This week we turn the spotlight away from HuBMAP to focus on the COVID-19 vaccination roll out. While there remains a great deal of effort left for the United States and other nations, we'd like to thank and acknowledge all of those who have spent countless hours on vaccine research & development and the healthcare workers and volunteers responsible for administering the doses.
HuBMAP Awards Three JumpStart Grants / Eight Summer Internships
HuBMAP has awarded two sets of exciting new awards to well deserving young researchers!
The JumpStart awards are going to three junior investigators who will undertake independent projects in HuBMAP labs. Yang Liu will undertake a project entitled: Spatial multi-omics profiling of human kidney tissue using DBiT-seq as part of the Yale TMC, under the guidance of PI Rong Fan. Angela Kruse will explore: 3D Multimodal Analysis of Eye and Pancreas Blocks Using Light Sheet Microscopy and Imaging Mass Spectrometry in the Vanderbilt TMC with PI Jeffrey Spraggins. Hang Hu will be completing a project titled: Self-supervised Mass Spectrometry Imaging Clustering with Convolutional Neural Network and Contrastive Learning as part of the Purdue TTD with Julia Laskin. Congratulations to these researchers!
The Underrepresented Undergraduate Internship program is a summer internship where students will get to undertake mentored scientific research in a HuBMAP lab. Eight students have been chosen for this inaugural program, out of 60 candidates! They will be hosted at six labs amongst Harvard Medical School, Stanford University and University of Pennsylvania. Thank you to the PI's who have agreed to host these outstanding students: Junhyong Kim, Garry Nolan, John Hickey, Nils Gehlenborg, Alison Pouch, James Gee, Kate O'Neill, and Brian Gregory!
Stay tuned for more information about all of the awardees as their research projects and internships progress.
HuBMAP Guest Speaker: Integrating single-cell lipidomics and single-cell RNA-seq
Gioele La Mannohas accepted an invitation to present at the next Integrated Data Analysis and Interpretation Working Group meeting on April 14 @ 10 AM. Gioele has done incredible work on collecting single-cell lipidomic profiles (with mass-spec) and integrating them with scRNA-seq profiles. This addresses a key challenge for HuBMAP and it may be of broad interest beyond the members of the WG.
Center for Integrated Cellular Analysis: Virtual Series
This seminar series will introduce deep-learning based approaches to register spatial 'omics' datasets into a common space. Each seminar will focus on a recently published manuscript or preprint and be presented by one of the lead authors. Talks will be openly broadcast online, with a public Q&A session after each seminar.
Next Event: April 13 @ Noon (Eastern).
Featured Speaker: Aidan Daly - Alignment, Registration, and Annotation of Spatial 'Omics' Datasets
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
CFDE Portal Demo Featuring HuBMAP Data
A 1-hour pop-up demo of newly released CFDE Data Portal that allows you to search across data from HuBMAP, Kids First Data Resource Center, Metabolomics, LINCS, exRNA, GTEx, and HMP from a single website is planned for Wednesday, April 14, at 11am PDT / 2pm EDT. Come check out what the portal has to offer and where we'll be taking it next. You can sign up for the event by clicking on the event calendar link.
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.
API for Molecular and Cellular Queries of HuBMAP Data
CMU TC, Sean Donahue, presented "Cells: An API for Molecular and Cellular Queries of HuBMAP Data" at yesterday's Steering Committee Meeting.
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.
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 email@example.com.