Introduction to the Computational Biology Core (CBC)
Welcome to the January 2025 edition of the CBC newsletter! The Computational Biology Core (CBC) housed in the Institute for Systems Genomics at the University of Connecticut provides computational power and technical support to UConn/UCH researchers and affiliates. We support over 400 users across campuses and departments, and work closely with the Center for Genome Innovation and the High Performance Computing Core within the Institute for Systems Genomics. We encourage researchers to reach out to us if you have any questions about future experiments and how best to plan for downstream analysis.
Support Offered
● Helpdesk: For any assistance, reach out to us at cbcsupport@helpspotmail.com.
● Slack Channel: Connect with our team and other researchers by joining our Slack workspace (open to UConn and UCH emails) at uconn-cbc.slack.com.
● Data Therapy Sessions: Offered on the first Friday of each month (in-person and online), these informal sessions are co-hosted by Noah Reid and Mia Nahom. Bring your data questions and get live support from our experts. Learn more here.
● Full Project Support: We collaborate with both internal and external researchers, offering guidance on data submission, best practices, and advanced analysis across RNA-Seq, single-cell, variant detection, metagenomics, and more. Learn more about our rates and services.
Data storage review (and updates!) on our HPC systems
Home directories on Xanadu/Mantis are intentionally small and most ideal for storing scripts, configuration files, intermediate files, and small data sets.
Lab/Project Directories (/core or /isg): For active or shared projects, PIs are encouraged to request dedicated lab or project directories, which allow collaboration among team members and provide more space for project data.
SeqData (/seqdata): Our new filesystem for raw (original) sequencing data from MARS, CGI, and external sources. This data is stored in a read-only format and can be symlinked so users can run analyses in their home or project/lab directories. By avoiding unnecessary copies, data remains in its original form (preventing accidental deletion) and frees up space in your working directories. If you’d like to move existing raw data to this location or store data from external
sequencing centers, please email us at cbcsupport@helpspotmail.com. Archive (/archive): Designed for long-term storage of completed projects, the archive filesystem is currently read-only while the CBC and HPC teams migrate data to free up space. Regular archive access is expected to resume in the next 5 weeks.
Important Archive Details: Directories under /archive/users have been moved to a filesystem that is not currently mounted. If you need access to files in these directories, please contact us at cbcsupport@helpspotmail.com. Archive directories that remain mounted are still readable.
Virtual Training Workshops
Our intensive training workshops run for 3–4 days and feature live instruction from experienced bioinformaticians. These sessions cover both the basics of high-throughput sequencing (HTS) and the specifics of analytic workflows. Intro to HPC and R will be provided as self-guided with pre-recorded videos intended to be completed before the start of live instruction. Registered participants gain access to all materials, including end-to-end tutorials, slides, and recordings.
Schedule for 2025
● RNA-Seq: February 4-6, 2025 – 10:00 AM to 2:00 PM
● Genome Assembly: March 5-7, 2025 – 10:00 AM to 2:00 PM
● Single-Cell Transcriptomics: April 8-10, 2025 – 10:00 AM to 2:00 PM
● Genome Annotation: April 15-17, 2025 – 10:00 AM to 2:00 PM
● Variant Detection: May 20-22, 2025 – 10:00 AM to 2:00 PM
● ChIP-Seq/ATAC-Seq: May 27-29, 2025 – 10:00 AM to 2:00 PM
To learn more about workshop content and register, please visit our CBC Workshops page.
Welcome to Our New Associate Director – Dr. Noah Reid
We are thrilled to announce Dr. Noah Reid as the new Associate Director of the Computational Biology Core! Noah joined the CBC in 2019 and has provided support to the research community at all levels. His contributions include:
● Designing and instructing our new graduate certificate program in Genomic Data Analysis
● Developing and leading training workshops focused on variant detection and high throughput genomics analyses
● Providing support for projects ranging from RNA-Seq to RAD-Seq.
● Hosting regular Data Therapy Sessions, bioinformatics journal clubs, and working groups on advanced analysis/technologies, including pangenome assembly and Nextflow.
In addition, Dr. Reid has provided daily support to users of our HPC resources, ensuring that scientists across UConn/UCH have the computational expertise needed to support their research.
Coming Soon: The CBC looks forward to announcing a new scientist who will join our team in the next few months, dedicated to supporting the UCH research community.
New certificate program launched in Fall of 2024
We are proud to announce our new Certificate Program in Genomic Data Analysis, developed under the guidance of Dr. Noah Reid. This one-year program (two courses per semester) is designed for early and mid-career scientists seeking intensive training in genomics and bioinformatics.
● Comprehensive curriculum covering core topics in genomics and computational biology
● Hands-on learning with real-world datasets and HPC resources
● Skills-focused approach to prepare you for emerging challenges in genomic data analysis
To learn more or apply, please visit the official page: Graduate Certificate in Genomics Data Analysis
Welcome to the new HPC cluster, Mantis!
Last year, our research community voted to name the new HPC cluster “mantis.” Since that time, the CBC and HPC cores have been providing on-request access as we bring it fully online.
● GPU Access: Mantis includes new GPU nodes for cutting-edge computational approaches (add stats here).
● Up-to-Date Software: Mantis runs current versions of Slurm and associated libraries, ensuring a more efficient and user-friendly environment.
● Shared Storage and Credentials: Mantis and Xanadu share the same back-end storage and login credentials, so files can be moved seamlessly.
● VPN Requirement: Researchers external to UCH must use the UCH VPN before connecting.
Interested in using Mantis? Reach out on Slack or via the Helpdesk to request an account. Please note that while storage is shared, individual modules may not work as expected on Mantis.
Coming Soon: In the near future, Mantis will be expanded to provide additional GPU capacity, enhanced memory nodes, and further integrations with emerging HPC technologies.
Introducing the HPC Ambassadors
This year, the CBC and HPC cores partnered to provide intensive SLURM HPC training to a group of 16 end users and staffmembers. After completing the training, all trainees are now recognized as HPC Ambassadors. They will offer guidance on best practices on both Xanadu and Mantis to the Slack user community and contribute to decision making in cluster management.
We would like to take this opportunity to welcome these members:
● Ziming Cao, PhD Student, UConn Health
● Jing Yuan, Postdoctoral Researcher, CAES
● Katie Kyle, PhD Student, UConn Storrs
● Sandy Garrett, Assistant Professor, UConn Health
● Yuping Zhang, Associate Professor, UConn Storrs
● Anthony He, Undergraduate, UConn Storrs
● Allyson Voelker, Research Assistant, UConn Health
● Gabrielle Stack, MS Student, UConn Storrs
● Lucas Jones, PhD Student, UConn Avery Point
Applications for the Biodiversity and Conservation Genomics Training Program due Feb 2nd
Led by the Institute for Systems Genomics in collaboration with research labs in EEB and MCB, the Biodiversity and Conservation Genetics (BCG) Training Program is accepting applications for its third cohort. The program provides specialized training in bioinformatics, conservation biology, and scientific writing. This year-long program begins in Summer 2025 and ends in Spring 2026. Since 2021, the BCG Training Program has trained 16 students in conservation genomics and generated genetic resources for 18 endangered species across North America. Learn more and apply here. Faculty, please spread the word!
Happy New Year!
We look forward to supporting your research in the coming year. If you have any questions or would like more information on any of the above items, please contact us at cbcsupport@helpspotmail.com or join us on Slack at uconn-cbc.slack.com.
