Loren Data's SAM Daily™

FBO DAILY ISSUE OF APRIL 17, 2009 FBO #2699
SOLICITATION NOTICE

D -- BioNumerics Additional Licenses - Techn. Eval Criteria

Notice Date

4/15/2009
 

Notice Type

Combined Synopsis/Solicitation
 

NAICS

511210 — Software Publishers
 

Contracting Office

Department of Health and Human Services, Food and Drug Administration, Office of Acquisitions and Grants Services, 5630 Fishers Lane, Room 2129, Rockville, Maryland, 20857-0001
 

ZIP Code

20857-0001
 

Solicitation Number

1055011
 

Point of Contact

Vida - Niles, Phone: 301-827-2476, Doreen Williams ,, Fax: 301-827-7106
 

E-Mail Address

vida.niles@fda.hhs.gov, doreen.williams@fda.hhs.gov
 

Small Business Set-Aside

Total Small Business
 

Description

Technical Evaluation Criteria The Food and Drug Administration (FDA) is seeking 100% total small business set-aside vendors that can provide quotes/proposals. This is a combined synopsis/solicitation for commercial items prepared in accordance with the format in FAR 12.6, simplified acquisition procedures and the resultant purchase order will include all applicable provisions and clauses in effect through the Federal Acquisition Circular 05-29. This announcement constitutes the only solicitation and a written solicitation will not be issued. The synopsis, NAICS code 511210, is to notify contractors that the government intends to issue a Purchase Order in accordance with FAR Part 13.106, for the following statement of work, under the simplified acquisition procedures. The Food and Drug Administration intends to award a purchase order on a sole source basis to: Applied Maths, Inc. Not withstanding, any vendor that believes it is capable of providing the required service as stated herein may submit a capability statement to document its ability to provide the required product(s). A determination to compete this procurement based on a response to this notice is solely within the discretion of the Government. The Government reserves the right to award a contract without discussions if the Contracting Officer determines that the initial offer(s) is/are providing Best Value and discussions are not necessary. The Government’s period of performance is for thirty (30) days effective ARO. The Food and Drug Administration (FDA) intends to award a fixed price purchase order for a BioNumerics Module version 5.1 for Fingerprint Types. Project Title: BioNumerics Additional Licenses Background: The Office of Regulatory Science, Divisions of Microbiology, intends to purchase six additional licenses of BioNumerics software. We currently use a 2-user BioNumerics network license to interface with the PulseNet databases housed at the CDC. We use this interface to share DNA fingerprint data from food-related bacterial isolates with our state and federal partners. As our needs grow, we are requiring additional Division of Microbiology personnel to use this software to contribute data to this growing database as well as assist with data analysis and interpretation. Additional licenses are required to allow for growth of our databases. Six additional licenses will allow eight Division of Microbiology users to be accessing the software simultaneously. Our current BioNumerics licenses consist of the following v. 5.1 modules: Fingerprint Types, Character Types, Sequence Types, Comparison and Cluster Analysis, Identification and Libraries and Database Sharing Tools. Additionally, we have needed the use of the v 5.1 Dimensioning and Statistics Module for further data analysis. Any future add-on licenses of this software must be an equivalent version of BioNumerics and identical module configuration to our existing license in order to be compatible. Statement of Work: Requirements: The following software modules are required to address our needs: 1. BioNumerics Module v5.1 - Fingerprint Types: QTY 6 a. Image processing and normalization. Input of 8-bit, 12-bit and 16-bit TIFF images, densitograms, and chromatograms of unlimited filesize. Automatic lane finding on images for all types of gels. Gelstrip borders and tracking splines adjustable for each individual lane. Automated and manual alignment by pattern recognition using external reference patterns and/or internal reference bands. On-screen normalization of TIFF images with indication of reliability and possible misalignments. Direct processing of ABI, Beckman and Amersham chromatogram files with inline reference tracks. Adjustable background subtraction using rolling disk method. Adjustable curve smoothing by Arithmetic, Median and Mode filters and Least Square filtering algorithms. Adjustable Richardson-Lucy deconvolution. b. Database. Entry description by up to 60 information fields, up to 80 characters long each. Easy drag & drop linkage of multiple experiments to database entries. Powerful search engine for combined database searches on different information fields and experiment presence, character values, and ranges. Storage and management of composite database queries. Imaging of any selection of patterns by normalized 2D-bitmap strips, densitograms