Attachment3SOWAugust2009.pdf

Attachment # 3 – August 13, 2009 Page 1

Statement of Work

Operation and Maintenance of the Biological Data Processing System

A. Overall Objectives

The purpose of this contract is to provide software engineering, database design, commercial-off-the-shelf product support, mathematical and statistical support for the Information Technology Branch (ITB). This includes design and or/redesign of application programs as well as initial coding, revising, testing, documenting, operating and maintaining all custom software. The Contractor will work at their own location, but frequently be required to attend meetings with Contracting Officer’s Technical Representative(s) (COTRs) at Government offices in Frederick and Rockville, MD.

Data communication between the Contractor's site and the NCI- Frederick, located in Frederick, MD will be the responsibility of the contractor. Technical support for troubleshooting and maintaining communications with NCI-Frederick computers will be available to the contractor, but the contractor will be responsible for obtaining and maintaining adequate Internet services.

The database operates in an Oracle RDBMS environment on a HP Integrity Server rx8620 using the VMS operating system. The software suite spans several generations of computing technologies. These technologies include:

host based programs running in the VMS environment web-based applications running under Microsoft Windows IIS/ASP web-based applications running under Java2 Enterprise Edition CambridgeSoft Enterprise/Desktop Suite

Figure 1:

Environment Tools

Oracle10G SQL*Net, PL/SQL

VAX/VMS Digital Command Language (DCL), Module Management System (MMS), Code Management System (CMS), TCP/IP

Windows (MS, NT) Visual Basic, Active Server Page, HTML, Adobe PDF Professional

JDK 1.5.0, WebLogic 9.2.0 JBuilder X, Java Server Page (JSP), Extensible Markup Language(XML), Java 2 Enterprise Edition (J2EE), Concurrent Versions System (CVS)

Cambridgesoft Enterprise Suite E-notebook, BioAssay, BioSAR, Biological Inventory

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The goal of the ITB is to consolidate this wide variation of technologies into a consistent architecture. The contractor shall be knowledgeable in the following products and technologies and shall migrate legacy applications from these technologies to the J2EE and/or CambridgeSoft architecture using programming languages and tools listed below:

Tools

SVG, XSLT, JavaScript, HTML, CSS, EJB, Struts, Hibernate, BEA Weblogic Server, Tomcat, Oracle RDBMS

B. Description of Work

1.0 Software Development

Independently, and not as an agent of the Government, the Contractor shall perform the services described below. The Contractor shall provide qualified personnel, material, equipment and facilities not otherwise provided by the Government during performance of this contract. The Contractor shall perform work on all phases of the software life cycle, including requirements analysis, system design, software development, testing, and implementation. The contract will require that solutions be implemented in a wide range of software environments (see figure 1) using many different programming tools.

1.1 General Principals for Software Development (includes new software and upgrades to existing software)

1.1.1 All software databases shall be compliant with current and future ITB data standards.

1.1.2 All applications and data shall be designed to assure integration and interoperability.

1.1.3 All applications shall be delivered in a timely fashion determined by the Contracting Officer’s Technical Representative.

1.1.4 All applications shall be user-friendly and meet the needs of staff as outlined during the project development.

1.1.5 All new software shall be compliant with section 508 of the Rehabilitation Act.

1.1.6 The Contractor shall design, develop and deliver software applications to address scientific, operational, and administrative needs. These applications shall be developed utilizing best practices and methodologies.

2.0 Software Testing

2.1 General Principals regarding Software Testing:

2.1.1 The Contractor shall develop and implement a process to validate that all new custom software or custom software upgrades perform as designed and do not adversely impact other custom applications.

2.1.2 The Contractor shall develop and implement processes and procedures to maintain the integrity and quality of new data.

3.0 Documentation

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3.1 The Contractor shall develop, update and maintain all system documentation including technical system documentation.

4.0 Software Maintenance

4.1 Maintenance of all current and future applications is critical for continuous successful operations. Maintenance includes, but it not limited to the following:

Corrective Maintenance - Correct any identified bugs in the system.

Preventive - Modify system to maintain both effectiveness and reliability.

Adaptive - Provide any modifications required to accommodate physical changes in the software environment. These might include, adapting to a new network topology, or reconfiguration to accommodate a new release of

ORACLE.

Perfective Maintenance - Add new functions to accommodate change in the requirements.

Structural Reengineering – Modify systems to take advantage of new technology and improve software readability and modularity.

4.2 The Contractor shall perform all periodic operational tasks required to maintain the proper level of performance and integrity of all systems. This shall include all design and/or redesign of system program, verification and validation; initial coding; revision; testing; debugging; documentation for all system software.

4.3 All maintenance to the BDPS system shall be planned and executed with appropriate consideration paid to security issues.

4.4 The Contractor shall deploy all source code and documentation to the application server.

5.0 Transition: Phase-In/Phase-out

The transition plan is to define the required activities and to lay out a schedule as to how the current organization will transition to a new contractor.

