We're checking in with some HuBMAP team members at their home offices to tell us a bit about their work within HubMAP and to share how they're handling social distancing protocol.
Deb started her User Services career just before the advent of electricity. She began in what was then the central computing center at Carnegie Mellon University and moved to the Pittsburgh Supercomputing Center in 1986, where she and fellow HIVE IEC member Joel Welling were the entire User Support team for quite some time. Along the way, she’s given training classes, consulted with faculty on computing needs, written documentation, and of course, answered a lot of tickets.
As part of her PSC duties, she joined the HuBMAP HIVE IEC team about a year ago and has focused mainly on the website and the help desk. If you send email to help@hubmapconsortium.org, you have a fifty-fifty chance of her handling your ticket. She tries to always remember what her mother used to say about vinegar vs. honey in her replies, but apologizes in advance if you catch her on a vinegar day.
She’s very grateful that she visited San Diego in early March to see her son and his family, since God only knows when she’ll have that chance again. In the meantime, she is thankful for video calling and spends her free time in her garden or at her cabin in Ohio, where she practices her swimming strokes while her husband drowns worms.
Countdown to Data Release
Feedback is still being accepted and tracked from those responsible for reviewing submitted datasets.
Please continue to send email to: help@hubmapconsortium.org for issues with missing or incorrect data as early as possible.
Last week’s edition was inspired, but what about papers that are on arXiv and not biorXiv? Is there a way to easily find papers there?
Sincerely,
A Wicked Smart HuBMAP PI
Dear Learn Something New Every Day,
I had no idea such a thing as arXiv existed, but now that I know, I will go about tagging HuBMAP papers there, as well!
So I would like to rephrase my earlier advice: Please let me know if you have papers on either so I can tag them!
Signed,
Thanks for the tip!
Job Opportunities:
HuBMAP Postdoc Position
The Department of Intelligent Systems Engineering at Indiana University, Bloomington, is seeking a Postdoctoral Fellow join an interdisciplinary research team working on 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 postdoctoral fellow will help identify and catalog knowledge about the structure of the vascular pathways in the human body (arteries, veins, capillaries, and lymph vessels). This will be conducted primarily through a literature search to find (1) descriptions of the named vascular pathways and microvascular architecture in different organs of the body; (2) descriptions of the variability of the vascular system across different individuals; (3) imaging studies that show the physical 3D structure of vascular pathways; and (4) studies that identify biomolecular signatures unique to different parts of the vascular system, such as how gene expression varies in endothelial cells across the body. The postdoctoral fellow should have a background in human anatomy or related fields such as systems biology, cell biology, radiology, or pathology.
The position is for 12 months initially and can start as soon as August 2020 (negotiable).
If you have questions or wish to apply, please contact Prof. Katy Borner, katy@indiana.edu
Use ‘HuBMAP-Postdoc’ insubject header.
HIVE Demo Day Registration
Hosted by Indiana University
HIVE Demo Day (open to all consortium members): September 21-22, 2020
The agenda and general information can be foundhere.
Watch for Zoom links and a call for posters and/or recorded demos as the date of the event approaches.
The Hackathon focused on identification of cell types has been postponed until later this year. Stay tuned for me details.
Yearly Progress Reports (RPPRs) are due 6-8 weeks in advance of the end of the funding period. For your reference, here are the end dates for the different Components:
* RTIs - August 31, 2020
HuBMAP Haha
What type of fish is made up of only two sodium atoms?
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 and 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
