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FBO DAILY - FEDBIZOPPS ISSUE OF FEBRUARY 13, 2013 FBO #4099
MODIFICATION

D -- Development and Support for NTP Databases

Notice Date

2/11/2013
 

Notice Type

Modification/Amendment
 

NAICS

541512 — Computer Systems Design Services
 

Contracting Office

Department of Health and Human Services, National Institutes of Health, National Institute of Environmental Health Sciences, Office of Acquisitions, Office of Management, 530 Davis Drive, Durham, North Carolina, 27713, United States
 

ZIP Code

27713
 

Solicitation Number

NIHES2013164
 

Point of Contact

Laura E. McGrew, Phone: (919)541-3813, Brian J. Souter, Phone: 919-541-0401
 

E-Mail Address

mcgrewl@niehs.nih.gov, brian.souter@nih.gov
(mcgrewl@niehs.nih.gov, brian.souter@nih.gov)
 

Small Business Set-Aside

N/A
 

Description

The purpose of this modification/amendment is as follows: To CORRECT paragraph 6. Other Important Consideration NAICS Code 541512 size standard to read $25.5M. All other terms and conditions remain unchanged. 1. Introductory. This is a Small Business Sources Sought notice. This is NOT a solicitation for proposals, proposal abstracts, or quotations. The purpose of this notice is to obtain information regarding: (1) the availability and capability of qualified small business sources; (2) whether they are small businesses; HUBZone small businesses; service-disabled, veteran-owned small businesses; 8(a) small businesses; veteran-owned small businesses; woman-owned small businesses; or small disadvantaged businesses; and (3) their size classification relative to the North American Industry Classification System (NAICS) code for the proposed acquisition. Your responses to the information requested will assist the Government in determining the appropriate acquisition method, including whether a set-aside is possible. An organization that is not considered a small business under the applicable NAICS code should not submit a response to this notice. 2. Background. The National Institute of Environmental Health Sciences (NIEHS) is one of 27 Institutes and Centers of the National Institutes of Health (NIH), Department of Health and Human Services (DHHS). The mission of the NIEHS is to reduce the burden of human illness and disability by understanding how the environment influences the development and progression of human disease. The National Toxicology Program (NTP) is an interagency program whose mission is to evaluate agents of public health concern by developing and applying tools of modern toxicology and molecular biology. The Division of the NTP supports the program. The NTP maintains an objective, science-based approach in dealing with critical issues in toxicology and is committed to using the best science available to prioritize, design, conduct, and interpret its studies. To that end, the NTP is continually evolving to remain at the cutting edge of scientific research and to develop and apply new technologies. 3. Purpose and Objective. (A) In carrying out its mission, the NTP studies the effects of environmental agents in laboratory studies, which are performed predominantly at contract laboratories and then reviewed by the NTP. The NTP carries out a number of testing paradigms, covering high-throughput testing, in-life testing, in vitro models, and other biological systems, with the aim of generating high-quality data to support the mission of the NTP. On an annual basis, NTP selects approximately 10 new chemicals for testing, has 20 to 30 subchronic studies and 30 to 40 chronic studies in different stages of testing and evaluation, and presents approximately 15 subchronic and chronic studies for public peer review. An additional 10 to 30 reproductive and developmental studies and 20 immunotoxicology studies is also peer reviewed on an annual basis. (B) The NTP receives data from contract laboratories, and houses these data in a Laboratory Information Management Systems (LIMS) or in local or ad hoc systems. The LIMS currently used are the hosted Provantis database and the custom legacy LIMS. The Hosted LIMS is provided by Instem LSS while the legacy LIMS was developed under contract and has two components: Toxicology Data Management System Enterprise (TDMSE), and Laboratory Data Management System (LDAS). Once the data are made public, the entire dataset (data and metadata) from the study is transferred to the Chemical Effects in Biological Systems database (CEBS) where the study data and conclusions are presented to the public and made available for download. (C) In addition, up to 50 high-throughput assays are performed, and up to 50 genetic toxicology studies are completed each year. The NTP also performs investigational studies using emerging technologies, with one-off designs, will perform studies to investigate other areas of toxicology and environmental health science, and has legacy data not currently housed in a relational database which must be included in a data stream to CEBS. (D) The NTP must manage, house, and report the data from this scientific work. The NTP requires the Contractor to perform this task. The Contractor shall be capable of (1) providing user support for the NTP for CEBS and the LIMS and for members of the public for the use of CEBS and (2) maintaining normal operating processes for NTP's use of the LIMS and CEBS. (E) Also, CEBS currently does not contain the complete set of functionality desired by the NTP. The Contractor shall design and incorporate new functionality into CEBS at the request of the NTP. 4. Project Requirements. 1. (Operational Tasks) Operational tasks are performed throughout the lifespan of the contract. Successful completion of these tasks requires an understanding of toxicological science in addition to strong understanding of computer science and information technology (IT). 