bioinformatics

Mentors and Regional Facilitators

Name	Region	Skills	Interests
Brett Milash	RMACC	bioinformatics hpc python
Larry Feinstein	Northeast	bioinformatics simulations
Ying Zhang	CAREERS	bioinformatics hpc	bioinformatics deep-learning hpc
Jacob Pessin	Northeast	aws bash batch-jobs big-data bioinformatics cloud cloud-storage cluster-support more...
Juan Vanegas	Northeast	bash batch-jobs bioinformatics compiling conda environment-modules hpc hpc-cluster-build more...
Rob Harbert	Northeast	anaconda array-job batch-jobs big-data bioinformatics biology cluster distributed-computing more...
Diana Dugas	RMACC, SWEETER, Campus Champions	bioinformatics biology cyberinfrastructure genomics hpc-getting-started proposal-development research-computing research-facilitation more...
Carrie Brown	CAREERS	bioinformatics cleanup community-outreach data-wrangling distributed-computing genomics github github-pages more...	hpc-getting-started htc
Shane Sanders	Campus Champions	bioinformatics c c++ containers cyberinfrastructure hpc hpc-tools machine-learning more...	archiving big-data data-analysis data-compliance data-facing data-lifecycle data-management data-reproducibility more...
Jordan Hayes	Campus Champions	acls administering-hpc amber anaconda api array-job atlas aws more...
Nick Dusek	Campus Champions	administering-hpc anaconda bash batch-jobs bioinformatics cloud compiling containers more...

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Affinity Groups

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Users

Name	Roles	Skills	Interests
Chris Hemme	researcher/educator	anaconda big-data bioinformatics biology data-analysis genomics r research-computing more...	anaconda big-data bioinformatics biology data-analysis genomics python r more...
Ying Zhang	mentor researcher/educator	bioinformatics hpc	bioinformatics deep-learning hpc
Kenneth Acosta	student facilitator	bash bioinformatics biology conda genomics github pip python more...	batch-jobs cloud cluster cluster-management cluster-support data-management data-transfer distributed-computing more...
Younes Shafter	student facilitator	anaconda big-data bioinformatics computational-chemistry ddocent deep-learning fastx gatk more...	hpc
Carrie Brown	mentor steering committee	bioinformatics cleanup community-outreach data-wrangling distributed-computing genomics github github-pages more...	hpc-getting-started htc
Vinayak Mathur	researcher/educator	bioinformatics biology genomics
Eren Ada	student facilitator	anaconda array-job bash big-data bioinformatics biology collaboration community-outreach more...
Emma Strand	student facilitator	anaconda archiving bash big-data bioinformatics biology cluster community-outreach more...
Xiaoluo Jiao	student facilitator	bioinformatics biology cleanup data-management data-reproducibility data-science-support data-wrangling genomics more...	python sql
Ifeoma Ugwuanyi	student facilitator	bioinformatics biology data-analysis genomics hpc notebooks python r more...	anaconda big-data bioinformatics biology data-analysis data-wrangling genomics hpc more...
Hening Cui	student facilitator	bioinformatics biology cleanup data-analysis java machine-learning natural-language-processing neural-networks more...

Resources

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Projects

Project Title	Project Institution	Project Owner	Tags	Status
Metagenomic analysis to identify gene clusters associated with IgA production	SUNY Upstate Medical University	Joel Wilmore	bioinformatics, biology, collaboration, genomics, python, r, research-computing, research-facilitation	In Progress
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, cluster, genomics	In Progress
High throughput Python pipeline to identify Horizontal Gene Transfer	Cabrini University	Vinayak Mathur	bioinformatics, biology, data-wrangling, genomics, github, python, workflow	In Progress
Deep convolutional neural networks (dCNN) for image segmentation, instance labeling, and tracking.	University of Delaware	Anita Schwartz	bash, bioinformatics, computational-chemistry, debugging, domain-specific, hpc, machine-learning, programming, programming-languages, python, researcher-facing, scripting, slurm, software-installation, tensorflow, visualization	Complete
Parallel analysis of variants in multiple bear genomes: algorithmic solutions	Rutgers University–Camden	Galen Collier	Data-Facing, bioinformatics, domain-specific, researcher-facing	Complete
Assembly and Taxonomic Profiling of Metagenomic Sequences using Deep Learning	University of Rhode Island	Gaurav Khanna	ai, bioinformatics, biology, deep-learning, domain-specific, gpus, hardware, machine-learning, neural-networks, python	Complete

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