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.

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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

Antibody Portal

NCI CSSI

Scientific Catalogs

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

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.

Bioinfo

NCI OD-Frederick

Other Resources

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

CCBR

NCI CCR

Other Resources

A resource group which provides a mechanism for CCR researchers to obtain many different types of bioinformatics assistance to further their research goals

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.

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

CyPRUS

NCI OD-Frederick

Biomedical Annotations

Visualize protein annotations from Uniprot; Comparisons across ortholog sequences; Visualize custom annotations on protein sequences.

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

Functional Heatmap

USACEHR/WRAIR

Visual Analytics and Analysis

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

GAU

NCI CCR

Other Resources

Genome Analysis Unit Provides bioinformatics assistance to CCR investigators by engaging in long-term collaborative projects; Developing custom tools and pipelines and by providing training opportunities

HapFerret

NCI CCR

Genomics Workflows

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

iSCAP

NCI CCR

Genomics Workflows

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

MAAPster

NCI CCR

Genomics Workflows

Comprehensive web tool for transcriptome analysis of human or mouse Affymetrix microarray data; supports local files and GEO IDs

MoCha cBioPortal

NCI DCTD

Data Analysis and Management

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

NCBR

NIAID

Other Resources

The NIAID Collaborative Bioinformatics Resource is a group with expertise in a broad range of bioinformatics topics to provide a mechanism for researchers to obtain bioinformatics assistance.

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

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.

OSTR

NCI CCR

Other Resources

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

PanoromiX

USACEHR/WRAIR

Visual Analytics and Analysis

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

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

Protein Capture

NCI CSSI

Scientific Catalogs

An NCI community resource to provide low-cost, high-quality renewable affinity reagents for human proteins for the scientific community.

PSD

NCI CCR

Data Analysis and Management

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

Quick2Insight

NCI OD-Frederick

Image Analysis

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

RID

NCI CCR

Data Analysis and Management

Retrovirus Integration Database; query retrovirus integration sites in host genomes

RNAScope

NCI OD-Frederick

Image Analysis

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

ROI Extraction

NCI OD-Frederick

Image Analysis

Extracts sub-images defined on Aperio SVS images and saves these sub-images to separate TIFF image files for downloading; 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

SysBioCube

USACEHR/WRAIR

Data Analysis and Management

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

TIE

NCI CCR

Data Analysis and Management

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

ToTeM

NCI OD-Frederick

Biomedical Annotations

Tool for Text mining; Queries MEDLINE; Integrates bioDBnet and AVIA to provide enhanced gene based and variant based literature searches