1.1 User Support 1.1.1 CEBS Support Current Issue: Members of the public and of the NTP require assistance in obtaining data from CEBS. Objective: The Contractor shall provide staff to assist users in routine use of CEBS. Desired Outcomes: CEBS users have a point of contact for questions, common questions are captured and rendered in CEBS as a help or workflow, bugs are identified and resolved expeditiously, questions requiring direct database access are answered in a timely manner, and modifications are made to the CEBS UI to allow users to address similar questions in the future. 1.1.2 SIFT File Creation Current Issue: Users provide data in various formats for deposition into CEBS. Objective: Data received by the NTP for CEBS shall be formatted for entry into CEBS. Desired Outcomes: The Contractor shall support this process by converting the deposited data into a validated SIFT (Simple Investigation Formatted Text) file for loading into CEBS. The process of SIFT creation may be manual, or automated for numerous data files in a consistent format, at the discretion of the COR. Approximately 100 - 150 such files are presented in a year. 1.1.3 CEBS Presentations at Meetings Current Issue: Every year the NTP demonstrates CEBS at the Annual Meeting of the Society of Toxicology (SOT). Objective: The Contractor shall provide staff to assist with the demonstration of CEBS at scientific meetings. Desired Outcomes: The contractor shall supply staff knowledgeable about toxicology and the use of CEBS to attend scientific and/or technical meetings and provide a daily session during the meeting where CEBS is demonstrated to the scientists attending the meeting. One to two meetings are expected annually. 1.1.4 User Support for the Hosted LIMS Current Issue: The contractor supplying the Hosted LIMS provides user support, but does not support the needs of the NTP to have data presented in specific report formats and who need advice about protocol templates or work schedules. Objective: The Contractor shall assist users in use of the Hosted LIMS for NTP users requiring special help. Desired Outcomes: The staff provided will create tables for NTP users using for example the Business Objects tool supplied by Instem and attached to the Provantis database. This task requires understanding of as well as experience with Provantis itself. The Contractor shall provide assistance for NTP staff or contractors who may have questions about using the Hosted LIMS, if requested by the COR. The Contract staff will communicate closely with the COR and NTP staff to fully gather requirements and constraints for the tables and staff support. 1.1.5 The Hosted LIMS User Support for NTP Protocol Templates Current Issue: Studies are created in the Hosted LIMS from specific NTP protocol templates within the Hosted LIMS database. Objective: The Contractor shall understand and advise NTP personnel about the impact of suggested changes in NTP protocol templates in the Hosted LIMS. Desired Outcome: If a change is required, the Contractor shall make the change in the NTP template, and, if requested by the COR, perform testing to determine if the change functions as expected. Changes made to the Hosted LIMS database templates will follow the established GLP change control process, be thoroughly documented and coordinated with the NTP Validation Team and the Hosted LIMS database Administrator. 1.1.6 The Hosted LIMS User Support for the Hosted LIMS System Libraries and System Security Current Issue: The NTP will identify changes or additions required in the system configuration or library content of the Hosted LIMS. Objective: The Contractor shall implement changes to the Hosted LIMS System Libraries and System Security, using either the NTP Change Control process or the NTP Process for Making Administrative Changes in the Hosted Database as directed by the COR. Desired Outcome: Changes made to the Hosted LIMS libraries will follow the established GLP change control process, be thoroughly documented and coordinated with the NTP Validation Team and the NTP Hosted LIMS Administrator. 1.1.7 Legacy LIMS User Support Current Issue: Legacy LIMS must be maintained and supported. Objective: Legacy LIMS shall be maintained, and staff shall be provided to respond to user-identified issues or account maintenance requests, security needs, changes in operating systems and other similar changes. Desired Outcome: Contractor shall assign a liaison to each lab collecting NTP data using LDAS, with the responsibility to solve or capture any issues that the lab personnel encounter while using the Legacy LIMS. Liaisons are expected to be on-call and available for work on an ad hoc basis during evening and weekend hours. User-identified issues, security needs, changes in operating systems, and other similar changes will be collected in a Government-provided task management system currently Jira, and reviewed with the COR for prioritization and inclusion into a maintenance release. The Contractor shall carry out such a release as directed. It is anticipated that the NTP will end the use of LDAS to collect data from new studies after one year from the start of the contract. The Contractor shall retire TDMSE as directed; house the data in such a way that the data can be searched if need be. 1.2 Data Management 1.2.1 Loading of Production CEBS Current issue: The NTP constantly updates NTP data. Objective: The NTP data shall be refreshed in the production CEBS database at least quarterly. Desired Outcomes: Regularly, and at least quarterly, re-build one of the two production databases, validate the build, and then point the CEBS user interface to the newest database. Currently there are approximately 2500 studies in CEBS, and the number is expected to grow annually. With every update of the CEBS database, a parallel update of the CEBS bulk data download "Bundles" is also required. Each update requires debugging, post-processing and validation. A report of the number and type of studies loaded successfully, and a report of the CEBS data dictionary shall be included with each load. 1.2.2 NTP File Management Current issue: The NTP data is stored in a variety of files. Objective: Create and manage an orderly file management system for NTP data files Desired outcomes: The Contract shall perform an inventory of files associated with CEBS studies, and develop a central point for storing all data files. The files shall be managed using both manual and automated processes, and an inventory maintained. A report of the data file inventory shall be produced with each new load of CEBS production. 