BioHPC Lab at Cornell
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1 BioHPC Lab at Cornell Jaroslaw Pillardy CBSU, Life Sciences Core Laboratories Center Cornell University
2 Practical exercises for the workshop will be carried out using CBSU BioHPC Lab Software used during the workshop can be downloaded from
3 Brief introduction to using BioHPC Lab is available on the workshop page
4 BioHPC Laboratory is a computational cloud-like resource configured and optimized for the needs of computational biology
5 Hardware (general access): BioHPC Laboratory 3 Linux interactive workstations. Dell Precision T3500n, Quad Core Intel Xeon W GHz CPU, HDD SATA controller with 2 2TB HDD, 24GB RAM, NVIDIA Quadro NVS 295 Graphics Card, 24in LCD monitor. 1 Windows interactive workstation. Dell Precision PWS T5400, Quad Core Intel Xeon E GHz CPU, HDD SATA controller with total of 10TB HDD storage, 16GB RAM, NVIDIA Quadro FX570 Graphics Card, 24in LCD monitor. 31 Linux remote workstations. Dell PowerEdge M600 blade server, two quad-core Intel Xeon E GHz CPUs, 16GB RAM, 1TB HD local storage. 2 Linux large RAM remote workstation. Dell PowerEdge R710 with four quad-core Intel Xeon E GHz, 1TB HD, 64GB RAM. Red Barn Server with four 12-core AMD Opteron 6172 SKT G34 2.1GHz, 13TB HD, 512GB RAM. File server. Dell Precision T110, Intel Xeon X3430, 2.4 GHz, HDD SATA controller with 4 2TB HDD, 36 TB SATA enclosure, 8GB RAM.
6 Software: Linux: 454 gsassembler, ABySS, AllPaths, Annovar, ATSAS, bamtools, BEDtools, BioPerl, BLAST, BLAT, Bowtie, BWA, CBSU RNAseq, CLUSTALW, Cufflinks, FASTX, GATK, iassembler, IGV, LUCY, MACS, MAQ, Netbeans, Novoalign (Novocraft), Oases, Picard, plink, prinseq, QIIME, R, RSEM, Samtools, SOAPdenovo, stacks, tabix, TASSEL, TopHat, Trinity, vcftools, Velvet. Windows: NextGENe (SoftGenetics), NGen (DNAStar), GenomeStudio (SoftGenetics). Up to date software list with additional information (version etc.) is online
7 BioHPC Laboratory
8 Remote workstations Interactive workstations
9 BioHPC Laboratory BioHPC Lab website allows for managing your account, make and manage reservations and connect to the workstations.
10 BioHPC Laboratory BioHPC Lab website allows for managing your account, make and manage reservations and connect to the workstations.
11 BioHPC Lab workstations must be reserved before using. Reservations for this workshop have been pre-arranged, workstation assignments are published on the workshop web pages: (on web page for session 2)
12 BioHPC Laboratory
13 Workstations feature two kinds of storage: o Network storage /home/<your_id> /programs /shared_data o Local storage /workdir /local_data
14 Remember: /workdir should be treated strictly as scratch space, i.e, files created there are not guaranteed to be preserved after the workshop (more generally, when your reservation expires). After completing the calculations, you will have to copy any important result files you wish to save to your home directory, where they will be preserved and accessible from other workstations. Create your own subdirectory /workdir/<my_lab_id> /home/<your_id> is NOT for computations they will be painfully slow there!
15 Connecting to workstations 1. ssh (PuTTY) 2. X-Windows (Xming on Windows) 3. VNC (must first connect from My Reservations ) Connecting from outside Cornell network: VPN required.
16 BioHPC Laboratory
17 Transferring files to and from workstations 1. FileZilla 2. WinScp 3. sftp
18 Running programs in Linux environment. Slides from our Linux workshops are available online: CBSU organizes Linux for Biologists workshops (two parts) check our website for next installment or sign up for CBSU mail list
19
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