Happy St. Patrick's Day everyone! As part of our efforts to get our "green on" we present this week's Image of the Week. This week we have a seqFISH image from CalTech that shows RNA transcripts in a section of healthy human (or possibly leprechaun) small intestine. To see this image and others like it, check the Data Portal.
Enable Medicine (enablemedicine.com) is a new company out of Menlo Park, CA that runs CODEX-based image acquisition and analysis in their labs, and have a pipeline that performs single-cell segmentation, characterizes marker expression, and interprets cell-cell interaction maps. If you would be interested in speaking to them about their software platforms, please contact Archit Sheth-Shah
Save the Date(s):
HuBMAP Annual Meeting
This is a reminder to mark you calendars for May 19-21, 2021for the HuBMAP Annual Meeting. The meeting will be held virtually. Stay tuned for additional details.
Pediatrics and Ancestry RFA
Please spread the word about exciting funding opportunities from the Chan Zuckerberg Initiative (CZI).
These RFAs will support collaborative networks of researchers for three-year projects. Teams should consist of at least three and up to 10 principal investigators, including at least one computational biologist or data scientist and one expert in single-cell biology. They strongly encourage community-engaged researchers to be involved in the collaboration as Co-PIs
to help provide, promote, and build culturally competent connections with the research participants and members of their community. The RFA builds off of CZI’s learnings from supporting 10 collaborative research teams to study tissue samples from a diversity of populationsas an initial step in addressing representation in the HCA.
HCA is also looking for reviewers to provide input on proposals for the Ancestry and Pediatrics Networks RFAs. If you're interested in reviewing, please contact Ellen Todres.
Notice of Intent to Publish: (AMP AIM)
The Accelerating Medicines Partnership in Autoimmune and Immune Mediated Diseases has recently published a Notice of Intent to Publish that may be of interest to HuBMAP investigators. The FOA is expected to be released later this month.
AMP AIM will cover diseases including RA, SLE, psoriatic spectrum diseases and Sjogren's syndrome. The Program will pioneer the concept of 'disease reconstruction' by bringing in novel multi-modal analytics to elucidate how immune cells and tissue-resident cells network with each other to cause tissue injury and clinical disease. Among the program objectives, the following may be of interest to the HuBMAP investigators:
Conduct spatial mapping of cell types and states to identify the pathways of crosstalk between cells that drive inflammation and tissue damage.
Model integrated single cell multi- 'omics data in a spatial context and identify inflammatory mediators to uncover the regulatory mechanisms governing functions within and between cells that cause disease.
Single Cell Genomics Day: A (Virtual) Practical Workshop
Save the date for the Satija Lab's fifth annual Single Cell Genomics Day - Friday, March 26 from 10 AM to 5 PM EST. HuBMAP members presenting include Cole Trapnell, Fei Chen and Shila Ghazanfar.
Description: Recent developments in molecular biology, microfluidics, and computational biology have transformed the field of single cell genomics, and have widespread biological applications. However, the breathtaking pace of technology development has given rise to a multitude of molecular protocols, commercial systems, and computational challenges.
This workshop will begin with an overview of exciting developments in the field over the past year, followed by in-depth presentations on exciting methods and techniques. The goal is to empower the audience to utilize single cell genomics in their work. The workshop is free and open to beginners and experts alike.
All talks will be openly live-streamed; registration is not required. More information.
This guide provides the process a data provider should follow when submitting data to HuBMAP for it to be displayed in the portal.
Since the goal is to continue enhancing the capabilities of the portal, this document will be versioned as changes are made. The HIVE recommends accessing the document via the link to ensure you are viewing the most up to date version.
Suggestions regarding the messaging within this document can be sent to the Help Desk.
Intra-Consortia Junior Investigator's Meeting: Seeking Planning Committee Members
Are you a graduate student or a postdoc? Are you interested in working with members from HTAN, CZI, as well as other HuBMAP members to create a junior investigator's meeting? Here is the advertisement for you!
We are soliciting three HuBMAP graduate students or postdocs to join the planning committee for an intra-consortia Junior Investigator's Meeting, which will virtually take place September 22-24.
The HuBMAP Tools Component at Harvard Medical School will be hosting a virtual workshop for members of cell atlas projects and the broader community. The goal of the workshop is to discuss and prioritize interactive visualization and analysis functionality that should be integrated into the HuBMAP Portal and other related data resources. The information gathered in this workshop will be incorporated into a roadmap for the HuBMAP Portal.
The event will include a presentation of the tools that are currently available in the HuBMAP Portal and future directions.
The next Human Cell Atlas General Meeting will be held June 28-30 and will take place virtually. To maximize participation from the global audience, main sessions will be scheduled between 9:00 AM - 1:00 PM EST each day. Recordings of talks will be available later for viewing on the event platform, as well as onYouTubeandBilibilichannels.
Please visit thewebsiteoremail for more information. Further details about HCAeventsare available.
Reminders, Links to Resources, etc.
When does Valentine's Day come after St. Patrick's Day?
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.