1.2.3 Management of CEBS Bins Current issue: Public access to and the administration of the CEBS private file system ("Bins") is inefficient. Objective: Develop a user interface for CEBS Bins to allow users to manage their data. Desired outcome: Develop a user interface with at a minimum the following features: • A system for authorizing users to upload or remove data files from their CEBS bin • A means for authorized users can create sub-bins, and can select the users authorized to view/delete/upload data in these bins from the list of authorized users in CEBS. • A means for an authorized user to upload individual files or directories. 1.2.4 CEBS Administrative Page Current Issue: Maintenance of the CEBS data dictionary is a manual process Objective: Develop a tool to permit CEBS curators to review and update the CEBS databases Desired Outcome: A tool for adding terms to the CEBS data dictionary shall be created. Additionally a process for term review shall be created; this process shall include the COR and members of the NTP staff as directed by the COR. Generate SOPs for adding terms to the dictionary. On a regular basis, or at least bi-annually, survey the dictionary to identify incorrect or redundant terms. 1.3 Validation 1.3.1 Validation of Code Changes Current Issue: Code changes can have unintended consequences or unwarranted assumptions. Objective: Code shall be tested prior to release. Desired Outcome: With every code change in either CEBS or TDMSE/LDAS, prior to release of the code, the Contractor shall demonstrate that the changes have not impacted the validity of the data in CEBS or the presentation of data to the CEBS user. The process of validating code shall be converted to an automated protocol where possible. 1.3.2 Validation of Data Streams Current Issue: Data streams must be validated to ensure that no data are dropped or coded incorrectly. Objective: The data transfer process shall be validated as part of developing code to handle the data stream for every new data stream coming to CEBS or to the PWG module. Desired Outcome: Each data stream for each load will be tested for complete data transfer to ensure that no new data were added to the input form and that all data are correctly captured in CEBS. When possible, the validation should be performed using automated methods and incorporated into routine testing at each loading. 1.3.3 Validation of the CEBS Database Functioning Current Issue: The CEBS database is non-responsive at erratic times. Objective: Contractor shall monitor CEBS performance on an automated basis. Desired Outcomes: The Contractor shall have a suite of tools which verifies the response and user experience of CEBS and establish automated methods to carry out CEBS validation. This includes a system to monitor CEBS system availability and response time in real time, and to verify the accuracy and completeness of data in CEBS in user interface search pages. The Contractor shall maintain logs from such methods and summarize weekly for the COR. 1.3.4 Validation of Changes to the Hosted LIMS Current Issue: The hosted database is housed in a GLP validated environment, meaning that it is in compliance with the guidance from the US Food and Drug Agency (FDA) for Good Laboratory Practice as outlined in 21 CRF Parts 11 and 58, and from the US Environmental Protection Agency (EPA) 40 CFR Parts 160 and 792. Objective: When changes are needed in the templates, in security settings, roles or endpoints, when a new release or update of the Hosted LIMS is received, or any other change is required in the Hosted LIMS, the Contractor shall validate these changes as directed by the NTP Validation Team, the NTP Hosted LIMS Administrator, in coordination with the COR. Desired Outcome: Contractor shall follow the NTP GLP Validation Change Control Process or, when appropriate, following the NTP Administrative Change process. Additionally, new statistical methods in the Hosted LIMS must be validated as they are added to the Hosted LIMS by Instem. The Contractor shall verify that the method returns the expected value for a particular set of test data. This verification shall conform to the NTP Change Control process. The COR shall direct all changes made to the Hosted LIMS. 1.4 Work Environment The NTP is a responsive government agency which acts in the public interest. As such, it is likely that changing NTP priorities will impact the priority and sequence of tasks. It is likely that the NTP will add additional tasks not specifically listed here, but which are within scope of the Contract. The Contractor is expected to be accommodating to changes of this nature, and to work with the COR to prioritize and incorporate tasks. 