BIOINFORMATICS & COMPUTATIONAL BIOLOGY SERVICES & RESOURCES


The NIAID Office of Cyber Infrastructure and Computational Biology (OCICB) offers scientific services and resources through its Bioinformatics and Computational Biosciences Branch (BCBB). These offerings include: collaborative data analysis; provisioning of commercial software; development of custom software systems and automation; advanced 3D visualization technologies; and hands-on trainingand support. These services are provided at no direct cost to the NIAID research community and its collaborators.


COLLABORATION AND TRAINING


The BCBB team collaborates with NIAID researchers on a wide variety of projects to process and analyze almost every kind of biomedical data type in the larger context of information found in public repositories and databases. Collaborative data analysis and software training services in the areas listed below are available to researchers at all levels of experience.

For inquiries, please LOGIN and return to this page.

Data Science & Machine Learning


Maximize the value and knowledge contained in your data to identify patterns, prioritize experimental variables, and perform predictive modeling.

Data Analysis
  • Identify patterns and outliers within numerical, text, or sequence-based data sets
  • Use AI/ML algorithms and experimental design
  • Data processing (e.g. feature engineering, transformation, normalization and imputation)
  • Developing and evaluating supervised and unsupervised machine learning models
  • Variable ranking and prioritization
  • Deep Learning and AI approaches
  • Reproducible data science workflows
Software Training
  • Python and Jupyter Notebooks
  • R, R Markdown, and Shiny
  • Weka, TensorFlow, Keras
  • AI/ML and Deep Learning
  • Natural language processing
  • Time series analysis

Genomics, Transcriptomics & Microbiome Analysis


Identify genetic variants (SNPs, indels, CNVs) and changes in gene expression, perform comparative genomics and microbiome analyses, and characterize functional elements.

Data Analysis
  • Assembly and mapping of short- and long-read sequencing data
  • RNA-Seq, scRNA-Seq, CHiP-Seq, miRNA-Seq, variant discovery
  • Metagenomic analyses (16S, ITS, WGS)
  • Pathways and network analyses
Software Training
  • Genomics: STAR, HiSAT2, BWA, MACS, minimap2, RSEM, cellRanger, CITE-seq, CITE-seq, Bowtie, miRge2.0, GATK, GEMINI, plink, EPACTS, SPAdes
  • Pathways & Networks: IPA, BIOBASE, clusterProfiler, Cytoscape, Gephi
  • Transcriptomics: R/Bioconductor, Seurat, DEseq2
  • Metagenomics: QIIME2, DADA2, Kraken, Nephele, MetaSPAdes, MEGAN, CheckM, MetaBAT, etc.

Phylogenetics & Evolutionary Analysis


Place your research in an evolutionary context. Understand the development of pandemics and antimicrobial resistance.

Data Analysis
  • DNA and protein sequence alignment
  • Tree building
  • Selection analysis
Software Training
  • Alignment: BLAST, ClustalW, MUSCLE, MAFFT, Lasergene, MacVector, Sequencher
  • Phylogenetics: MEGA, MrBayes, HyPhy, BEAST
  • Visualization: FigTree, iToL

Molecular Modeling, Simulation, & Analysis


Understand binding interactions and the effect of mutations; contribute to the development of bioactive small molecules and peptides.

Data Analysis
  • Model Building: template-based, loop modeling, de novo
  • Drug Design: docking, QSAR, pharmacophore modeling
  • Interfaces: docking and design
  • Visualization: virtual reality, figures, animations, 3D printing
Software Training
  • Visualization: PyMOL, UCSF Chimera, ChimeraX, VMD
  • Modeling: NAMD, Rosetta

Imaging Analysis & Advanced Visualization


Understand the structure and distribution of components and processes at the sub-cellular, cellular, or gross anatomical levels.

Data Analysis
  • Image classification and segmentation (Deep Learning)
  • Image registration
  • Workflow development
Software Training
  • SimpleITK, Slicer

Biostatistics & Experimental Design


Design experiments and choose the right statistical method for analysis.

