genomics

Mentors and Regional Facilitators

Name	Region	Skills	Interests
Alyssa Pivirotto	ACCESS CSSN, Campus Champions	Recursion, stop!	arcgis machine-learning
Carrie Brown	CAREERS, ACCESS CSSN, CCMNet	Recursion, stop!
Cindy Cheng	Campus Champions	abstract affiliations ai archiving artificial-intelligence azure backup benchmarking more...	Recursion, stop!
David Carlson	ACCESS CSSN, Open OnDemand	bash bioinformatics biology gatk genomics ookami python r more...	Recursion, stop!
Daniel Morales	Campus Champions	ACCESS ACCESS-allocations ACCESS-credits adding-users allocation-management anaconda bash batch-jobs more...	Recursion, stop!
Diana Toups Dugas	Campus Champions	bioinformatics biology genomics proposal-development research-facilitation software-carpentry training workforce-development	Recursion, stop!
Feseha Abebe-Akele	CCMNet	abstract ACCESS ACCESS-account ACCESS-allocations ACCESS-credits ACCESS-website adding-users affiliations more...	Recursion, stop!
Jordan Hayes	Campus Champions	acls administering-hpc amber anaconda api atlas aws bash more...
Jeremiah Olugbami		abstract affiliations bioinformatics biology chemistry citation genomics hardware more...
Konda Reddy Karnati	Campus Champions	ACCESS ACCESS-account artificial-intelligence bash big-data bioinformatics campus-champions centos more...
shuai liu	ACCESS CSSN	ai anaconda azure big-data bioinformatics biology containers data-analysis more...
Nil Mu	CCMNet	artificial-intelligence bioinformatics computer-science data-science genomics hpc-arch-and-perf hpc-cluster-architecture hpc-operations more...	artificial-intelligence bioinformatics genomics hpc-cluster-architecture performance-tuning workflow
Nicholas Panchy	Campus Champions	bash bioinformatics biology conda easybuild genomics modules open-ondemand more...
Russell Hofmann	ACCESS CSSN, CCMNet	computational-chemistry data-analysis data-science dft gaussian genomics gromacs kubernetes more...	administering-hpc cluster-support computational-chemistry data-analysis data-science dft gaussian genomics more...
Rob Harbert	Northeast	anaconda batch-jobs big-data bioinformatics biology distributed-computing genomics gis more...
Xiaoqin Huang	ACCESS CSSN	ACCESS-account ACCESS-credits adding-users affinity-group allocations-extension allocations-proposal amber anaconda more...	ACCESS-credits ACCESS-website adding-users affinity-group allocations-extension allocations-proposal amber anaconda more...
Vijay Shankar	Campus Champions	administering-hpc archiving backup bash big-data bioinformatics biology centos more...	ACCESS ansible aws azure campus-champions cgroups cifs cloud more...
Wesley Brashear	ACCESS CSSN, Campus Champions, Open OnDemand	bioinformatics biology genomics python r
William Lai	ACCESS CSSN	administering-hpc ai anaconda archiving backup bash bioinformatics biology more...	administering-hpc ai archiving bash benchmarking big-data bioinformatics biology more...
Yun Shen	CAREERS, Northeast, ACCESS CSSN, CCMNet	big-data bioinformatics data-analysis data-science genomics open-ondemand programming Programming more...

Users

Name	Roles	Skills	Interests
Carrie Brown	mentor steering committee	bioinformatics cleanup community-outreach data-wrangling distributed-computing genomics github github-pages more...	Recursion, stop!
Emma Strand	student facilitator	anaconda archiving bash big-data bioinformatics biology community-outreach data-analysis more...
Chris Hemme	researcher/educator	Recursion, stop!	anaconda big-data bioinformatics biology data-analysis genomics python r
Ifeoma Ugwuanyi	student facilitator	Recursion, stop!	anaconda big-data bioinformatics biology data-analysis data-wrangling genomics python more...
Kenneth Acosta	student facilitator	Recursion, stop!	batch-jobs cluster-management cluster-support data-management data-transfer distributed-computing programming-best-practices scheduling
Vinayak Mathur	researcher/educator	Recursion, stop!
Lenore Martin	researcher/educator	Recursion, stop!	administering-hpc ai amber anaconda bioinformatics biology charmm community-outreach more...
Xiaoluo Jiao	student facilitator	Recursion, stop!	python sql
Matt Ferguson	researcher/educator	Recursion, stop!	ACCESS ACCESS-account ACCESS-allocations ACCESS-credits ACCESS-website ai amber anaconda more...
Sanguthevar Ra…	researcher/educator	Recursion, stop!
Stanley Nwoji	researcher/educator	Recursion, stop!	big-data community-outreach conda data-analysis deep-learning genomics image-processing julia more...
William Feng	student facilitator	Recursion, stop!
Yun Shen	mentor	Recursion, stop!

Projects

Project Title	Project Institution	Project Owner	Tags	Status
High throughput Python pipeline to identify Horizontal Gene Transfer	Cabrini University	Vinayak Mathur	bioinformatics, biology, data-wrangling, genomics, github, python, workflow	Halted
Metagenomic analysis to identify gene clusters associated with IgA production	SUNY Upstate Medical University	Joel Wilmore	bioinformatics, biology, genomics, python, r, research-facilitation	Finishing Up
Host-symbiont population genomics - analyzing the intraspecific variability of methanogenic archaeal endosymbionts of genus Methanocorpusculum hosted by a marine anaerobic ciliate Metopus sp. (Metopida)	University of Rhode Island -- Bay Campus	Gaurav Khanna	bioinformatics, biology, genomics	Complete
Discovering the Structure, Function, and Evolution of Sirtuins and Associated Proteins in Aiptasia: A Deep Learning and Integrative Genomics Approach	Wilmington University	Anita Schwartz	deep-learning, genomics, hpc-tools, NSF ACCESS Resources	Complete
Develop a data portal for the organization of molecular and imaging data	University of Rhode Island -- Bay Campus	Gaurav Khanna	archiving, aws, bioinformatics, biology, Cloud, Data Storage, docker, genomics	Complete
Coral Genomics: An assessment of metabolic pathways and genes influencing coral bleaching. Implications for the development of hydra as a model organism.	Wilmington University	Anita Schwartz	genomics	Complete

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Announcements

Title	Date
Ookami Webinar	02/14/24

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Topics from Ask.CI

Knowledge Base Resources

Title	Category	Tags	Skill Level
Biopython Tutorial	Learning	bioinformatics, genomics, python	Beginner, Intermediate, Advanced
MATLAB bioinformatics toolbox	Tool	visualization, data-analysis, bioinformatics, genomics, matlab	Beginner, Intermediate, Advanced
Samtools Documentation	Docs	documentation, data-analysis, bioinformatics, data-science, genomics	Beginner, Intermediate, Advanced