A Containerized Software System for Generation, Management, and Exploration of Features from Whole Slide Tissue Images
This article describes a suite of services and web applications that allow users to select regions of interest in whole slide tissue images, run a segmentation pipeline on the selected regions to extract nuclei and compute shape, size, intensity, and texture features, store and index images and analysis results, and visualize and explore images and computed features. All the services are deployed as containers and the user-facing interfaces as web-based applications. The set of containers and web applications presented in this article is used in cancer research studies of morphologic characteristics of tumor tissues. The s...
Source: Cancer Research - October 31, 2017 Category: Cancer & Oncology Authors: Joel Saltz, Ashish Sharma, Ganesh Iyer, Erich Bremer, Feiqiao Wang, Alina Jasniewski, Tammy DiPrima, Jonas S. Almeida, Yi Gao, Tianhao Zhao, Mary Saltz, Tahsin Kurc Tags: Focus on Computer Resources Source Type: research
The Digital Slide Archive: A Software Platform for Management, Integration, and Analysis of Histology for Cancer Research
Tissue-based cancer studies can generate large amounts of histology data in the form of glass slides. These slides contain important diagnostic, prognostic, and biological information and can be digitized into expansive and high-resolution whole-slide images using slide-scanning devices. Effectively utilizing digital pathology data in cancer research requires the ability to manage, visualize, share, and perform quantitative analysis on these large amounts of image data, tasks that are often complex and difficult for investigators with the current state of commercial digital pathology software. In this article, we describe ...
Source: Cancer Research - October 31, 2017 Category: Cancer & Oncology Authors: David A. Gutman, Mohammed Khalilia, Sanghoon Lee, Michael Nalisnik, Zach Mullen, Jonathan Beezley, Deepak R. Chittajallu, David Manthey, Lee A.D. Cooper Tags: Focus on Computer Resources Source Type: research
Platform for Quantitative Evaluation of Spatial Intratumoral Heterogeneity in Multiplexed Fluorescence Images
We introduce THRIVE (Tumor Heterogeneity Research Interactive Visualization Environment), an open-source tool developed to assist cancer researchers in interactive hypothesis testing. The focus of this tool is to quantify spatial intratumoral heterogeneity (ITH), and the interactions between different cell phenotypes and noncellular constituents. Specifically, we foresee applications in phenotyping cells within tumor microenvironments, recognizing tumor boundaries, identifying degrees of immune infiltration and epithelial/stromal separation, and identification of heterotypic signaling networks underlying microdomains. The ...
Source: Cancer Research - October 31, 2017 Category: Cancer & Oncology Authors: Daniel M. Spagnolo, Yousef Al-Kofahi, Peihong Zhu, Timothy R. Lezon, Albert Gough, Andrew M. Stern, Adrian V. Lee, Fiona Ginty, Brion Sarachan, D. Lansing Taylor, S. Chakra Chennubhotla Tags: Focus on Computer Resources Source Type: research
The Mouse Tumor Biology Database: A Comprehensive Resource for Mouse Models of Human Cancer
Research using laboratory mice has led to fundamental insights into the molecular genetic processes that govern cancer initiation, progression, and treatment response. Although thousands of scientific articles have been published about mouse models of human cancer, collating information and data for a specific model is hampered by the fact that many authors do not adhere to existing annotation standards when describing models. The interpretation of experimental results in mouse models can also be confounded when researchers do not factor in the effect of genetic background on tumor biology. The Mouse Tumor Biology (MTB) da...
Source: Cancer Research - October 31, 2017 Category: Cancer & Oncology Authors: Debra M. Krupke, Dale A. Begley, John P. Sundberg, Joel E. Richardson, Steven B. Neuhauser, Carol J. Bult Tags: Focus on Computer Resources Source Type: research
PDX-MI: Minimal Information for Patient-Derived Tumor Xenograft Models
Patient-derived tumor xenograft (PDX) mouse models have emerged as an important oncology research platform to study tumor evolution, mechanisms of drug response and resistance, and tailoring chemotherapeutic approaches for individual patients. The lack of robust standards for reporting on PDX models has hampered the ability of researchers to find relevant PDX models and associated data. Here we present the PDX models minimal information standard (PDX-MI) for reporting on the generation, quality assurance, and use of PDX models. PDX-MI defines the minimal information for describing the clinical attributes of a patient's tum...
