This week's image is courtesy of the lab of Sean Bendall at Stanford. This human colon image shows immune cells in yellow, the cell membranes of the villi in cyan, nuclei in white and muscle cells in magenta. It was captured as part of a study that established a new approach to investigate cellular metabolism in human tissues.
This week HuBMAP hosted our second external Sci/Tech Webinar which featured demos of Azimuth, the RUI and the Visible Human MOOC. A big thank you goes out to Rahul, Katy and Andreas for their time and informative presentations.
If you were not able to join us at the webinar you can find the recording on our website and on the HuBMAP YouTube channel.
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.
Seminar: Multimodal Imaging Mass Spectrometry: Advanced Technologies for the Construction of Biomolecular Tissue Atlases
Join HuBMAP PI Jeff Spraggins for an online seminar on Wednesday, March 10 @ 1 PM ET. Zoom Link. Meeting ID: 912 0099 4500. Password: Research
Azimuth is Live
Azimuth, developed by the New York Genome Center Mapping Component, is now available.
The web application uses an annotated reference dataset to automate the processing, analysis, and interpretation of a new single-cell RNA-seq experiment. Azimuth leverages a 'reference-based mapping' pipeline that inputs a counts matrix of gene expression in single cells, and performs normalization, visualization, cell annotation, and differential expression (biomarker discovery). All results can be explored within the app, and easily downloaded for additional downstream analysis.
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.
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.
If you eat too much pi you'll end up with a big circumference.
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.