ABCS | Scientific Applications
Advanced Biomedical Computational Science specializes in providing informatics solutions for simple to advanced scientific challenges. The solutions are scalable, modular and flexible, such that they can be easily adopted and/or integrated into other environments.

ABCS Publications

NCI OD-Frederick

ABCS Publications

List of peer-reviewed publications by ABCS researchers

AVIA

NCI OD-Frederick

Biomedical Annotations

Genomic location based annotations; Variant impact analysis; Annotate variants in VCF and BED formats; Recognizes codon and protein variant formats

bioDBnet

NCI OD-Frederick

Biomedical Annotations

Gene based identifer conversions; Organism wide; Ortholog conversions; Recognizes hundreds of data types

CyPRUS

NCI OD-Frederick

Biomedical Annotations

Visualize protein annotations from UniProt; Comparisons across ortholog sequences; Visualize custom annotations on protein sequences

non-B

NCI OD-Frederick

Biomedical Annotations

non-B DNA annotations; External and custom annotations from in-house algorithms; All mammalian genomes; Annotate custom sequences

MoCha cBioPortal

NCI DCTD

Biomedical Data Integration

Local instance of cBioPortal with CTEP and NIH authentication supporting the National Clinical Lab Network (NCLN) studies

RARe-SOURCE

NCATS

Biomedical Data Integration

Rare disease and associated gene details, related variant annotations, literature mining using language models

SysBioCube

USACEHR/WRAIR

Biomedical Data Integration

Data sharing for ongoing collaborations; Raw, temporary and analyzed files; Clinical data analytics; Interactive tracking of samples and assays status

CSSI DCC

NCI CSSI

Data Analysis and Management

Data sharing using standardized metadata; Open access and controlled access; Ontologically enhanced searches; Flexible downloads and API access

IC50 to Ki

NCI OD-Frederick

Data Analysis and Management

Computes Ki values from experimentally determined IC50 values for inhibitors of enzymes that obey classic Michaelis-Menten kinetics and protein-ligand interactions

PSD

NCI CCR

Data Analysis and Management

Pro-Viral Sequence Database; meta-analysis of HIV RNA and proviral sequences in donors on antiretroviral therapy

RID

NCI CCR

Data Analysis and Management

Retrovirus Integration Database; query retrovirus integration sites in host genomes

TIE

NCI CCR

Data Analysis and Management

Tumor IsomiR Encyclopedia for querying and comparing isomiR expression across TCGA and TARGET miRNA datasets

ASCENT

NCI CCR

Genomics Workflows

Alternate SpliCing EveNt Tools; multi-sample alternative splicing identification

ASPEN

NCI CCR

Genomics Workflows

Atac Seq Analysis Pipeline is CCBR's pipeline to calls peaks for ATACseq datasets

CARLISLE

NCI CCR

Genomics Workflows

Cut And Run anaLysIS pipeLinE; prediction tool for murine cancer neoantigens

CHARLIE

NCI CCR

Genomics Workflows

circRNA Detection Annotation and Quantification

Docker Containers for NGS Analysis

NCI CCR

Genomics Workflows

Docker containers for ATACSeq, ChIPSeq, ExomeSeq, RNASeq; to be executed on the DNANexus cloud platform; GitHub repo

HapFerret

NCI CCR

Genomics Workflows

Haplotype inference program; Expectation-Maximization algorithm; uses a natural format for input genotypes and output haplotypes; GitHub repo

iCLIP

NCI CCR

Genomics Workflows

Individual-nucleotide resolution Cross-Linking and ImmunoPrecipitation; multi-sample peak identification and annotation analysis; differential analysis using DIFFBIND and MANORM

iSCAP

NCI CCR

Genomics Workflows

Integrated Single Cell RNA-Seq analysis pipeline; multi-sample differential expression analysis; marker gene and subpopulation identification; GitHub repo

Longread Somatic Analysis Pipeline

NCI CCR

Genomics Workflows

This pipeline processes long-read (LR) sequencing data to identify somatic mutations including single nucleotide variants (SNVs), structural variants (SVs), and copy number alterations (CNAs) using various bioinformatics tools

MAAPster

NCI CCR

Genomics Workflows

MicroArray Analysis Pipeline, also known as MAAPster, is a comprehensive Shiny application and R package that performs transcriptome analysis of human or mouse Affymetrix gene expression data

METRO

NCI CCR

Genomics Workflows

Mouse nEoanTigen pRedictOr; prediction tool for murine cancer neoantigens

miRNA Mapping and Abundance Estimation

NCI CCR

Genomics Workflows

Workflow for handling small RNA sequencing analysis

MNaseSeq

NCI CCR

Genomics Workflows

MNase-seq Analysis PipeLinE: multi-sample DYAD fragment identification and quantification

NGS_SV_CNV

NCI CCR

Genomics Workflows

Next Gen Sequencing analysis pipeline for structural variant and copy number variation detection, annotation and visualization: GitHub repo

