The OMNITEC CIO-SP3 Team

OMNITEC Solutions, Inc.

OMNITEC provides program management,development, and ongoing operation services to the National Database for Autism Research (NDAR) for its collaborative biomedical informatics web portal (http://ndar.nih.gov). The contract is both an expansion of and a follow-up to OMNITEC’s previous consultative services, which included the provision of strategic guidance during the planning and creation of the NDAR web portal. The primary objective of NDAR, which was established by the National Institutes of Health (NIH), is to provide broad access to all quality research data relevant to the field of autism spectrum disorders (ASD) – regardless of where the data is located or its funding source. As a collaborative biomedical informatics platform, NDAR also provides researchers with collaboration opportunities, research tools, and a channel for the publication of research results. It has won the HHS Innovates award for “best innovations” in 2011 from Secretary Sebelius.

While the NDAR portal requires collaborative web technologies, support of complex data types, cross-platform database federation, and the rapid movement of terabytes of data, the key challenge was not primarily technological. It was a matter of overcoming legal, policy, and data-sharing roadblocks that limited significant collaboration. Historically, scientific research, including research into ASD, had been conducted in small labs on limited numbers of subjects. There was little emphasis on data definition standards, infrastructure to support data accumulation, or collaboration among many researchers. These limitations constituted a significant barrier to data sharing and scientific advances among the larger community of researchers. OMNITEC was charged by the NIH to overcome these roadblocks. Our objective was to lead the large, diverse stakeholder community to adopt, support, and help extend a bioinformatics platform that would advance scientific discovery. In response, OMNITEC defined an optimal solution that focused on three critical areas: (1) database definition and organization, (2) collaborative workflow, and (3) the development of information-sharing policies and procedures that would be acceptable to NDAR’s many stakeholders.

UCSD

A key emphasis of the National Center for Microscopy and Imaging Research UCSD (NCMIR) is the application of advanced imaging technologies to the nervous system in health and disease.Affiliated with UCSD’s Center for Research in Biological Systems (CRBS), the NCMIR is a recognized authority in the development of technologies for high throughput, multi-scale imaging and analysis of biological systems at the mesoscale, the dimensional range spanning 5 nm3 and 50µm3. Macromolecules, organelles, and multi-component structures like synapses, which are encompassed in this dimensional range, have traditionally been challenging to study because they fall in the resolution gap between X-ray crystallography at one end and medical imaging at the other. While maintaining a focus on neurobiology, NCMIR also conducts research that addresses the cellular and molecular underpinnings of biological systems relevant to cancer, diabetes, and heart disease, to name a few. NCMIR welcomes requests for collaborative projects that will drive development in its core research areas designed to develop and enhance technologies, including:

  • novel and traditional specimen preparation methods for intermediate voltage electron microscopy (IVEM) and correlated microscopies.
  • computer-aided methods for the acquisition of data from the microscopes.
  • enhancement of image contrast and extraction of accurate 3D information from biological specimens prepared for light and electron microscopy.
  • reconstruction of larger structural complexes using electron tomography and correlated microscopies.

RNSolutions

RNSolutions has been providing IT services involving Bioinformatics support to the following Government clients: The Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD) and the United States Food and Drug Administration (FDA) Center for Food Safety and Applied Nutrition (CFSAN).

With a CMMI level II certification, they utilize state-of-the-art technologies such as J2EE, STRUTS, and Oracle 10g RDBMS. RNSolutions is maintaining, enhancing, and/or developing multiple web and other based systems for these customers. These systems are in the areas of clinical trial information, biomedical data extraction, transformation and load (ETL), data formation, accuracy validation, clinical data warehouse, replication, scientific reporting, and thesaurus management. In addition, RNSolutions is involved in the efforts of maintaining reliable, secure, and HIPAA-compliant systems.

The Unit on Computer Support Services (UCSS) located within the Division of Intramural Research (DIR), NICHD at NIH, provides information technology services to support NICHD’s clinical and basic research programs. RNSolutions supports the overall goal of the UCSS to provide capabilities for DIR scientists to manage basic and clinical research information related to child health and human development. The UCSS supports Internet and database projects that allow for scientific data collection and analysis. The current environment utilizes Unix, Java, Oracle, and Veritas technologies.

