NBIS Compute and Storage
The Bioinformatics compute and storage facility provides
high-performance computing and storage resources, maintain relevant
bioinformatics software and data (e.g. reference genomes), and offer
associated user support. The facility is hosted at Uppsala
Multidisciplinary Center for Advanced Computational Science
(SNIC-UPPMAX), which is Uppsala University’s resource for
high-performance computing and related know-how. Its reference group
makes strategic and policy decisions, while a manager is responsible
for daily operations.
Services
- Bioinformatics software
- Maintenance of an extensive suite of bioinformatics software
applications. Assistance with installation and updates
- Computing and storage
- High-performance computing and large-scale storage for
bioinformatics, primarily for the Next Generation Sequencing (NGS)
community in Sweden
- Hardware and system administration
- Expert management of high-performance computational hardware
- Reference data
- Maintenance of reference genomes and other shared data sources
- Training services
- Participates in various SciLifeLab workshops and courses, such as
“Computational Methods for Massively Parallel Sequencing”. Provides
computational resources for several other courses
- User support
- Provides technical user support for high-performance computing and
NGS analyses on UPPNEX systems
Equipment
- Access to SweStore National Storage
- Mainly for archiving data for longer periods of time.
- Alignment programs
- E.g. BWA, Mosaik, Bowtie, Tophat, MAQ, Bioscope and Lifescope
- Backup system
- Each project has a file area that every night is backed up on
magnetic tapes in Linköping
- Computational resources
- Computer cluster with 2 000 000 computing hours per month
- De novo assembly software
- E.g. Abyss, Velvet and Mira
- Downstream analysis programs
- E.g. Cufflinks, MrBayes, SAM-tools, and Annovar
- General software tools
- E.g. BioPerl, Picard and GATK
- High-bandwidth network
- Fast connection to Swedish University Network (SUNET) backbone
- High-memory computer
- Large memory SMP with 2 TB RAM
- Storage resources
- Storage resources of 7 PB
Applications
- Next-generation sequencing data analysis and management
- Large-scale storage and archiving of image data
- Management and analysis of drug screening data