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  • Integrated Virtual Microscopy and Molecular Analysis Software for Enhanced Cancer Diagnosis
    Educators Online OCS Lecture Series Press Releases Headlines Calendar of Events About OSC Media Kit OSC Media Contacts Staff Directory Visit OSC Supercomputing Support Networking Support Analytics Research Current Projects Contact Us Related Links Research Home Get an Account Research Reports 2009 Research Highlights 2008 Research Report 2007 Research Report Analytics Research Integrated Virtual Microscopy and Molecular Analysis Software for Enhanced Cancer Diagnosis Principal Investigator Ashok Krishnamurthy Ph D Ohio Supercomputer Center Funding Source U S Department of Health and Human Services through the Ohio Board of Regents The acronym VM2M might stand for Virtual Microscopy to Microarray but for cancer researchers it means revolutionizing a part of the investigative process Expert pathologists depend on microscopy or the latest use of microscopes to examine and review diseased tissue Their conclusions help oncologists form the foundation for treatments The different research teams involved are working to create a tool that provides multi modal views of cancer biopsies that show pathologies of cancerous cells alongside their genetic information said Dave Billiter PMP The Research Institute at Nationwide Children s Hospital Our portion involves taking microscopy data virtual by digitizing the slides of the cancerous biopsies and providing a tool to view them via the Web After The Research Institute at Nationwide Children s Hospital creates the microscopy image from the specimen the tissue sample is sent to the Childrens Hospital Los Angeles where that research team creates the microarray portion of the project by identifying the genetic information for each tumor The Ohio Supercomputer Center researchers meanwhile are expanding the capabilities of VIPER Virtual microscopy Image Pilot EndeavoR which is the pathology review component of VM2M The Web based portal they created enables pathologists to review annotate and share tissue specimen images Ultimately VIPER and VM2M will provide cancer researchers with searchable

    Original URL path: http://archive.osc.edu/research/analytics/projects/VM2M/index.shtml (2013-06-13)
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  • Interfacing PC-based MATLAB Directly to HPC Resources

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    Original URL path: /research/analytics/projects/matlab/index.shtml (2013-06-13)


  • Remote Backup of Critical Administrative Data for Disaster Recovery
    s Summer Institute HPC and Software Training Current Training and Events Educators Online OCS Lecture Series Press Releases Headlines Calendar of Events About OSC Media Kit OSC Media Contacts Staff Directory Visit OSC Supercomputing Support Networking Support Networking Research Current Projects Past Projects Collaborators Contact Us Related Links Research Home Get an Account Systems Research OSC Networking Research Reports 2009 Research Highlights 2008 Research Report 2007 Research Report Cyberinfrastructure and Software Development Research Remote Backup of Critical Administrative Data for Disaster Recovery Principal Investigator Steve Gordon OSC Funding Source Ohio Board of Regents OBR Duration 2 2003 8 2005 Description Disaster recovery imputations can be very costly and time consuming A number of Institutions in Ohio are in need of an off site storage facility for part of their disaster recovery needs This project takes a look at using OSCnet Solaris 10 Containers and ZFS together for a cost effective way for institutions to store their data off site Using Shared hardware and partitioning the hardware using Solaris 10 Containers and ZFS provides excellent platform for data management on a large scale Institutions want their autonomy and want full control of their data Solaris Containers allows the dynamic allocation of

    Original URL path: http://archive.osc.edu/research/networking/projects/disaster/index.shtml (2013-06-13)
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  • NSF Network Connections Project
    Calendar of Events About OSC Media Kit OSC Media Contacts Staff Directory Visit OSC Supercomputing Support Networking Support Networking Research Current Projects Past Projects Collaborators Contact Us Related Links Research Home Get an Account Systems Research OSC Networking Research Reports 2009 Research Highlights 2008 Research Report 2007 Research Report Cyberinfrastructure and Software Development Research NSF Network Connections Project Central State University Cedarville University Wilberforce University and the Ohio Supercomptuer Center Project Summary A grant from the National Science Foundation and Ohio Board of Regents Action Fund financed new high performance network connections HPNC to Central State University Cedarville University and Wilberforce University to accommodate growth and allow them to benefit from high performance networking and computing Central State is leading the HPNC project management and collaboration among the three schools The network connections will be in full production and will help to facilitate a number of new collaborations among the institutions and OSC Several kinds of activities are envisioned Lectures and seminars delivered over the network beginning with subjects relating to networking and high performance computing and then extending into other areas Experience with cluster computing using hardware acquired through the grant and the existing infrastructure at OSC Opportunites for