RNSolutions supports both information technology infrastructure and the complex business workflows for the UCSS. They are applying a software development lifecycle (SDLC) that involves requirements gathering and authoring, domain modeling, rapid prototype development/proof of concept, software architecture design and documentation, and database design and implementation. RNSolutionshase successfully developed several software products for the UCSS including bioinformatics, genomic analysis, and molecular genetics tools, as well as business process automation tools. Each of these tools is a mature software product deployed within the organization. They continually provide quality assurance oversight for all our software products and fix bugs as identified or provide software enhancements when necessary. Their technical and business support includes business areas such as:

  • Clinical trials research
  • Bioinformatics and genomics
  • Medical imaging and bio-visualization (research animations, figures, diagrams)
  • Photography/videography (including DVD production)
  • Publishing, including poster/flyer design, annual reports, and scientific journals
  • Administrative management systems (including budgetary and personnel systems which interface with the NIH New Business System (NBS)
  • Architecture and application support to maintain the NICHD server architecture, including ad-hoc technical assistance with database and web server applications, configuration of firewalls, and backup/recovery.

Clinical Informatics

The UCSS Clinical Informatics program delivers a set of web-based applications and an experienced team of research staff trained to assist Principal Investigators (PIs) conduct natural history or interval-based protocols.

Clinical Trials Database (CTDB)
The CTDB is a web-based application used to design, collect, and report research protocol data. The system supports 150 protocols, with 110 protocols at the NICHD, and is utilized by the National Institute of Mental Health (NIMH), the National Institute of Nursing Research (NINR), the National Institute of Dental and Craniofacial Research (NIDCR), the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), and the Clinical Center. Integration with the NIH Clinical Center Biomedical Translational Research System (BTRIS) is planned for FY2011. The application provides the following key modules:

  • Clinical trials research
  • Bioinformatics and genomics
  • Medical imaging and bio-visualization (research animations, figures, diagrams)
  • Photography/videography (including DVD production)
  • Publishing, including poster/flyer design, annual reports, and scientific journals
  • Administrative management systems (including budgetary and personnel systems which interface with the NIH New Business System (NBS)
  • Architecture and application support to maintain the NICHD server architecture, including ad-hoc technical assistance with database and web server applications, configuration of firewalls, and backup/recovery.

Clinical Data Mart (CDM)
The CDM consists of a star schema reporting structure that supports research and hospital data integration. The design accommodates clinical and laboratory results, genomic family history data, and bio-specimens. The reporting engine includes 300 custom reports with integration to Cognos and Business Objects for additional ad-hoc reporting functionality.

Clinical Wiki (cWiki)
The cWiki is a Web 2.0 collaboration platform developed to improve communication and knowledge management for clinical projects. Currently, web portals support OB/GYN services, pediatric endocrinology, biomedical education, and other laboratories within the DIR. The cWiki will complement the multi-site module of the CTDB to bring researchers together from universities, hospitals, non-profit groups, and the NIH.

Bioinformatics
This scientific informatics group develops research tools to assist investigators with genomic data management and analysis.

Molecular Genetics Core Support
RN Solutions is currently establishing a computing cluster and hardware/software environment to capture,process, and analyze data for high throughput sequencing (SOLID, Illumina).

Family History Genomics Tool
This tool is a web-based system for collecting disease patterns in patient families. The application includes a unique pedigree reporting feature that accommodates multiple family structures.

Genomic Analysis
The team is currently researching the interaction network of the NEF-SP protein, including the extraction of biological meaning, pathways and networks from interacting proteins by applying sequence alignment, identifying protein motifs, analyzing protein configurations, and analyzing the distribution of conserved amino acids at binding sites.

TileMapper
This tool is designed for mapping various genomic annotation features to the tiling microarray data derived from transcriptome, Chip-chip, or MeDIP studies. The data are visualized in a tabulated format, which permits flexible processing, and further analyzed by downstream pipelines to relate the data and perform interaction analysis. TileMapper accepts transcribed fragments (transfag) information in Browser Extensible Display (BED) format generated from Affymetrix Integrated Genome Browser (IGB) or downloaded from the UCSC server.

GermSage
This web application automates access to a collection of male germ cell transcriptome information derived from Serial Analysis of Gene Expression (SAGE). The application includes the three key germ cell stages in spermatogenesis; mouse type Aspermatogonia (Spga), pachytene spermatocytes (Spcy), and round spermatids (Sptd). A total of 452,095 SAGE tags are represented in all the libraries, making them by far the most comprehensive resource available.

