BioNumerics

General Information

Technologies must be operated and maintained in accordance with Federal and Department security and privacy policies and guidelines. More information on the proper use of the TRM can be found on the TRM Proper Use Tab/Section.

Website:	Go to site
Description:	BioNumerics is a platform for the management, storage and statistical analysis of biological data. BioNumerics consists of software modules used for the analysis of all major applications in bioinformatics: one-dimensional electrophoresis gels, chromatographic and spectrometric profiles, phenotype characters, microarrays, and sequences. BioNumerics is able to combine information from various genomic and phenotypic sources into one global database and conduct conclusive analyses. Version 6 of this product uses Microsoft Access as the default backend database for data storage. Versions 7 and above use SQLite. The installation directory for the BioNumerics application and the database home directory can be configured on installation. Two default locations can be selected for the database home directory: In Common Documents and In My Documents.
Technology/Standard Usage Requirements:	Users must ensure their use of this technology/standard is consistent with VA policies and standards, including, but not limited to, VA Handbooks 6102 and 6500; VA Directives 6004, 6513, and 6517; and National Institute of Standards and Technology (NIST) standards, including Federal Information Processing Standards (FIPS). Users must ensure sensitive data is properly protected in compliance with all VA regulations. Prior to use of this technology, users should check with their supervisor, Information Security Officer (ISO), Facility Chief Information Officer (CIO), or local Office of Information and Technology (OI&T) representative to ensure that all actions are consistent with current VA policies and procedures prior to implementation.
Section 508 Information:	This technology has been assessed by the Section 508 Office and found non-conformant. The Implementer of this technology has the responsibility to ensure the version deployed is 508-compliant. Section 508 compliance may be reviewed by the Section 508 Office and appropriate remedial action required if necessary. For additional information or assistance regarding Section 508, please contact the Section 508 Office at Section508@va.gov. Please see reference tab for more information concerning product versions.
Decision:	View Decisions

Decision Source:	TRM Mgmt Group
Decision Process:	One-VA TRM v23.2
Decision Date:	02/22/2023 at 19:05:51 UTC
Introduced By:	TRM Request
Vendor Name:	Applied Maths

Vendor Release Information

The Vendor Release table provides the known releases for the TRM Technology, obtained from the vendor (or from the release source).

Version	Release Date	Vendor End of Life Date	Vendor Desupport Date
6.6.x	12/11/2013
7.1	09/09/2014
7.5	06/26/2015
7.6.x	01/09/2017
8.1.x	10/06/2022

Current Decision Matrix (02/17/2023)

Users must ensure their use of this technology/standard is consistent with VA policies and standards, including, but not limited to, VA Handbooks 6102 and 6500; VA Directives 6004, 6513, and 6517; and National Institute of Standards and Technology (NIST) standards, including Federal Information Processing Standards (FIPS). Users must ensure sensitive data is properly protected in compliance with all VA regulations. Prior to use of this technology, users should check with their supervisor, Information Security Officer (ISO), Facility Chief Information Officer (CIO), or local Office of Information and Technology (OI&T) representative to ensure that all actions are consistent with current VA policies and procedures prior to implementation.

The VA Decision Matrix displays the current and future VA IT position regarding different releases of a TRM entry. These decisions are based upon the best information available as of the most current date. The consumer of this information has the responsibility to consult the organizations responsible for the desktop, testing, and/or production environments to ensure that the target version of the technology will be supported. Any major.minor version that is not listed in the VA Decision Matrix is considered unapproved for use.

