biology

Mentors and Regional Facilitators

Name	Region	Skills	Interests
Anoop Arunagiri		ACCESS ACCESS-account ACCESS-allocations ACCESS-credits allocations-proposal biology biophysics physiology more...	biology biophysics physiology structural-biology
Alyssa Pivirotto	ACCESS CSSN, Campus Champions	bash bioinformatics biology conda data-analysis data-science genomics github more...	arcgis machine-learning
Cindy Cheng	Campus Champions	abstract affiliations ai archiving artificial-intelligence azure backup benchmarking more...
Carolina Roe-Raymond	CCMNet	anaconda arcgis big-data biology conda css data data-analysis more...	big-data image-processing paraview visIt
David Carlson	ACCESS CSSN, Open OnDemand	bash bioinformatics biology gatk genomics ookami python r more...	ACCESS bash bioinformatics containers genomics
diana Trotman	CAREERS	benchmarking biology cloud-open-source cloudlab community-outreach computational-chemistry cybersecurity data-analysis more...	benchmarking bioinformatics biology cleanup cloud-commercial computational-chemistry containers cybersecurity 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...
Deborah Penchoff	Campus Champions	abstract ACCESS ACCESS-account adding-users affiliations ai allocation-management allocation-time more...
Diana Toups Dugas	Campus Champions	bioinformatics biology genomics proposal-development research-facilitation software-carpentry training workforce-development
Elie Alhajjar	ACCESS CSSN, CCMNet	biology c++ community-outreach data-science julia mathematica matlab professional-development more...	ai big-data biology c++ community-outreach data-analysis data-science deep-learning more...
Feseha Abebe-Akele	CCMNet	abstract ACCESS ACCESS-account ACCESS-allocations ACCESS-credits ACCESS-website adding-users affiliations more...	ACES administering-hpc ai artificial-intelligence aws azure bash batch-jobs more...
Jeremiah Olugbami		abstract affiliations bioinformatics biology chemistry citation genomics hardware more...
Jeffrey Weekley	Campus Champions	administering-hpc archiving biology community-outreach condo containers cybersecurity data-compliance more...
Amy Koshoffer	Campus Champions	biology data-lifecycle data-management doi file-formats workflow	archiving backup biology data-lifecycle data-management doi file-formats file-transfer more...
shuai liu	ACCESS CSSN	ai anaconda azure big-data bioinformatics biology containers data-analysis more...
Maureen Donlin	Great Plains, Open OnDemand	bioinformatics biology research-facilitation research-grants	ACCESS-allocations administering-hpc cluster-support cui docker federated-authentication jetstream management more...
Nicholas Danes	Campus Champions, MINES	anaconda biology compiling cpu-bound distributed-computing fluid-dynamics fortran job-array more...	ai aws azure benchmarking big-data c c++ deep-learning more...
Nicholas Panchy	Campus Champions	bash bioinformatics biology conda easybuild genomics modules open-ondemand more...
Renée F. Brown	ACCESS CSSN	bash big-data biology compiling computer-science data data-analysis data-lifecycle more...	ai deep-learning edge-computing generative-ai gis llm machine-learning python 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...
Tessa Fisher	CCMNet	astronomy astronomy and planetary sciences atmospheric-physics biology earth-sciences linux python slurm	astronomy and planetary sciences atmospheric-physics biology earth-sciences hpc linux machine-learning python more...
Thomas Pranzatelli		bash batch-jobs bioinformatics biology c c++ cloud-computing cluster-management more...	bash biology cuda deep-learning distributed-computing gpu IO-issue julia 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...

Users

Name	Roles	Skills	Interests
Aidan McCrillis	student facilitator	bioinformatics biology data-science python
Chitral Samala	student facilitator	biology community-outreach data-transfer jupyterhub management matlab netcdf programming more...	c c++ cybersecurity gis java julia science-gateway software-installation more...
diana Trotman	student facilitator rcf mentee	benchmarking biology cloud-open-source cloudlab community-outreach computational-chemistry cybersecurity data-analysis more...	benchmarking bioinformatics biology cleanup cloud-commercial computational-chemistry containers cybersecurity more...
Emma Strand	student facilitator	anaconda archiving bash big-data bioinformatics biology community-outreach data-analysis more...
Eren Ada	student facilitator	anaconda bash big-data bioinformatics biology community-outreach compiling dependencies more...
Gregory Ezike	student facilitator	bash biology c c++ github java mpi programming more...
Chris Hemme	researcher/educator	anaconda big-data bioinformatics biology data-analysis genomics r	anaconda big-data bioinformatics biology data-analysis genomics python r
Hening Cui	student facilitator	bioinformatics biology cleanup data-analysis java machine-learning natural-language-processing neural-networks more...
Ifeoma Ugwuanyi	student facilitator	bioinformatics biology data-analysis genomics python r sql	anaconda big-data bioinformatics biology data-analysis data-wrangling genomics python more...
John Acheampong	student facilitator	biology conda github programming-best-practices python software-installation
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...
William Feng	student facilitator	bioinformatics biology data-analysis genomics java programming programming-best-practices python more...
Zoe Reich	student facilitator	biology data-analysis r	bioinformatics community-outreach genomics professional-development project-management python research-facilitation research-grants

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
Simulating 21st century boreal forests and fire with a state-of-the-art process-based model	Cary Institute	Winslow Hansen	biology, cluster-support, dependencies, deployment, netcdf, performance-tuning, r	Finishing Up
Assembly and Taxonomic Profiling of Metagenomic Sequences using Deep Learning	University of Rhode Island	Gaurav Khanna	ai, bioinformatics, biology, deep-learning, gpu, hardware, machine-learning, neural-networks, python	Complete
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
Detecting Covid-19 Misinformation on Social Media	Bryant University	Gaurav Khanna	ai, bash, batch-jobs, big-data, biology, cuda	Complete
Computational pipelines for the analysis of plastic-degrading genes	University of Rhode Island	Gaurav Khanna	bioinformatics, biology, workflow, workforce-development	Complete
Development of personalized healthy food incentives to improve diet and cardiovascular risk	University of Rhode Island	Gaurav Khanna	biology	Complete

Blog Entries

There are no Blog Entries associated with this topic.

Organizations

"/themes/nect-theme/img/neutral-images/affinity-groups-default.png"

ERN

Website

https://www.ernrp.org

big-data data-access-protocols data-compliance data-management data-analysis

Affinity Groups

There are no Affinity Groups associated with this topic. View All Affinity Groups.

Announcements

Title	Date
Register for HTC25: Connect with the High Throughput Computing Community	03/18/25
Ookami Webinar	02/14/24
Open Call: Minisymposia for PASC24	10/05/23

Upcoming Events & Trainings

No events or trainings are currently scheduled.

Topics from Ask.CI

Knowledge Base Resources

Title	Category	Tags	Skill Level
Data Analysis with R for Educators	Video	data-analysis, data-science, psychology, biology, training, workforce-development, r	Beginner
phenoACCESS-24 workshop program materials	Website	big-data, data-management, metadata, biology, professional-development, workforce-development	Intermediate
Trinity Tutorial for Transcriptome Assembly	Learning	biology	Beginner