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biology

Mentors and Regional Facilitators
Name Region Skills Interests
diana Trotman CAREERS
Diana Toups Dugas RMACC, SWEETER, Campus Champions
Elie Alhajjar ACCESS CSSN
Jason Wells Campus Champions
Jeffrey Weekley Campus Champions
Amy Koshoffer Campus Champions
shuai liu ACCESS CSSN
Nicholas Danes Campus Champions, MINES
Nicholas Panchy Campus Champions
Rob Harbert Northeast
Xiaoqin Huang ACCESS CSSN
William Lai ACCESS CSSN
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Users
Name Roles Skills Interests
Aidan McCrillis
student facilitator
Chitral Samala
student facilitator
diana Trotman
student facilitator
rcf
mentee
Emma Strand
student facilitator
Eren Ada
student facilitator
Gregory Ezike
student facilitator
Chris Hemme
researcher/educator
Hening Cui
student facilitator
Ifeoma Ugwuanyi
student facilitator
John Acheampong
student facilitator
Kenneth Acosta
student facilitator
Vinayak Mathur
researcher/educator
Lenore Martin
researcher/educator
Xiaoluo Jiao
student facilitator
William Feng
student facilitator
Zoe Reich
student facilitator

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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