The Bioinformatics core at the Genome Center of UC Davis is hosting several largest computer clusters in campus specifically for biological applications. The core has numerous computers for various software and database development and services.
We offer a number of in-depth 2-day workshops on topics such as RNASeq analysis, data visualization, and cloud computing for bioinformatics using Amazon Web Services. You can find information on these courses and a number of other training resources at training.bioinformatics.ucdavis.edu.
- High Performance Scientific Computing Cluster: 111 nodes dual socket dual core Opteron 270, 4GB or 8GB RAM runing ROCKS 5.0 & 6TB storage
- Bioinformatics Applications & Training cluster: 10 nodes dual socket qual core Opteron 2346, 8GB RAM running ROCKS 5.1 & 10TB storage
- High Throughput Bioinformatics Applications: 24 nodes dual socket dual core Opteron 248, 4GB RAM and 10 nodes of 4-socket quad core Opteron 8356 with 32GB RAM & 4TB local storage running ROCKS 5.0 & 3.2 TB storage
- Large Genome Assembly: Sun Fire x4600 with 128GB RAM for large Genome Assembly and memory intensive applications
- Ultra-high Memory Use Applications: Sun Fire x4600M2 with 512GB RAM for ultra-high memory-use applications
- Advanced high-content scientific data visualization: 6-node visual processing system with 50 megapixel display wall
- 20 TB Disk to Disk backup capacity at two separate physical locations in UC Davis campus
- 20TB/year tape backup capacity, One Sun Fire x4500 (48TB) for Illumina GA seqeuence
- Dozens Virtual Machines for Web sites, File System Services (NFS/AFS), DNS, DHCP, KDC, CVS/SVN, Terminal Service, Firewall and Databases
- 10 Gigabit Ethernet network service with direct access to National Lamda Rail (NLR) network. UC Davis is a member of the Corporation for Education Network Initiatives in California (CENIC).
- Active bioinformatics tools at the Bioinformatics Core wiki
- create fake sequences (e.g. for CAP3 / PCAP) from a fasta file
- remove blank spaces from filenames
- sort sequence in fasta format by their length
- quick/dirty simulation of Illumina reads from a fasta reference
- remove extended ASCII characters from files (like genepix microarray .gpr files!)
- reformat fasta sequences or qualities to have fixed width
- find single character frequencies in a text file