Center for Computation & Visualization

The Center for Computation and Visualization is located at Brown University and led by Executive Director Gucharan Khanna.

If your research applies to EPSCoR themes and you could use these resources, apply today for access as an EPSCoR user. Fill out the computational resource user initial application or renewal application and submit to Rhode Island NSF EPSCoR. Requests will be processed by the Steering Committee.

EPSCoR users are given access to these resources as well as bioinformatics support:

  • Highest priority access to the EPSCoR 1000+ core condo maintained and supported by the CCV
  • Access to a Galaxy portal with 128 cores and 512 GB memory per node (2 nodes)
  • Data Storage purchase (CCV priced at $750 per TB) and includes automatic backup and storage for up to six years
  • Highest priority access to the Scale-MP “Fat Node” of 1.5 TB which is extremely useful for de novogenome assembly from fragment reads
  • Access to over 100 bioinformatics/genomics applications and general applications
  • Collection and assembly of data for genomic analysis and for gene expression profiling
  • General source of advice on existing tools for genome analysis, gene expression analysis, gene annotation, and epigenetic analysis
  • Analysis of basic biological research and biomedical data using existing tools
  • Evaluation and development of new and advanced bioinformatics tools and analytical software
  • Development and description of data workflows and pipelines
  • Flexibility to work with data streams from various major instrumentation platforms
  • Technical and analytical methods  preparation for assembly of grant applications

See the collection of available software tools and more at the bioinformatics wiki.

  • MicroArray software:  Bioconductor
  • Pathway analysis:  IPA
  • RNA-Seq software: CASAVA, Tophat/Cufflinks, CrossBow, Erange, GATK
  • CHIP-Seq software: PeakSeq, SPP package, MACS
  • De Novo Assembler: ABYSS, SOAPDenovo, Velvet, InchWorm, Rnnonator,  Agalma
  • Aligner: Eland, Bowtie, MAQ, Blast, BWA
  • CNV analysis: CNVnator
  • MicroRNA analysis: miRExpress
  • Other tools: samtools, igvtools, bfast, bamtools, Bioperl, BioPython
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