RFC_unrestricted_11_26_2014.docx

Request for Capabilities CODIS Development and Maintenance Purpose:

The purpose of this Request for Capability Statements (RFC) is to understand the industry capabilities (business size) for meeting the future development objectives of the Federal Bureau of Investigation’s (FBI’s) Combined deoxyribonucleic acid (DNA) Indexing System (CODIS.) RFC responses will assist the Government in determining potential industry sources capable of providing a sufficient technical solution based on the requirements contained in this RFC. The Government may issue a future solicitation for services for IT system development including (but not limited to) integration of Rapid DNA technology, match rarity estimation calculation, allelic dropout search enhancement, pedigree auto search performance enhancement, Popstats pedigree likelihood ratio calculations, interoperability with external application improvements, and general usability improvements. These enhancements to CODIS represent a sample of the enhancements planned for future releases of CODIS to meet the FBI law enforcement mission of helping solve and prevent violent crimes and aid in missing person/disaster victim identification. This RFC does not represent a solicitation by the Government for offers, but may be used for market research purposes to inform a potential future solicitation. This RFC is not to be construed as a commitment by the Government to issue a formal solicitation or ultimately award a contract.

Background:

CODIS allows forensic laboratories to exchange and compare DNA profiles electronically, thereby linking serial crimes to each other and to identify potential suspects by matching DNA from crime scenes to offenders. CODIS can be considered the more generic term used to describe the FBI's program of support for criminal justice DNA databases as well as the software and telecommunications backbone used to run these databases. CODIS has a three tiered hierarchy of Index Systems; the National DNA Index System (NDIS), State DNA Index System (SDIS), and Local DNA Index System (LDIS). The highest level in the CODIS hierarchy is NDIS which contains the DNA profiles contributed by federal, state and local participating forensic laboratories in the U.S. There are currently over 13 million searchable profiles from 192 NDIS participating laboratories consisting of 137 local DNA index systems and 54 state DNA index sites which include the FBI, United States Army, other Federal Agencies and Puerto Rico. In addition, the CODIS software is deployed to over 80 laboratories in over 50 international countries resulting in a sizable customer base of over 290 domestic and international laboratories. The current statistics for NDIS can be found on www.FBI.gov.

The concept behind CODIS is to create a database of the Federal and states’ offender DNA profiles and uses it to assist in linking and solving crimes for which there are no identified suspects. CODIS enables Federal, State and local forensic laboratories to exchange and compare DNA profiles electronically, thereby linking serial crimes to each other and to known offenders. CODIS uses several indices to generate investigative leads in crimes where biological evidence is recovered from the crime scene. The Offender Index contains DNA profiles of individuals convicted, arrested or detained. The Forensic Index contains DNA profiles developed from crime scene evidence.

In addition, the CODIS software facilitates the identification of human remains through the use of DNA. The National Missing Persons DNA Database (NMPDD) was initially outlined in 1996 and was funded by Congress in 1999. This program facilitates the collection and DNA typing of reference samples from relatives of missing persons which are placed in a database managed by CODIS. This program determines the DNA types of human remains in an attempt to associate those remains to missing persons. The Missing Person Index contains DNA records from missing persons. The Unidentified Human Remains (UHR) Index contains DNA records recovered from unidentified human remains. The Relatives of Missing Person Index contains DNA records voluntarily contributed from relatives of missing persons. The DNA profiles from missing persons and relatives are entered into CODIS for Pedigree Analysis. The goal of Pedigree analysis is to link an unidentified person or UHR to the missing person’s DNA. This is accomplished by generating a DNA profile from some personal item or the DNA from a biological relative. The most common type of DNA profile entered into CODIS is the STR DNA profile; however, a DNA profile cannot always be accomplished using only Short Tandem Repeats (STR) data. In some instances when the UHR are very old or degraded the STR data may not be able to be developed. Analysts are less likely to obtain STR data from older and more compromised UHR. When STR data is limited or unavailable, genetic analysts rely upon mitochondrial DNA (mtDNA) to tie unidentified persons or remains to a biological relative. This functionality was originally developed as Next Generation CODIS (NGCODIS) 6.0.

NGCODIS 7.0 replaced the legacy version of CODIS 5.7.4. The re-architecture of CODIS 7.0 was built upon the CODIS 6.0 framework and graphical user interface (GUI) standards. Due to the demands on the system through additional legislative requirements, expanding user base and the requirement to update legacy code, there was a need to re-architect the system. The CODIS 7.0 architecture is designed to support CODIS searches of the entire database of at least 50 million profiles against itself in 8 hours or less. It continues to support one-time searching, provide data exchange through uploads and messaging and manage data migration from existing systems. CODIS 7.0 completed the development effort initiated with the design of CODIS 6.0. The user friendly GUI, the use of Pedigree trees, and the robust search engine that leverages the Combined Likelihood Ratio solution for ranking and matching specimens to pedigrees has been maintained.

