Services

Pipelines & Workflows: Out-of-the-box execution for Nextflow and Snakemake (including full nf-core suite compatibility via Singularity).

Compute Specialization: High-memory nodes (up to 2 TB RAM) for de novo assembly and single-cell RNA-Seq, plus GPU-accelerated nodes for AlphaFold and structural modeling.

Data Management: High-speed parallel storage coupled with automated archival tiers for raw FASTQ, BAM/CRAM, and VCF files.

This comprehensive ecosystem of software tools supports advanced research across disciplines including bioinformatics, imaging, AI/ML, and data science. These tools are optimized for high-performance computing (HPC) environments and enable scalable, reproducible, and efficient scientific workflows.

In addition to HPC resources, researchers also have access to a broader collection of software applications through the Weill Cornell Medicine Library Scientific Software Hub. See Learn More link

Registration: Scientific Computing Training Series

Workflow Automation & Pipeline Development – Guidance and templates for building automated, scalable, and reproducible workflows using Snakemake, Nextflow, CWL, or custom scripts.

Data Transfer & Synchronization – Best practices and tools for secure, high-speed data movement between HPC clusters, cloud resources, and collaborator sites, including parallel transfers and checkpointed syncing for very large datasets.

Containerized Pipelines – Support for Singularity/Apptainer containers to make workflows portable and reproducible across systems.

Job Orchestration & Monitoring – Tips for efficient scheduling, monitoring, and optimizing pipeline execution on HPC and hybrid cloud resources.

Data Management Guidance – Recommendations on organizing, documenting, and versioning datasets to support reproducibility, collaboration, and long-term accessibility.

Interactive Sessions – Launch RStudio, Jupyter notebooks, MATLAB, or terminal sessions on the cluster without using SSH.

File Management & Transfers – Upload, download, and manage large datasets directly via the portal.

Job Submission & Monitoring – Submit SLURM jobs, monitor progress, and check outputs with a graphical interface.

Visualization Tools – Use remote desktop sessions or GPU-backed visualization for large-scale imaging and simulations.

User-Friendly Interface – Designed for researchers who prefer point-and-click access over command-line operations.

Secure & Integrated – Single sign-on access that works with existing HPC authentication and preserves data security.

At Weill Cornell Medicine (WCM), cloud services via AWS are structured into three distinct support tiers to align with technical expertise and project complexity:

SSOD (Standard Solutions on Demand): Fully managed by a dedicated support team. Designed for low-complexity, standalone instances (EC2, S3, RDS) on shared accounts with minimal user effort required.

Managed Solutions: Managed by an extended Cloud Team (covering Cloud, Security, Ops, and white-glove hosting). Ideal for medium-to-high complexity production apps and sensitive data handling.

Co-Managed Solutions: You manage your own dedicated account and resources directly, backed by basic infrastructure and monitoring support from the Cloud Team for a minimal service fee

Large-Scale Storage Access – Leverage over 26 PB of high-performance storage across Lustre, GPFS, and NFS systems for genomics, imaging, simulation, and other large datasets.