Legend:

White	Approved: The technology/standard has been approved for use.
Yellow	Approved w/Constraints: The technology/standard can be used within the specified constraints located below the decision matrix in the footnote[1] and on the General tab.
Gray	Unapproved: This technology or standard can be used only if a POA&M review is conducted and signed by the Authorizing Official Designated Representative (AODR) as designated by the Authorizing Official (AO) or designee and based upon a recommendation from the POA&M Compliance Enforcement, has been granted to the project team or organization that wishes to use the technology.
Orange	Divest: VA has decided to divest itself on the use of the technology/standard. As a result, all projects currently utilizing the technology/standard must plan to eliminate their use of the technology/standard. Additional information on when the entry is projected to become unapproved may be found on the Decision tab for the specific entry.
Black	Prohibited: The technology/standard is not (currently) permitted to be used under any circumstances.
Blue	Planning/Evaluation Constraint:The period of time this technology is currently being evaluated, reviewed, and tested in controlled environments. Use of this technology is strictly controlled and not available for use within the general population. If a customer would like to use this technology, please work with your local or Regional OI&T office and contact the appropriate evaluation office displayed in the notes below the decision matrix. The Local or Regional OI&T office should submit an inquiry to the TRM if they require further assistance or if the evaluating office is not listed in the notes below.

Release/Version Information:

VA decisions for specific versions may include a ‘.x’ wildcard, which denotes a decision that pertains to a range of multiple versions.

For example, a technology approved with a decision for 7.x would cover any version of 7.(Anything) - 7.(Anything). However, a 7.4.x decision would cover any version of 7.4.(Anything), but would not cover any version of 7.5.x or 7.6.x on the TRM.

VA decisions for specific versions may include ‘+’ symbols; which denotes that the decision for the version specified also includes versions greater than what is specified but is not to exceed or affect previous decimal places.

For example, a technology approved with a decision for 12.6.4+ would cover any version that is greater than 12.6.4, but would not exceed the .6 decimal ie: 12.6.401 is ok, 12.6.5 is ok, 12.6.9 is ok, however 12.7.0 or 13.0 is not.

<Past

CY2017

CY2018

CY2019

Future>

Release

Q1

Q2

Q3

Q4

Q1

Q2

Q3

Q4

Q1

Q2

Q3

Q4

6.6.x

Unapproved

Approved w/Constraints
[1, 2, 3, 4]

Approved w/Constraints
[1, 3, 5, 6]

Approved w/Constraints
[3, 5, 6]

Divest
[3, 5, 6, 7]

7.1

Unapproved

Approved w/Constraints
[1, 2, 3, 4]

Approved w/Constraints
[1, 3, 5, 6]

Approved w/Constraints
[3, 5, 6]

Divest
[3, 5, 6, 7]

7.5

Unapproved

Approved w/Constraints
[1, 2, 3, 4]

Approved w/Constraints
[1, 3, 5, 6]

Approved w/Constraints
[3, 5, 6]

Divest
[3, 5, 6, 7]

7.6.x

Unapproved

Approved w/Constraints
[1, 2, 3, 4]

Approved w/Constraints
[1, 3, 5, 6]

Approved w/Constraints
[3, 5, 6]

Approved w/Constraints
[3, 5, 6, 7]

8.1.x

Unapproved

Decision Constraints


[1]	For Microsoft Access 2010 and prior versions, usage is limited to databases supporting individual user`s personal productivity and/or training as database administrators. For Microsoft Access 2010 and prior versions, Microsoft Access must not be used to support line of business operations requiring data durability/persistence. Further, when properly configured as a front-end client, no data at rest is permissible to be stored by Microsoft (MS) Access 2010 and prior. These older versions must only be used with sensitive data as part of a secured system when Access is configured as a client front-end to an appropriately secured MS SQL Server or MS SharePoint Server following VA security configuration baselines and connected via a Federal Information Processing Standard (FIPS) 140-2 certified encrypted connection. For Microsoft Access 2016 and subsequent versions, the security configuration baseline must comply to the DISA STIG for Microsoft Access 2016 or subsequent version. When Microsoft Access 2016 and subsequent versions are used for business processes OR used with VA sensitive data including PHI and PII, the data files must be stored in storage location encrypted by FIPS 140-2 certified encryption. Further, the files must be securely backed up on a regular basis for recovery purposes, and access controls to that encrypted storage location must be restricted to only those individuals that are allowed access to the data. Users must not solely rely on Microsoft Access application passwords to protect sensitive data from unauthorized access. Appropriate authorization and role-based access control should be enforced to ensure only authorized staff have access to the data files and controls. There must be a clear delineation of duties for staff supporting and utilizing the tool. For example, access to the security controls must be restricted to certain staff who require it to accomplish assigned tasks. All instances used for business processes OR VA sensitive data including PHI and PII, must be reviewed and approved by the local ISO and privacy officer.