CODIS 7.0 continues to support import and export functions. These include the use of xml files such as CMF and Interpol formats that are used as mechanisms for input/output of data into other systems. CODIS 7.0 maintains a sound security posture by ensuring the operating environment is maintained securely through the implementation of FTP-S and the application of operating system/Commercial of the Shelf (COTS) security patches.

In the years following the development and successful deployment of NGCODIS 7.0, the CODIS Program has lacked a development funding source, despite having an existing backlog of development objectives. During this interim period additional system objectives have been and continue to be collected. The CODIS software must be developed further to continue to comply with applicable policies, as well as to adapt and comply with emergent ones. CODIS will be required to take advantage of industry technological advances through integration and interoperation. Concurrently, improvements in search capabilities and efficiencies will be needed to enable the CODIS database to continue to grow without degradation to search and other performance aspects. For more information about CODIS, please see http://www.fbi.gov/about-us/lab/biometric-analysis/codis.

System Description:

The current CODIS architecture will be evolved by following a technical roadmap that delivers incremental releases over the period of performance. Each incremental release will deliver key enhancements supporting the overall long-term FBI CODIS strategic mission. Figure 1 High-level CODIS Architecture depicts the current CODIS high level application architecture.

Figure 1 High-level CODIS Architecture The following enhancements are a subset of requirements being considered for execution under a future contracting vehicle, and comprise a sample task for purposes of response. The enhancements are listed from highest to lowest priority. This sample task has a targeted duration of two years. A new release of CODIS is anticipated to occur during each year of the period of performance. Contractor responses to this RFC shall reflect an understanding of each enhancement objectives and demonstrate the Contractor’s capabilities and experience required to deliver each enhancement. The Contractor response shall describe the plan/capability to deliver all of the following enhancements within the two year period of performance for this sample task.

Enhancement #1: Merge Rapid DNA Prototype functionality with the current CODIS release.

Enhancement Background Rapid DNA, or Rapid DNA Analysis, describes the fully automated (hands free) process of developing a CODIS Core STR profile from a reference sample buccal swab. The “swab in – profile out” process consists of automated extraction, amplification, separation, detection and allele calling without human intervention. The goal of the FBI’s Rapid DNA initiative is to develop commercial instruments capable of producing a CODIS-compatible DNA profile within two hours and to integrate those instruments effectively within the existing CODIS structure to search unsolved crimes while an arrestee is in police custody during the booking process. The FBI has been working on how to integrate this technology first into CODIS laboratory operations and then into police agency booking locations. See http://www.fbi.gov/about-us/lab/biometric-analysis/codis/rapid-dna-analysis for more information on rapid DNA.

In order to validate the FBI and various law enforcement stakeholders understanding of the requirements related to using a rapid DNA (R-DNA) instrument in a booking station environment, the FBI created a prototype application that provides interoperability between an R-DNA instrument and the CODIS application. A software application referred to as the “CODIS Rapid Workstation (CRW)” was created as part of the Rapid DNA Prototype. See Figure 2 CRW Architecture for an overview of the CRW architecture.

Figure 2 CRW Architecture The CRW automatically validates and processes files (Rapid Common Message Format (CMF)) produced by R-DNA instruments to enroll and search specimens in the CODIS database. The CRW application is configurable to control what users, specimen categories, kits, and loci/alleles are acceptable. The CRW application was developed using C# communicating with a MS SQL Express database installed on a standard Windows client workstation.

As part of the Rapid DNA Prototype, the CODIS server application was modified to provide services to process the specimen enrollment requests (SERs) and rapid search requests (RSRs) sent by the CRW application. If a hit occurs when processing the RSR, a hit notification response is returned to the CRW. See Figure 3 CODIS Rapid Server Architecture for an overview of the CODIS Rapid Server architecture.

Figure 3 CODIS Rapid Server Architecture The CODIS application was also modified to allow users to rapid enable single source forensic profiles by entering casework metadata within the CODIS Analyst Workbench (AWB) user interface. The AWB also allows users to view arrestee metadata that was provided in the SER message. The CODIS server application is configurable to control the agencies that are allowed to submit SERs and RSRs. The CODIS server performs various validation rules to determine if the requests are acceptable. These SERs and RSRs are generated automatically and submitted to CODIS using Representational State Transfer (REST) Application Programming Interface (API) via HTTPS. Based on various business rules, specimens enrolled at SDIS are then transmitted to the National DNA Database (NDIS) for enrollment and searching. See Figure 4 CODIS Laboratory Hierarchy for a description of the CODIS laboratory hierarchy including the new local Rapid DNA Index System (RDIS) tier composed of booking agencies using R-DNA instruments.

Figure 4 Proposed CODIS Laboratory Hierarchy The Rapid DNA Prototype will send Rapid Hit Notification (RHNs) to the Criminal Justice Information Services (CJIS) Message Manager (CMM) in order to inform local law enforcement agencies of a hit between an arrestee being enrolled and a rapid enabled forensic profile.

