The accelerating progress in cancer research has been driven by rapid developments in technology, and with it, an associated influx of data, emphasizing the growing importance of computing, machine learning, and data analysis in biomedicine. The collected works below, published online-only in the November 1, 2017 issue of Cancer Research, introduce computing tools and resources that non-bioinformaticists can incorporate into their work. These articles are freely available thanks to support from the NCI. We intend for this collection to be the beginning of many more computational resource papers that will be published and highlighted in future issues of Cancer Research.

Here, the articles are grouped by subject matter: Genomics, Proteomics, Animal Models, Imaging, and Clinical.

Read the Focus Editorial from Juli Klemm, NCI; Warren Kibbe, Duke University; and John Quackenbush, Harvard University and Senior Editor, Cancer Research.

Genomics

• The Cancer Genomics Cloud: Collaborative, Reproducible, and Democratized—A New Paradigm in Large-Scale Computational Research
  Jessica W. Lau…Brandi Davis-Dusenbery
• The ISB Cancer Genomics Cloud: A Flexible Cloud-based Platform for Cancer Genomics Research
  Sheila M. Reynolds…Ilya Shmulevich
• WebMeV: a Cloud Platform for Analyzing and Visualizing Cancer Genomic Data
  Yaoyu E. Wang…John Quackenbush
• Developing Cancer Informatics Applications and Tools Using the NCI Genomic Data Commons API
  Shane Wilson…Robert L. Grossman
• Cistrome Cancer: A Web Resource for Integrative Gene Regulation Modeling in Cancer
  Shenglin Mei…X. Shirley Liu
• A Galaxy Implementation of Next-Generation Clustered Heatmaps for Interactive Exploration of Molecular Profiling Data
  Bradley M. Broom…John N. Weinstein
• Integrating DNA Methylation and Hydroxymethylation Data with the Mint Pipeline
  Raymond G. Cavalcante…Maureen A. Sartor
• Variant Review with the Integrative Genomics Viewer (IGV)
  James T. Robinson…Jill P. Mesirov
• CRAVAT 4: Cancer-Related Analysis of Variants Toolkit
  David L. Masica…Rachel Karchin
• Software for the Integration of Multiomics Experiments in Bioconductor
  Marcel Ramos…Levi Waldron
• TIMER: A Web Server for Comprehensive Analysis of Tumor-Infiltrating Immune Cells
  Taiwen Li…X. Shirley Liu

Proteomics

• An Accessible Proteogenomics Informatics Resource for Cancer Researchers
  Matthew C. Chambers…Timothy J. Griffin
• P-MartCancer—Interactive Online Software to Enable Analysis of Shotgun Cancer Proteomic Datasets
  Bobbie-Jo M. Webb-Robertson…Karin D. Rodland
• Explore, Visualize and Analyze Functional Cancer Proteomic Data Using The Cancer Proteome Atlas
  Jun Li…Han Liang
• DINC 2.0: A New Protein–Peptide Docking Webserver Using an Incremental Approach
  Dinler A. Antunes…Lydia E. Kavraki
• NDEx 2.0: A Clearinghouse for Research on Cancer Pathways
  Dexter Pratt…Trey Ideker

Animal Models

• PDX-MI: Minimal Information for Patient-Derived Tumor Xenograft Models
  Terrence F. Meehan…Carol J. Bult
• The Mouse Tumor Biology Database (MTB): A Comprehensive Resource for Mouse Models of Human Cancer
  Debra M. Krupke…Carol J. Bult

Imaging

• Platform for Quantitative Evaluation of Spatial Intratumoral Heterogeneity in Multiplexed Fluorescence Images
  Daniel M. Spagnolo…S. Chakra Chennubhotla
• The Digital Slide Archive: A Software Platform for Management, Integration and Analysis of Histology for Cancer Research
  David A. Gutman…Lee A.D. Cooper
• A Containerized Software System for Generation, Management and Exploration of Features from Whole Slide Tissue Images
  Joel Saltz…Tahsin Kurc
• An Image Analysis Resource for Cancer Research: PIIP—Pathology Image Informatics Platform for Visualization, Analysis and Management
  Anne L. Martel…Metin N. Gurcan
• dcmqi: An Open Source Library for Standardized Communication of Quantitative Image Analysis Results Using DICOM
  Christian Herz…Andriy Fedorov
• Integrative Analysis of Histopathological Images and Genomic Data Predicts Clear Cell Renal Cell Carcinoma Prognosis
  Jun Cheng…Kun Huang
• SlicerDMRI: Open Source Diffusion MRI Software for Brain Cancer Research
  Isaiah Norton…Lauren J. O'Donnell
• Computational Radiomics System to Decode the Radiographic Phenotype
  Joost J.M. van Griethuysen…Hugo J.W.L. Aerts

Clinical

• TumorMap: Exploring the Molecular Similarities of Cancer Samples in an Interactive Portal
  Yulia Newton…Joshua M. Stuart
• DeepPhe - A Natural Language Processing System for Extracting Cancer Phenotypes from Clinical Records
  Guergana K. Savova…Rebecca S. Jacobson
• LesionTracker: Extensible Open-Source Zero-Footprint Web Viewer for Cancer Imaging Research and Clinical Trials
  Trinity Urban…Gordon J. Harris
• "Personalized Cancer Therapy": A Publicly Available Precision Oncology Resource
  Katherine C. Kurnit…Funda Meric-Bernstam