    Original URL path: http://archive.osc.edu/research/networking/projects/connections/index.shtml (2013-06-13)
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  • OSC Research Report

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    Original URL path: /research/report/biological.shtml (2013-06-13)




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    Original URL path: /research/bioinformatics/compsci_survey.shtml (2013-06-13)


  • Larg-Scale Systems Biology Research at OSC
    Archive Related Links Collaborations Get an Account Research Partners Research Video Library Research Reports 2010 Research Highlights 2009 Research Highlights 2008 Research Report 2007 Research Report Bioinformatics Software Development Projects Large Scale Systems Biology Research at OSC Principle Investigators Dr Said Sif Assistant Professor Department of Molecular and Cellular Biochemistry Ohio State University Dr Shiyuan Cheng Associate Professor University of Pittsburgh Cancer Institute Dr Chunming Liu Assistant Professor University of Texas Medical Branch Co PI Weisong Gu OSC Funding Agency OSC In house Research Description Traditional molecular biology approach to study gene expression and gene regulation is based on an ad hoc individual analysis that is very laborious Moreover the data collected in this way is of isolated status and thus may not truly reflect the real characteristics of the cell or organism With the advent of genome sequencing and high throughput measurement technologies comprehensive data can be collected at the system level or at the whole genome scale Particularly gene expression microarray technology is revolutionizing many aspects of biological research as it allows monitoring many thousands of gene transcripts simultaneously This provides powerful tools for the genome wide correlation of gene transcript levels with physiological responses and alterations in physiological states to assess various biological models including disease therapy or experimental manipulation Recently chromatin immunoprecipitation technology has been coupled with the high throughput DNA microarray CHIP on Chip to study the protein DNA binding assay at the genome scale level With the combined high throughput data in both gene expression and bind assay the gene regulatory network could be solidly constructed at the genome wide level using sophisticated computer algorithms such as GRAM REDUCE modified MOTIF REGRESSOR etc OSC has been integrating a Systems Biology infrastructure to assist Ohioan and national biological researchers in Genomics Computation Analysis and Technology

    Original URL path: http://archive.osc.edu/research/bioinformatics/projects/gene_expression/index.shtml (2013-06-13)
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  • HIPPA Compliant Web-based Framework for the Ohio BioRepository
    Software Training Current Training and Events Educators Online OCS Lecture Series Press Releases Headlines Calendar of Events About OSC Media Kit OSC Media Contacts Staff Directory Visit OSC Supercomputing Support Networking Support Research Blue Collar Computing Analytics Bioinformatics Biomedical Sciences and Visualization Computational Science Engineering Research Cyberinfrastructure and Software Development Systems Research Research Archive Related Links Collaborations Get an Account Research Partners Research Video Library Research Reports 2010 Research Highlights 2009 Research Highlights 2008 Research Report 2007 Research Report Bioinformatics Software Development Projects HIPPA Compliant Web based Framework for the Ohio BioRepository Principal Investigator Bill Tacon Omeris Funding Source Ohio Department of Development Duration December 2003 December 2006 The Ohio BioRepository OBR comprising a human tissue specimen repository and associated searchable database is led by Omeris in partnership with the Ohio Supercomputer Center OSC with support from Ohio State University s Human Tissue Resource Network HTRN The repository provides researchers ready access to tissues stored under a variety of preservation techniques ensuring the presence of low abundance mRNAs and a separate formalin fixed paraffin block tissue archive The repository will become a unique asset for fast turnaround on human research studies The Ohio BioRepository initiative needed a secure way of capturing annotated pathology report data The annotated data or protected heath information PHI was to later be converted to non PHI and be accessible by researchers interested in conducting research on the tissue specimens The Ohio Supercomputer Center OSC had the tasks of designing the web interfaces creating and hosting the web sites and maintaining the database for the Ohio BioRepository The developed annotation system allows for the secure capture of PHI data viewing the reports and searching on the data The subsequent public site used to search sanitized information was built using a flexible framework that allows for a

    Original URL path: http://archive.osc.edu/research/bioinformatics/projects/obr/index.shtml (2013-06-13)
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