CODIS is widely used by law enforcement agencies in both the United States and in over 50 international countries. The Government is actively involved with various domestic and international agencies to establish standards for biometric DNA data exchange. The FBI CODIS program is a stakeholder participating in the governance of the biometric exchange formats used by FBI CJIS Division, National Institute of Standards and Technology (NIST), National Information Exchange Model (NIEM), and International Organization for Standardization (ISO).

Requirements are still evolving related to messaging between the State CJIS Systems Agency (CSA), the CODIS Server, and the CJIS Message Manager. See https://www.fbibiospecs.org/ebts.html for more information on the FBI CJIS Electronic Biometric Transmission Specification (EBTS). See http://biometrics.nist.gov/cs_links/standard/ansi_2012/Update-Final_Approved_Version.pdf for more information regarding the NIEM Type 18 DNA record.

In order to protect data in transit, the Rapid DNA Prototype SER/RSR interface utilizes Hypertext Transfer Protocol Secure (HTTPS). This ensures that all communications will be secured by the Transport Layer Security (TLS) protocol, which underlies HTTP and uses asymmetric cryptography to encrypt and decrypt data. The use of encrypted requests and responses allows for secure transmission over both secure (e.g. CJIS WAN/SEN (Shared Enterprise Network)) or non-secure (i.e. public internet) networks. The SER/RSR interface employs application layer security to authenticate the entity submitting SERs and RSRs. The external system must supply its X.509 certificate with each request. The X.509 certificate in combination with other request contents (detailing the instrument and user that generated the supplied genetic data) allows for the destination Rapid Service to programmatically ensure that such transactions are permitted with the requesting entity. See Figure 5 Rapid DNA Messaging Co-ops for a description of the overall Rapid DNA messaging flow.

Figure 5 Rapid DNA Messaging ConOps

Enhancement Description Merge Rapid DNA Prototype The primary objective of this enhancement is to merge the Rapid DNA Prototype functionality with the CODIS baseline application functionality. The capability to integrate R-DNA instruments with CODIS is considered a major enhancement to the CODIS application. The resulting application needs to be thoroughly tested to meet critical performance requirements. The CODIS application is required to process SERs and RSRs concurrently while operations such as processing uploads and performing autosearches are occurring in parallel. It is critical that SERs and RSRs containing a single specimen be processed in less than one minute when searching at least one million rapid enabled single source forensic profiles at high stringency with no missed STR loci. The current performance requirement for processing uploads and performing autosearches at NDIS must be satisfied while concurrently processing SERs and RSRs.

The current CODIS maintenance code base and the Rapid DNA Prototype code base are under configuration management (CM) control by using the Microsoft Team Foundation Server (TFS). Separate branches in TFS exist for the maintenance code base and the Rapid DNA prototype code base. The Contractor will be required to use MS TFS for source code control in order to create the new version of CODIS that includes all existing functionality and the rapid DNA functionality as well as the functionality for the other enhancements identified within this RFC. The Contractor is expected to use continuous integration to detect defects early in the software development life cycle (SDLC). Continuous integration refers to the practice of automatically performing regression tests as new code is checked into the source code repository, so that developers immediately know if someone “broke the build”.

The Rapid DNA Prototype has the following capabilities that need to be merged with the main CODIS code base:

1. Process Specimen Enrollment Requests (SERs) at SDIS from CRW

2. Process Rapid Search Requests (RSRs) at SDIS from CRW

3. Process Specimen Enrollment Requests (SERs) at NDIS from SDIS

4. Process Rapid Search Requests (RSRs) at NDIS from SDIS

5. Send Rapid Match Messages from NDIS to SDIS and LDIS

6. Update Options to Configure RSR Processing

7. Update Options to Configure Autoexecution of SERs and RSRs

8. Update Options to Configure Specimen Categories to be SER Acceptable

9. Update Options Reports due to Rapid Prototype Integration

10. Update Metadata Entry to Enter Casework Metadata and Display Arrestee Metadata

11. Update Specimen Manager to Rapid Enable Forensic Specimens

12. Update Upload to Process Specimens with Rapid Information

13. Create New Reports in CODIS to include Rapid DNA Information

14. Existing automated unit tests need to be merged

15. Update CODIS Server Installation program to Support Rapid DNA Functionality Create CMM Prototype The CMM is currently in a conceptual phase. Requirements for the CMM are being elicited from law enforcement stakeholders. A prototype version of the CMM service needs to be created to facilitate the elicitation and validation of requirements. The CMM service will process RHNs sent by the CODIS SDIS server. The CMM service will generate Unsolicited DNA Notifications (UDNs) to local law enforcement agencies informing them of the hit between an arrestee currently in custody at a booking agency and a rapid enabled forensic specimen from a crime of special concern. Mockups of the UDN messages need to be created to validate law enforcement stakeholder requirements. These UDN messages are envisioned to be similar to messages sent by the Interstate Identification Index (III) system or the National Crime Information Center (NCIC) system related to watches and warrants. Collaboration with law enforcement stakeholders is needed to define interface specification documents (ISDs) and interface control documents (ICDs) that will be used for messaging between federal, state, and local law enforcement agencies in order to meet the FBI rapid DNA mission objectives.