Source: Cancer Research - October 31, 2017 Category: Cancer & Oncology Authors: Terrence F. Meehan, Nathalie Conte, Theodore Goldstein, Giorgio Inghirami, Mark A. Murakami, Sebastian Brabetz, Zhiping Gu, Jeffrey A. Wiser, Patrick Dunn, Dale A. Begley, Debra M. Krupke, Andrea Bertotti, Aleȷandra Bruna, Matthew H. Brush, Annette Tags: Focus on Computer Resources Source Type: research
NDEx 2.0: A Clearinghouse for Research on Cancer Pathways
We describe innovations addressing the challenges of an online data commons: scalability, data integration, data standardization, control of content and format by authors, and decentralized mechanisms for review. The practical use of NDEx is presented in the context of a novel strategy to foster network-oriented communities of interest in cancer research by adapting methods from academic publishing and social media. Cancer Res; 77(21); e58–61. ©2017 AACR. (Source: Cancer Research)
Source: Cancer Research - October 31, 2017 Category: Cancer & Oncology Authors: Dexter Pratt, Jing Chen, Rudolf Pillich, Vladimir Rynkov, Aaron Gary, Barry Demchak, Trey Ideker Tags: Focus on Computer Resources Source Type: research
DINC 2.0: A New Protein-Peptide Docking Webserver Using an Incremental Approach
Molecular docking is a standard computational approach to predict binding modes of protein–ligand complexes by exploring alternative orientations and conformations of the ligand (i.e., by exploring ligand flexibility). Docking tools are largely used for virtual screening of small drug-like molecules, but their accuracy and efficiency greatly decays for ligands with more than 10 flexible bonds. This prevents a broader use of these tools to dock larger ligands, such as peptides, which are molecules of growing interest in cancer research. To overcome this limitation, our group has previously proposed a meta-docking strategy...
Source: Cancer Research - October 31, 2017 Category: Cancer & Oncology Authors: Dinler A. Antunes, Mark Moll, Didier Devaurs, Kyle R. Jackson, Gregory Lizee, Lydia E. Kavraki Tags: Focus on Computer Resources Source Type: research
Explore, Visualize, and Analyze Functional Cancer Proteomic Data Using the Cancer Proteome Atlas
Reverse-phase protein arrays (RPPA) represent a powerful functional proteomic approach to elucidate cancer-related molecular mechanisms and to develop novel cancer therapies. To facilitate community-based investigation of the large-scale protein expression data generated by this platform, we have developed a user-friendly, open-access bioinformatic resource, The Cancer Proteome Atlas (TCPA, http://tcpaportal.org), which contains two separate web applications. The first one focuses on RPPA data of patient tumors, which contains>8,000 samples of 32 cancer types from The Cancer Genome Atlas and other independent patient cohor...
Source: Cancer Research - October 31, 2017 Category: Cancer & Oncology Authors: Jun Li, Rehan Akbani, Wei Zhao, Yiling Lu, John N. Weinstein, Gordon B. Mills, Han Liang Tags: Focus on Computer Resources Source Type: research
P-MartCancer-Interactive Online Software to Enable Analysis of Shotgun Cancer Proteomic Datasets
P-MartCancer is an interactive web-based software environment that enables statistical analyses of peptide or protein data, quantitated from mass spectrometry–based global proteomics experiments, without requiring in-depth knowledge of statistical programming. P-MartCancer offers a series of statistical modules associated with quality assessment, peptide and protein statistics, protein quantification, and exploratory data analyses driven by the user via customized workflows and interactive visualization. Currently, P-MartCancer offers access and the capability to analyze multiple cancer proteomic datasets generated throu...
Source: Cancer Research - October 31, 2017 Category: Cancer & Oncology Authors: Bobbie-Jo M. Webb-Robertson, Lisa M. Bramer, Jeffrey L. Jensen, Markus A. Kobold, Kelly G. Stratton, Amanda M. White, Karin D. Rodland Tags: Focus on Computer Resources Source Type: research
An Accessible Proteogenomics Informatics Resource for Cancer Researchers
Proteogenomics has emerged as a valuable approach in cancer research, which integrates genomic and transcriptomic data with mass spectrometry–based proteomics data to directly identify expressed, variant protein sequences that may have functional roles in cancer. This approach is computationally intensive, requiring integration of disparate software tools into sophisticated workflows, challenging its adoption by nonexpert, bench scientists. To address this need, we have developed an extensible, Galaxy-based resource aimed at providing more researchers access to, and training in, proteogenomic informatics. Our resource br...
