Software Resources for Analysis of Data: We offer a variety of services and support for analysis of data using both commercial and internally developed software that include the following: Commercial sequence analysis bundle: A collection of sequence analysis software is provided to CHOP researchers through an arrangement with the Bioinformatics Group of PENN Microarray Facility (http://core.pcbi.upenn.edu/index.html) This software bundle provides comprehensive functionality for analysis and management of nucleic acid and protein sequence. The package consists of the following programs:

• MacVector 10.6
• Sequencher 4.8
• Lasergene 7.0

Click here to sign up for the sequence analysis bundled package. Please contact us

CNV Workshop: CNV Workshop is a web-based CNV analysis, annotation, and visualization platform. It was designed as a chromosomal copy number variation (CNV) analysis tool using the SNP genotyping arrays. CNVs represented by as few as 2 SNPs can be detected reliably. Using multiple genomic resources, these CNVs are automatically annotated for gene content and potential disease labels, among others. The CNV Workshop web portal is integrated with the UCSC Genome Browser, which provides intuitive visualization capability and a rich context of genomic annotations. For more information on the tool or to request access to CNV Workshop, please contact us.

Other: Other bioinformatics specialty software that we have access to includes GCOS, GTYPE, GSEA, dChip, PartekPro, SpotFire Decision Site Functional Genomics Package, BLAST and BLAT, EMBOSS, Phred/Phrap/Consed, MacVector, VectorNTI, and a variety of NGS bioinformatics tools such as SOLiD System Open Source Software Tools (mapreads, Corona Lite, SAB, matoGff, solid2srf, and rna2map), Solexa Pipeline, MAQ, Bowtie, FindPeaks, SSAHA, RMAP, and SOAP. BiC servers host locally maintained versions of public databases (e.g. UCSC Genome Browser). We also have licenses for accessing Ingenuity Pathway Analysis (IPA) and BIOBASE Knowledge Library (BKL) + Explain. Software available without charge through the Stokes Research Institute includes but is not limited to Oracle 9i, SAS, and SPSS.

High-Performance Computing Access: Some bioinformatics analyses involve a large amount of legacy data in terms of numbers of samples, numbers of parameters, numbers of variables or all of these. The BiC maintains a multi-CPU cluster solution. Please contact us if you would like to have access to such resources.

The cluster consists of 12 servers. Each server is configured with the latest Intel Xeon CPU, boasting aither dual-quad core configurations or dual-dual core configurations. The cluster has a total of 84 available CPU/Cores for processing, and a grand total of 260GB of RAM memory. The cluster is running Centos 5 Linux through an installation of Rocks Cluster Suite. This suite provides torque PBS for batch processing of data and is equipped with a wide range of tools for advanced research. Internally the system has approximately 4.5 terabytes of disk space. It is also attached to the CHOP SAN infrastructure via optical fiber high-speed connections to increase available disk space to several terabytes, which can be expanded upon demand. The server is capable of running in a dual boot configuration enabling such operating systems as Open Mosix, which create a single super computer image that runs across all available systems.