Test Rapid DNA Functionality The CODIS application needs to be thoroughly regression tested when merging the Rapid DNA Prototype functionality. Automated unit tests shall exist for new functionality being added to the CODIS baseline application and for the CRW application. System testing of both the legacy functionality and the new Rapid functionality shall be performed.

Usability Improvements to the CRW While the current Rapid DNA Prototype has been developed using an Agile SDLC over the past two years, additional usability improvements are anticipated for the CRW. The CRW application is intended to be used by law enforcement agents with no CODIS or DNA experience and minimal IT knowledge. It is critical that the CRW application be very simple to use with minimal training. This enhancement includes the effort to conduct usability reviews including demonstrations of the new CODIS application to elicit usability feedback from law enforcement stakeholders. The Government will identify and approve all law enforcement stakeholders that need to participate in these usability reviews.

Maintainability Improvements to the CRW Prior to deployment to booking agency production environments, enhancements to the CRW are needed to improve maintainability. Error handling and logging shall be improved to facilitate helpdesk troubleshooting. It is likely that the Operations helpdesk will not be able to remotely access the CRW at booking agencies not connected to the CJIS WAN. CRW error messages shall clearly identify the cause of the error and provide clear direction to the user if the helpdesk needs to be contacted. The CRW shall support a debug mode that creates detailed error logging information for the helpdesk and tier 3 support analysts to investigate problems.

This enhancement includes the effort to analyze ways to proactively monitor the workstation environment to alert the user if insufficient hard disk space or memory is available. Since the CRW is using a SQL Express database, analysis is needed to determine database backup COTS tools and disaster recovery instructions. Requirements related to data retention on the CRW are still evolving.

Installation Packaging of the CRW In addition to updating the CODIS server application to include rapid DNA functionality, the CRW application shall be packaged in a manner that allows law enforcement users at booking agencies with minimal IT experience to install the CRW application. A user guide, online help, release notes, and installation kit shall be created for the CRW. The CODIS application is supported on multiple versions of the Windows operating system including Windows Server 2008/2012 R2 64 bit, Windows 7, and Windows 8 64 bit. The CODIS application supports multiple versions of the Microsoft SQL Server Database including SQL Server 2008/2012 R2 64 bit and SQL Server Express. Both the CRW application and the CODIS application need to be packaged to allow easy installation and maintainability on all supported platforms. This enhancement includes the effort to support the latest version of the MS Windows operating systems and MS SQL Server databases.

Rapid Messaging Interface and Security Enhancements This enhancement includes the effort to create and evolve the messaging interface standards used to support the Rapid DNA mission. As usability reviews and prototype demonstrations are conducted, new requirements are anticipated and existing requirements may need to be modified. The Rapid message interface specifications (Rapid CMF, Specimen Enrollment Request, Rapid Search Request, and Rapid Hit Notification) will need to be updated based on emergent requirements. Analysis is needed to maintain conformity with the NIEM biometrics message standards and the EBTS message standards.

This enhancement includes effort to collaborate with CJIS to determine acceptable security measures for messaging between CODIS and CMM. Analysis is needed to determine how the CMM service can authenticate the identity of each CODIS lab that is sending RHN messages. Even though the current Rapid DNA Prototype is using PKI/X.509 certificates, changes to security enhancements related to Rapid DNA messaging are anticipated. Interface control documents related to Rapid DNA messaging shall be updated due to evolving security requirements.

Performance Improvements for Rapid Messaging While this enhancement is primarily focused on merging the existing Rapid DNA Prototype functionality, the capability to process SERs and RSRs could be used in the future to improve the existing CODIS incremental upload process and the incremental Autosearch process by providing faster messaging to synchronize and search specimens within the CODIS lab hierarchy. For reference purposes, the NDIS database is growing at a rate of about one million (1,000,000) specimens per year. The design of the Rapid DNA messaging architecture shall be scalable to accommodate the increasing size of the NDIS database. This enhancement includes effort to improve the performance of processing Rapid DNA related messages at all CODIS lab levels.

Rapid DNA Documentation All functional specifications, architecture documentation (SSAD), system design documents (SDDs), database design/model documentation, default data, test cases, online help, CBTs, and training materials shall reflect the new rapid DNA functionality. The CODIS ConOps must be maintained to reflect new functionality. Interface specifications and interface control documents must be maintained. Installation kits and release notes shall be available for all new CODIS releases.

Contractor Capability Requirements (See attached Capabilities response table)

1. The Contractor shall have experience with the latest version of MS Visual Studio (C#, VB.Net, and C++) and the .Net Framework.

2. The Contractor shall have experience with the latest version of MS SQL Server including the Enterprise and Express editions.