[2]	Veterans Affairs (VA) users must ensure VA sensitive data is properly protected in compliance with all VA regulations. All instances of deployment using this technology should be reviewed by the local ISO (Information Security Officer) to ensure compliance with VA Handbook 6500.

[3]	Technology must remain patched and operated in accordance with Federal and Department security policies and guidelines in order to mitigate known and future security vulnerabilities.

[4]	Per the May 5th, 2015 memorandum from the VA Chief Information Security Officer (CISO) FIPS 140-2 Validate Full Disk Encryption (FOE) for Data at Rest in Database Management Systems (DBMS) and in accordance with Federal requirements and VA policy, database management must use Federal Information Processing Standards (FIPS) 140-2 compliant encryption to protect the confidentiality and integrity of VA information at rest at the application level. If FIPS 140-2 encryption at the application level is not technically possible, FIPS 140-2 compliant full disk encryption (FOE) must be implemented on the hard drive where the DBMS resides. Appropriate access enforcement and physical security control must also be implemented. All instances of deployment using this technology should be reviewed to ensure compliance with VA Handbook 6500 and National Institute of Standards and Technology (NIST) standards. It is the responsibility of the system owner to work with the local CIO (or designee) and Information Security Officer (ISO) to ensure that a compliant DBMS technology is selected and that if needed, mitigating controls are in place and documented in a System Security Plan (SSP).

[5]	Veterans Affairs (VA) users must ensure VA sensitive data is properly protected in compliance with all VA regulations. All instances of deployment using this technology should be reviewed by the local ISO (Information Security Officer) to ensure compliance with VA Handbook 6500.

[6]	Per the May 5th, 2015 memorandum from the VA Chief Information Security Officer (CISO) FIPS 140-2 Validate Full Disk Encryption (FOE) for Data at Rest in Database Management Systems (DBMS) and in accordance with Federal requirements and VA policy, database management must use Federal Information Processing Standards (FIPS) 140-2 compliant encryption to protect the confidentiality and integrity of VA information at rest at the application level. If FIPS 140-2 encryption at the application level is not technically possible, FIPS 140-2 compliant full disk encryption (FOE) must be implemented on the hard drive where the DBMS resides. Appropriate access enforcement and physical security control must also be implemented. All instances of deployment using this technology should be reviewed to ensure compliance with VA Handbook 6500 and National Institute of Standards and Technology (NIST) standards. It is the responsibility of the system owner to work with the local CIO (or designee) and Information Security Officer (ISO) to ensure that a compliant DBMS technology is selected and that if needed, mitigating controls are in place and documented in a System Security Plan (SSP).

[7]	Users should check with their supervisor, Information Security Office (ISO) or local OIT representative for permission to download and use this software. Downloaded software must always be scanned for viruses prior to installation to prevent adware or malware. Freeware may only be downloaded directly from the primary site that the creator of the software has advertised for public download and user or development community engagement. Users should note, any attempt by the installation process to install any additional, unrelated software is not approved and the user should take the proper steps to decline those installations.

Note:

At the time of writing, 8.1.1 is the most current version, released 10/06/2022.