1.4.1 Regulatory Compliance Current issue: The NTP is part of the NIEHS computer infrastructure, and subject to regulations related to computer and infrastructure security and compliance with federal regulations such as Section 508 of the Americans with Disabilities Act. The NTP is also subject to records management regulations. Objective: The Contractor is expected to be compliant with NIEHS, NIH and HHS regulations. Desired Objectives: The Contractor shall be compliant with NIEHS, NIH and HHS regulations. These include but are not limited to Section 508, security and records management. The Contractor shall perform all work in compliance with regulations and document this compliance with an annual security and 508 compliance reports, and responsiveness to interim security requirements which may arise. The Contractor shall maintain files in accordance with the appropriate current National Archives and Record Administration (NARA), and General Records Schedule (36 Code of Federal Regulations (CFR) 122014 and 44 U.S.C. 3301). All contractor files, records, and documents maintained in the performance of the resultant contract are Government Property and the Contractor shall return them upon completions or termination of the work. However, internal proprietary contractor business files are not Government property. 1.4.2 Collaboration with Government Staff and Other Contractors Current issue: The NTP details government staff to work on parts of the overall CEBS and the Hosted LIMS projects, in parallel with the Contractor. The Computer Technology Branch (CTB) details staff and contractors to work on CEBS support. Instem details staff to work on the Provantis database. This work environment requires close communication among these groups in order to accomplish these separate tasks in an efficient manner. Objective: NTP staff and Contractor staff working on CEBS and the Hosted LIMS shall communicate regularly and transparently about the technical details of work relating to CEBS and the Hosted and legacy LIMS. Contractor staff shall communicate with CTB and other components of NIEHS, Instem and their delegates, as needed and in coordination with the COR. Desired Outcomes: A 10 minute response time from Contractor staff during normal business hours (9am to 6pm, eastern local standard time). Weekly meetings to ensure that the Government and Contractor teams work is coordinated, not-overlapping, and separated by function. It is expected that some members of contractor staff shall be stationed at the NTP facility. The Contractor shall interface with other contractors and federal employees as necessary to perform daily operations. 1.4.3 Documentation and Version Control Current issue: Contractor using government tools to manage work. Objective: Contractor shall use government supplied tools to manage work tickets, version control and non-end user documentation. Desired Outcome: The Contractor staff shall use government-supplied tools for work tickets, version control and non-end user documentation. Currently, these are Jira, Confluence, and Subversion. 1.4.4 Knowledge Transfer Current issue: The NTP and NIEHS provide training and other opportunities for knowledge transfer which permit Contractor staff to more properly fulfill their tasks. Objective: Contractor staff shall participate in training and local seminars at the discretion of the COR at their own expense. Desired Outcome: Contract staff shall participate in opportunities for learning provided by the NIEHS and NTP or other local ICs and companies. Typically, these have no costs associated with them. These are provided so that the Contract staff may perform their tasks with more efficiency and understanding. 1.5 IT Support. 1.5.1 Inventory Current Issue: The LDAS in-life and administrative workstations in contractors' labs must function well while they are in use for work under NTP contracts. The Government requires an inventory of Government Furnished Equipment (GFE) and Contractor Acquired Purchases (CAP). Objective: Maintain and support the inventory associated with the contract. Desired Outcome: Maintain LDAS units in labs in good working order. Maintain an inventory of parts to support LDAS workstations. Collect or abandon-in-place LDAS in-life and admin workstations, and dispose of these once all in-life work using LDAS has ceased or the Contractor Laboratory no longer has need for them. 1.5.2 Security Current Issue: There are rare instances of security incidents involving the systems managed under this contract. Objective: All security incidents will be identified rapidly, communicated to the NTP, and resolved efficiently in accordance with the contract. Desired Outcome: The Contractor shall provide immediate notification of any security incident, followed by a report within 48 hours of the remediation. Additionally, the Contractor shall provide weekly reports of failed access to CEBS private data and all LIMS, and weekly summaries of log files. 1.5.3 Hardware/Software Support Current Issue: Contractor staff requires good capacity workstations and servers, high-speed access to the internet in order to access the NIEHS computational facility, and up-to-date software. Objective: The Contractor shall provide all necessary services, hardware and software licenses for the contract, and training in necessary systems at no cost to the Government. Desired Outcome: The Contractor staff shall have the necessary support to be able to work efficiently. The Government recommends the use of COTS products where possible, to avoid unnecessary expense involved in developing and supporting software, however, the CEBS database is currently so unique that no commercial analog can be identified. 1.5.4 The Hosted LIMS Exports Current issue: The LIMS supplier provides a copy of the Hosted LIMS database on a weekly basis. Objective: The Contractor shall receive the copy of the Hosted LIMS database export, verify that it is accurate and complete, and store it safely at the NIEHS. Desired Outcome: The NTP shall have a current copy of the Hosted LIMS data available to ensure data continuity. 1.5.5 Use of the Internet Cloud Current issue: Development options are wider if some development work is performed on the cloud. Objective: Establish a cloud instance of CEBS which contains data of size and complexity equivalent to production CEBS but which is not actual NIH data. Desired Outcome: Use this to prototype different options for warehouse architecture, queries, bioinformatics tools, Tox21 data presentation, and other tasks for which the NIEHS network is less well suited than the internet cloud. 