3. The Contractor shall have experience with MS Windows Communication Foundation (WCF).

4. The Contractor shall have experience with creating automated unit tests (i.e. NUnit, CSUnit, etc.) for .Net solutions that are invoked as part of a continuous integration (CI) strategy as new builds are created. Experience with automated user graphical user interface (GUI) testing is highly desirable.

5. The Contractor shall have experience with using automated tools to perform load testing to simulate a large number of users simultaneously using an application based on a service oriented architecture (SOA).

6. The Contractor shall have experience in both concurrency testing and performance testing.

7. The Contractor shall be able to create realistic test datasets with synthetic DNA profiles using allelic population database frequencies.

8. The Contractor shall be able to create test scenarios reflecting typical CODIS operations that occur in parallel in order to meet concurrency requirements.

9. The Contractor shall have MS TFS experience.

10. The Contractor shall have experience in managing and merging code branches with no disruption and/or degradation of existing code.

11. The Contractor shall have experience in continuous integration in order to detect defects early in the software development life cycle (SDLC).

12. The Contractor shall demonstrate they have experience creating screen mockups, interactive prototypes, and conducting usability reviews.

13. The Contractor shall have current human factors engineering experience to guide the design of the CODIS application so that user productivity is efficient while minimizing the need for CODIS application training.

14. The Contractor shall have installation packaging experience using Windows Installer (MSI) technology and experience releasing application updates (patches, hotfixes, etc.).

15. The Contractor shall be able to describe a technical approach to maintaining the CRW at booking agencies not connected to the CJIS SEN with minimal assistance from the Operations helpdesk.

16. The Contractor shall be able to create realistic test environments for each CODIS release being developed reflecting the types of environments that will be used in the production environment for CODIS operations.

17. The Contractor shall demonstrate the capability to create realistic system (end-to-end) test cases that exercise the CODIS functionality when sending SERs/RSRs from a booking agency to SDIS and NDIS.

18. The Contractor shall have experience using virtualization and supporting large SQL Server databases in order to adequately test rapid DNA functionality to meet the FBI rapid DNA mission objectives.

19. The Contractor shall be able to describe how the capabilities to process SERs and RSRs could be used in the future to improve the existing CODIS incremental upload process and the incremental Autosearch process.

20. The Contractor shall have experience implementing scalable messaging solutions that are reliable and secure.

21. The Contractor shall have experience in developing XML schema (XSDs) used to define interface specifications.

22. The Contractor shall have experience with secure messaging using industry standard web services.

23. The Contractor shall have experience with HTTPS and Public Key Infrastructure (PKI) using X.509 certificates.

24. The Contractor shall have experience in security testing to verify the security posture of the CODIS application is constantly maintained as the CODIS application is enhanced.

25. The Contractor shall be able to describe a technical approach for merging Rapid DNA Prototype functionality with the CODIS main code base while verifying that software quality is not compromised.

26. The Contractor shall be able to describe a technical approach to incrementally delivering business value using an Agile SDLC.

Enhancement #2: Develop Match Rarity Enhancement (MRE).

Enhancement Background The current CODIS 7.0 SP6 release has the capability to calculate a moderate match estimate (MME) for specimens. The MME value is an indicator of how rare the specimen profile is. Specimen profiles that are common could result in the creation of fortuitous matches that degrade the productivity of CODIS users and negatively impact the CODIS mission. The MME value shown in Specimen Manager is the same value that can be calculated using the Popstats Match Estimation calculation when evaluating loci at moderate stringency. The current MME calculation is based only on the 13 core NDIS loci being evaluated at moderate stringency. The current MME calculation is limited to using only the NIST population database frequencies for the “Combined” population group with a constant theta value.

Enhancement Description This enhancement to calculate an MRE value is in addition to the capability of calculating the MME value. The MRE calculation will be configurable per specimen category. Users will be able to select what STR loci will be calculated at a specified stringency (moderate or high) per STR locus using a user specified population database, population group, and theta value per specimen category. The MRE value will be shown in Specimen Manager, Specimen Details, and STR Data Entry/Combined Data Entry. The MRE value will automatically be calculated when adding and modifying specimens with STR loci. The MRE value will be automatically calculated when processing uploads based on the configuration settings at the processing lab. SDIS and NDIS CODIS administrators will have the ability to configure both an MME and MRE threshold value for upload acceptance. If specimens do not meet the configured MRE upload threshold, then the specimen should be rejected and shown on the upload recon report with a clear indicator for why the specimen was rejected.

This MRE value will allow users greater control over what specimens should be marked for inclusion in uploads. The MRE value could also be used to control what specimens are evaluated during searches.

This enhancement includes the effort to update test datasets to use an increased number of loci such as all GlobalFiler or PowerPlex Fusion loci. Automated unit tests shall be created to verify the MRE value by comparing to the Popstats Match Estimation calculation results when using multiplex kits and varying locus stringency, population databases, population groups, and theta values.

