biology

Mentors and Regional Facilitators

Name	Region	Skills	Interests
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...
Diana Toups Dugas	RMACC, SWEETER, Campus Champions	bioinformatics biology genomics proposal-development research-facilitation software-carpentry technical-training-for-hpc training more...
Elie Alhajjar	ACCESS CSSN	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...
Jason Wells	Campus Champions	administering-hpc api bash batch-jobs biology cluster-management cluster-support computational-fluid-dynamics 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...
Nicholas Danes	Campus Champions, MINES	anaconda biology compiling computational-fluid-dynamics cpu-bound distributed-computing 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 ondemand more...
Rob Harbert	Northeast	anaconda batch-jobs big-data bioinformatics biology distributed-computing genomics geographic-information-system more...
Xiaoqin Huang	ACCESS CSSN	access-acount 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...

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Affinity Groups

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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 geographic-information-system 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
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

CI Links

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, ondemand, science gateway, c++, jupyterhub, python	Beginner, Intermediate, Advanced
Data Analysis with R for Educators	Video	data-analysis, data-science, psychology, biology, technical-training-for-hpc, training, workforce-development, r	Beginner
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
Recommended Libraries for Cyberinfrastructure Users Developing Jupyter Notebooks	Website	ai, big-data, data-analysis, machine-learning, data-sharing, data-lifecycle, data-management, data-management-software, data-reproducibility, data-wrangling, github-pages, workflow, astrophysics, data-science, computational-chemistry, genomics, materials-science, gravitational-waves, oceanography, particle-physics, physiology, psychology, quantum-computing, quantum-mechanics, biology, science gateway, conda, jupyterhub, python	Beginner, Intermediate, Advanced
Research Software Development in JupyterLab: A Platform for Collaboration Between Scientists and RSEs	Learning	ai, visualization, big-data, data-analysis, deep-learning, machine-learning, astrophysics, data-science, novel-accelerators, computational-chemistry, genomics, materials-science, gravitational-waves, oceanography, particle-physics, physiology, psychology, quantum-computing, quantum-mechanics, biology, ondemand, science gateway, c++, jupyterhub, python, r	Beginner, Intermediate
Research Software Engineering Training Materials	Website	astrophysics, data-science, novel-accelerators, computational-chemistry, genomics, materials-science, gravitational-waves, oceanography, particle-physics, physiology, psychology, quantum-computing, quantum-mechanics, biology, git, training, workforce-development, programming, programming-best-practices, version-control	Beginner, Intermediate, Advanced
Science Gateway Tool/Web App Template (Jupyter Notebook + ipywidgets)	Learning	data-analysis, github, astrophysics, data-science, novel-accelerators, computational-chemistry, genomics, materials-science, gravitational-waves, oceanography, particle-physics, physiology, psychology, quantum-computing, quantum-mechanics, biology, ondemand, science gateway, jupyterhub, python	Beginner

Projects

Project Title	Project Institution	Project Owner	Tags	Status
Computational pipelines for the analysis of plastic-degrading genes	University of Rhode Island	Gaurav Khanna	bioinformatics, biology, workflow, workforce-development	Reviewing Applicants
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 MGMT and MVMT, docker, genomics	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
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
Detecting Covid-19 Misinformation on Social Media	Bryant University	Gaurav Khanna	ai, bash, batch-jobs, big-data, biology, cuda	Complete

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