5.1 Phase-In. The incumbent Contractor shall assist the successful contractor in the transition of this contract. The transition period shall consist of the final 30 calendar days of the current contract. On the 31 calendar day, the successful contractor shall assume all responsibilities. The following shall apply only to a transition wherein the incumbent contractor is not the successful contractor.

5.1.1 The incumbent Contractor shall provide the successor with detailed briefings regarding the structure of the database tables and software required continuing maintenance and operation of systems developed under this contract.

5.1.2 The incumbent Contractor shall transfer all project materials, to include but not limited to, source codes, course files, computer programs, project materials, documentation, operating manuals, etc. to the successor Contractor upon direction from the Contracting Officer and in a

Attachment # 3 – August 13, 2009 Page 4 manner prescribed by the Contracting Officer’s Technical Representative (COTR). Transfer shall be completed by the expiration date of the contract and shall include provision by the incumbent Contractor of accurate and complete data files and pertinent documentation.

5.1.3 The incumbent Contractor shall transfer the source files and documentation for all software developed on this contract to the successor Contractor. Transfer shall be completed by the expiration date of the contract and shall include provision by the incumbent Contractor of accurate and complete source files and documentation for all software developed.

5.1.4 For a contractor other than the incumbent provide a detailed plan and timetable for implementing the transition from the current facility to the proposed facility. The Incumbent Contractor shall be responsible for the physical move of all inventories. The move shall be accomplished prior to the effective date of the contract.

5.2 Phase-Out. At the conclusion of this effort, the Contractor shall assist in the transition of this contract to a successor contractor. The transition period shall consist of the final 30 calendar days of the contract. On the 31 calendar day, the successor will assume all responsibilities. The following shall apply only to a transition wherein the contractor is not the recipient of the successor award.

5.2.1 The Contractor shall provide the successor with detailed briefings regarding the structure of the database tables and software required continuing maintenance and operation of systems developed under this contract.

5.2.2 The Contractor shall transfer all project materials, to include but not limited to, source codes, course files, computer programs, project materials, documentation, operating manuals, etc. to the successor Contractor upon direction from the Contracting Officer and in a manner prescribed by the Contracting Officer’s Technical Representative(s).

Transfer shall be completed by the expiration date of the contract and shall include provision by the incumbent Contractor of accurate and complete data files and pertinent documentation.

5.2.3 The Contractor shall transfer the source files and documentation for all software developed on this contract to the successor Contractor.

Transfer shall be completed by the expiration date of the contract and shall include provision by the incumbent Contractor of accurate and complete source files and documentation for all software developed.

5.2.4 Provide a detailed plan and timetable for implementing the transition from the current facility to the proposed facility. The Incumbent Contractor shall be responsible for the physical move of all inventories.

The move shall be accomplished prior to the effective date of the contract.

6.0 Miscellaneous

6.1The Contractor shall participate, as needed, in joint government personnel and government contractor’s software development efforts, which include software development, database integration, and implementation of shared information management resources

Attachment # 3 – August 13, 2009 Page 5

7.0 Staff Experience Requirements

The Project Manager shall be considered a key person and should devote 50% of his or her time to this project. The Project Manager shall be expected to perform as a senior level developer as well as manage the overall efforts of the development team. The Project Manager shall have extensive experience with the full life cycle of large applications projects and the following experience:

Within the last ten (10) years, the Project Manager shall demonstrate eight (8) years of experience with application systems design and development, three (3) of which are at the management level.

Within the last seven (7) years, the Project Manager shall have five (5) recent years working in an ORACLE environment on a VAX/VMS platform.

Experience managing the development of large biological database systems within the last four (4) years.

Experience managing a software development team in a J2EE environment using web-based BEA WebLogic application server front end tools and ORACLE as a database server within the last four (4) years

Experience developing in a J2EE environment.

Programmer Analysts

The two Analysts shall be committed full time to this project.

Within the last eight (8) years, the Analysts shall demonstrate six

(6) years of experience with application system design and development. Within the last six (6) years the Analysts shall demonstrate four (4) years of experience designing and developing systems in an ORACLE/Java/J2EE environment.

At least one (1) analyst shall possess experience implementing solutions using the CambridgeSoft Enterprise Software Suite. The experience should document requirements analysis, template configuration and processing, as well as support for subsequent data mining techniques.

Programmer

The Programmer shall be committed full-time to this project and shall have experience with full life cycle of large application projects. Within the last six (6) years, the Programmer shall have six (6) years experience with ORACLE within the last six (6) years and two (2) years experience with J2EE/Java environment.