Contractor Capability Requirements (See attached Capabilities response table)

1. The Contractor shall have expertise with DNA forensic statistical calculations used to determine human identity.

2. The Contractor shall be knowledgeable of how population database frequencies impact random match probability and how the number of expected matches is calculated when searching at different stringencies and when allowing a specified number of STR loci to miss.

3. The Contractor shall be able to independently validate MRE calculation results for scientific and statistical accuracy.

4. The Contractor shall be able to describe a testing strategy for MRE functionality.

5. The Contractor shall be able to update relevant CODIS design documentation to explain how the MRE value is calculated and how CODIS business rules are impacted by the MRE capability.

Enhancement #3: Allelic dropout search capability.

Enhancement Background The current version of CODIS allows users to specify various identity search criteria to control what matches are returned such as the following:

1. minimum number of STR loci required to report a match

2. number of missed STR loci

3. the search stringency per STR locus The CODIS search engine is an in-memory database that organizes specimen data into a tree-structured index using naturally occurring patterns and clusters within the DNA data to support efficient search and retrieval strategies of DNA data. The CODIS search engine supports logarithmic scale up and parallelization.

Enhancement Description The allelic dropout search enhancement is intended to augment the existing identity search capabilities of CODIS by allowing the user(s) to specify a “floating number” of STR loci that are allowed to match at moderate stringency when all STR loci are being evaluated at high stringency. This enhancement works in conjunction with the MRE enhancement. When configuring specimen categories to calculate MRE, users will have the option to specify that loci designed as partial or loci with more than 2 alleles should automatically be evaluated at moderate stringency regardless of the specified locus search stringency. As part of the effort to implement this enhancement, the MRE calculation will need to be updated to evaluate partial loci and loci with more than 2 alleles at moderate stringency based on the configuration of the specimen category in Options.

The need for this search capability is based on the increasing size of the CODIS database and the need to reduce fortuitous matches. As of 10/1/2014, the NDIS database contains over 14 million specimens including offender, arrestee, and forensic profiles. Many of these specimen profiles were added to CODIS years ago before the capability to designate a locus as partial existed. This search enhancement will allow for searches to be performed while accommodating for the possibility of allelic dropout without needing to search all specimen loci at moderate stringency. The number of STR loci allowed to match at moderate stringency is cumulative of the number loci matching at moderate stringency due to being partial or having more than two alleles and the number of loci matching at moderate stringency due to the typical CODIS search evaluation rules. If the number of loci matching at moderate stringency is greater than the specified number in the search configuration, then the match will be filtered (not reported).

This enhancement requires that the match details module be updated to indicate the new search setting being used. Match messages will need to include this information. The match details and Autosearch reports need to reflect this new setting. Existing match information will need to be migrated in a manner to accommodate this new search criteria option. Backward compatibility with the previous of CODIS will need to be maintained when introducing this new identity search capability.

Performance testing must be done to verify that existing performance objectives related to identity searches and autosearches are satisfied after changing the CODIS search engine.

Based on SME analysis, CODIS searching capabilities may be further enhanced in the future by implementing a threshold based identity search configuration. See Subject Matter Expertise (SME) Support section for further details on threshold based identity searches.

Contractor Capability Requirements (See attached Capabilities response table)

1. The Contractor shall possess bioinformatics expertise (recent within the last year) to understand how stringency and missed STR loci search configuration settings impact search results and the CODIS search engine (Next Generation Indexing Search Service (NGISS)) performance.

2. The Contractor shall be knowledgeable in multi-dimensional and tree structured indexing methods to support future optimizations to the CODIS search engine.

3. The Contractor must have an understanding of naturally occurring patterns in DNA genotypes and haplotypes in order to support efficient, high performance search and retrieval strategies of DNA profiles.

Enhancement #4: Interoperability Service Enhancements.

Enhancement Background The current CODIS application does not expose any services that can be used by external applications. Commercial DNA outsourcing vendors wishing to exchange DNA profiles with the CODIS application use the CMF 3.2 Interface Specification to create files in a format that can be processed by the CODIS application. CODIS users import files by browsing and selecting files to import within the AWB user interface.

Enhancement Description After merging the Rapid DNA Prototype code, CODIS will have services to process specimen enrollment requests and rapid search requests. This enhancement is intended to improve CODIS interoperability with other external COTS applications such as laboratory information management systems (LIMS) and expert systems. This enhancement will create and expose new services that can be used by external applications to automate common CODIS operations in order to improve specimen throughput. The following services will be created within the scope of this enhancement:

1. Specimen enrollment service – allows users to add new specimens including all supported genetic technologies (STR, Y-STR, and mtDNA) to CODIS

2. Specimen modification service – allows users to modify an existing specimen in CODIS

3. Specimen delete service – allows users to delete a specimen from CODIS based on a specified lab ID and specimen ID

4. Specimen existence service – allows users to determine if a specimen exists in CODIS based on a specified lab ID and specimen ID

5. Identity search service – allow users to provide a target specimen with any combination of genetic technologies (STR loci, mtDNA, and Y-STR loci) to search CODIS and return matches. This identity search service is envisioned to work similarly to the existing remote search capability that allows users to specify a search configuration that is validated against the processing lab’s business search constraints.