or reconstructed patterns. Multi-database system, each database can contain many different fingerprint types. Direct comparison of differently normalized patterns through automatic MW remapping functions. Advanced database exchange functions using the Bundles concept and XML exchange packets. Compatibility with external databases via ODBC. c. Quantification. Approved band-search algorithms with adjustable sensitivity for shoulder and double-band finding based on curve. Possibility to find and mark uncertain bands. Quantification of molecular sizes or any other metric unit using linear, logarithmic, combined logarithmic-third power regression, cubic spline or pole functions. Accurate expression of protein or nucleic acid quantities or concentrations based on cubic spline regression using known calibration bands. Extensive anatomy and comparative quantification of bands between groups of patterns. Generation of characteristics tables and extensive comparative reports between unlimited numbers of patterns, with indication of molecular weight, fragment length, and absence/presence or absolute protein or DNA amount per band. Search for discriminative bands between selected groups of patterns; search for unique and common bands within selections. Binary and quantitative band matching tables of multiple combined fingerprints. 2. BioNumerics Module v5.1 - Character Types: QTY 6 Universal import tools and programmable routines (scripts) for all kinds of text-oriented character data. Character types may include any existing test panel, binary, multi-state or continuous within any range, with fixed or variable number of characters. Character names may be entered by the user or automatically imported. Unlimited length of character arrays. Direct processing of densitometric arrays (spots), test panels, microtiter plates, dot blots, etc. from TIFF files. Character profiles are displayed in a panel with user-defined color scales or in a list with values. Display of truthful image of any test panel and easy data input on-screen. 3. BioNumerics Module v5.1 - Sequence Types: QTY 6 Project-based contig assembly and consensus editing from sequencer chromatogram files (ABI, Beckman, MegaBace). Direct import of EMBL, GenBank, Flat A, and FASTA formats. Import of nucleic acid and amino acid sequences. Easy paste from clipboard, and manual editing. Contig projects can be opened directly from entry editor, comparison and multiple alignment 4. BioNumerics Module v5.1 - Comparison & Cluster Analysis: QTY 6 a. Methods. Creation of dendrograms including up to 10,000 database entries using product-moment Pearson correlation, cosine correlation, Dice or Nei and Li, Jaccard, Jeffrey's X, Ochiai and area sensitive relatives for banding patterns, Gower, Canberra metric, Simple Matching, etc. Categorical coefficient for multi-state character data such as MLST or VNTR. Unweighted pair-grouping (UPGMA), complete linkage (furthest neighbor), single linkage (nearest neighbor), Ward or Neighbor Joining clustering. Adjustable trace-to-trace optimization and tolerance settings for banding patterns. Statistical determination of most justified tolerance settings for banding patterns. Phylogenetic inference methods: Generalized Parsimony, Maximum Likelihood. Population modelling: Analysis of categorical data such as MLST or VNTR (MLVA) using Minimum Spanning Trees to reconstruct evolutionary models. Advanced presentation and editing tools. b. Interpretation. Combined display of character images, sequences, normalized pattern images, with similarity matrices and sorted according to dendrogram(s). Indication of statistical error at all linkage levels and calculation of co-phenetic correlation. "Seaweed" and pseudo-rooted representation for unrooted trees. Bootstrap analysis for single or composite datasets. Display of sorted similarity matrices, shaded or with numerical similarity values. Comprehensive edit and publishing functions. Professional presentation and printing facilities, in a WYSIWYG environment. Direct interaction between database and dendrogram. Incremental and decremental clustering: new entries can be added to or deleted from existing cluster analyses, without having to recalculate the complete analysis. All features of a comparison are stored to disk. c. Congruence between techniques. Calculation of global similarity or congruence between different techniques as matrix or dendrogram. Easy visualization of taxonomic depth or level of each technique by pairwise regression plots of similarities. d. Composite cluster analysis. Different data sets of the same type and of different types (fingerprint, character, sequence and matrix) can be combined into one consensus clustering. Calculation of global similarity by merging characters or by averaging experiment-related similarities. Optional weighting based on number of characters or defined by the user. e. Plots and graphs. Creation of 2-D and 3-D bar graphs, contingency tables, 2-D and spatial 3-D scatterplots or feature plots from database fields and characters. Professional presentation, printing and exporting tools. 