1.5.6 Technology Assessment and Refreshment Current Issue: IT technology and NTP requirements develop rapidly, making new tools available and current technologies obsolete. Objective: Collect suggestions from the NTP and from IT professionals and incorporate into proposals for updates and improvements to CEBS. Implement these proposals as directed. Desired Outcome: Capture user needs, and then assist COR in evaluating suggested improvements/refreshments. Contractor shall ensure that Contractor staff remains current with IT technology through reading, communication with other IT professionals, and through attendance at technical meetings. As requested by the COR, develop proposals to incorporate new functionality and/or new technology into CEBS. These proposals will be incorporated into the tasks in the next section of this document. 2 (Development Tasks) In addition to operational tasks done on a continuing basis throughout the lifespan of the contract, the NTP requires that the following tasks be completed, starting at the time of contract award. The COR shall work with the Contractor to fully define the requirements and assumptions for each task, and the priority of tasks with in this list. These tasks are performed in support of the NTP mission and rely on strong science as well as strong IT understanding. It is possible that the order of tasks, and the exact requirements of these various tasks, will vary as the priorities of the NTP are changed. The COR shall work with the Contractor to accommodate these changes. 2.1 New Data Types Current issue: New data types, new technologies, and new study designs are used by the NTP in support of the NTP mission. Objective: As new data types and study designs are received, it is necessary to model these for incorporation into the CEBS and for proper display in the CEBS user interface and then incorporate them into CEBS. Desired Outcome: The new data shall be added to the CEBS database using the SIFT (Simple Investigation Formatted Text) file format and the CEBS loader. This process requires thoughtful discussion by the Contractor with the COR and members of NTP staff prior to incorporation. The CEBS database may need to be changed by the addition of a new table or field to accommodate such requests. New presentation of the data shall be added to CEBS user interface in addition to the standard CEBS view of the data. The NTP anticipates changes needed to display study phases, generations, and results of data transformations, results of assay panels, data from new NTP legacy study types, and additional data which will be encountered over the course of the contract. Successful completion of these tasks requires an understanding of the various data found in different NTP studies, and how these same data are captured and represented in CEBS, in addition to a strong background in IT. 2.2 Data Pipelines Current Issue: Current data streams to CEBS may be error-prone, and do not encompass all NTP data. Objective: Ensure that all NTP data flows into CEBS in an accurate and complete manner. Desired Outcomes: Current methods shall be validated, NTP legacy data not currently in CEBS, which at a minimum will include data from ADME (Absorption, Distribution, Metabolism, Excretion), TK (Toxicokinetic) studies, Immunotoxicology and historical comet studies, and clinical chemistry and reproductive data stored in a legacy relational database, shall be moved to CEBS. Methods to capture data from NTP contract labs shall be established and validated. Data from legacy database, contract labs, and the Hosted LIMS database shall be linked to the corresponding animal ID. 2.3 Computations Current Issues: The computations in CEBS do not encompass all that are needed by the NTP. Instem will incorporate new statistical methods into the Hosted LIMS database suite which must be validated. Objective: Add and validate statistical and computational methods to CEBS user interface and backend analysis server in consultation with COR. Desired Outcomes: This task is to incorporate and validate existing software in the public domain rather than to develop new statistical methods, however strong understanding of the CEBS database schema and of statistical and visual data mining methods is required for successful completion of this task. Software to incorporate include at a minimum (1) the EPA's Benchmark Dose Software (BMDS) software, (2) the functionality of the Genetic Alterations in Cancer user interface, (3) the signature calling algorithm from Drug Matrix, (4) visual methods for viewing data in CEBS using a software package such as the Spotfire package from TIBCO, (5) supervised statistical analyses such as ANOVA or trend tests, (6) genome-wide association tools such as EMMA and QTLRel. Provide CEBS workflows restricting the user to the correct method for each data type. 2.4 CEBS features Current issues: CEBS does not contain all the features required by the NTP. Objective: Incorporate new features identified by the NTP into the CEBS user interface and database. Desired Outcomes: The features to be added will be described by the NTP; examples include the following: • CEBS shall have a historical control database for all NTP study types including appropriate meta-data. • NTP conclusions shall be incorporated into the CEBS database where possible, and made available to the user for searching. • After discussion with NTP staff about methods to generalize; add new workflow to CEBS to allow users to carry out common queries. • A CEBS view shall exist for each of the NTP Search pages (see http://ntp-apps.niehs.nih.gov/ntp_tox/index.cfm). Ensure that all data included on NTP Search pages are also displayed by CEBS. • Transfer all