Immune Epitope and Analysis Resource Program

The purpose of this Amendment is to extend the solicitation due date. The solicitation due date is now February 21st, 2018 3:00pm Eastern Standard Time

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Added: Feb 16, 2018 3:28 pm

The purpose of this Amendment is to extend the solicitation due date. The solicitation due date is now February 21st, 2018 3:00pm Eastern Standard Time

Introduction

The National Institute of Allergy and Infectious Diseases (NIAID), National
Institutes of Health (NIH), of the Department of Health and Human Services
(DHHS) supports research related to the basic understanding of microbiology and
immunology leading to the development of vaccines, therapeutics, and medical
diagnostics for the prevention, treatment, and diagnosis of infectious and immunemediated diseases. The NIAID, has a requirement for continue support of the
Immune Epitope and Analysis Resource Program, formerly known as the Immune Epitope Database and Analysis Program (IEDB), which provides the research community an easy resource for searching experimental data characterizing antibody and T cell epitopes studied in humans, non-human primates, and other animal species, involved in infectious disease, allergy, autoimmunity, and transplant, and tools to assist in the prediction and analysis of B cell and T cell epitopes.

Description

The NIAID Division of Allergy, Immunology and Transplantation (DAIT) supports
extramural grants and contracts for basic, pre-clinical, and clinical research on
immune system development and function, and host immune responses in
infectious and immune-mediated disorders (e.g., autoimmunity, allergy/asthma,
and transplant rejection). This mission includes support of various reagent facilities,
repositories, and databases that provide resources for biomedical researchers. As a
part of this continuing effort to support the scientific enterprise, the NIAID
announces the renewal of the Immune Epitope and Analysis Resource Program to
further develop, populate, and maintain a public resource containing antibody/B cell
and T cell epitope information, B cell receptor (BCR/T cell receptor (TCR) repertoire
analyses, and epitope prediction and analysis tools for use by the research
community worldwide. For this RFP, immune epitopes are defined as molecular
structures recognized by specific antigen receptors of the immune system, namely
antibodies, BCRs, and TCRs. Immune epitopes involved in infectious and immunemediated diseases and the accompanying biological information will be included in the Immune Epitope and Analysis Resource Program (IEDB).

The effectiveness of adaptive immune responses is related to the diverse functions
of B and T cells as well as to interactions with cells of the innate immune system.
With respect to diversity, B cells secrete antibodies with different functions and T
cells differentiate into subsets that lyse infected target cells, secrete inflammatory
and regulatory cytokines, and promote powerful antibody responses. Knowledge of
antigen specificity is very important in understanding the generation, maintenance
and control of adaptive immunity in infection or immune-mediated diseases. In
addition, immune epitopes can be difficult to reliably and accurately predict using
current epitope prediction algorithms, especially for antibodies and for MHC
molecules that have limited ligand binding data. Therefore, development of
improved prediction tools will be greatly enhanced by better information on the
epitopes recognized by antibodies/BCRs and TCRs/MHC molecules. Such advances
would potentially include better ways to interrogate the repertoire of different B and
T cell receptors and their relation to epitope binding in humans and other model
immune systems. Overall, understanding the nature of immune epitopes recognized
by T and B cells will expedite the development of new therapies to prevent and
treat infection, organ and tissue transplant rejection, and autoimmune and allergic
disorders.

In December 2003, the NIAID awarded the original IEDB contract to the La Jolla
Institute of Allergy and Immunology (N01-AI-40006) and subsequently awarded
the successor contract to the same contractor in December 2011
(HHSN272201200010C). The IEDB website, containing immune epitope information
and analysis tools, became publicly available in 2005 (www.iedb.org) and currently
contains detailed information for over 298,000 unique immune epitopes curated
from more than 18,000 journal references or direct submissions from the research
community related to infectious and immune-mediated diseases. The Analysis
Resource includes the following computational/bioinformatics tools:

1. Epitope prediction tools:
a. T cell epitope predictions based on MHC class I or class II binding, or
peptide processing, or immunogenicity predictions
(http://tools.iedb.org/main/tcell/)
b. B cell epitope and structure predictions
(http://tools.iedb.org/main/bcell/)
2. Epitope analysis tools (http://tools.iedb.org/main/analysis-tools/):
a. Population coverage - calculates the fraction of individuals predicted to
respond to a given set of epitopes with known MHC restrictions.
b. Conservancy analysis - determines the degree of conservancy of an
epitope within a related protein sequence set at different degrees of
sequence identity.
c. Cluster analysis - groups epitopes into clusters based on a degree of
sequence identity.
d. Computational methods for mapping mimotopes to protein antigens -
provides information on available methods for mimotope mapping,
how to search the IEDB for mimotopes, and an example of a mimotope
dataset and the results of its mapping, using other publicly available
web servers.

