Hang Hu is a 4th year Ph.D. candidate in Dr. Julia Laskin's research group at Purdue University. He investigates nano-DESI mass spectrometry imaging (MSI) and participates in the Computational Interdisciplinary Graduate
Program. He is interested in the application of machine learning, computer vision and lab automation for MSI. Outside the lab, Hang usually runs 15 miles a week and enjoys cooking!
Learn more about Hang's JumpStart Project and this year's other awardees on our website.
Image of the Week
This week we present a seqFISH image of healthy human small intestine from Long Cai's lab at CalTech. The bright yellow dots in the image are fluorescent probes that seqFISH uses to find RNA within the cell. Hope this image brings a bright spot to your day! Explore the image within the Data Portal.
Send your best birthday wishes to Dena and thank her for her various contributions to the Consortium!
HuBMAP Annual All-Hands Meeting
The meeting will take place on *Wednesday, Thursday and Friday May 19-21,
The Annual Meeting Websitehas all of the information you need to know . Note that you'll need to be logged into the Member Portal to view the website. Below are the themes of each day (all times in EDT):
Day 1, Wednesday 5/19, 12:00pm-6:00pm: *Harmonizing HuBMAP*
Day 2, Thursday 5/20, 12:00pm-6:00pm: *How do we build an atlas*?
Day 3, Friday 5/21, 10:30am-6:00pm: *External Collaboration and Engagement:
Cell Type Identification & Annotation*
We have an agendapacked full of presentations, breakout sessions, and plenty of opportunities to chat with fellow Consortium members! With many opportunities for
discussion, we are excited to hear from a diverse range of voices from across the Consortium, including from our HuBMAP junior investigators.
There's no need to register for this meeting - you can access it from the following Zoom links:
The next Cell Atlas Curation WG call will be held May 4 @ 10 AM EST and will continue a Workshop Planning Discussion. Zoom link. Running Notes.
Begin building a master list of use cases for the workshop:
Nils has provided a summary of HuBMAP use cases to use as a starting point for developing use cases for the workshop (link in the notes). Starting with this, the goal is to create a master list of strawman use cases and perhaps present it to the workshop for expansion.
Prepare and outline for the workshop agenda:
What is the output of a query?
Discuss proposed specific topics for the workshop:
Constraining queries on a cell type:
Constrain the cell types we begin with.
All cells that express this marker (to some degree).
T-cells are a common use case.
Then expand to other cell-type leveraging ontologies to focus on branches below.
Providing a resource for discovering data based on ontologies.
Notices of Intent to Publish - BRAIN Initiative Cell Atlas Network (BICAN)
The following three Notices are provided to allow potential applicants sufficient time to develop meaningful collaborations and responsive projects. Please note the estimated application due date is November 9, 2021 for all BICAN FOAs.
Estimated Publication Date of Funding Opportunity Announcement: July 01, 2021. First Estimated Application Due Date: November 09, 2021.
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.
Reminders, Links to Resources, etc.
When the lab smells like rotten eggs a lot of people have to sulfur through it.
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.