SOLICITATION NOTICE
B -- ASSIST DEVELOPING A CYTOGENETIC BIODOSIMETRY SYSTEM - COPY OF THE SOLICITATION
- Notice Date
- 5/23/2013
- Notice Type
- Combined Synopsis/Solicitation
- NAICS
- 541690
— Other Scientific and Technical Consulting Services
- Contracting Office
- Other Defense Agencies, TRICARE Management Activity, USUHS CONTRACTING OFFICE, 4301 JONES BRIDGE ROAD, Bethesda, Maryland, 20814-4799, United States
- ZIP Code
- 20814-4799
- Solicitation Number
- HT9404-13-Q-0676
- Archive Date
- 7/6/2013
- Point of Contact
- Christina Johnson, Phone: 3012953069, Zamora Olin, Phone: 301-295-3922
- E-Mail Address
-
christina.johnson@usuhs.edu, Zamora.Olin@usuhs.edu
(christina.johnson@usuhs.edu, Zamora.Olin@usuhs.edu)
- Small Business Set-Aside
- Total Small Business
- Description
- A COPY OF THE COMBINED SYNOPSIS/SOLICITATION IS PROVIDED. PLEASE SEE THE ATTACHED COPY OF THIS SYNOPSIS. This requirement is set-aside for small businesses only. The Uniformed Services University of the Health Sciences (USUHS), located on the Walter Reed National Military Medical Center (WRNMMC), Bethesda, MD, intends to solicit offers for a consultant/s to assist developing a cytogenetic biodosimetry system to estimate radiation doses in radiation accidents and overexposures. This is a combined synopsis/solicitation for commercial items prepared in accordance with the format in Subpart 12.6, as supplemented with additional information included in this notice. This announcement constitutes the only solicitation; offers are being requested and a written solicitation will not be issued. The solicitation number is HT9404-13-Q- 0676, and it is being issued as a Request For Quotations (RFQ). This request for quotes (RFQ) for commercial items is in accordance with FAR Part 12 - Acquisition of Commercial Items and FAR Part 13 - Simplified Acquisition Procedures. The solicitation document and incorporated provisions and clauses are those in effect through Federal Acquisition Circular (FAC) 2005-66, effective April 1, 2013. This document is available for download at Federal Business Opportunities (FedBizOpps) website, https://www.fbo.gov, reference number: HT9404-13-Q-0676. In accordance with FAR Subpart 16.4, this is a firm-fixed price contract. This requirement will be competed as a set-aside for small businesses. The following North American Industry Classification System (NAICS) code is applicable: 541690, Other Scientific and Technical Consulting Services, with a size standard of $14.0 541990, All other Professional, Scientific and Technical Services, with a size standard of $14.0 E-mail or mailed offers are acceptable. Facsimile offers will not be accepted. All correspondences shall be submitted to Christina Johnson via e-mail at christina.johnson@usuhs.edu. Offerors shall ensure the RFQ solicitation number, HT9404-13-Q-0676, is referenced. POINT OF DELIVERY Location: Armed Forces Radiobiology Research Institute (AFRRI) 8901 Wisconsin Avenue Building 42 Bethesda, MD 20889-5603 I. Price Schedule: The contractor shall furnish all required materials, equipment, documentation and transportation listed herein to accomplish the requested services required for the Uniformed Services University of the Health Sciences. Services shall be performed in accordance with the statement of work as set forth in this solicitation. Price Schedule: The contractor should provide pricing as set up below: Contract Line Number (CLIN), description, and unit of issue. CLIN 0001 Unit of Issue Unit Cost Total Cost Development of High-throughput Interphase Dicentric Chromosome Aberration biodosimetry system JOB $ $ Contract Total $ II. STATEMENT OF WORK 1.0 General 1. The contractor shall provide all technical support within the scope of this statement of work. The contractor shall perform tasks, as specified by the individual deliverables areas: Task 1: IDCA (Interphase Dicentric Chromosome Aberration) & LIMS (Laboratory Information Management System), Hardware/Software, Platform Design & Implementation; and Task 2: Database Design, and Development and JAVA based Implementation. The Contractor shall be capable of performing a range of Bioinformatics/Systems biology, computational programming, and robotic and high-throughput instrumentation work to accomplish the project deliverables. 2. The tasks which will be issued through work assignments commonly require expertise in multiple disciplines such as; High-throughput Imaging, Radiation biology, Cytogenetics, Biodosimetry, Robotics, Bayesian systems, Neural Networking systems, Artificial Intelligence, Pathology, Molecular biology, Genetics, Physiology, Decision analysis, Quantitative dose-response assessment, Quantitative uncertainty analysis, GLP, Computer Science & Programming. 