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The application portfolio listed in the table below has documentation available in the electronic reading room at:

http://dtp.nci.nih.gov/BDPSAcqusitionPlan2009ReadingRoom/

System Name Description System Tools

Aids Decisions Supports the evaluation of Aids screening results

J2EE

Antimicrobial Activity Antimicrobial DB and reporting of activity reports

J2EE

Assignment Support the assignment and availability of Cancer compounds

J2EE

BEC Minutes Supports maintaining detail minutes, action items, and monthly reports

J2EE

Cancer Decisions Supports the evaluation of Cancer screening results

PL/SQL

Combination/Fractionation Supports assignment of Combination/Fractionation compounds

J2EE

COMMON Lookup tables and functions that are referenced BDPS systems

Oracle Database Only

Data Warehouse Supports common data architecture for biological data available to public researchers

PL/SQL

Generic Plate Loader Supports the screening laboratories plate data

J2EE

High Throughput Prescreen Supports the cell-based anti-cancer compound 384 well plate format for screening

Oracle Database Only

Hollow Fiber Analysis/Spreadsheet Support the Hollow Fiber in vivo assay. It involves implanting hollow fibers contain cancer cell lines into animals, treating the animals with drugs and then removing the fibers and testing them in vitro

J2EE

Hollow Fiber Scoring Supports data summarization of the in vivo hollow fiber assay

J2EE

Hollow Fiber Setup Supports initial indices of in vivo drug efficacy Hollow Fiber screen

J2EE

Hollow Fiber Calculation Supports calculation module for Hollow Fiber screen

PL/SQL

In vivo Presentation Produces presentation-quality graphs for the in vivo screen.

J2EE

In vivo Detailed Graphics Produces graphs of the animals in an in vivo test group

In vivo Calculation Supports the evaluation of PL/SQL

Attachment # 3 – August 13, 2009 Page 7 clinical efficacy in vivo screening results

Material Safety Data Sheets Supports know hazard and safety information on each compound for NCI repository

Active Server Page JavaScript

Molecular Target Screening Supports for a cell based screen for inhibitors

J2EE

Natural Product Tracking Supports Natural Products processing and shipments of extracts

Active Server Page JavaScript

Natural Product Raw Material Supports Natural Products collection of extracts

J2EE

Natural Products Plant Header Supports the protocols from 1959-1972 for screening Natural Products against in vitro biological system

J2EE

PreScreen (Natural Products and Synthetic)

Supports the cell-based anti-cancer compound Prescreen screening database

Oracle Database Only

Screening System Aids Support the cell-based antiviral screenings assays, which examine the anti-HIV activity of synthetic and pure natural product compounds

Oracle Database Only

Screening System Cancer Support the cell-based anti-cancer compound screening, which examine activity of synthetic and pure natural product compounds

Database modules packages, procedures, functions, triggers, DCL scripts, SQL*Plus scripts

Screening System OneDose Support the cell-based anti-cancer compound screening program for 60 cell lines at a single dose which examine the activity of synthetic and pure natural product compounds

Database modules packages, procedures, functions, triggers, DCL scripts, SQL*Plus scripts

Screening System in vitro in vitro Cell Line Screening System (IVSS). IVSS is designed to screen compounds for potential anticancer activity

Database modules packages, procedures, functions, triggers, DCL scripts, SQL*Plus scripts, J2EE

Supplier Report Maintains and support the Supplier Reporting System (SRS) providing graphical and tabular reports used for in-house evaluation of anti-cancer and anti-AIDS screens

Supplier Report Cancer Package Two procedures called from with Java modules

Oracle

PL/SQL

Stanford/ARL Oracle Oracle Database Only

Attachment # 3 – August 13, 2009 Page 8

Supplier Notification Oracle Batch Job sends email to suppliers about data availability

Oracle Database/Oracle Batch Jobs

Task Tracking Support the assign compounds to a branch for a particular task.

J2EE

Test Counts Supports the reporting of statistics for screening

J2EE

Test History

Supports the reporting of compounds complete in the different anti-cancer screens

J2EE

Time Course Assay Support the web-based system to facilitate data capture, calculation, analysis, presentation and efficient database retrieval for allowing a ranking of cell line sensitivities on the basis of time-relevant drug exposure conditions

Active Server Pages JavaScript

Appendix 1: Glossary of Terms

ASP - Active Serve Page

BDPS - Biological Data Processing System

BEA - WebLogic - Application Server

CMS - Code Management System

CSS - Cascading Style Sheets

CO - Contracting Officer

COTR – Contracting Officer’s Technical Representative

COTS – Commercial-off-the-shelf Software

CVS - Concurrent Versions System

DBMS - Database Management System

DCL - Digital Command Language

DCTD - Division of Cancer Treatment and Diagnosis, NCI

DHHS - Department of Health and Human Services

EJB - Enterprise Java Beans

Hibernate - Object-relation mapping library for the Java language

Attachment # 3 – August 13, 2009 Page 9

HTML - Hyper Text Markup Language

ITB - Information Technology Branch

JSP - Java Server Page

J2EE - Java 2 Enterprise Edition

LAN - Local Area Network

MMS - Module Management System

NCI - National Cancer Institute

NIH - National Institutes of Health

PBSC - Performance-Based Service Contracting

ORADIS - NCI Drug Information System

PDF - Portable Document Format

PL/SQL - Procedural Language/Structured Query Language

PRS - Performance Requirements Summary

Struts - open-source web application framework for developing web applications.

QA - Quality Assurance

QASP - Quality Assurance Surveillance Plan

RDBMS - Relational Data Base Management System

SVG - Scalable Vector Graphics

XML - Extensible Markup Language

XSLT - Language for transforming XML documents into other XML documents.