Data Analysis
  • Experimental design
  • Statistical testing (t test, ANOVA, multiple comparisons, Chi-squared, Fisher’s Exact
  • Regression analysis
  • Curve fitting
  • Survival analysis
Software Training
  • Prism, R, SAS, SPSS

ADVANCED 3D VISUALIZATION


Improve data insight via virtual and augmented reality applications (VR/AR), high-pixel-count displays, and 3D printing.

Applications
  • 3D molecular structures
  • Microscopy image stacks
  • 3D radiological images (e.g., CT scans)
Software
  • Virtualitics, ChimeraX, Enduvo, Medical Holodex, Slicer
  • Analysis: online tools

AUTOMATION, SCRIPTING & SOFTWARE DEVELOPMENT


The BCBB creates novel bioinformatics applications and can aid in extending existing applications. Examples of custom software applications developed by the OCICB include tools for extracting, processing, and analyzing data from “messy” data sources, querying and retrieving data from public repositories, web portals for the publication or sharing of data, and applications for automation of lab tasks.

SCIENTIFIC SOFTWARE


Workstation and network-based software is selected and provisioned based on the identified needs of NIAID researchers.

Now Available
  • Proteomics Analysis: PEAKS
  • Sequence Analysis: Lasergene, MacVector, Geneious, Sequencher
  • Statistics: PRISM, JMP, SAS, R
  • Pathway Analysis: Ingenuity (IPA), Biobase, TRANSFAC
  • Imaging: Fiji

Scientific Consultants


Phil-Cruz
Phil Cruz, Ph.D.

Computational Structural Biologist

Andrew-Oler
Andrew Oler, Ph.D.

Computational Biologist

Mariam-Quinones
Mariam Quinones, Ph.D.

Computational Biologist

Kurt-Wollenburg
Kurt Wollenberg, Ph.D.

Computational Biologist

Amit-Roy
Amit Roy, Ph.D.

Computational Structural Biologist

Brendan-Jeffrey
Brendan Jeffrey, Ph.D.

Computational Biologist

Poorani-Subramanian
Poorani Subramanian, Ph.D.

Computational Biologist

Tony-Armstrong
Tony Armstrong, Ph.D.

Computational Structural Biologist

Claire-Wang
Claire Wang, M.S.

Clinical Biostatistician

Jingwen Gu
Jingwen Gu, M.S.

Clinical Biostatistician

Karthik-Kantipudi
Karthik Kantipudi, M.S.

Imaging Specialist

David-Chen
David Chen, Ph.D.

Visualization Scientist

Ziv-Yaniv
Ziv Yaniv, Ph.D.

Imaging Scientist

Yunhua-Zhu
Yunhua Zhu, Ph.D.

Transcriptomics Specialist

Angelina-Angelova
Angelina Angelova, Ph.D.

Metagenomics Analysis Specialist

David-Stern
David Stern, Ph.D.

Computational Biologist

Hernan-Lorenzi
Hernan Lorenzi, Ph.D.

Computational Functional Genomics Specialist

Isaac-Raplee
Isaac Raplee, Ph.D.

Transcriptomics Specialist

Samuel-Li
Samuel Li, Ph.D.

Computational Biologist

Kai-Zhang
Kai Zhang, M.S

Research Engineer

Yong-Sok-Lee
Yong Sok Lee, Ph.D.

Computational Chemist

Madeline-Galac
Madeline Galac, Ph.D.

Computational Microbial Genomics Specialist

Peter-Steinbach
Peter Steinbach, Ph.D.

Computational Structural Biologist

Sergio-A.-Hassan
Sergio A. Hassan, Ph.D.

Computational Structural Biologist


For assistance with a NIAID bioinformatics or computational biology project, please LOGIN and return to this page

Application Hosting


Are you a NIAID researcher interested in hosting your application at NIAID? Navigating the security and technical requirements can be confusing and we are here to help. Below is a typical workflow for taking your application from the "idea" stage to "going live to the public."