3. Under the DoD 5200.2, DoD Personnel Security Program, the Government is responsible for maintaining security within AFRRI. All Contractors' personnel will adhere to AFRRI security requirements. All Contractors' personnel must have AMERICAN CITIZENSHIP and valid I. D. to work within AFRRI and to enter the facility. 2.0 Introduction and Overview Armed Forces Radiobiology Research Institute (AFRRI), a tri-service biomedical research laboratory chartered in 1961 and a major component of the Uniformed Services University of the Health Sciences, conducts research in the field of radiobiology and related matters essential to the operational and medical support of the U.S. Department of Defense and the military services. The institute collaborates with other governmental facilities, academic institutions, and civilian laboratories in the United States and other countries. Its findings have broad military and civilian applications. In support of AFRRI/USU and the DoD military mission, the project Principal Investigator (PI) and his lab has established international protocols and have identified the use of gold standard radiation biomarkers to estimate radiation doses in radiation accidents and overexposures. The PI is a subject matter expert (SME) of Artificial Intelligence (AI) and Automated systems and has set up a high-throughput prototype system CLASP (Cytogenetic Laboratory Automation System Platform) that has been recognized as a great tool for use during a radiation or nuclear mass-casualty emergency. The entire system demands the use of many robotic instruments and high-throughput automated systems to meet the sample analysis demands and throughput. The whole system is supported by a high-performing computing infrastructure controlled by AI and Bayesian system using neural networking and contextual image mapping framework integrated with high performing computing architecture. 3.0 Project Background Nuclear/radiological exposure risk is eminent and several thousands of individuals may be exposed to radiation in worst-case scenarios. Radiation mass casualties will demand high-throughput individual diagnostic dose assessment for medical management of exposed subjects. Many established cytogenetic assays are generally manually performed, either in part or in whole, and are inadequate for high-throughput requirements, particularly during radiation mass casualty. Because current medical intervention guidelines encourage early administration of cytokines and supportive therapy, timely identification of radiation casualties who will benefit from medical intervention in radiation disasters is critical. Cytogenetic techniques are considered as the "Gold Standard" biological dosimeters for medical management and triage during nuclear radiation mass casualty. In the last decade, a variety of new biodosimetric assays have evolved; Gamma-H2AX, micronuclei, premature chromatin condensation assays etc. Besides these established assays, several new reliable technologies like electron paramagnetic resonance (EPR) dosimetry, gene expression profiling, nanovesicle hydrocell and DNA microarrays are rapidly gaining importance. These technologies are also very useful for the clinical assessment of biological effects of Ionizing Radiation, understanding transcriptome modulations, relational analysis of gene expression data, establishing gene signatures for early transient responses which are of very high interest to the radiobiology and military community and can assist during triage of radiation mass casualty. 4.0 Goals or Objectives The purpose of this project is to develop a rapid, high-throughput, radiation-specific diagnostic cytogenetic biodosimetry system Inter-phase Dicentric Chromosomes Aberrations (IDCA) for individual diagnostic dose estimation, highly specific to radiation exposure, and with a better operating dose-range than the current gold-standard metaphase-spread Dicentric Chromosomes Abberations (DCA). The project wants to establish an independent ultra-high-throughput radiation dose specific analytical system which can be operational and usable on a cytogenetic laboratory automation platform. The system prototype developed should be integrated with Laboratory Information Management System (LIMS) and should be inter-reportable with complementary biodosimetric assays. The prototype should be able to enumerate and score the image attributes, spatial and spectral features for IDCA. An automatic feature extraction algorithm to support and enhance the specificity and sensitivity of the platform has to be developed and integrated. The system should be able to validate the large-scale sample processing capabilities of the automated high-throughput robotic cytogenetic system for the preparation of abridged short-term whole-blood micro-culture and metaphase spreads for the IDCA. The entire system should be ready to be tested and validated against manual scoring of the samples, should be capable of integration into existing platform and be scalable based on the timely requirements and demands. The prototype should adapt Rational Unified Process and Machine Learning approaches using Vector training and Bayesian algorithms. 