NTP search page functionality to CEBS. This will include moving the statistical methods including trend tests and poly-k test run on data from CEBS. It is possible that the NTP will augment the current statistical tests with others; if this is the case these new tests shall also be included. • Automate the transfer of data from the static Sites and Associations workflow currently in CEBS to include all studies in CEBS. • Develop methodology to capture, manage and report data from literature curation derived by NTP and/or from external scientists • Permit the user to enter in CEBS a list of test articles or conclusions to retrieve results, rather than restricting the query input to one item. Validate the query input terms against terms in CEBS prior to executing the query. Build a new workflow in the CEBS user interface to support this. • Develop a secure method for expert NTP staff to search all of the data in CEBS. The Contractor shall deliver a document outlining the requirements and technical approach and gain approval from the COR before initiating work. 2.5 CEBS Ontology Current issue: The CEBS Ontology is not complete. Objective: Create a CEBS Ontology that can be used to draw conclusions and reason about NTP studies. Desired Outcome: Complete creation of the CEBS SIFT Ontology by ensuring that the terms used in CEBS to describe neoplastic, non-neoplastic, clinical pathology endpoints and organs are mapped to existing external ontologies, and that the data needed to support each study conclusion is expressed as an RDF triple. Leverage the CEBS ontology to draw conclusions about CEBS data using the semantic web and logical reasoning, and integrate this data stream into CEBS. Identify to the user which conclusions are computationally derived. Develop tools to carry out natural language processing (NLP) to derive conclusion data from NTP Technical Reports provided in electronically readable format and deposit in CEBS. Add toxicological knowledge to CEBS by surveying the literature as directed by the COR. Ensure that the terminology used in the Hosted LIMS database is aligned with current requirements defined by the COR and the Provantis Steering Team. Ensure that the vocabulary used in CEBS is aligned with current NTP requirements as defined by COR and the NTP ABC (Advisory Board for CEBS). 2.6 Bioinformatics Current issue: CEBS does not leverage bioinformatics knowledge in delivering information to users. Objective: Bioinformatics annotation and tools will be incorporated into CEBS. Desired Outcomes: Add bioinformatics capability to CEBS - align sequence IDs among transcriptomics platforms and across species. Add tools to link genes to the relevant pathway and function described in the Gene Ontology. Add tools for users to identify gene signature expression changes (signature), and to determine if the associated changes in annotated pathways and sets show significant changes in a particular gene signature. Incorporate these results in the CBS user interface. Add gene-centric queries to the user interface - permit the user to load or compute a gene signature and then to identify test articles related to the signature. Implement clustering or other unsupervised methods to permit users to combine high capacity data such as high-throughput or transcriptomics data with phenotype data such as histopathology findings for analysis. Use software packages such as Spotfire or Bioconductor for this task. Add network analysis/connectivity analysis capability to the CEBS UI, using tools such as those in the public domain. 2.7 Warehouse Current issue: CEBS is currently based on a relational database design. Objective: Build a data warehouse or appropriate system linked to CEBS to permit users to draw conclusions and find relationships across studies and data domains while still being able to drill down to access the underlying individual animal data. Desired Outcomes: Prototype and develop CEBS warehouse to capture/compute NTP conclusions and link to supporting data. Ensure that the technology selected supports real-time use by standard users. Assess the technology used to build the CEBS user interface and back-end code. If this technology requires updating to leverage new technology and to more smoothly interface with the CEBS warehouse user interface, then develop a plan for this in collaboration with NTP staff and the COR. Put this plan into place as directed by the COR. Add data mining tools to identify correlations in responses seen in CEBS and then augment a search by suggesting additional terms (e.g. if a user enters a list of test articles into CEBS, and the CEBS data mining routine has identified a test article with similar (R>.8) result, return this new test article and determine if the user would like to include / see results for this test article). Develop and test a user interface to the CEBS Warehouse. Permit the users to search conclusions at the Study, Trial, Group, and Subject or Assay Input/organ level, Gene, across studies and data domains. Permit search of Test Article by use and class. 2.8 Link-out Current issue: CEBS should be a resource to bring users to other external databases. Objective: CEBS users can be directed to other data resources relating to environmental health science from the CEBS user interface. Desired Outcome: Align CEBS with external data resources relating to environmental health science. Develop an API for CEBS to permit it to communicate with other databases containing data relevant to the environmental health sciences at the NIEHS and other ICs. Develop tools to allow the user to navigate from CEBS to government databases of environmental health sciences data and to other public databases to access relevant data. External databases may include CTD, PubChem, ToxNet, AcTOR, DSSTox, SNP databases, PubMed, GEO. Leverage data in PubChem to support structure-based queries via the CEBS user interface. 