SageWorks
This application allows investigators to leverage the robust public databases available in combination with their SAGE data to assist with the acceleration of gene and pathway discovery. This workspace can accommodate any SAGE data and provides the scientific community with the opportunity to minimize the redundancy of manual manipulation.

BioSilico
This integrative, web-based, functional genomics platform has a compendium of bioinformatics modules for statistical analysis and functional prediction. The application utilizes statistical methods and gene set enrichment algorithms to analyze gene expression data from public experiments to identify disease-causing genes. The tool also provides a Bayesian net module that uses gene expression to identify novel regulatory networks. Using the application, the team confirmed and identified known and potential novel candidate genes for a variety of metabolic and reproductive disorders (e.g., prostate cancer).

Biovisualization
Lab journals, experimental data, research notes, lab protocols, reference lists, images, and videos are commonly generated during the research process. E-mail, word documents, PDFs, notes, conferences and conversations via phone or video, the use of forums, wikis, and blogs are common methods of collaborating in the production of research. Publications, photographs, videos, computer graphics, figures, graphs, posters, fliers, reports, and presentations are used for disseminating information and research.The management of this information relies on the use of multiple applications, platforms, and websites. Solutions to the organization of, and access to, content are designed not to be Mac- or PC-specific or bottleneck users into one interface only. Solutions allow information to be ported in or out and remain dynamic and inclusive.The biovisualization team provides services for efficiently collaborating, capturing, presenting, and disseminating information by facilitating the use of forums, blogs, microblogs, wikis, and mashups to aggregate information and move researchers beyond simple e-mail and static documents (such as Microsoft Word and PowerPoint).

Microscopy
The amount of data being generated from microscopy is growing exponentially. Increased resolution in CCDs (charged coupled devices) and improved optics allow transmission electron microscopes and confocal microscopes to generate huge amounts of data (up to 2 terabytes per afternoon per instrument). Storage and management is complicated by the wide range of imaging devices, software applications for processing and viewing data, and proprietary file formats in which the data is stored.One possible solution for managing these digital assets is OMERO, an open-source, server-based Digital Asset Management (DAM) application developed as a joint project between a number of research teams. RN Solutions are currently testing the use of OMERO.

KForce

In addition to our highly productive internal HR department and our well established relationships within the health and technology business environment, we have full access to the resources at Kforce, one of our CTA members. Kforce is a billion dollar national staffing firm with over 45 years of experience providing qualified resources for a variety of clients and industries across the Nation. Backed by more than 1,000 recruiting professionals, an internal database of over 2.5 million resumes, and a results-proven disciplined process, Kforce has proven their ability to understand the tangible and intangible skills required by client organizations and to make the “right match” in:

  • Technology Development, Enterprise Data Management, and Infrastructure
  • Finance & Accounting
  • Professional Administrative Services
  • Healthcare Information Management
  • Clinical Research

Annually, they complete approximately 44,000 successful matches as temporary engagements, temporary-to-hire placements, and permanent placements. Kforce has a team of over 1,000 sales and recruiting associates working in 60 field offices in 40 major markets around the country, with a centralized ISO 9001:2008 Certified National Recruiting Center on call for any surge staffing demands that require a quick turnaround.

Kforce is also a Top Secret cleared firm. Utilizing our internal FSO team, Kforce can process, verify, and hold Top Secret clearances for all of our consultants. Kforce can also run background checks and skills testing to fit each client’s unique needs. Available and staffed personnel include:

In addition to 60 offices in 41 major markets across the Nation, Kforce has a Global Solutions Center which staffs personnel around the world easily fulfilling any OCONUS requirements. All of these staff members have a Bachelor of Science or Master’s Degree, at minimum. Their Global Solutions Center is CMM level 2 and ISO 27001 Certified (Information Security Management System).

Prometheus Research

The OMNITEC Team has a deep, successful relationship with Prometheus Research. We are very proud to add them on our CIO-SP3 team as a subcontractor. For the last ten years, they’ve been developing software and offering research informatics services to clients looking for low-cost, easy-to-use, web-based data access integration tools. Their software products and services are designed to empower knowledge workers by making existing databases easily accessible on the web, and doing it fast and at low cost.