5.0 Personnel Qualifications Except as otherwise authorized in writing by the Contracting Officer, the Contractor shall ensure that each employee meets the following minimum criteria: 5.1 The consultant MUST be ready and have the ready expertise to start on the project right away; ZERO tolerance for learning on the job or inflated expertise. 5.2 The consultant will contribute to systems programming and support application development, working closely with Project Principal Investigator (PI) in his AI and computational programming efforts, applied biostatistics, data mining, and algorithm development efforts to automate cytogenetic analysis and develop IDCA. 5.3 The consultant MUST be expert in robotic instrumentation, shell scripting, JAVA or a C# developer. 5.4 The consultant will design, develop and code scripts, customize robotic high throughput equipment's, develop interfaces for robotic equipment and develop graphic user interfaces (GUI) and provide user friendly functionalities. 5.5 Should be an expert with Information Management System and help in the integration of SOW within the database architecture. 5.6 The consultant should be highly proficient in automation of existing laboratory manual processes into software pipelines under GLP is a MUST. 5.7 The Consultant MUST have extensive expertise in database (ORACLE/MySQL) development and administration in highly professional industrial environment. 5.8 Bioinformatics/Systems biology, implementation and support of algorithm development and automation of research designs are a MUST. 5.9 The consultant MUST have excellent programming, scripting, shell and web knowledge and experience. 5.10 The consultant should have expertise and prior experience with IIS 5/6, Apache 2.0, SSL, NAT, DNS, WINS, TCP/IP, FreeBSD, NetBSD, Linux, Solaris 7/8, HP-UX 10/11. 5.11 The consultant should be an expert with at least three of these languages C/C++, Python, AWK, VB & VBA, CSH, PERL, JAVA, ASP,.NET, and R. 5.12 The consultant should have experience in designing a secure network and GRID frame work for multi-processing architectures. 5.13 A strong knowledge of Bioinformatics and application development is necessary. 6.0 Technical Tasks and Deliverables The contractor shall design, develop and provide the management and technical expertise to ensure that all tasks and deliverables are performed efficiently, accurately, on time, and in compliance with the requirements of this document. 6.1 Task 1: IDCA & LIMS, Hardware/Software, Platform design & Implementation Design hardware architecture and infrastructure for base platform implementation. The system should support concurrent execution of multiple analysis jobs per biomarker/array and generation of per-well output. Platform should support high-quality data and attribute extraction. Perform Operating System implementation; hardware fabrication, network connectivity to local nodes; user control for information segregation. Fabricate and design a prototype platform implementation which will support multi-faceted and concurrent execution of numerous biomarker/array analysis jobs. Transform the manual laboratory biodosimetry assays into high-throughput Bayesian based platform. Design and develop IDCA assay for high-throughput analyses. Develop and code for high-throughput image acquisition. The system design should be capable of parallel execution and use of grid-based computing facilities such as SGE, MPI-CH or MPI-CH2. The platform should be able to utilize batch processing facilities and cross-cluster linkages for temporal information retrieval. Horizontal expansion of computation capacity should be supported through addition of array-worker nodes. A reporting console a.la web-based management dashboard should be provided in order to manage platform system components. Utilization of a component based architecture. Perform testing of platform prototype scalability; benchmark bandwidth and connectivity; hardware programming of platform resources to utilize I/O tunneling. Integrate with existing network and