Interface specifications and interface control documents shall be created to facilitate the adoption of these CODIS services. The ICD shall describe how user authentication and nonrepudiation will occur when using these new CODIS services. The confidentiality and integrity of CODIS data cannot be compromised. A clear audit trail in CODIS shall exist for all actions performed via these new services.

These new services must be thoroughly tested by creating test harnesses to simulate external applications invoking the CODIS services. Automated unit tests shall be created to support regression testing of this new functionality.

Contractor Capability Requirements (See attached Capabilities response table)

1. The Contractor shall have experience creating interface specifications and interface control documents to facilitate the adoption of industry standard services.

2. The Contractor shall have experience creating secure services that authenticate users, protect confidentiality, and maintain integrity of law enforcement sensitive data.

3. The Contractor shall have experience testing services accessed over both protected and unprotected networks.

4. The Contractor shall have experience creating automated unit tests that validates service layer business functionality.

Enhancement #5: Pedigree Autosearch Performance Improvement.

Enhancement Background CODIS currently has the capability to perform pedigree autosearches. During a pedigree Autosearch, all pedigrees in the selected target index are evaluated against the specimens in the selected candidate indexes to provide rank results. The current pedigree Autosearch algorithm is single threaded. The CODIS search engine is multithreaded but the process to Autosearch pedigrees is limited to a single thread.

Enhancement Description The objective of this enhancement is to reduce the time to complete pedigree autosearches through multithreading by leveraging all available processors on the CODIS server. As part of the effort to accomplish this enhancement, the pedigree Autosearch metrics shall be improved by tracking the amount of time required to search each pedigree included in the Autosearch. The time required to search a pedigree during the last pedigree Autosearch should be readily visible to the user. Users need the ability to determine what pedigrees are taking the most time to evaluate during an Autosearch. This information will allow users to determine if more typed nodes or genetic technologies need to be added to the pedigree to improve search performance. This information will allow users to identify pedigrees with only distant relatives or overly complex pedigree structure that need to be improved in order to reduce the time to search.

Performance testing shall be performed to determine if the pedigree Autosearch performance requirements are being satisfied. All changes to the CODIS search engine shall require regression testing to determine that the expected rank results are being returned. Automated unit tests shall be created for pedigree Autosearch functionality.

CODIS system design documents (SDDs) such as the AutoSearcher SDD and NGISS SDD shall be updated to reflect the current design.

Contractor Capability Requirements (See attached Capabilities response table)

1. The Contractor shall possess bioinformatics expertise (recent within the last year) to understand how the number of typed and untyped pedigree nodes impact pedigree search results and the CODIS search engine (Next Generation Indexing Search Service (NGISS)) performance.

2. The Contractor shall have recent (within the last year) experience in multi-threaded programming using multi-core processors.

3. The Contractor shall have an understanding of creating pedigree search algorithms for missing person identification that are logarithmically scalable.

4. The Contractor shall have an understanding of how different genetic technologies (STR, mtDNA, and Y-STR) impact missing person identification.

5. The Contractor shall have general experience with application performance monitoring and tuning when using large in-memory databases.

6. The Contractor shall be able to describe a technical approach to reducing pedigree Autosearch time. The technical approach shall consider implications to pedigree consistency checks needed to initialize the pedigree for evaluation during searching.

7. The Contractor shall be able to create valid test data using synthetic pedigrees with a user specified number of typed nodes that are genetically consistent across all genetic technologies.

Enhancement #6: Popstats Pedigree Calculation.

Enhancement Background The current CODIS Popstats module has the capability to perform the following calculations:

· Forensic Single Sample

· Forensic Mixture

· Paternity (Reverse and Trio)

· Kinship

· Match Estimation

· Partial Match The current CODIS application has the capability to perform pedigree searches that return ranks involving a pedigree and a candidate specimen. The ranks returned in CODIS include an STR LR, mtDNA LR, Y-STR LR, and Combined LR (CLR) value indicating the strength of the relationship between the pedigree and candidate specimen.

The rank LR values shown in CODIS use a government proprietary method that is not intended for legal/court reporting purposes.

Enhancement Description This enhancement shall update the existing CODIS Popstats capabilities to include legal/court reportable pedigree likelihood ratio calculations (STR LR, mtDNA LR, Y-STR LR, and Combined LR). The Government shall provide the pedigree likelihood ratio calculations as GFI. These new pedigree likelihood calculations are not the same as the existing LR calculations performed when doing pedigree searches in CODIS.