2.9 Use of Cloud for Production CEBS [Option] Option: To be exercised at the government's choosing, with at least 6 months' notice. Current issue: CEBS runs on the NIEHS network. It is possible that during the course of this contract the decision will be taken at the NIEHS to use the internet cloud to house production CEBS. Objective: Establish a cloud instance of production CEBS which complies with NIEHS/NIH regulations. Desired Outcome: If this were to become a possibility, the Contractor would provide support to prototype and install production CEBS in the cloud, monitor performance and cost, and if a decision were taken to support such an installation for CEBS, provide ongoing system administration, security, and patch management for CEBS cloud installation, with weekly reports and summaries of log files provided for the COR. Packaging and Marking Marking/Packaging shall be in accordance with industry standards unless otherwise stated. Deliveries Deliverables shall be in accordance with industry standards unless otherwise stated (Performance Requirements Summary). Deliveries shall be to the locations as specified throughout the contract. REPORTS DESCRIPTION FREQUENCY 1. Security Report Summary of failed access to CEBS private data, Hosted LIMS and log files - Weekly 2. Performance Report Summary of CEBS performance - Weekly 3. Cloud Report Progress and Summary of log files - Weekly 4. GLP Report Validation Reports - Ad-hoc 5. Security Plan As stated in contract - Annually 6. Section 508 Report As stated in contract - Annually 7. Green Purchasing Description, Purpose and Costs - Monthly 8. Key Personnel Education/Experience, Clearances, Departures, Replacements - In accordance with solicitation/contract and/or As Required/Requested Key Personnel In addition to highly experience d's computer science professionals familiar with CEBS and the LIMS in use - (i.e., Provantis and TDMSE/LDAS). The NTP requires that the Contractor staff include personnel with a master's degree in Biology, a master's degree in Statistics or Mathematics, and undergraduate degrees in Chemistry, Biology, Mathematics and experience handling similarly sized projects. Information Technology (IT) Laws, Policies, and Regulations Compliances The Contractor shall be aware and comply with all applicable federal, state and local information technology (IT) laws, regulations, and policies of the contract. 5. Anticipated Period of Performance (PoP) is as follows: Base Year 1 Aug 2013 thru 31 Jul 2014 Option Year One 1 Aug 2014 thru 31 Jul 2015 Option Year Two 1 Aug 2015 thru 31 Jul 2016 Option Year Three 1 Aug 2016 thru 31 Jul 2017 Option Year Four 1 Aug 2017 thru 31 Jul 2018 Option Year Five 1 Aug 2018 thru 31 Jul 2019 Option Year Six 1 Aug 2019 thru 31 Jul 2020 Option Year Seven 1 Aug 2020 thru 31 Jul 2021 Option Year Eight 1 Aug 2021 thru 31 Jul 2022 Option Year Nine 1 Aug 2022 thru 31 Jul 2023 If the performance under the resultant contract is delayed or suspended, the Government reserves the right in its discretion to exercise an option to extend the contract term for an additional period commensurate with the delay or suspension. 6. Other Important Consideration. The NAICS Code is 541512 with a size standard of $25.5M. The resultant contract is anticipated to be an Indefinite Delivery Indefinite Quantity (IDIQ) Commercial Contract under competitive procedures with Firm Fixed Labor Rates/Unit Prices, Fixed Priced with economical price adjustment, Labor Hour (LH) and maybe Time and Material (T&M) line items with Estimated Quantities, Not-To-Exceed Amounts and Over & Above Work line items (type of contract to be determined (TBD)) in accordance with FAR Part 12 Acquisition of Commercial Items and FAR Part 37.6 Performance-Based Acquisition. Over & Above Work (a) Definitions. As used in this clause - (1) "Over and above work" means work discovered during the course of performing that is- (i) Within the general scope of the contract; (ii) Not covered by the line item(s) for the basic work under the contract; and (iii) Necessary in order to satisfactorily complete the contract. (2) "Work request" means a document prepared by the Contractor which describes over and above work being proposed. (b) The Contractor and Contracting Officer (CO) shall mutually agree to procedures for Government administration and Contractor performance of over and above work requests. If the parties cannot agree upon the procedures, the CO has the unilateral right to direct the over and above work procedures to be followed. These procedures shall, as a minimum, cover - (1) The format, content, and submission of work requests by the Contractor. Work requests shall contain data on the type of discrepancy disclosed, the specific location of the discrepancy, and the estimated labor hours and material required to correct the discrepancy. Data shall be sufficient to satisfy contract requirements and obtain the authorization of the CO to perform the proposed work; (2) Government review, verification, and authorization of the work; and (3) Proposal pricing, submission, negotiation, and definitization. (c) Upon discovery of the need for over and above work, the Contractor shall prepare and furnish to the Government a work request in accordance with the agreed-to procedures. (d) The Government shall- (1) Promptly review the work request; (2) Verify that the proposed work is required and not covered under the basic contract line item(s); (3) Verify that the proposed corrective action is appropriate; and (4) Authorize over and above work as necessary. (e)The Contractor shall promptly submit to the CO, a proposal for the over and above work. The Government and Contractor will then negotiate a settlement for the over and above work. Contract modification(s) will be executed to definitize all over and above work. (f)Failure to agree on the price of over and above work shall