NIAID Bioinformatics Portal

Science Support Application Hosting Outreach Advanced Biovisualization Training and Support Supported Software Groups Computational Resources

Science Support

The NIAID Office of Cyber Infrastructure and Computational Biology (OCICB) offers scientific expertise 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 training and support. This support is provided at no direct cost to the NIAID research community and its collaborators.

BCBB has a team of Ph.D. and M.S level scientists that have been collaborating for many years with researchers working with biomedical data. Our team is available for research collaborations, short consultations to answer bioinformatics questions, assistance with script writing, providing training on methods or use of tools and more. The areas of expertise include genomics, imaging, data science, machine learning, structural biology, biostatistics, virtual reality and more. To learn more about the types of research support, explore the subject matter areas below.

Microbial Genomics

Metagenomics

Clinical Genomics

Imaging

Data Science & Biostatistics

Structural Biology

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."

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Workflow for developing an application at NIAID

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

What is the EPLC process?

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.

How do I pass the first part of the EPLC process?

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.

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.

What if the scan finds vulnerabilities?

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

Pass the second part of the EPLC review process.

How do I pass the second part of the EPLC process?

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).

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

Can I provide access to my application for manuscript reviewers before it is made available to the general public?

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.

This process seems onerous. Am I on my own in navigating all of these steps?

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.

Advanced Biovisualization

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

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

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.

Virtual and Augmented Reality

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).

References and Additional Information

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, Ph.D.

Computational Structure Biologist

Phil Cruz, Ph.D.

Computational Structure Biologist

Kai Zhang, M.S.

Research Engineer

Victor Starr Kramer

Visualization Technology Specialist

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

Website

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

Website

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

Website

NIAID Microbiome Program

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

Website

DataScience@NIH

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

Website

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

Website

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.

Website

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.

Website

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.

Website

The Bioinformatics and Computational Biology Core facility at NHLBI

The Bioinformatics and Computational Biology Core facility at the NHLBI

Website

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.