The Popstats pedigree calculation shall allow users to retrieve an existing pedigree from the CODIS database. Users can retrieve the candidate specimen that ranked to the unknown missing person node of the pedigree. Users can also keyboard enter or import/export the candidate specimen. The Popstats pedigree calculation shall be limited to one candidate specimen for a specified unknown missing person node even if the pedigree contains multiple unknown missing person nodes. Users shall be able to specify the Popstats frequency database, population group, and theta value to use. Users shall be able to specify the genetic technologies to be calculated. A Popstats pedigree calculation report shall be available that shows the following information (but not limited to):

1. Graphical representation of the pedigree reflecting typed, untyped, and missing person nodes

2. The lab ID, specimen ID, and genetic information for all typed nodes in the pedigree

3. The lab ID, specimen ID, and genetic information for the candidate specimen

4. The pedigree calculation parameters

5. A user specified comment for the pedigree

6. The pedigree calculation results for all genetic technologies If the candidate specimen is not a feasible rank (LR < 1) to the pedigree, then the user shall receive a clear message/results that the candidate specimen is not related to the pedigree.

The CODIS AWB application shall allow users to send pedigrees from Pedigree Manager, Pedigree Designer, and Rank Details to Popstats in Pedigree Calculation mode.

This enhancement includes the effort to conduct usability reviews including demonstrations of the new Popstats pedigree calculation and associated report to elicit usability feedback from CODIS users.

The system design documents, Popstats Functional Specification, online help, CBTs, and ILT materials shall describe this new functionality.

Automated unit tests shall be created to support regression testing of this enhancement.

Contractor Capability Requirements (See attached Capabilities response table)

1. Even though the Government is providing the pedigree likelihood calculation algorithm as GFI, the Contractor shall be knowledgeable of kinship statistics in order to support the implementation and validation of the pedigree likelihood calculation.

2. The Contractor shall have the expertise to implement and validate these new Popstats pedigree LR calculations.

3. The Contractor shall be knowledgeable of mutation models and the impact of mutations (STR, mtDNA, and Y-STR) to pedigree likelihood calculations.

4. The Contractor shall be knowledgeable of the impact of genetically linked loci (not independent) on kinship calculation results.

5. The Contractor shall be knowledgeable of approaches to determining identity by descent (IBD) for both genotypes and haplotypes.

6. The Contractor shall be knowledgeable of the current SWGDAM guidelines for both mtDNA and Y-STR interpretation. For more information on statistical calculations for haplotypes refer to Scientific Working Group on DNA Analysis Methods (SWGDAM) Interpretation Guidelines for Mitochondrial DNA Analysis by Forensic DNA Testing Laboratories and Scientific Working Group on DNA Analysis Methods (SWGDAM) Interpretation Guidelines for Y-Chromosome STR Typing.

Enhancement #7: Combined Data Entry.

Enhancement Background The current CODIS application uses separate modules to perform STR/Y-STR data entry, mtDNA data entry, and specimen metadata entry.

Enhancement Description In order to improve the usability of the CODIS application, this enhancement is intended to merge all specimen data entry capabilities into a single module/user interface that operates as an integral part of the AWB. Each genetic technology and metadata shall be shown on a separate tab within this Combined Data Entry (CDE) module. No loss of functionality shall occur when creating this new module. The CDE module shall support missing person metadata, custom missing person metadata, casework metadata, and arrestee metadata.

The current CODIS data entry modules are limited to editing a single specimen. This enhancement includes the effort to support multi-specimen navigation such that users can select multiple specimens for editing in Specimen Manager when invoking the CDE module. This enhancement includes the effort to update all existing CODIS functionality to invoke the new CDE module rather than the legacy data entry modules. This enhancement includes the ability to drag/drop specimens from any specimen grid in CODIS (Searcher, Popstats, and Specimen Manager) to the CDE module.

Online help, CBTs, and ILT materials shall need to describe this new functionality.

Automated unit tests shall be created to support regression testing of this enhancement.

This enhancement includes the effort to create screen mockups and conduct usability reviews of the proposed new user interface. This enhancement requires that documented Graphical User Interface (GUI) standards be followed. Human factors engineering design principles shall be followed to guide the design of this user interface enhancement to improve user productivity and reduce the need for CODIS application training.

Contractor Capability Requirements (See attached Capabilities response table)

1. The Contractor shall have current experience developing feature rich GUI interface applications using MS Visual Studio and the .Net framework. Experience with MS Windows Presentation Foundation (WPF) is desirable.

Enhancement #8: Specimen Import.

Enhancement Background The current CODIS application processes CMF 3.2 import files to add and modify specimens with STR/Y-STR loci in the CODIS database. CMF files are in a standard XML format.

Enhancement Description The Government will provide a new CMF 3.3 interface specification as GFI that allows users to specify the NCIC#, ViCAP#, and partial locus indicator. The CODIS STR Import application shall be updated to support the new fields in CMF 3.3.

This enhancement also includes the effort to configure CODIS to automatically process both STR and mtDNA import files in a specified file directory. The CODIS Options module shall allow users to specify a directory to “watch” to trigger automatic importing of files in this directory. Once the import file is processed, the file shall be moved to a different directory that is also configurable in Options. The Options module shall allow the user to specify an assign to user for the specimens in the CMF file. This import file watcher capability is in addition to the existing import functionality.