be a dispute within the meaning of the Dispute clause of the contract. Phase-In In the resultant contract the Government intends to allow 60 days for phase-in. The phase-in shall be in accordance with FAR Clause 52.237-3, Continuity of Services. This period allows for the establishment of operations and infrastructure in preparation for full performance, to include preparation and submission of proposals. Phase-In shall be Not-Separately Priced (NSP) and the cost attributable with phase-in shall be included in the fixed loaded hourly labor rates. Section 508 The anticipated requirement will be in accordance with Section 508 of the Rehabilitation Act of 1973 (29 U.S.C. 794d), as amended by the Workforce Investment Act of 1998, and the Architectural and Transportation Barriers Compliance Board Electronic and Information (EIT) Accessibility Standards (36 CFR Part 1194). Green Purchasing Green requirements shall apply if applicable to deliveries of supplies and/or services, such as: Services - require electronic deliverables; limit number of hard copes; and favor black/white, double-sided, soy based ink. Non-Personal Services The resultant contract is a "non-personal services contract" as defined in the Federal Acquisition Regulation (FAR) Subpart 37.1. It is, therefore, understood and agreed that the Contractor and/or employees of the Contractor: (1) shall perform the services specified in the contract as independent contractors, not as employees of the Government, (2) shall be responsible for their own management and administration of the work requirements and bear sole responsibility for complying with any and all technical, schedule, or financial requirements or constraints attendant to the performance of the contract; (3) shall be free from supervision or control by any Government employee with respect to the manner or method of performance of the services specified; but (4) shall, pursuant to the Government's right and obligation to inspect, accept, or reject the work, comply with such general direction of the Contracting Officer (CO), or duly authorized representative of the CO, as is necessary to ensure accomplishment of the contract objectives. 7. Capability Statement / Information Sought. Respondents must provide, as part of their responses, a capability statement, answers to questions/issues, as follows: a. Respondents' opinions about the difficulty and/or feasibility of the potential requirement or proposed acquisition, possible solutions and approaches that may currently exist in the marketplace, and information regarding innovative ideas or concepts; b. Information regarding respondents': (i) staff expertise, including their availability, experience, and formal and other training; (ii) current in-house capability and capacity to perform the work; (iii) prior completed projects of similar nature; (iv) corporate experience and management capability; and (v) examples of prior completed Government contracts, references, and other related information; c. Respondents' DUNS number, organization name, address, point of contact, and size and type of business (e.g., 8(a), HUBZone, etc) pursuant to the applicable NAICS code; d. Any other information that may be helpful in developing or finalizing the OPDIV's acquisition requirements; e. Capability statements are limited to 25 pages and must be submitted electronically. Telephone and facsimile responses are not acceptable unless otherwise directed by the Contracting Officer (CO); f. The information should be provided in Microsoft Word, and Adobe PDF, including 12 font size, 8.5 by 11, 1" margins and 1.0 spacing; g. The information should be outlined and material should be organized (e.g., cover page, title, index of topics addressed, executive summary, etc.); h. Respondents' technical and administrative points of contact, including names, titles, addresses, telephone and fax numbers, and e-mail addresses; and i. Written capability statements should be submitted to Laura McGrew, Contract Specialist/Contracting Officer via email at mcgrewl@niehs.nih.gov by 4pm local eastern standard time, 25 Feb 2013. Please note the title and reference number of the announcement on all related correspondence. All questions must be directed in writing, via email to Laura McGrew. 8. Disclaimer and Important Notes. This notice does not obligate the Government to award a contract or otherwise pay for the information provided in response. The Government reserves the right to use information provided by respondents for any purpose deemed necessary and legally appropriate. Any organization responding to this notice should ensure that its response is complete and sufficiently detailed to allow the Government to determine the organization's qualifications to perform the work. Respondents are advised that the Government is under no obligation to acknowledge receipt of the information received or provide feedback to respondents with respect to any information submitted. After a review of the responses received, a pre-solicitation synopsis and solicitation may be published in Federal Business Opportunities. However, responses to this notice will not be considered adequate responses to a solicitation. 9. Confidentiality. No proprietary, classified, confidential, or sensitive information should be included in your response. The Government reserves the right to use any non-proprietary technical information in any resultant solicitation(s).
 

Web Link

FBO.gov Permalink
(https://www.fbo.gov/spg/HHS/NIH/NIEHS/NIHES2013164/listing.html)
 

Place of Performance

Address: NIEHS, P.O. Box 12233, Research Triangle Park (RTP), North Carolina, 27709, United States

Zip Code: 27709
 

Record

SN02984559-W 20130213/130211234139-f7e8fbbbb512cf852591d13c36a8f231 (fbodaily.com)
 

Source

FedBizOpps Link to This Notice
(may not be valid after Archive Date)

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