Pipeliner

NCI CCR

Genomics Workflows

Provides a graphical interface for configuring and executing RNA-Seq, Exome-Seq and sc-RNA-Seq analysis pipelines on the NIH biowulf cluster

Polylox Barcode

NCI CCR

Genomics Workflows

The project utilizes the innovative Polylox barcode system in conjunction with PacBio sequencing and 10X cell barcodes for high-resolution lineage tracing and cell tracking

SF_ATAC-seq

NCI CCR

Genomics Workflows

The ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) pipeline analyzes paired-end sequencing data and identify regions of open chromatin (peaks)

SF_LR_Transcriptome

NCI CCR

Genomics Workflows

Workflow for handling long-read transcriptomic (LR_Transcriptome) sequencing analysis

SF_LR_VAP

NCI CCR

Genomics Workflows

The SF Long Read Variant Analysis Pipeline (SF_LR_VAP) integrates a suite of advanced tools and methodologies for the comprehensive analysis of long-read sequencing data, from raw reads to annotated variants

SF_MAS-SC

NCI CCR

Genomics Workflows

In the SF Multiplexed Arrays Sequencing (SF_MAS-SC) workflow, full-length cDNA sequences are processed and classified against a reference annotation database. This workflow identifies novel genes and isoforms, and outputs count matrices at both the gene and isoform levels.

TRANQUIL

NCI CCR

Genomics Workflows

TRna AbundaNce QUantification pIpeLine is a Snakemake pipeline which quantifies tRNA using the mim-tRNAseq tool

Quick2Insight

NCI OD-Frederick

Image Analysis

Semi-automatic classification guided 3D volumetric image data visualization tool; GitHub repo

RMS_AI

NCI OD-Frederick

Image Analysis

GitHub page for Predicting survival of rhabdomyosarcoma patients based on deep-learning of hematoxylin and eosin images manuscript

RNAScope

NCI OD-Frederick

Image Analysis

Interactive visualization and analysis results of virion counting on RNAscope and DNAscope images; GitHub repo

SSR Environment

NCI OD-Frederick

Image Analysis

Central imaging informatics platform for collaborators to interface with IVG; Adjust parameters; Download results; GitHub repo

ABCS Git Repo

NCI OD-Frederick

Other Resources

Git Repo with code and data from several ABCS projects including the biomarker discovery kit, image analysis and NGS workflows

ABCS Training

NCI OD-Frederick

Other Resources

Details on computational science, programming and statistics trainings available to NCI researchers

Bioinfo

NCI OD-Frederick

Other Resources

Web interface listing ABCS web applications and code repositories; Hosts small applications

CCR Bioinformatics

NCI CCR

Other Resources

CCR Bioinformatics is an integrated portal for CCR bioinformatics resources including Bioinformatics Training & Education Program (BTEP), CCR Collaborative Bioinformatics Resource (CCBR), Genome Analysis Unit (GAU), and NCI Bioinformatics Community (NCI BC)

CCR Genomics

NCI CCR

Other Resources

The CCR Genomics core provides investigators from NCI and other institutes within NIH with access to genomic technologies and Next-Generation Sequencing (NGS) with rapid turnaround on smaller-scale projects or projects that are not ready for production

CMM

NCI CCR

Other Resources

The Center for Molecular Microscopy (CMM) develops and utilizes new techniques and emerging technologies for high resolution 3-D electron microscopy in structural biology (high resolution imaging) and cell biology (volume EM)

Confocal

NCI CCR

Other Resources

NCI Optical Microscopy Laboratories provide advanced cancer research through optical measurements and analysis

CPTR

NCI CCR

Other Resources

An open core dedicated to developing and implementing cutting edge protein-based technologies to facilitate discovery, translational and clinical research

MTP

NCI CCR

Other Resources

The Molecular Targets Program (MTP) provides the focus and infrastructure that enables CCR investigators to pursue molecularly targeted drug discovery research by promoting an interdisciplinary, collaborative, team-oriented approach to identifying and validating potential cancer-pertinent targets

OAMS

NCI DCTD

Other Resources

The OCCPR Author Management System (OAMS) is an online resource for tracking publication authors across the DCTD community

OSTR

NCI CCR

Other Resources

Explores and evaluates the latest technologic advancements and then makes them available to all CCR investigators

Antibody Portal

NCI DCTD

Scientific Catalogs

An NCI community resource that provides access to a large number of standardized renewable affinity reagents and accompanying characterization data

ICPC

NCI DCTD

Scientific Catalogs

A voluntary scientific organization that provides a forum for collaboration among some of the world’s leading cancer and proteogenomic research centers

Functional Heatmap

USACEHR/WRAIR

Visual Analytics and Analysis

Transcriptomics analysis; Differentially expressed genes/metabolites/proteins; Categorize longitudinal data sets; Pathway and functional references

PanoromiX

USACEHR/WRAIR

Visual Analytics and Analysis

Network visualization of complex data sets; Interactive and customizable; Upload and visualize multiple aspects of custom data