LIMS architecture with scatter/gather-style capabilities; benchmark bandwidth & connectivity, feasibility, validation and proof-of-principle for VPN, debugging and system validation along with user documentation. Implementation of tools and programming to support modeling of biomarker data sets. Facilitate high-throughput performance requirements of analyzing incoming biomarker and dosimetry data points from multiple sources. Perform hardware and software programming for multi-core enhanced software libraries (MPI, OpenMP, etc.) and processor-specific data copy-in/copy-out assembly/op-codes. Rapid servicing and dispatch of incoming requests on timely basis to keep scheduling pipeline fully saturated. Use N-tier architecture for platform scalability and resource utilization flexibility in processing of numerous microarray configurations at a time. 6.2 Task 2: Database Design, Development and JAVA based Implementation Design Entity Relationship Models (ERMs) for the underlying cytogenetic database information store. Design and develop models to parallel compute cytogenetic image sync within and across other repositories for identifying, scoring and establishing sensitivity and specificities weights for each image. The Image and Contextual Image algorithm mapping should be performed in extreme high-throughput. Appropriate use case models should be developed for interaction with the DB entities and schemas. JAVA applets and user based interactive analyses window to be developed for monitoring and placing weights for analysis based on inputs. GRID based architecture for parallel processing of heavy images at high-throughput should be designed developed and established in support of the CLASP platform. Support storage of ephemeral or permanent data points and other information vectors onto MySQL-backend systems. Schema should utilize compact data types for space efficiency in order to support large data sets. Implement high-throughput DB-level clustering for latency reduction in I/O tunneling. Concurrent access from multi-core kernels should be supported on the Schemas. Implement a caching engine to mediate between the database servers and client processes and threads. Perform system compatibility analysis with POSTGRESS/SQL for object-oriented database management extensions; SQL scripts for data query and data analyses, optimized search organization, heterogeneous systems data portability checks. Integrate the database information views with existing LIMS backend storage. Perform user bandwidth testing; packet transmission checks; Read/Write/Update latency analysis and delay assessments. Implement entity and schema-level optimizations using partitioning and master/slave-style replication for performance. DB management system should perform load among multiple slaves to improve performance. In this environment, all writes and updates must take place on the master server. Reads, however, may take place on one or more slaves. Stored procedures and subroutines should be built into the DBMS to reduce query execution times for rapid analysis operations per array worker. Cross-link with external data sources and perform scheduled management for automatic update and synchronization, in order to facilitate rapid and updated cross-analysis. The software should interface with well-known Bioinformatics and Bio databank application programming interfaces, ABIs and libraries. In addition, the system should integrate with high-performance machine-optimized numerical integration and scientific computation packages. 7.0 Reporting, Timelines and Evaluation of Progress The Contractor is required to provide a detailed work progress report to the Project Principal Investigator (PI) upon completion of each listed deliverable in a timely fashion (mutually agreed upon). Demonstration (on-site or in some cases a VPN established WebEx with prior written approval from Project PI of the completed deliverable is mandatory before invoicing or start of the next deliverable. Upon successful completion of sequentially listed sub-tasks, the PI would recommend continuation or may request the changes or cancel the work effort by the consultant. All the deliverables listed under the scope of the project needs to be completed by October 30, 2013 along with the project report and documentation.
- Web Link
-
FBO.gov Permalink
(https://www.fbo.gov/notices/6052a2df773cfd22f950ae08ac4acf15)
- Place of Performance
- Address: BETHESDA, MD, United States
- Record
- SN03071031-W 20130525/130523235853-6052a2df773cfd22f950ae08ac4acf15 (fbodaily.com)
- Source
-
FedBizOpps Link to This Notice
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