genomics

Mentors and Regional Facilitators

Name	Region	Skills	Interests
Alyssa Pivirotto	ACCESS CSSN, Campus Champions	bash bioinformatics biology conda data-analysis data-science genomics github more...	arcgis machine-learning
Carrie Brown	CAREERS, ACCESS CSSN, CCMNet	bioinformatics cleanup community-outreach data-wrangling distributed-computing genomics github github-pages more...
David Carlson	ACCESS CSSN	bash bioinformatics biology gatk genomics ookami python r more...
Daniel Morales	Campus Champions	ACCESS ACCESS-allocations ACCESS-credits adding-users allocation-management anaconda bash batch-jobs more...	ACCESS ACCESS-allocations allocation-management bioinformatics biology community-outreach conda deep-learning more...
Diana Toups Dugas	RMACC, SWEETER, Campus Champions	bioinformatics biology genomics proposal-development research-facilitation software-carpentry training workforce-development
Feseha Abebe-Akele	CCMNet	abstract ACCESS ACCESS-account ACCESS-allocations ACCESS-credits ACCESS-website account adding-users more...
Jordan Hayes	Campus Champions	acls administering-hpc amber anaconda api atlas aws bash more...
shuai liu	ACCESS CSSN	ai anaconda azure big-data bioinformatics biology containers data-analysis more...
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...
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...
Emma Strand	student facilitator	anaconda archiving bash big-data bioinformatics biology community-outreach data-analysis more...
Chris Hemme	researcher/educator	anaconda big-data bioinformatics biology data-analysis genomics r	anaconda big-data bioinformatics biology data-analysis genomics python r
Ifeoma Ugwuanyi	student facilitator	bioinformatics biology data-analysis genomics python r sql	anaconda big-data bioinformatics biology data-analysis data-wrangling genomics python more...
Kenneth Acosta	student facilitator	bash bioinformatics biology conda genomics github pip python more...	batch-jobs cluster-management cluster-support data-management data-transfer distributed-computing programming-best-practices scheduling
Vinayak Mathur	researcher/educator	bioinformatics biology genomics
Lenore Martin	researcher/educator	administering-hpc amber anaconda backup bash bioinformatics biology charmm more...	administering-hpc ai amber anaconda bioinformatics biology charmm community-outreach more...
Xiaoluo Jiao	student facilitator	bioinformatics biology cleanup data-management data-reproducibility data-wrangling genomics git more...	python sql
Matt Ferguson	researcher/educator	ACCESS ai anaconda bash bioinformatics biology c charmm more...	ACCESS ACCESS-account ACCESS-allocations ACCESS-credits ACCESS-website ai amber anaconda more...
Sanguthevar Ra…	researcher/educator	ai big-data bioinformatics biology computational-chemistry data-analysis data-science deep-learning more...
Stanley Nwoji	researcher/educator	anaconda aws azure big-data c c++ community-outreach conda more...	big-data community-outreach conda data-analysis deep-learning genomics image-processing julia more...
William Feng	student facilitator	bioinformatics biology data-analysis genomics java programming programming-best-practices python more...
Yun Shen	mentor	big-data bioinformatics data-analysis data-science genomics open-ondemand programming Programming more...

Projects

Project Title	Project Institution	Project Owner	Tags	Status
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	In Progress
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
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

Blog Entries

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Affinity Groups

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Announcements

Title	Date
Ookami Webinar	02/14/24

Upcoming Events & Trainings

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Topics from Ask.CI

Knowledge Base Resources

Title	Category	Tags	Skill Level
Awesome Jupyter Widgets (for building interactive scientific workflows or science gateway tools)	Learning	ai, computer-graphics, plotting, visualization, big-data, data-analysis, deep-learning, image-processing, machine-learning, monte-carlo, neural-networks, data-sharing, data-lifecycle, data-management, data-management-software, data-reproducibility, github, astrophysics, data-science, novel-accelerators, computational-chemistry, genomics, materials-science, gravitational-waves, oceanography, particle-physics, physiology, psychology, quantum-computing, quantum-mechanics, biology, open-ondemand, science-gateway, c++, jupyterhub, python	Beginner, Intermediate, Advanced
Biopython Tutorial	Learning	bioinformatics, genomics, python	Beginner, Intermediate, Advanced
How the Little Jupyter Notebook Became a Web App: Managing Increasing Complexity with nbdev	Learning	data-sharing, data-management-software, data-reproducibility, github, workflow, astrophysics, data-science, novel-accelerators, computational-chemistry, genomics, materials-science, gravitational-waves, oceanography, particle-physics, physiology, psychology, quantum-computing, quantum-mechanics, biology, science-gateway, software-carpentry, jupyterhub, programming, python	Beginner, Intermediate, Advanced

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Engagements

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People with Expertise

Kenneth Acosta

Rutgers University - New Brunswick

Programs

CAREERS, ACCESS CSSN

Roles

student-facilitator

A portrait of Kenneth Acosta visiting Cold Spring Harbor Laboratory.

Expertise

bash

biology

conda

genomics

+9 more tags

Matt Ferguson

Boise State University

Programs

At-Large

Roles

researcher/educator, cssn

picture of Matt Ferguson

Expertise

access

ai

anaconda

bash

+34 more tags

David Carlson

SUNY at Stony Brook

Programs

ACCESS CSSN

Roles

researcher/educator, research computing facilitator, cssn

Expertise

bash

biology

gatk

genomics

+7 more tags

People with Interest

Daniel Morales

Florida International University

Programs

Campus Champions

Roles

research computing facilitator, student champion

Photo of Daniel Morales

Interests

access

access-allocations

allocation-management

bioinformatics

biology

+17 more tags

Christina Koch

University of Wisconsin-Madison

Programs

ACCESS CSSN

Roles

research computing facilitator, cssn, Affinity Group Leader

A white woman with dark hair is smiling at the camera.

Interests

astrophysics

biology

community-outreach

computational-chemistry

data-analysis

+14 more tags

Lenore Martin

University of Rhoide Island

Programs

CAREERS

Roles

researcher/educator

Lenore in office

Interests

administering-hpc

ai

amber

anaconda

bioinformatics

+53 more tags