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...	ACCESS ACCESS-allocations account ACES administering-hpc ai allocations-extension allocations-proposal 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

Blog Entries

There are no Blog Entries associated with this topic.

Affinity Groups

Logo	Name	Description	Tags	Join
	Genomics with OOD	This group is for anyone using Open OnDemand in genomics research. Whether you're working with sequencing data, analyzing genomic information, or optimizing workflows for bioinformatics tools, join us…	data-analysis genomics bioinformatics open-ondemand	Login to join

Announcements

Title	Date
Register for HTC25: Connect with the High Throughput Computing Community	03/18/25
Ookami Webinar	02/14/24
2024 HuBMAP Underrepresented Student Internship Program	10/31/23

Upcoming Events & Trainings

No events or trainings are currently scheduled.

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