The system architecture and software design specifications and entity relational
diagrams of the current IEDB system are available at the IEDB website:
http://help.iedb.org/hc/en-us/articles/114094150691-IEDB-System-Architectureand-
Design

The main goal of this solicitation is to continue support of the IEDB which provides
the research community an easy resource for searching experimental data
characterizing antibody and T cell epitopes studied in humans, non-human
primates, and other animal species, involved in infectious disease, allergy,
autoimmunity, and transplant, and tools to assist in the prediction and analysis of B
cell and T cell epitopes. No changes are anticipated to the scope of work from the
previous solicitation in terms of the types of immune epitopes to be included in the
IEDB. In addition, since this solicitation is a re-competition of an existing public
resource, there is no requirement to develop the IEDB and operating system de
novo. Offerors can access the specifications for the current IEDB operating system
at: http://help.iedb.org/hc/en-us/articles/114094150691-IEDB-System-
Architecture-and-Design. Subsequent contractors are expected to use/improve
upon the existing IEDB system. Funding under the prior solicitation is NOT required
for submission to this current solicitation.

Any responsible offeror may submit a proposal which will be considered by the
Agency. This RFP will be available electronically on/about 11/20/2017, and may be
accessed through FedBizOpps http://www.fedbizopps.gov/. This notice does not
commit the Government to award a contract. No collect calls will be accepted. No
facsimile transmissions will be accepted.

For this solicitation, the NIAID requires proposals to be submitted via two methods:
(1) Disc (CD or DVD) and;
(2) Online via the NIAID electronic Contract Proposal
Submission (eCPS) website. The content of the disc and online proposals must be
identical. Submission of proposals by facsimile or e-mail is not acceptable.
SOURCE SELECTION INFORMATION‐‐SEE FAR 2.101 and 3.104

For directions on using eCPS, go to the website https://ecps.nih.gov and then click
on "How to Submit."

.

Added: Nov 02, 2017 10:01 am Introduction

The National Institute of Allergy and Infectious Diseases (NIAID), National
Institutes of Health (NIH), of the Department of Health and Human Services
(DHHS) supports research related to the basic understanding of microbiology and
immunology leading to the development of vaccines, therapeutics, and medical
diagnostics for the prevention, treatment, and diagnosis of infectious and immunemediated diseases. The NIAID, has a requirement for continue support of the
Immune Epitope and Analysis Resource Program, formerly known as the Immune Epitope Database and Analysis Program (IEDB), which provides the research community an easy resource for searching experimental data characterizing antibody and T cell epitopes studied in humans, non-human primates, and other animal species, involved in infectious disease, allergy, autoimmunity, and transplant, and tools to assist in the prediction and analysis of B cell and T cell epitopes.

Description

The NIAID Division of Allergy, Immunology and Transplantation (DAIT) supports
extramural grants and contracts for basic, pre-clinical, and clinical research on
immune system development and function, and host immune responses in
infectious and immune-mediated disorders (e.g., autoimmunity, allergy/asthma,
and transplant rejection). This mission includes support of various reagent facilities,
repositories, and databases that provide resources for biomedical researchers. As a
part of this continuing effort to support the scientific enterprise, the NIAID
announces the renewal of the Immune Epitope and Analysis Resource Program to
further develop, populate, and maintain a public resource containing antibody/B cell
and T cell epitope information, B cell receptor (BCR/T cell receptor (TCR) repertoire
analyses, and epitope prediction and analysis tools for use by the research
community worldwide. For this RFP, immune epitopes are defined as molecular
structures recognized by specific antigen receptors of the immune system, namely
antibodies, BCRs, and TCRs. Immune epitopes involved in infectious and immunemediated diseases and the accompanying biological information will be included in the Immune Epitope and Analysis Resource Program (IEDB).