Prometheus’ foundational software innovation, HTSQL, is based on open-source technology and quickly translates the language of the web (HTTP) into the language of databases (SQL). As a result, HTSQL allows businesses, organizations, and biomedical researchers to securely increase their intelligence through dynamic, real-time, web-based database management. Their software tools dramatically simplify the problem of developing custom web pages to access rich data sources by automatically converting databases into interactive, flexible, agile, and adaptive websites.

Prometheus Research provides its customers two key product offerings: HTSQL and Research Informatics. Markets for the HTSQL product include businesses, organizations, and governments that rely heavily on database knowledge to manage sales and operations. Their Research Informatics products and services are designed specifically for biomedical and scientific researchers, research institutions, and research funding organizations. Prometheus Research Informatics is used by world-renowned researchers at major universities around the world looking to simplify the development of web-based custom informatics systems for quick collaboration, fast and agile information management, and secure access to their rich scientific data.

Hendall Inc.

Hendall Inc. is supporting the National Cancer Institute’s Office of Budget and Finance in maintaining, enhancing, applying, and documenting a Budget Execution and Formulation Support System (BEFSS). This system has been used extensively in budget execution/formulation/presentation and development of projections for inclusion in NCI planning documents for the past 34 years. The BEFSS can be logically divided into two major components: the Budget Formulation and Presentation Support System (BFPSS), and the Budget Execution Support System (BESS). The BFPSS has as its central component a specialized version of a general purpose, interactive Fiscal Projection Model (FPM) which facilitates the rapid development and analysis of fiscal profile data in many programmatic dimensions. The specialized FPM also includes algorithms for allocating overhead (administrative support) dollars and positions across the programmatic categories used in NCI budgets, and extensive report formatting software. The BESS contains three subsystems to assist NCI in 1) preparing and distributing current fiscal year operating budget/notification-of-allowances information; 2) accessing NIH-maintained accounting data and preparing and distributing monthly status-of-funds reports which show actual obligations compared with the operating budget/allowance data; and 3) allowing Division budget analysts to enter monthly estimates of expenditures for the remainder of the fiscal year.

Delta Resources Inc.

DELTA delivers Mission Assurance and Network Operations capabilities through requirements management and implementation planning, and ensuring continuity of critical missions in the face of cyber-attacks in a contested battle space.

Cyber Security
DELTA cybersecurity professionals are trusted partners and advisors with hands-on experience providing cyber strategy and operations to our government customers. We help mission owners reduce their cyber risks using a comprehensive Risk Management approach guided by DoD Instruction 8500.01 (Cybersecurity) and NIST Special Publication 800- 53 Revision 4 and executed by seasoned, certified, professionals. We support all aspects of Assessment and Authorization processes for data and risk categorization, hands-on system hardening, Risk Management evaluations, cybersecurity testing and improved cyber situational awareness, continuous monitoring and targeted cybersecurity capability implementations.

Our certified professionals include – Certified Information Systems Security Professional (CISSP®) and SANS certifications such as GIAC Certified Incident Handler (GCIH) and many more. While experience and certifications are important, at DELTA we focus on growing cyber talent by assessing candidates for technical aptitude, diligence, judgement and customer focus. We provide training and certification to ensure professional growth.

Cloud Computing
DELTA, an Amazon Consulting Partner, delivered DoD’s first operational Enterprise system at Cloud Security Level 4 on the Amazon GovCloud in November 2014. DELTA’s comprehensive solution included extensive testing to ensure the delivered solution met DoD’s evolving cloud cybersecurity requirements while providing cost savings of over $200K per year. DELTA cloud cybersecurity experts help refine the process for acquiring shared services and cloud cybersecurity to help pave the way for government cloud adopters.

Navy Shipbuilding
DELTA performs a full range of professional support services across the Program Executive Offices, shipbuilding and weapons systems program offices, resource sponsors, and Surface Warfare Enterprise stakeholders. DELTA supports the Navy’s shipbuilding programs and provides Fleet support in areas such as project management, systems engineering, combat systems development, and business management. DELTA analysts have been directly involved in several of the Navy’s most critical shipbuilding initiatives, and DELTA’s personnel also provide critical Fleet support efforts for the fielding of C5I improvements, ensuring that sailors have reliable and technologically and mature capabilities in order to deploy, execute missions while in harm’s way, and return home safely.

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