We wanted to take a moment to thank those groups and individuals who have helped with promoting the Data Release by posting, tweeting, and linking the Data Portal from their lab and institution websites.
If you haven't had the opportunity to promote the data release in your networks, don't worry it's not too late! Contact the help deskfor more information and resource to promote the data release
UC San Diego Institute for Genomic Medicine Symposium on Spatial Omics
The UC San Diego Institute for Genomic Medicine is holding a virtual symposium on Monday, October 26, 2020. This meeting calls scientists from across the United States to come together and contribute their cutting-edge ideas on "Spatial Omics.” As a platform for researchers to discuss the latest advancements on spatial gene expression, this meeting strives to glean novel insights into the role cell-type specific regulatory mechanisms play in complex traits. It is in conjunction with the virtual American Society of Human Genetics meeting occurring on October 27th through October 30th, 2020.
HuBMAP PIs Long Cai and Katy Börner will be presenting.
The course opened Tuesday, September 1, 2020 in parallel with the 1st HuBMAP Portal Release. It will welcome students continuously until the 2nd HuBMAP Portal Release begin of January 2021.
The course aims to provide you with:
Theoretical and practical understanding of different single-cell tissue analysis techniques.
Expertise in single-cell data harmonization used to federate data from different individuals analyzed using different technologies in diverse labs.
Hands-on skills in the design and usage of semantic ontologies that describe human anatomy, cell types, and biomarkers (e.g., marker genes or proteins).
Knowledge on the design and usage of a semantically annotated three-dimensional reference system for the healthy human body.
An understanding of how the HuBMAP reference atlas might be used to understand human health but also to diagnose and treat disease.
Wait! There are new people coming?! No one tells me anything! Are we supposed to anything about this?
Sincerely,
Haven't You Heard of ‘Stranger Danger’?!
Dear 'Don't Be so Paranoid',
In the words of J.J. Wilks “Success occurs when strangers become friends”. Fret not! Yes, the awards for the new TMCs and TTDs have either been awarded, or will be shortly, so we will be seeing new people at meetings and calls soon!
You don’t have to do anything except continue to be the spectacular people you are. All will be well...I hope.
Dena
Save the Date
December Demo Day
Mark your calendars for December Demo Day on December 14-15, details to follow as we get closer.
The National Human Genome Research Institute (NHGRI) and the Eunice Kennedy Shriver National Institute for Child Health and Human Development (NICHD) are co-collaborating on a new initiative, developmental Genotype-Tissue Expression (dGTEx), to catalog and analyze transcriptional profiles from a wide variety of tissues from the pediatric period, including neonates through adolescents, in a post-mortem setting.
Register for HIVE Demo Day -Submit a Poster or Demo
Registration for the September HuBMAP Demo Day event, taking place on September 21-22, 2020 is now open here. Event information can be found on the website.
There will be an opportunity to showcase your team's work through posters, pre-recorded videos, and live demos during the meeting. Please use this form to submit your posters and pre-recorded demos (videos), and to let us know if you'd like a time slot for a live demo by September 11th. There is not a limit on the number of submissions from one team.
The meeting for September 22nd has been cancelled due to the September Demo Day. Regularly scheduled meetings for this working group will resume on October 6.
HuBMAP VCCF Postdoc Position
HuBMAP VCCF Postdoc
Apply by September 10, 2020
Position Description
Using Data Science to Map the Entire Human Vasculature
Blood vessels are both the source of life for people, bringing oxygen and nutrients to all living cells, as well as pathways that lead to disease, including coagulopathies in COVID-19, vascular abnormalities in diabetes, and the spread of metastatic cancers. For 2000 years, scientists have been cataloging different parts of the vasculature, but no one has yet connected the dots to show the full network of vessels throughout the body. As a Postdoctoral Fellow in the Department of Intelligent Systems Engineering at Indiana University, Bloomington, you can be the first person in history to map the entire human vasculature using modern data science techniques! You will gain experience in using natural language processing to extract existing knowledge about the vascular system from the biomedical literature, mining biomolecular databases to obtain endothelial cell gene expression profiles, and creating interactive visualizations and anatomical ontology graphs. This is a key part of an ambitious national effort to create a detailed map of all the cells within the human body-the NIH funded Human BioMolecular Atlas Program (HuBMAP).
The position is for 12 months initially and can start as soon as September 2020 (negotiable). The postdoctoral fellow should have a background in human anatomy or pathology, or related fields such as systems biology, cell biology, or radiology.
If you have questions or wish to apply, please contact Prof. Katy Börner, katy@indiana.edu
As I suspected, someone has been adding soil to my garden...
the plot thickens.
HIVE Infrastructure
Developers in need of HIVE infrastructure may request access through the PSC web form, foundhere.
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
