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  1. The Digital Slide Archive

    13 Jun 2017 | Presentations | Contributor(s): Denise Warzel, Ann Christine Catlin, Sumudinie fernando

    Presentation at the 2017 Informatics Technology for Cancer Research Annual Meeting Advanced development of an open-source platform for web-based integrative digital image analysis in cancer.

  2. Activities to Promote Technology Research Collaborations (APTRC) PA-17-143 Pre-Application Webinar

    24 Feb 2017 | Presentations | Contributor(s): Denise Warzel, Ann Christine Catlin, Sumudinie fernando

    Pre-application seminar held February 24, 2017 for FOA PA-17-143 

  3. Life after MOOCS: Online Science Education Needs a New Revolution

    03 Feb 2017 | Presentations | Contributor(s): Denise Warzel, Ann Christine Catlin, Sumudinie fernando

    ITCR Monthly PI Meeting, February 3, 2017 Presentation by Phillip Compeau (Carnegie Mellon U.)

  4. Extending 3D Slicer to support ground truth pathology tissue segmentation data for integrated pathology/radiology image analysis competitions.

    06 Jan 2017 | Presentations | Contributor(s): Denise Warzel, Ann Christine Catlin, Sumudinie fernando

    ITCR PI Monthly Meeting January 6, 2017 Collaborative project goal: Improve support in 3D Slicer for pathology imaging, generate high quality, well curated “ground truth” annotations, integrate key aspects of the Stony Brook ITCR project (FeatureDB) into the MGH project and...

  5. Providing National Cyberinfrastructure to Biologists, esp. Genomicists

    02 Sep 2016 | Presentations | Contributor(s): Denise Warzel, Ann Christine Catlin, Sumudinie fernando

    National Center for Genome Analysis Support (NCGAS) provides access to High Performance Computing resources for biologists. NCGAS also maintains a curated set of applications and Galaxy instances of their software, as well as provides bioinformatics expertise.

  6. An Extensible and Scalable Knowledge System Architecture for Cancer Research

    06 May 2016 | Presentations | Contributor(s): Denise Warzel, Ann Christine Catlin, Sumudinie fernando

    ITCR May 2016 PI meeting presentation on development of an advanced knowledge system to capture, share and support reproducible analysis from the biomarker data results.  

  7. Resources on NCIP Hub (2016)

    02 Mar 2016 | Presentations

    This presentation is part of NCIP Hub's 2016 Webinar Series. It provides an overview of what resources are, when and why to use resources and how to upload resources to NCIP Hub.

  8. GenomeSpace Presentation

    08 Feb 2016 | Presentations | Contributor(s): Denise Warzel, Ann Christine Catlin, Sumudinie fernando

    GenomeSpace (http://www.genomespace.org) is a cloud-based, cooperative community resource that currently supports the streamlined interaction of 20 bioinformatics tools and data resources. To facilitate integrative analysis by non-programmers, it offers a growing set of 'recipes',...

  9. Trinity: RNA-Seq De novo Assembly Application

    30 Jun 2015 | External Applications | Contributor(s): Denise Warzel, Ann Christine Catlin, Sumudinie fernando

     Quick Guide for the ImpatientTrinity assembles transcript sequences from Illumina RNA-Seq data.Download Trinity here.Build Trinity by typing make : ; in the base installation directory.Assemble RNA-Seq data like so:Trinity --seqType fq --left reads_1.fq --right reads_2.fq...

  10. CRAVAT - Cancer-Related Analysis of Variants Toolkit

    23 Jun 2015 | External Applications | Contributor(s): Denise Warzel, Ann Christine Catlin, Sumudinie fernando

    cravat is a bioinformatics pipeline : ; that performs high-throughput cancer-related analysis of variants. it : ; utilizes three applications: CHASM (Cancer-Specific Analysis of Somatic Mutations), VEST and SVN-Get. More information on these tools is available at CHASM Software.Release...

  11. Tools for Creation of Integrated Data Repository for Cancer Research

    16 Jun 2015 | Presentations | Contributor(s): Denise Warzel, Ann Christine Catlin, Sumudinie fernando

    Admin Supplement Proposal Parent Projects: DeepPhe (PIs: Savova and Jacobson) caCDE-QA (PI: Jiang)

  12. A Semantic Web-based Quality Assurance Tool for Cancer Study Common Data Elements

    16 Jun 2015 | Presentations | Contributor(s): Denise Warzel, Ann Christine Catlin, Sumudinie fernando

    A poster presentation from the caCDE-QA project (PI: Jiang)  

  13. Notes from the ITCR Annual Meeting May 27-28, 2015

    10 Jun 2015 | Downloads | Contributor(s): Denise Warzel, Ann Christine Catlin, Sumudinie fernando

    Notes from the ITCR Annual Meeting May 27-28, 2015

  14. NCIP Hub QIN Workshop - March 3, 2015

    19 Mar 2015 | Presentations

    Mike McLennan, director of HUBzero, presented an overview of basic NCIP Hub functionality to the QIN group on March 3, 2015. The presentation included an overview of the "hub" and HUBzero, and touched upon functionality such as projects, groups, resources and information sharing. The...

  15. Introduction to the Trinity Cancer Transcriptome Analysis Toolkit

    05 Feb 2015 | Teaching Materials | Contributor(s): Denise Warzel, Ann Christine Catlin, Sumudinie fernando

    This short video provides an overview of our ITCR-funded effort to leverage RNA-Seq and de novo transcriptome assembly to assist researchers in studying cancer transcriptomes.  Visit our NCGAS Trinity/Galaxy portal to access these compute...

  16. CRAVAT Introduction Video - Cancer Related Analysis of Variants

    03 Dec 2014 | Teaching Materials | Contributor(s): Denise Warzel, Ann Christine Catlin, Sumudinie fernando

    This video provides a brief overview of the CRAVAT web service(http://www.cravat.us/).  CRAVAT provides annotation and analysis of cancer mutations. CRAVAT is free, very easy to use, and can handle large volumes of mutations.[[Youtube(xovmIy11Bcs)]]Please switch to 1080 resolution and watch...

  17. Databases on NCIP Hub

    21 Nov 2014 | Teaching Materials

    Overview and demo of the database functionality on NCIP Hub. Further documentation on database functionality is included in the "Supporting Documentation" section.

  18. Building Online Scientific Communities via NCIP Hub

    17 Nov 2014 | Teaching Materials

    Overview of how NCIP Hub can be used to build online scientific communities.

  19. Tools to Analyze Morphology and Spatially Mapped Molecular Data

    03 Oct 2014 | Presentations | Contributor(s): Denise Warzel, Ann Christine Catlin, Sumudinie fernando

  20. Resources on NCIP Hub

    22 Sep 2014 | Teaching Materials

    This is a presentation given as part of the NCIP Hub Webinar Series. It reviews at a high level what resources are, why and when to use them, and how to contribute.