Workflow for developing an application at NIAID


  1. Understand the recommended workflow for developing applications at NIAID. See the Developer’s Guide.
  2. Develop application (make use of the Monarch platform if possible).
  3. Pass the first part of the EPLC review process.

  4. The Enterprise Performance Lifecycle Process (EPLC) is a solid project management methodology that incorporates best government and commercial practices through a consistent and repeatable process, and provides a standard structure for planning, managing and overseeing IT projects over their entire life cycle. The HHS Enterprise Performance Life Cycle (EPLC) framework provides that methodology for HHS. NIH has adopted the HHS EPLC framework.

    A slide deck must be completed and presented to members at an OCICB EPLC meeting which takes place on Wednesdays at 10AM at 5601 Fishers Ln. Download slide deck here. For assistance in filling out the slides or to schedule a time to present at an OCICB EPLC meeting contact us.


  5. Pass security scans and review. Maintaining cyber security standards is not just for application owners, but is everyone's responsibility and to everyone's benefit.

  6. Vulnerabilities will be communicated back to you which must be corrected. OCICB can work with you to tackle these fixes.


  7. Pass the second part of the EPLC review process.

  8. A slide deck must be completed and presented to members at an OCICB EPLC meeting which takes place on Wednesdays at 10AM at 5601 Fishers Ln. Download slide deck here. For assistance in filling out the slides or to schedule a time to present at an OCICB EPLC meeting contact us.


  9. The PI must sign a Memorandum of Understanding (MOU) acknowledging that the application container (if on Monarch) must be run at least monthly, responsibility for fixing security vulnerabilites, and completing any outstanding Plan of Action and Milestones (POA&M).

  10. A change request (CR) is made and the Change Advisory Board (CAB) approves making the application publicly accessible.

  11. Yes. We understand that journal reviewers must be able to see your application before a manuscript is accepted for publication. Contact us and we can discuss the steps needed to make an application accessible to a subset of the public.

    No. OCICB is here to assist you through any or all of these steps.

African Centers of Excellence (ACE)



The African Centers of Excellence (ACE) in Bioinformatics and Data Intensive Science is a research and training collaborative established by NIAID in partnership with public and private industry partners to deliver high performance computing infrastructure and training to capable research and academic institutions in Africa. Through this partnership, services and in-kind donations are provided to build, deliver, install, and maintain the ACE compute infrastructure and deliver training and research support. The ACE collaborative provides African researchers with computing resources and bioinformatics tools necessary for performing advanced biomedical data analysis and provides a platform for sharing data, best practices, and scientific research projects.

For more information click here.

About ACE

Advanced Biovisualization


Advanced-Visualization

3D Technologies for Research and Discovery


As part of NIAID's mission to make bioscientific and clinical data more accessible and usable, we are applying a variety of 3D technologies to enhance understanding and communication in basic and clinical research. We are also working to implement and extend existing open source applications and develop new tools that help users to maximize the utility of that content. Visit NIAID's flagship 3D resource, the NIH 3D Print Exchange, to find thousands of bioscientific and medical 3D models available for free download, as well as web tools to create your own 3D models from experimentally-derived structure data, medical imaging scans, or published molecular and microscopy data.

3D printing allows for rapid, and relatively low-cost, fabrication of objects that are either impractical, expensive, or even impossible to produce using traditional manufacturing methods. 3D printing is already making an impact in bioscience and medicine:

  • Tangible models of complex biomolecules facilitate new research discoveries
  • Physical models of a patient's unique anatomy inform physician decision-making and surgical planning
  • Custom and open-source laboratory eq¬uipment provide substantial savings in cost and time, and improve experimental reproducibility
  • 3D-printable prostheses and assistive devices improve patient care and quality of life
3d-model

Custom 3D Modeling and 3D Printing Services


For over 10 years, NIAID structural biologists and visualization specialists have used 3D printers to complement NIAID research projects. The 3D modeling and printing service includes fabrication of digital 3D models, as well as technical help in the design and preparation of models. Three types of printer technologies support creation of objects in a range of materials:

  • Full-color "sandstone," best suited for visualization of complex structures
  • Durable 1- to 2-color prints available in a range of materials, including ABS, PLA, polycarbonate, nylon, and other specialty materials
  • Monochrome, ultra-high-resolution models produced from transparent or flexible photopolymer resin

3D printing services are provided to the NIAID community free of charge; appropriate models are those derived from molecular, microscopy, or medical imaging data, or those created using computer-assisted design (CAD) software for use in the lab or clinic. Non-NIAID requests are subject to additional approval. NIAID and other NIH staff can submit requests by contacting us.

Phil-Bill
Dr. Phil Cruz and Bill Gates

Virtual and augmented reality (VR, AR) technologies combine a computer-generated environment with wearable hardware in the form of a head-mounted display (HMD), to create an interactive experience. VR and AR provide viewpoints and stereoscopic depth information that cannot be grasped from a traditional stereo-3D view on a 2D display. NIAID is at the forefront of applying these technologies, traditionally used in gaming and entertainment, to advance bioscientific and clinical research.


NIAID Biovisualization Laboratory


The NIAID Biovisualization Laboratory, or "BioViz Lab," is a pilot program aimed toward developing a dedicated facility to provide NIAID staff with various options for advanced visualization experiences. Currently located at 5601 Fishers Lane, the BioViz Lab hosts four workstations, each with high-end computational and graphics processing hardware to support the most advanced requirements of VR and AR devices and applications. The BioViz Lab incorporates several types of HMDs for VR and AR, including a Dell Mixed Reality Visor, four HTC Vive headsets, a Metavision Meta2, a Microsoft HoloLens, and an Oculus Rift Touch.

We support advanced visualization of several different types of raw data using applications designed for the VR and AR experience, including:

  • UCSF ChimeraX for molecular visualization and drug discovery
  • ConfocalVR for viewing and interacting with microscopy data stacks
  • Enduvo, a platform for creating and consuming training and teaching modules in VR
  • Medical HoloDeck provides a rich interface for dynamic visualization of volumetric data, such as CT or MRI scans in DICOM format
  • More applications coming soon!

NIAID staff can LOGIN and return to this page to find out more, and to book a visualization session.


High-Resolution, Large-Scale Displays


Large-scale (4K, 8K) displays allow for visualization of more data at the same time, and at high resolution. They also facilitate communication and foster collaboration. The Biomedical Advanced Research and Discovery Authority, part of the HHS Assistant Security for Preparedness and Response, hosts a Visualization Hub featuring a CAVE2 (Cave Automated Virtual Environment).

  • Poster, "3D Printing and Biovisualization at the NIH: Research, Development, and Resources from the National Institute of Allergy and Infectious Diseases." 2017.
  • Tyrwhitt-Drake J, et al. Molecular spelunking: exploration of biological structures in a virtual reality environment. Poster presented at the 2017 NIH Research Festival, Bethesda, MD. 2017 Sep 14. doi: 10.13140/RG.2.2.27616.12803.
  • Bramlet and Coakley. Utility of a 3D File Database. Chapter in Rapid Prototyping in Cardiac Disease: 3D Printing the Heart. Ed. K. Farooqi. Springer International Publishing. doi: 10.1007/978-3-319-53523-4.
  • Bramlet et al., Impact of 3D Printing on the Study and Treatment of Congenital Heart Disease. Circ Res. 2017 Mar 17. PMC5439501 .
  • Beltrame et al., 3D Printing of Biomolecular Models for Research and Pedagogy. J Vis Exp. 2017 Mar 13. PMC5408980 .
  • Coakley MF and Hurt DE, 3D Printing in the Laboratory: Maximize Time and Funds with Customized and Open-Source Labware. J Lab Autom. 2016 Aug 2. PMC5380887 .
  • Coakley MF, et al. The NIH 3D Print Exchange: A Public Resource for Bioscientific and Biomedical 3D Prints. 3D Printing and Additive Manufacturing. 2014 Sept 1. PMC4981148 .