5. BioNumerics Module v5.1 - Identification and Libraries: QTY 6 a. Database screening. Fast identification of batches of entries with entire databases or selections from databases, using all available coefficients. b. Libraries. Creation of highly characteristic identification libraries using the open unlimited multi-library system. Specific similarity measures and settings can be defined for specific experiment types. Comprehensive identification reports showing results for each available experiment. Many different viewing options and statistical tools to facilitate interpretation. c. Neural Networks. Neural Networks can be trained per experiment type and used for quick and accurate identification of complex groupings. 6. BioNumerics Module v5.1 - Database Sharing Tools: QTY 6 a. Connected Databases. Possibility to plug BioNumerics onto ODBC compatible database systems such as Oracle, Microsoft Access, SQL Server, MySQL, PostgrSQL. Bundles. Any selected information and experiment data for selections of entries from the database can be condensed into a Bundle. Bundles can be exchanged over internet and opened in a recipient database. Automatic remapping makes full comparison between different fingerprint systems possible. b. Client-Server setup. Client functions come with the Database Sharing Tools. Functions include querying and downloading entries from the central Server database; Upload of data to the Server for identification; Receipt of detailed identification report from Server. Call for prices of BioNumerics Server package. c. XML export/import. Creation of XML files from any selection of entries and techniques from the database. Received XML files can be imported as fully editable database entries. XML exchange is the preferred way of exchanging database entries in a peer-to-peer network. 7. BioNumerics Module v5.1 - Dimensioning and Statistics: QTY 6 a. Principal Components Analysis. Non-hierarchic grouping by PCA. Spatial representation of clouds of entries in X-Y-Z coordinate system. Indication of total discrimination of axes. Real-time rotation of coordinate system to enhance perception of 3-D structures. Advanced Open-GL presentation and layout for publication. Delineation of populations using colors and/or codes. Plotting of dendrogram branches on PCA for advanced grouping comparisons. b. Multi-Dimensional Scaling. Non-hierarchic grouping by MDS. Same presentation features as for PCA. Iterative optimization of distances according to similarity matrix. c. Self-Organizing Maps. Non-hierarchic grouping by the technique of SOM (Kohonen maps), a sort of neural network. MANOVA. Advanced statistical analysis of discriminative features between selected groups with indication of confidence based on multivariate analysis of variance. d. Statistics. A number of parametric and non-parametric statistical tests can be performed in an easy and intuitive environment (Chi-square test, T-test, Wilcoxon signed-ranks test, Kruskal-Wallis test, ANOVA, Pearson correlation test, Spearmann rank-order test. Automatic display available tests for each input data type. Kolgomorov-Smirnov test for normality of character data. Deliverables: The contractor shall deliver after receipt of order. CCR: Vendor must be registered in the Central Contractor Register (CCR) prior to the award of the contract. You may register by going to www.ccr.gov. You will need to your Tax ID, Duns Number, Bradstreet number and banking information. QUESTIONS DEADLINE: All questions are to be submitted via email to Vida.Niles@fda.hhs.gov, no later April 20, 2009, 4:30 pm EST. QUOTATIONS DUE: All quotations are due to: Vida.Niles@fda.hhs.gov, no later than 4:30 pm, EST on Thursday, April 30, 2009. PROVISIONS and CLAUSES: The provision at FAR 52.212-1, Instructions to Offerors Commercial Items applies to this solicitation. The following agenda has been attached to this provision: None. The clause at FAR 52.212-4, Contract Terms and Conditions, Commercial Items applies to this acquisition. The following agenda has been attached to the clause: None. The clause at FAR 52.212-5 Contract Terms and Conditions Required to Implement Statues or Executive Orders, Commercial Items applies to this acquisition. The following FAR clauses cited are applicable: FAR 52.217-8, FAR 52.222-26, FAR 52.222-35, FAR 52.222-36, FAR 52.232-33, FAR 52.246-9 and FAR 52.246-18. Clauses and provisions are incorporated by reference and apply to this acquisition. Responses to this notice shall be sent via email to Vida.Niles@fda.hhs.gov, Telephone calls will not be accepted.
 

Web Link

FedBizOpps Complete View
(https://www.fbo.gov/?s=opportunity&mode=form&id=c2e7d39a0ab579bdffce5d00bb049852&tab=core&_cview=1)
 

Place of Performance

Address: 5100 Paint Branch Parkway, College Park, Maryland, 20740, United States

Zip Code: 20740
 

Record

SN01793444-W 20090417/090415222815-c2e7d39a0ab579bdffce5d00bb049852 (fbodaily.com)
 

Source

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

---

| FSG Index  |  This Issue's Index  |  Today's FBO Daily Index Page |