The effectiveness of adaptive immune responses is related to the diverse functions
of B and T cells as well as to interactions with cells of the innate immune system.
With respect to diversity, B cells secrete antibodies with different functions and T
cells differentiate into subsets that lyse infected target cells, secrete inflammatory
and regulatory cytokines, and promote powerful antibody responses. Knowledge of
antigen specificity is very important in understanding the generation, maintenance
and control of adaptive immunity in infection or immune-mediated diseases. In
addition, immune epitopes can be difficult to reliably and accurately predict using
current epitope prediction algorithms, especially for antibodies and for MHC
molecules that have limited ligand binding data. Therefore, development of
improved prediction tools will be greatly enhanced by better information on the
epitopes recognized by antibodies/BCRs and TCRs/MHC molecules. Such advances
would potentially include better ways to interrogate the repertoire of different B and
T cell receptors and their relation to epitope binding in humans and other model
immune systems. Overall, understanding the nature of immune epitopes recognized
by T and B cells will expedite the development of new therapies to prevent and
treat infection, organ and tissue transplant rejection, and autoimmune and allergic
disorders.

In December 2003, the NIAID awarded the original IEDB contract to the La Jolla
Institute of Allergy and Immunology (N01-AI-40006) and subsequently awarded
the successor contract to the same contractor in December 2011
(HHSN272201200010C). The IEDB website, containing immune epitope information
and analysis tools, became publicly available in 2005 (www.iedb.org) and currently
contains detailed information for over 298,000 unique immune epitopes curated
from more than 18,000 journal references or direct submissions from the research
community related to infectious and immune-mediated diseases. The Analysis
Resource includes the following computational/bioinformatics tools:

1. Epitope prediction tools:
a. T cell epitope predictions based on MHC class I or class II binding, or
peptide processing, or immunogenicity predictions
(http://tools.iedb.org/main/tcell/)
b. B cell epitope and structure predictions
(http://tools.iedb.org/main/bcell/)
2. Epitope analysis tools (http://tools.iedb.org/main/analysis-tools/):
a. Population coverage - calculates the fraction of individuals predicted to
respond to a given set of epitopes with known MHC restrictions.
b. Conservancy analysis - determines the degree of conservancy of an
epitope within a related protein sequence set at different degrees of
sequence identity.
c. Cluster analysis - groups epitopes into clusters based on a degree of
sequence identity.
d. Computational methods for mapping mimotopes to protein antigens -
provides information on available methods for mimotope mapping,
how to search the IEDB for mimotopes, and an example of a mimotope
dataset and the results of its mapping, using other publicly available
web servers.

The system architecture and software design specifications and entity relational
diagrams of the current IEDB system are available at the IEDB website:
http://help.iedb.org/hc/en-us/articles/114094150691-IEDB-System-Architectureand-
Design

The main goal of this solicitation is to continue support of the IEDB which provides
the research community an easy resource for searching experimental data
characterizing antibody and T cell epitopes studied in humans, non-human
primates, and other animal species, involved in infectious disease, allergy,
autoimmunity, and transplant, and tools to assist in the prediction and analysis of B
cell and T cell epitopes. No changes are anticipated to the scope of work from the
previous solicitation in terms of the types of immune epitopes to be included in the
IEDB. In addition, since this solicitation is a re-competition of an existing public
resource, there is no requirement to develop the IEDB and operating system de
novo. Offerors can access the specifications for the current IEDB operating system
at: http://help.iedb.org/hc/en-us/articles/114094150691-IEDB-System-
Architecture-and-Design. Subsequent contractors are expected to use/improve
upon the existing IEDB system. Funding under the prior solicitation is NOT required
for submission to this current solicitation.

Any responsible offeror may submit a proposal which will be considered by the
Agency. This RFP will be available electronically on/about 11/20/2017, and may be
accessed through FedBizOpps http://www.fedbizopps.gov/. This notice does not
commit the Government to award a contract. No collect calls will be accepted. No
facsimile transmissions will be accepted.

For this solicitation, the NIAID requires proposals to be submitted via two methods:
(1) Disc (CD or DVD) and;
(2) Online via the NIAID electronic Contract Proposal
Submission (eCPS) website. The content of the disc and online proposals must be
identical. Submission of proposals by facsimile or e-mail is not acceptable.
SOURCE SELECTION INFORMATION‐‐SEE FAR 2.101 and 3.104

For directions on using eCPS, go to the website https://ecps.nih.gov and then click
on "How to Submit."