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, CCMNet, Campus Champions	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
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

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Organizations

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ERN

Website

https://www.ernrp.org

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

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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

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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