Program Overview
Mission Summary
- Converge legacy CBSD delivery items with refreshed rack, power, and network layouts.
- Guarantee dual-room resiliency: Sequencer Room (instrument + UPS) and Datacenter Room (compute, storage, data protection).
- Stand up automated transfers to Crown AWS tenant for analytics and partner sharing.
Key Highlights
- 10 Gb production VLAN4, 40 Gb data VLAN7, VLAN2 IPMI, VLAN10 work area.
- Three 500 TB tiers (primary, secondary, clinical isolation) with the data-protection bridge.
- Crown-standard TACACS+, syslog, RBAC enforcement on the management fabric.
Business & Data Flow
Sequencing Capture
NextSeq 2000 captures production runs today while the NovaSeq X lane is staged; both write via CIFS to the sequencer switch and post health/control data over 1 Gb management links.
Dual-Fabric Transit
10 Gb data and 25 Gb storage fabrics (Catalyst 9200L + Nexus 9300) carry payloads into the HPC rack while IPMI/OOB stays isolated on VLAN2.
HPC Processing
Dell PowerEdge R760xs blades execute pipelines under Slurm, writing to the NetApp HA pair and flagging workloads for discovery vs. clinical storage.
Collaboration & Cloud
Bioinformaticians access results via the legacy Netgear core, Cohesity snapshots replicate to clinical storage + AWS, and job submissions keep the loop closed.
Global Architecture
The architecture view now mirrors the provided “NGS IT Infrastructure & Data Flow” reference: Sequencing and data generation on the left, HPC and primary storage at the center, and existing infrastructure/AWS services on the right, tied together by the same color-coded fabrics.
Design Principles & Delivery Milestones
NGS Readiness Timeline
Physical environment prep, procurement, on-site deployment, and go-live support.
Dec '25 – Apr '26
Dec '25
Jan '26
Feb '26
Mar '26
Apr '26
Physical Environment
- Sequencer Lab (Room #124): Place NextSeq 2000, lock UPS and power whip, and keep floor space reserved for the later NovaSeq X install; 10 Gb cabling quote underway with install finishing by January.
- Server room: Repurpose document archive into the additional NGS data center pending approval—Lonnie coordinating.
- Cooling: Datacenter stack (5× Dell R760xs @ ~8.2k BTU/h each, 3× NetApp FAS2820 @ ~3.4k, dual Nexus 9300 + dual Catalyst 9200L @ ~5.5k, APC rack UPS overhead ≈2.5k, NextSeq 2000 ≈6.8k) drives ≈62,000 BTU/h. Recommend at least a 7-ton (≈24 kW) expansion coil/CRAH with 20% headroom. Lonnie owns procurement.
- Power: Distribution looks good to go.
Hardware and Procurement
- Review and validate hardware spec: Confirm sizing, resiliency, and vendor lead times before release.
- Place order: Kick off procurement so hardware lands by late January.
On-site Deployment
- Network: Implement on-prem routing, segmentation, and service connectivity for the deployment window.
- Switches / IP subnets / VLAN: Data 25 Gb, IPMI 1 Gb, and sequencer 10 Gb fabrics validated with updated IP plan.
- Cabling: Pull and certify intra-rack and inter-room runs to support compute, storage, and sequencers.
- Internet: Stand up AWS split-network connectivity paths.
- NGS — Crown interconnect: Enable bioinformatic workstation access with the agreed Crown link.
- Server / cluster: Rack-mount hardware, install OS, and build the 5-node cluster.
- Data analysis testing: Execute representative pipelines to verify throughput and validation criteria.
- Storage: Install physical shelves and configure lifecycle rules for backup and retention.
- Data flow automation: Wire up sharing, access, and restriction policies end-to-end.
Go-live & Post-launch
- Go-live 1 Feb: Cut NextSeq 2000 production traffic and validate NovaSeq X staging paths, then deliver managed support through April.
