bioinformatics

Mentors and Regional Facilitators

Name	Region	Skills	Interests
Alyssa Pivirotto	ACCESS CSSN, Campus Champions	bash bioinformatics biology conda data-analysis data-science genomics github more...	arcgis machine-learning
Brett Milash	RMACC	bioinformatics python
Carrie Brown	CAREERS, ACCESS CSSN, CCMNet	bioinformatics cleanup community-outreach data-wrangling distributed-computing genomics github github-pages more...
Bala Desinghu	ACCESS CSSN, Campus Champions, CAREERS, Northeast	ai anaconda api bash batch-jobs benchmarking big-data bioinformatics more...	affinity-group ai allocations-proposal amber anaconda archiving backup bash more...
David Carlson	ACCESS CSSN, OnDemand	bash bioinformatics biology gatk genomics ookami python r more...	ACCESS bash bioinformatics containers genomics
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...
Diana Toups Dugas	RMACC, SWEETER, Campus Champions	bioinformatics biology genomics proposal-development research-facilitation software-carpentry training workforce-development
Feseha Abebe-Akele	CCMNet	abstract ACCESS ACCESS-account ACCESS-allocations ACCESS-credits ACCESS-website account adding-users more...
Gil Speyer	ACCESS CSSN, RMACC, Campus Champions	bash bioinformatics c computational-chemistry conda cuda debugging fortran more...	bash c computational-chemistry cuda gpu matlab mpi nvidia more...
Juanjo Garcia Mesa	Campus Champions, CCMNet, ACCESS CSSN	ACCESS-allocations bash batch-jobs bioinformatics c++ git jetstream job-array more...	generative-ai job-accounting llm mpi NAIRR-pilot natural-language-processing openmpi programming-best-practices more...
Jordan Hayes	Campus Champions	acls administering-hpc amber anaconda api atlas aws bash more...
Jacob Pessin	Northeast	aws bash batch-jobs big-data bioinformatics cloud-storage cluster-support cyverse more...
Juan Vanegas	Northeast	bash batch-jobs bioinformatics compiling conda environment-modules hpc-cluster-build hpc-operations more...
Larry Feinstein	Northeast	bioinformatics
shuai liu	ACCESS CSSN	ai anaconda azure big-data bioinformatics biology containers data-analysis more...
Nick Dusek	Campus Champions	administering-hpc anaconda bash batch-jobs bioinformatics compiling containers data-transfer more...
Nect Admin	Great Plains, Northeast, RMACC	astrophysics bioinformatics cgroups data-lifecycle deep-learning file-transfer	science-gateway
Nicholas Panchy	Campus Champions	bash bioinformatics biology conda easybuild genomics modules open-ondemand more...
Rob Harbert	Northeast	anaconda batch-jobs big-data bioinformatics biology distributed-computing genomics gis more...
Shane Sanders	Campus Champions	bioinformatics c c++ containers machine-learning programming python research-grants more...	archiving big-data data-analysis data-compliance data-lifecycle data-management data-reproducibility data-retention 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...
William Sanders	Campus Champions	bioinformatics c c++ containers machine-learning programming python research-grants more...	archiving big-data data-analysis data-compliance data-lifecycle data-management data-reproducibility data-retention 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...
Wesley Brashear	ACCESS CSSN, Campus Champions	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...
Ying Zhang	CAREERS	bioinformatics	bioinformatics deep-learning
Yun Shen	CAREERS, Northeast, ACCESS CSSN, CCMNet	big-data bioinformatics data-analysis data-science genomics open-ondemand programming Programming more...

Users

Name	Roles	Skills	Interests
Bala Desinghu	mentor researcher/educator rcf	ai anaconda api bash batch-jobs benchmarking big-data bioinformatics more...	affinity-group ai allocations-proposal amber anaconda archiving backup bash more...
Jacob Pessin	mentor	aws bash batch-jobs big-data bioinformatics cloud-storage cluster-support cyverse more...
Juan Vanegas	mentor	bash batch-jobs bioinformatics compiling conda environment-modules hpc-cluster-build hpc-operations more...
Kendra Batchelder	student facilitator	bioinformatics r	image-processing
Larry Feinstein	mentor	bioinformatics
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...
Michael Sundue	researcher/educator	bioinformatics
Nect Admin	cise	astrophysics bioinformatics cgroups data-lifecycle deep-learning file-transfer	science-gateway
Rob Harbert	mentor	anaconda batch-jobs big-data bioinformatics biology distributed-computing genomics gis more...
Yun Shen	mentor	big-data bioinformatics data-analysis data-science genomics open-ondemand Programming programming more...

Projects

Project Title	Project Institution	Project Owner	Tags	Status
Understanding Mechanical Properties of Bio-interfaces with HPC Molecular Simulations	University of Vermont	Juan Vanegas	bioinformatics, computational-chemistry, gromacs, molecular-dynamics, mpi, python	Complete
Genome Sequencing of the Bornean Rock Frog	Smith College	Lisa Mangiamele	big-data, genomics, bioinformatics	Complete
Analyzing Pathogenic Clinical Isolates Genomes to Identify Horizontal Gene Transfer of Antibiotic-Resistance Genes	University of Maine at Presque Isle	Larry Whitsel	big-data, bioinformatics, hpc-storage	Complete
Big Data Portal For Sharing Real-world Bioinformatics Data Sets to the Public Domain	University of Maine, Augusta	Bruce Segee	big-data, bioinformatics, data-management, data-wrangling, hpc-storage, metadata, science-gateway, storage	Complete
Developing Portable and Reusable Computational Biology Modules		Chris Wilson	bioinformatics, data-reproducibility, docker, genomics	Complete

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Announcements

Title	Date
Ookami Webinar	02/14/24
2024 HuBMAP Underrepresented Student Internship Program	10/31/23
Open Call: Minisymposia for PASC24	10/05/23

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Topics from Ask.CI

Knowledge Base Resources

Title	Category	Tags	Skill Level
Bioinformatics Workflow Management with Nextflow	Docs	cloud-computing, parallelization, data-management, bioinformatics, training	Beginner, Intermediate
Biopython Tutorial	Learning	bioinformatics, genomics, python	Beginner, Intermediate, Advanced
CI Computing Module For All	Learning	ai, computer-vision, neural-networks, visualization, big-data, gis, parallelization, data-management, data-science, bioinformatics, open-ondemand, hpc-getting-started, cpu-architecture, distributed-computing, job-submission, jupyterhub, python, r, cybersecurity, containers	Beginner