Biovisualization Specialists


Meghan-McCarthy
Meghan McCarthy, Ph.D.

Computational Structure Biologist

Phil-Cruz
Phil Cruz, Ph.D.

Computational Structure Biologist

Kai-Zhang
Kai Zhang, M.S.

Research Engineer

Victor-Starr-Kramer
Victor Starr Kramer

Visualization Technology Specialist

Ramandeep-Kaur
Ramandeep Kaur

Technical Lead: Continuous Integration and Dockerization

David-Liou
David Ta-Ming Liou

Technical Lead: Cloud Technologies


For more information, contact Dr. Meghan McCarthy.


Training and Support


BCBB offers deskside application training for NIAID researchers who wish to quickly get up to speed with certain programs. Be sure to look at our Training Resources page for self-guided tutorials. If a tutorial for an application for which you are interested is not available, contact us and we will schedule a time to meet with you to guide you through an application.

Supported Software


NIAID supports several software packages including:

  • JMP
  • Mathematica
  • Prism
  • SAS
  • Spotfire S+
  • GeneSpring GX
  • BIOBASE
  • IPA
  • Geneious
  • Lasergene
  • MacVector
  • Sequencher

For more information see Inside NIAID or contact us directly.

Groups


The following are bioinformatics and computational biology laboratories, centers, programs and projects associated with NIH.

The NIH Library Bioinformatics Support Program

Provides researchers with powerful tools to analyze and understand the biological significance of a variety of data

NIAID Bioinformatics and Computational Biology Branch

Supports the NIAID research mission by leveraging the latest computational technologies to accelerate discovery and remain at the forefront of today's rapid scientific pace

National Centers for Biomedical Computing

Part of the U.S. National Institutes of Health plan to develop and implement the core of a universal computing infrastructure that is urgently needed to speed progress in biomedical research

NIAID Microbiome Program

A microbiome sequencing facility with bioinformatics support and a gnotobiotic mouse facility

DataScience@NIH

Harnessing the potential of the computational and quantitative sciences to elevate the impact and efficiency of biomedical research

NIAID VRC Structural Bioinformatics Core Section (SBIS)

Seeks to apply the tools of computational biology and structural bioinformatics to the design of an effective HIV-1 vaccine

NIH Human Microbiome Project

The Data Analysis and Coordination Center (DACC) for the National Institutes of Health (NIH) Common Fund supported Human Microbiome Project (HMP). This site is the central repository for all HMP data.

NHLBI: The Laboratory of Computational Biology

An interdisciplinary group of scientists who study biological processes via computer simulation. Part of the Biochemistry and Biophysics Center Division of Intramural Research National Heart, Lung, and Blood Institute in the National Institutes of Health.

NIAID Bioinformatics Resource Centers

The BRC program collects, archives, updates, and integrates a variety of research data and provides information through user friendly interfaces and computational analysis tools which are made freely available to the scientific community.

The Bioinformatics and Computational Biology Core facility at NHLBI

The Bioinformatics and Computational Biology Core facility at the NHLBI

Computational Resources


Locus

The NIAID Office of Cyber Infrastructure and Computational Biology (OCICB) maintains a high performance computing (HPC) cluster environment for next generation sequencing, phylogenetics, structural biology, and other high-throughput, data-intensive analyses. This resource is currently freely available to NIAID researchers and their collaborators. More information can be found here.


Biowulf

The NIH HPC group plans, manages and supports high-performance computing systems specifically for the intramural NIH community. These systems include Biowulf, a 105,000+ processor Linux cluster; Helix, an interactive system for file transfer and management, Sciware, a set of applications for desktops, and Helixweb, which provides a number of web-based scientific tools including a wide range of computational applications for genomics, molecular and structural biology, mathematical and graphical analysis, image analysis, and other scientific fields. For more information, click here.