Network Subnet Plan
| Domain | Function | Subnet / Mask | Gateway | Remark |
|---|---|---|---|---|
| NGS | Machine / Sequencer |
Subnet: 179.15.53.0/24 Mask: 255.255.255.0 Gateway: 179.15.53.254 |
Seq Switch | 172.15.53.253 as the L3 interconnect IP of Storage Switch. |
| HPC | Storage for NGS & HPC |
Subnet: 179.15.52.0/24 Mask: 255.255.255.0 Gateway: 179.15.52.254 |
Storage Switch | Storage shares disks for NGS & HPC via the CIFS protocol. |
| HPC | Data for HPC |
Subnet: 179.15.51.0/24 Mask: 255.255.255.0 Gateway: 179.15.51.254 |
OA Core |
|
| IPMI | Mgmt for NGS & HPC |
Subnet: 179.15.50.0/24 Mask: 255.255.255.0 Gateway: 179.15.50.254 |
OA Core | Out-of-band management of NGS & HPC infrastructure. |
Hardware Stack (Dec 2025 quotation)
Line items are transcribed from San Diego HPC&NGS-20251219.xlsx. Pricing is intentionally removed so this page focuses on scope, capacity, and deployment readiness.
| Item | Brand / Model | Qty | Function | Notes |
|---|---|---|---|---|
| Server & Storage | ||||
| Analysis Servers | Dell PowerEdge R760xs | 5 | Compute blades | Dual Intel Gold 6526Y, 8×64 GB RDIMM, 3×1.92 TB SSD (RAID5), Broadcom 57414 10/25 Gb, iDRAC Enterprise. |
| NGS Storage (HA) | NetApp FAS2820 (25 Gb SFP28) | 2 | Primary & secondary landing tiers | Dual controller, 48×22 TB, SnapMirror HA, 3-year 4‑hour support. |
| NGS Storage (Option) | Dell PowerVault ME5212 + ME412 | 1 | Alternate HA landing tier | Dell ME5212 storage with 25 Gb FC Type‑B dual controllers, 2×2 SFP+ FC25 optics, 28×24 TB 12 Gb SAS 7.2K drives, 5U rack kit, dual 2200 W PSU, ProSupport Plus 4‑hour/36‑month. |
| NAS / Clinical Storage | NetApp FAS2820 (10 Gb SFP+) | 1 | Isolated clinical / NAS tier | Dual controller, 48×22 TB, 10 Gb data path for segregated workloads. |
| NAS Storage (Option) | Dell PowerVault ME5212 | 1 | Alternate NAS tier | Dell ME5212 storage with 25 Gb FC Type‑B dual controllers, 2×2 SFP+ FC25 optics, 28×24 TB 12 Gb SAS 7.2K drives, 5U rack kit, dual 2200 W PSU, ProSupport Plus 4‑hour/36‑month. Notes: confirm SAN switch, add 25 Gb NIC + 2×SFP to any server needing this array. |
| Precision Consoles | Dell Precision 3680 Tower | 2 | Bioinformatics workstations | Intel i7‑14700, 64 GB RAM, 2×2 TB SSD RAID1, Windows 11 Pro, 3‑year onsite support. |
| OS & Platform Stack | RHEL 9 Subscription | 5 | Cluster OS & middleware | Includes Slurm 23, GPFS entitlement, data-protection tooling, and AWS CLI/Snowball integration. |
| Network & Optics | ||||
| Sequencer Fabric Switch | Cisco N9K-C93108TC-FX3 | 1 | Sequencer aggregation | 48×100M/1/10G-T plus 6×40/100 G QSFP28; dual PSUs and fans. |
| Storage Fabric Switch | Cisco N9K-C93180YC-FX3 | 1 | 25 Gb storage/data fabric | 48×1/10/25 Gb SFP28 plus 6×40/100 G QSFP28; dual PSUs and fans. |
| Data Access Switch | Cisco C9200L-48T-4X-E | 1 | Production VLAN4 | 48×1 Gb, 4×10 Gb uplinks, Network Essentials license, DNAC subscription. |
| Management / IPMI Switch | Cisco C9200L-48T-4X-E | 1 | VLAN2 + work access | 48×1 Gb, 4×10 Gb uplinks, dual PSU. |
| QSFP Active Optical Cable | Cisco QSFP-100G-AOC5M | 2 | Fabric interconnect | 5 m 100 Gb AOC connecting the Nexus pair. |
