Want to give your guts a visceral thrill? This week we feature a CODEX image of healthy colon tissue from John Hickey of Garry Nolan's lab at Stanford. We also remind you to wear your shades of blue for National Colorectal Cancer Awareness Month.
In the image, the blue indicates nuclei of cells, green - goblet cells, gray - nerve cells, red - smooth muscle cells, yellow - epithelial cells, magenta - immune cells, and cyan - proliferating cells.
Are you looking for fame and notoriety? Send your best images to email@example.com.
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.
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.
There will be a virtual poster room with two interactive poster viewing sessions: One session in a time zone convenient to Asia and Australia and the other in a time zone convenient to Africa, Americas, and Europe. Interested poster presenters will need to submit abstracts via the registration site (coming soon).
HCA is aiming to have a public engagement social hour, as well as interactive sessions on challenges and issues for the research community and how these may be addressed. If you and your team would like to showcase your public engagement work, or are facing a challenge, or have ideas for discussion topics, pleasereach outto us; it would be great to hear from you!
Please visit thewebsiteoremail for more information. Further details about HCAeventsare available.
HCA Bionetworks Seminars
The next seminar in the series is scheduled for March 11 @ 10:30 AM EST and will feature Development and Organoid Bionetworks.
The two featured speakers are:
Hans Clevers (Hubrecht Institute) - "Adult stem cell-based organoids at single cell resolution”
Paola Arlotta (Department of Stem Cell and Regenerative Biology, Harvard University) - "Development and disease of the human brain at single cell resolution"
The talks will be followed by three concurrent breakout sessions:
1. Bioinformatics challenges: Data management / in vivo in vitro comparisons / meta-data / quality control
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.
We're spotlighting work being completed by various groups who are deep in the software development process.
This week we're featuring the starting point of the data submission process completed by representatives from HuBMAP data generation sites - the Data Ingest Portal (Ingest UI). The portal houses both the ID System for donor information and the Data Ingest tool for dataset submission. Development of the UI is handled by HIVE members from CMU, IU, Pitt and PSC. The data is securely housed within Globus and is integrated into the Ingest UI.
After data is successfully submitted, the data producers work with HIVE members in a reconciliation process to ensure that only high quality data is moved forward.
Check out their Github repositoryfor a look at the deployment environment and API information. Next time you're browsing the Data Portal take a moment to reflect on the tremendous efforts put forth to centralize, protect and publish HuBMAP data.
Reminder to Register
External Sci-Tech Webinar: March 8 @ 3PM EST
Registration is now open for the next external webinar. HuBMAP members must register for this event to attend.
The first presentation will be delivered by Rahul Satija of HIVE New York Genome Center Mapping Component who will present Azimuth: An App for Reference-Based Single-Cell Analysis.
Katy Börner and Andreas Bueckle of HIVE Indiana University Mapping Component will then feature the Registration User Interface (RUI) and Visible Human Massive Open Online Course (VHMOOC).
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.
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.