Welcome to the March 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 700 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 hosted by Noah Reid. 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.
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 detailed tutorials, slides, and recordings.
Schedule for 2025
- Genome Assembly: April 15-17, 2025 – 10:00 AM to 2:00 PM
- Variant Detection: May 20-22, 2025 – 10:00 AM to 2:00 PM
- Genome Annotation: May 27-29, 2025 – 10:00 AM to 2:00 PM
- Single-Cell Transcriptomics: June 24-26, 2025 – 10:00 AM to 2:00 PM
- RNA-seq Analysis (w/ reference genome & annotation): July 29-31, 2025 – 10:00 AM to 2:00 PM
- ChIP-Seq/ATAC-Seq: Aug. 19-21, 2025 – 10:00 AM to 2:00 PM
To learn more about workshop content and register, please visit our CBC Workshops page. Please see and share the attached flyer for the full schedule.
Welcome to the team Dr. Kerry Cobb!
We are excited to welcome Dr. Kerry Cobb to our team! Kerry joins us on March 21st as a computational biologist with a strong background in developing bioinformatics workflows to ask questions of genomic datasets. With a Ph.D. in Biological Sciences from Auburn University, his research has spanned evolutionary genomics, machine learning, and high-performance computing for large-scale data analysis. We are thrilled to have Kerry on board and look forward to his contributions to the UCH research community! UCH researchers – please stop by and welcome him later this month.
Bidding Farewell to Mia Nahom
We would like to take this opportunity to thank Mia Nahom for her valuable (and substantial) contributions to the Computational Biology Core. Since joining us in December 2022, she has led multiple training workshops, installed many complex software packages, and supported hundreds of users with HPC access and end-to-end project assistance. We sincerely appreciate her efforts and wish her all the best in her new role in conservation genetics at NOAA.
We’re Hiring! Research Technician (Bioinformatics Analyst)
The Computational Biology Core at UConn’s Institute for Systems Genomics is looking for a Bioinformatics Analyst to support cutting-edge research. This role involves data analysis, workflow management, HPC support, and training workshops for the research community. The position is available at the MS-level and above. Please see the flyer for details and share broadly with interested parties.
To apply, send your resume & cover letter to karelyn.lambert@gmail.com with the subject “Research Technician Application.” Screening starts immediately!
Registration open for Fall 2025: Genomic Data Analysis (Certificate Program)
We are proud to announce that we are welcoming applications for our 2nd year of the 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
Upcoming Information Sessions:
- Friday, March 7th, 2025 at 12 pm ET
- Friday, April 4th, 2025 at 12 pm ET
- Friday, May 2nd, 2025 at 12 pm ET
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 (four new nodes, added this month!)
- Current 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.
Contact us
We look forward to supporting your research. 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.