| 25 Gb SFP28 Optics | Cisco SFP-25G-SR-S | 18 | Server & storage uplinks | Fan-out to 5 servers (2 each) plus two NetApp HA pairs (4 each). |
| 10 Gb SFP+ Optics | Cisco MA-SFP-10GB-SR | 4 | Clinical NAS connectivity | Merges clinical NetApp shelves into legacy fabric. |
| OM4 Fiber (2 m) | LC-LC, MM | 8 | Storage patching | Short links between NetApp controllers and Nexus. |
| OM4 Fiber (5 m) | LC-LC, MM | 10 | Server uplinks | 2×5 runs for compute racks. |
| OM4 Fiber (10 m) | LC-LC, MM | 4 | NAS reach | NAS shelves to storage switch. |
| Cat6 Copper (2 m) | Factory bundle | 10 | Server management | IPMI and console jumpers (two bundles of five). |
| Cat6 Copper (5 m) | Factory bundle | 6 | Storage + Nexus | 2×2 storage runs plus 2× management uplinks. |
| Cat6 Copper (10 m) | Factory bundle | 4 | NAS + Catalyst | NAS redundancy and Catalyst uplinks. |
| Cat6A Copper (10 m) | Factory bundle | 5 | Sequencer data | High-bandwidth copper paths from sequencer room. |
| Accessory Materials | Cable trays / labels | 1 | Structured cabling kit | Includes ladder tray hardware, tie-downs, and labeling stock. |
| Facility & Power | ||||
| Dedicated Cold Aisle / HVAC | Facility scope | 1 | Cooling | Load recompute: ≈54,000 BTU/h for NextSeq 2000 + planned NovaSeq X + compute/storage; spec ≥5-ton coil. |
| 42U Racks + Dual PDUs | Standard cabinets | 2 | Rack footprint | Includes blanking panels, monitoring strips, and A/B PDUs. |
| UPS · Datacenter | APC Smart-UPS Online SRT10KXLI | 2 | Rack-level UPS | One 10 kVA online UPS per rack delivering dedicated power paths with N+1 coverage across the pair. |
| UPS · Sequencer / Lab | APC Smart-UPS Online SRT3000XLA | 1 | Instrument UPS | 3 kVA online UPS dedicated to the single NextSeq 2000 with circuits ready for future NovaSeq X. |
| Structured Cabling | Network link works | 1 | Fiber & copper plant | Part of facility build; ties sequencer room to datacenter. |
| Services & Support | ||||
| Remote Implementation Service | Dongke Service | 1 | Architecture & integration | WAN/HPC design, NetApp HA configuration, validation testing. |
| On-site Service | Dongke Deployment Block | 1 | Hands-on install | Rack/stack, OS installs, cutover support. |
| Annual Maintenance | Dongke Service | 1 | Run & support | Remote monitoring, updates, and escalation coverage. |
Execution Anchors
Each delivery stage below maps directly to the Physical Environment → Hardware & Procurement → On-site Deployment → Go-live & Post-launch timeline bands.
Physical Environment
Ready Room #124 for the NextSeq 2000, keep NovaSeq X footprint reserved, finish 10 Gb cabling quotes, confirm UPS/power paths, and release the ≥5-ton cooling upgrade.
Hardware & Procurement
Review the Dec 2025 quotation, validate specs, lock BTU + power inputs, and place orders for Dell, NetApp, Cisco, cabling, and services.
On-site Deployment
Rack the two 42U cabinets, install the five-node cluster plus NetApp shelves, terminate optics/copper, and stand up network/services through data-flow testing.
Go-live & Post-launch
Cut over the NextSeq 2000 data path on 1 Feb, pilot NovaSeq X prep flows, monitor SLAs, and deliver ongoing maintenance + support through April.