References

The following reference(s) are associated with this entry:
Type	Name	Source	Description

Technology Components

Note: This list may not be complete. No component, listed or unlisted, may be used outside of the technology in which it is released. The usage decision for a component is found in the Decision and Decision Constraints.
Name	Description
Character Data module	This module enables users to define any array of named characters, binary or continuous, with fixed or undefined length. The size of a character experiment in BioNumerics can range from one single character, such as a morphological feature, to microarray experiments of many thousands of gene expression values. There is no limit to the size of the character array and the software is optimized to analyze large data sets. This module includes features to: import character data from a text file, spreadsheet, or any Open Database Connectivity compatible database; create a customized display of test panels; and import distance and similarity matrices.
Classifiers and Identification module	This module provides identification, supervised learning, or classification technology. It introduces the possibility to identify unknown organisms based upon various available experiment data sets. Fingerprints, characters, and sequences, along with classifiers such as Naive Bayesian classifiers and Support Vector Machines, can be used for identification. This module also features automated identification via decision networks.
Fingerprint Data module	The Fingerprint Data module includes parts for the processing of one dimensional electrophoresis profiles and spectra, including all types of electrophoresis gels, sequencer trace files, Matrix Assisted Laser Desorption/Ionization (MALDI) profiles, spectrophotometric and chromatographic profiles. The module includes the ability for: importing any bitmap images, densitograms and chromatograms; reading graphical and desitometric file formats from image files; automated lane finding; alignment of patterns through normalization; band finding and quantification; and band matching.
Sequence Data module	The Sequence Data module enables users to assemble sequence reads ranging from single genes obtained via classical Sanger sequencing to full genomes via Next Generation Sequencing (NGS). It also recognizes sequence file formats including European Molecular Biology Laboratory (EMBL), GenBank, Flat A, and FASTA, and stores the full header and feature information of annotated sequences. This enables BioNumerics to use a variety of analysis applications such as multiple sequence alignment, phylogenetic clustering, chromosome comparison and alignment, automated annotation, chromosome-wide single nucleotide polymorphism (SNP) analysis, polymerase chain reaction (PCR) primer design, restriction enzyme analysis, and open reading frame analysis.
Tree and Network Inference module	This module includes parts for cluster analysis, or unsupervised learning. These are featured in the comparison window, which presents an overview of all available experiments for a selection of entries and to show and compare any combination of experiments. These features, which include dendrograms, phylogenetic trees, population modelling graphs, consensus trees and networks, and cluster significance analysis, can be stored to disk.

VA Categories View the VA Categorization Framework

Domain Area	Category	Customer Guidance	Category Locked By ELT Date
Information Management Technologies Business Intelligence and Data Warehouse Platforms	Data Analytics (Statistical Analysis, Prediction, and Modeling)

Operating Systems Supported by the Technology

Windows Client - Approved w/Constraints
Windows Server - Approved w/Constraints

Technologies/Standards Relationships

Runtime Dependencies:

Comparable Technologies:

Companion Technologies/Supported Standards:

General Analysis

Adoption Benefits

At the time of writing, no National Institute of Standards and Technology (NIST) vulnerabilities had been reported and no VA Cyber Security Operations Center (CSOC) bulletins had been issued for the latest versions of this technology.
This is a well-documented technology.

Adoption Risks

System scans indicate that this technology is no longer in use within the VA network.
There is no indication based on available vendor documentation that this technology is Federal Information Processing Standard (FIPS) 140-2 compliant.
This technology involves the use Universal Serial Bus (USB) connections and proper security precautions must be taken when used.
This technology can potentially use Secure Sockets Layer (SSL), an unapproved protocol.
The potential exists to store Personally Identifiable Information (PII), Protected Health Information (PHI) and/or VA Sensitive data and proper security standards must be followed in these cases.
Due to the rapid release schedule of this product, the VA may be unable to update to the most recent patch and may require a deployment model requiring the use of specific versions.
This technology can integrate with and alter database technologies.
The technology is available as freeware. As such, the technology will be without clearly defined support options which may result in suboptimal enterprise level support.

Architectural Risks

This technology is not portable as it runs only on Windows platforms.

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