Collaboration


The Bioinformatics and Computational Biosciences Branch (BCBB) partners with NIAID researchers by applying bioinformatics and computational biology methods to generate new hypotheses and data, analyzing existing data, and ultimately elevating the use of these methods and resources throughout the NIH. We offer expert assistance in the following major areas:

  • Genomics
  • Transcriptomics
  • Biostatistics
  • Phylogenetics
  • Computational Structural Biology
  • Virtual and Augmented Reality

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


Science Support Computational Biology Services


The NIAID Science Support Section provides professional bioinformatics and computational biology consulting to researchers. We offer the following three tiers of services:

  • Tier 1 - access to commercial resources such as genomics tools and statistical software.
  • Tier 2 - group training, consultation or assistance with scripting for high performance computing.
  • Tier 3 - data analysis collaboration. Our goal is to greatly facilitate the process between data generation and interpretation.

What we do


Bioinformatics and data analysis consulting

We work with researchers to provide analysis of their high-throughput sequencing, genomics, gene expression, structural modeling/simulation and other biological data. Most importantly, we can provide customized analyses and mentor all lab members to build confidence in bioinformatics analysis.

Pipeline development

We will help to create custom pipelines and work closely with the Bioinformatics Software Development team to create interfaces for web services.

Consulting prior to experiments

We will meet with you to offer guidance on experimental design, direct you to existing tools/pipelines available or discuss a plan for custom data analysis.

Training in Bioinformatics

We offer training sessions regularly but also prepare custom trainings upon request. Our goal is to assist researchers in learning the computational tools that can be applied in their daily research.


Examples of analytical serves we provide


Genome mapping and de novo assemblies

  • Comparative analysis of genome assemblies
  • WGS and exome mapping
  • SNP/indels, CNV discovery and variant annotation

Phylogenomics

  • Sequence alignments
  • Phylogeny reconstruction
  • Analysis of evolutionary effects, such as selection, recombination, or migration

Epigenetics

  • Whole genome bisulfite mapping
  • Identification of differentially methylated regions

Transcriptomics/RNA-Seq

  • Data quality assessment
  • Differential expression
  • Heatmap visualizations
  • Pathway and network analyses

Metagenomics

  • Assembly of shotgun metagenomics
  • Functional annotation of metagenomes
  • Data denoising, clustering and taxonomic assignments of 16S/ITS data
  • Statistical analysis and visualization of outputs

Modeling and simulations

  • Protein structure and interactions prediction
  • Combining experimental structural data to produce atomic-resolution structures that are otherwise impossible
  • Protein-ligand, protein-protein interactions design and predictions
  • Docking and virtual screening of small molecule ligands against protein targets of interest

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


Scientific Consultants


Phil-Cruz
Phil Cruz, Ph.D.

Computational Structure 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 Structure 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


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. Complete initial set of security documents. Download security document templates here.
  4. Pass the first part of the EPLC review process.

  5. 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.


  6. 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. Submit a completed security package to the NIAID ISSO.

  7. Applications are scanned using IBM AppScan Enterprise, Netsparker Web Application Security Scanner and/or others.

    OCICB. To request a security scan of your application, contact us.

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

    A member of the Software Engineering Branch (SEB) at OCICB will submit the completed security package to the NIAID ISSO for review. Once the application has passed ISSO review the second part of the EPLC process can be scheduled.


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

  9. 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.


  10. Review of signed On-Going Authorization, Certification Memo, and POA&M

  11. The application developer and/or stakeholder must make any final corrections. Once the documents have been reviewed they are returned to OCICB.

  12. NIAID CIO approves making the application publicly accessible.

  13. 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)



About 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.

About ACE

Our Mission


To drive incremental and transformative change in the performance, training, and operation of computational biosciences in Sub-Saharan Africa. We exist to create a sustainable, independent community of bioinformatics specialists to encourage sharing of data, best practices, and collaborative projects.

Our Mission

Our Services


  • We provide advanced computing infrastructure and software to enable storage, retrieval and analysis of data from next-generation sequencing (NGS), microarrays, proteomics, and imaging experiments.
  • We provide a variety of bioinformatics trainings to include: seminars, train-the-trainer workshops, remote instruction and online content.
  • We provide technical assistance with grant proposals and publications.
  • We provide bioinformatics service support to researchers, including technical assistance and implementation support for bioinformatics related projects.
Our Services

Timeline of Program Activities


2017

  • 1. First cohort of students graduating from Master’s Program in Bioinformatics at USTTB.

    2. Student accepted into PhD fellowship program working under Dr. Nicola Mulder of H3 Africa.

    3. Student accepted in PhD fellowship program in Tunisia.

  • 4. Coordination of MaliREN to support computational research for academic and research institutions.

    5. Second cohort of students enroll in Master’s Program in Bioinformatics at USTTB.

    6. BioCompACE imaging available on local workstations and laptops using SALT.

2016

  • 1. Developed and delivered over 60 bioinformatics courses and seminars in Mali.

    2. Poster at the American Society of Tropical Medicine in collaboration with the University of Dakar.

  • 3. DELGEME collaboration established with ACE.

    4. Growth of interest in the ACE model this included requests for collaboration from co the DRC, Malawi and other countries.

2015

  • 1. A strategic public-private partnership was finalized with NIAID, BioTeam, Intel Corporation’s Health and Life Sciences Group, EMC Corporation, the Foundation for NIH, and USTTB.

    2. A high-performance computing server has been installed at the first collaborative center at USTTB.

  • 3. Built a world class telelearning in an environment engineered for optimal communication and remote learning.

    4. The first African Center of Excellence (ACE) in bioinformatics is launched at the University of Sciences, Techniques, and Technologies of Bamako (USTTB) in Mali, West Africa.

    5. First cohort of students enrolled in MSc Bioinformatics Degree Program at USTTB.


Our Team


The African Centers of Excellence has a multidisciplinary team where each member presents a different profile and provides expert knowledge in area necessary to develop novel products, from ideas to market launch. We have a strong multidisciplinary team, with, many years of experience in bioinformatics, computational biology, and data science, ensuring that we can offer a full range of training, consulting, and collaboration services. Contact us if you have any question.


Darrell-Hurt
Darrell Hurt

Chief, Bioinformatics and Computational Biosciences Branch, NIAID

Chris-Whalen
Chris Whalen

Program Lead, International Biomedical Research Support Program

Latrice-Ware
Latrice Ware

Program Coordinator

Karlynn-Noble
Karlynn Noble

Communications & Outreach Lead

Burke-Squires
Richard Squires

Computational Genomics Specialist

Brian-Moyer
Brian Moyer

Project Manager, International Biomedical Research Support Program (IBRSP)


Servers provisioned with the help of CDWG, Mali Service Center, and The Mitchell Group for use in Kenya and Mali with the DELGEME Project.

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 contact us 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

Hunde-Keba
Hunde Keba

Full Stack Drupal Engineer


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.

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

NIAID Clinical Proteomics

A collaborative resource to identify predictive biomarker panels of outcome or therapeutic in humans with NIAID Category A-C agents or new/emerging infectious agents

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

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