Source: Cancer Research - October 31, 2017 Category: Cancer & Oncology Authors: Matthew C. Chambers, Pratik D. Jagtap, James E. Johnson, Thomas McGowan, Praveen Kumar, Getiria Onsongo, Candace R. Guerrero, Harald Barsnes, Marc Vaudel, Lennart Martens, Bȷorn Gruning, Ira R. Cooke, Mohammad Heydarian, Karen L. Reddy, Timothy J. Tags: Focus on Computer Resources Source Type: research
Software for the Integration of Multiomics Experiments in Bioconductor
Multiomics experiments are increasingly commonplace in biomedical research and add layers of complexity to experimental design, data integration, and analysis. R and Bioconductor provide a generic framework for statistical analysis and visualization, as well as specialized data classes for a variety of high-throughput data types, but methods are lacking for integrative analysis of multiomics experiments. The MultiAssayExperiment software package, implemented in R and leveraging Bioconductor software and design principles, provides for the coordinated representation of, storage of, and operation on multiple diverse genomics...
Source: Cancer Research - October 31, 2017 Category: Cancer & Oncology Authors: Marcel Ramos, Lucas Schiffer, Angela Re, Rimsha Azhar, Azfar Basunia, Carmen Rodriguez, Tiffany Chan, Phil Chapman, Sean R. Davis, David Gomez-Cabrero, Aedin C. Culhane, Benjamin Haibe-Kains, Kasper D. Hansen, Hanish Kodali, Marie S. Louis, Arvind S. Mer, Tags: Focus on Computer Resources Source Type: research
CRAVAT 4: Cancer-Related Analysis of Variants Toolkit
Cancer sequencing studies are increasingly comprehensive and well powered, returning long lists of somatic mutations that can be difficult to sort and interpret. Diligent analysis and quality control can require multiple computational tools of distinct utility and producing disparate output, creating additional challenges for the investigator. The Cancer-Related Analysis of Variants Toolkit (CRAVAT) is an evolving suite of informatics tools for mutation interpretation that includes mutation mapping and quality control, impact prediction and extensive annotation, gene- and mutation-level interpretation, including joint prio...
Source: Cancer Research - October 31, 2017 Category: Cancer & Oncology Authors: David L. Masica, Christopher Douville, Collin Tokheim, Rohit Bhattacharya, RyangGuk Kim, Kyle Moad, Michael C. Ryan, Rachel Karchin Tags: Focus on Computer Resources Source Type: research
Variant Review with the Integrative Genomics Viewer
Manual review of aligned reads for confirmation and interpretation of variant calls is an important step in many variant calling pipelines for next-generation sequencing (NGS) data. Visual inspection can greatly increase the confidence in calls, reduce the risk of false positives, and help characterize complex events. The Integrative Genomics Viewer (IGV) was one of the first tools to provide NGS data visualization, and it currently provides a rich set of tools for inspection, validation, and interpretation of NGS datasets, as well as other types of genomic data. Here, we present a short overview of IGV's variant review fe...
Source: Cancer Research - October 31, 2017 Category: Cancer & Oncology Authors: James T. Robinson, Helga Thorvaldsdottir, Aaron M. Wenger, Ahmet Zehir, Jill P. Mesirov Tags: Focus on Computer Resources Source Type: research
Integrating DNA Methylation and Hydroxymethylation Data with the Mint Pipeline
DNA methylation (5mC) plays important roles in mammalian development, oncogenesis, treatment response, and responses to the environment. DNA hydroxymethylation (5hmC) is also an informative epigenetic mark with distinct roles in regulation and cancer. Gold-standard, widely used technologies (bisulfite conversion, followed by deep sequencing) cannot distinguish between 5mC and 5hmC. Therefore, additional experiments are required to differentiate the two marks, and in silico methods are needed to analyze, integrate, and interpret these data. We developed the Methylation INTegration (mint) pipeline to support the comprehensiv...
Source: Cancer Research - October 31, 2017 Category: Cancer & Oncology Authors: Raymond G. Cavalcante, Snehal Patil, Yongseok Park, Laura S. Rozek, Maureen A. Sartor Tags: Focus on Computer Resources Source Type: research
A Galaxy Implementation of Next-Generation Clustered Heatmaps for Interactive Exploration of Molecular Profiling Data
Clustered heatmaps are the most frequently used graphics for visualization of molecular profiling data in biology. However, they are generally rendered as static, or only modestly interactive, images. We have now used recent advances in web technologies to produce interactive “next-generation” clustered heatmaps (NG-CHM) that enable extreme zooming and navigation without loss of resolution. NG-CHMs also provide link-outs to additional information sources and include other features that facilitate deep exploration of the biology behind the image. Here, we describe an implementation of the NG-CHM system in the Galaxy bio...
Source: Cancer Research - October 31, 2017 Category: Cancer & Oncology Authors: Bradley M. Broom, Michael C. Ryan, Robert E. Brown, Futa Ikeda, Mark Stucky, David W. Kane, James Melott, Chris Wakefield, Tod D. Casasent, Rehan Akbani, John N. Weinstein Tags: Focus on Computer Resources Source Type: research
