census Network (BICCN) Scalable Technologies and Tools for Brain Cell Census

Link to additional information here.

Pilot Projects Enhancing Utility and Usage of Common Fund Data Sets (RFA)

Link to additional information here.
KidneyX Launches 2 New Prize Competitions
 
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 NCI Innovation Lab on Modeling Emergent Cellular Behavior in Cancer
 
Please help spread the word about an upcoming virtual Innovation Lab on Modeling Emergent Cellular Behavior in Cancer sponsored by the National Cancer Institute's Cancer Systems Biology Consortium.

The National Cancer Institute is hosting an Innovation Lab to generate creative strategies and new research collaborations aimed at improving understanding, prediction, and validation of dynamic cell-cell communication and emergent behaviors of cell ensembles in cancerous tissues. This 5-day virtual event will take place in February 25-26 and March 1-2 and 5, 2021. PI-level cancer researchers and clinician scientists, cell and developmental biologists, systems biologists, evolutionary biologists, engineers, physical scientists, and computer scientists, etc. are strongly encouraged to apply.

This announcement is targeted to faculty-level participants. Please share this information with any colleagues you think may be interested.
More information here.
Single Cell Job Opportunity:

Data Focused Research Associate at NCI Bethesda

More information about the roles and expected qualifications can be found at this link.

Please contact Kimia Dadkhah (kimia.dadkhah@nih.gov) or Michael Kelly (michael.kelly3@nih.gov) about this position.
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. 
Help Desk Holidays

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.
Dates for reduced hours included:
November 26 - 29
December 24 - January 3.
Reminders, Links to Resources, etc.
New Members to Your Team?

Please have them register for an account at: https://profile.hubmapconsortium.org/register
HuBMAP Haha

A biologist, a physicist, and a programmer stand in front of an empty house. Suddenly, two people walk into the house. A few minutes later, three people emerge.

The biologist says - "They must've reproduced!"

The physicist says - "This must be a measurement error."

The programmer says - "I think I left the back door open..."
HIVE Infrastructure

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 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
HuBMAP Consortium
 

View Previous Newsletters

Return to Collaboration Portal.

Collaboration Portal