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