Above is a CODEX MIF image of the cortex from a human kidney using 19 antibodies from Elizabeth Neuman at Vanderbilt TMC that shakes us to the core, no kidneying.
Data Science WG Call
Concluded
Future meetings have been cancelled, as the new Working Groups are beginning to launch.
It has been a pleasure working with you - please consider membership in these new efforts.
- Margaret Vella
Policy Working Group
Meeting Agenda
Wednesday, October 7 @ 3 PM
A discussion on HuBMAP Editorial Controls of Data Publication (timing and “packet” size), Assignment of DOIs, Authors, Contacts and Attributions.
Virtual Symposium on LINCS Perturbation-Response Community Resources: Science, Utility, Challenges
The NIH Common Fund’s Library of Integrated Network-based Cellular Signatures (LINCS) program is holding a Virtual Symposium November 19-20.
The Common Fund’s Library of Integrated Network-based Cellular Signatures (LINCS) program was launched in 2010. Its focus is perturbational biology undertaken at scale to create community resources for query and analysis. By using a multi-omic approach, LINCS investigators have built a catalog of cellular responses (signatures) from various assays (transcriptomics, proteomics, imaging) performed on hundreds of different cell types following tens of thousands of genetic and small molecule perturbations.
The LINCS Virtual Symposium will feature presentations from LINCS investigators that address: (1) major scientific achievements and insights on signatures for drug action and prediction of drug related adverse events, (2) additional value addition from approaches to integration of multiple data types including proteomics and transcriptomics data to identify biological states, (3) development of methodologies for doing rigorous reproducible biological research including with iPS differentiated cells within a consortium, (4) new computational tools for data integration & data FAIRness, (5) future challenges in perturbational biology.
The symposium will also include presentations from users of LINCS data and tools from both academia and industry. Short presentations that describe continued accessibility of LINCS tools and data will also be an area of emphasis during the symposium.
Visit the LINCS Virtual Symposium webpage here for updates and registration information.
Visit the SPARC Art Contest Voting page hereto see the variety of images and videos inspired by SPARC's goal of advancing bioelectronic medicine through precise control of the autonomic nervous system. Be sure to click through every image and video to see the full size artwork, view the short videos, and cast your vote by October 9, 2020.
NIH-HCA: CCF ASCT+B Tables Meeting
When: October 10, 2020 @ 1:30 PM ET.
If you would like to attend but don't see a Zoom invite in your calendar, please register and share more info on your expertisehere.
(RFA) 3D Technologies to Accelerate HTAN Atlas Building Efforts
The overarching goal of this FOA is to accelerate research efforts conducted and led by the Human Tumor Atlas Network (HTAN, humantumoratlas.org) via the implementation of three-dimensional (3D) imaging technologies that will allow for a comprehensive view of the dynamic multidimensional ecosystems that define tumors in humans.
Each project will lead to the multiplexed 3D characterization of at least one cancer transition investigated by the HTAN (pre-malignant to malignant, primary to metastatic, therapy responsive to resistant). The data and analytical tools generated through this FOA will be made available for use by the research and clinical communities through the activities of the HTAN Data Coordinating Center.
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.
A position is available within the NCI Single Cell Analysis Facility that provides dedicated support to the NCI Center for Cancer Research. The person in this position would work closely with the rest of the Single Cell Analysis Facility team to support state-of-the-art single cell methods such single cell gene expression profiling, vdj sequencing, epigenomic profiling, and proteogenomic and multimodal analyses, as well as spatial expression profiling and other emerging methods. This work is in support of both basic science and translational research projects.
More information about the roles and expected qualifications can be found at this link on the Leidos Biomedical Research Inc career website. Leidos operates the Frederick National Laboratory for Cancer Research (a FFRDC) through a long-standing contract with NCI.
Please contact Kimia Dadkhah (kimia.dadkhah@nih.gov) or Michael Kelly (michael.kelly3@nih.gov) about this position.
HuBMAP Visible Human MOOC
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.
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.
What did Yoda say when he first saw himself in 4K video?
"HDMI"
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
