ABSS Statement of Work (SOW) - SSN Draft Version.pdf

United States Patent and Trademark Office (USPTO) Automated Biosequence Search System (ABSS)

Statement of Work (SOW)

Draf t

CUI//SP-PROCURE

Form # USPTO-OP-020 (08/2020) Page 1 of 22

Table of Contents Background

Purpose

Scope

Cloud Services Requirements

High Level Cloud Migration Roadmap:

Service Level Agreement:

Impacts

Deliverables

Period of Performance

Place of Performance

Special Requirements

Travel

Key Personnel

Training

Cybersecurity Requirements

Revision Date Revision Number Description

Form # USPTO-OP-020 (08/2020) Page 2 of 22

Background

The Automated Biosequence Search System (ABSS) is the current system used by the U.S.

Patent and Trademark Office (USPTO) since 1997 to examine claims including biosequences.

Its mission is to provide to the examining corps the capability to search electronic sequence listing data submitted by applicants, and support searching of molecular sequences using data stored from both applicant submissions and public/commercial databases of published sequence information.

The vision and mission of the ABSS is to enhance and sustain USPTO business function of performing prior art searching of polynucleotide and polypeptide sequences claimed in patent applications by providing a seamless, integrated, and efficient platform used by the Patents Examining Corps. ABSS is the searching system for Biosequence data that comprises polynucleotide molecular sequences using data stored from both applicant submissions and public and commercial databases of published sequence information.

Purpose

The purpose of this statement of work is to procure ABSS software and services. USPTO has determined that there is a need for ABSS Software for the purposes listed below, this includes continued license maintenance services, installation, applicable trainings, and premier operation and support to the Patent Examining Corps. The Contractor will be expected to perform the cloud migration of ABSS and shall comply with the USPTO requirement to migrate from the on-premise location to the Amazon Web Service (AWS) cloud.

Scope

USPTO requires a contract that will allow the use of Automated Biotechnology Sequence Search (ABSS) system, its software, maintenance, and operational support in accordance with the specifications listed below:

1.0. Capability to perform one-to-one nucleotide and protein sequence alignment searching against large databases e.g., single sequence vs. GenBank Nucleotide Collection databases.

1.1 Using at least the following sequence alignment algorithms/heuristics or their equivalents, including but not limited to Smith-Waterman and Basic Local Alignment Search Tool (BLAST), for local alignments; Needleman-Wunsch for global alignments; and Hidden Markov Model (HMM), including creating HMM profiles.

• For nucleotide searches, search both the query sequence and its complement

(searched in the 5’ to 3’ direction, a.k.a. reverse complement).

• Ensure that all search results clearly distinguish between hits to the original sequence and those to the reverse complement. Report these distinctions in a detailed table of scores and alignments. Please see section 1.5 for alternative search parameters.

Form # USPTO-OP-020 (08/2020) Page 3 of 22

1.1.1 Capability to search a nucleotide query against a nucleotide database (n2n search) and against a protein database (“n2p search”). Alignments displayed in search results for n2p searches must align three letter abbreviations for amino acids with their corresponding codon.

1.1.2 Capability to search a protein query against a protein database (p2p search) and against a nucleotide database (“p2n search”). Alignments displayed in search results for p2n searches must align three letter abbreviations for amino acids with their corresponding codon.

1.1.3 Capability to add and run a search using any other alignment algorithm/heuristic.

1.1.4 All algorithms and heuristics must be subject to independent, public review for soundness.

1.1.5 Algorithms and heuristics must be optimized so as to minimize computational requirements (e.g., SSE extensions for Smith-Waterman).

1.2 Capability to search databases stored in common formats, at least Intelligenetics

(IG), FASTA, and BLAST formats.

1.3 Capability to set a specific algorithm/heuristic and set of search input and output parameters as the default condition for each of n2n, n2p, p2n, and p2p searches.

• Must be configurable at an administration level.

1.4 Capability to set a default set of search input and output parameters as the default conditions for each alternative algorithm/heuristic available for n2n, n2p, p2n, and p2p searches.

1.5 Capability to set one or more alternative sets of search input and output parameters for each available algorithm/heuristic as alternative defaults for each of n2n, n2p, p2n, and p2p searches.

1.6 Capability to rank and save hits based upon “Percent Query Match” parameter.

1.7 Percent Query Match=(calculated score for best local alignment / perfect score)*100

Capability to rank and save hits based upon the metric "Score Over Length" (Score Over Length=(calculated score for best local alignment / hit database sequence length)*100)

1.8 Capability to rank and save hits based upon “Score” parameter.

Form # USPTO-OP-020 (08/2020) Page 4 of 22

1.9 Capability to search with a fragment of a biosequence as query, where the position numbering from the original sequence is maintained and displayed in the alignment output.

1.10 Capability to filter database sequences by minimum and/or maximum length.

E.g., database sequences that are not from 15-100 residues in length are excluded from the search.

1.11 Capability to score pairings between an ambiguity symbol and a corresponding defined residue as a match, conservative mismatch or mismatch.

• E.g., X in protein query paired with A in database sequence; y in nucleotide query paired with c or t in database sequence.

1.12 Capability to search sequence patterns with following capabilities.

1.12.1 Search PROSITE-style patterns in nucleotide or amino acid sequences, equivalent to EMBOSS “fuzznuc” & “fuzzpro”.

1.12.2 Search regular expression patterns in nucleotide or amino acid sequences, equivalent to EMBOSS “dreg” and “preg”.

1.12.3 Search with a query containing alternate residues at each of one or more positions.

• For example, position 5 can be Ala, Leu, Gly; and position 20 can be Arg or Lys.

1.12.4 Search with a query that excludes a specified residue or string of residues at a specified location.

• For example, position 5 is anything except His; position 10 is anything except Glu or Phe; position 15 is followed by anything other than the string Pro-Ser-Lys.

1.12.5 Search with a query with the beginning and/or the end of the sequence being marked.

• E.g., the N-terminus must be Gly; the C-terminus must be Thr; the N-terminus is Val and the C-terminus must be Trp.

1.12.6 Search with a query containing a wildcard residue at each of one or more positions.

• E.g., position 13 is any amino acid.

1.12.7 Capability to specify the size of a gap in a query.

• E.g., 0-20 repeats of any amino acid; 3-5 repeats of Trp

Form # USPTO-OP-020 (08/2020) Page 5 of 22

1.12.8 Search with a query containing a specified number of perfect or imperfect repeats (as with EMBOSS “dreg” and “preg”.)

• E.g., 3-10 consecutive copies of an imperfect repeat that is gatc or gatt.

1.12.9 Capability to combine any or all of these features:

• A combination of features/capabilities provided under items 1.12.1-1.12.5.

1.12.10 The output must display each alignment along with the bibliographic and annotation information associated with the database sequence(s). Not like GCG FindPatterns output.

1.12.11 Capability to select multiple databases to search a query in a single operation, as opposed to entering a separate search for each database – applies to general searching and EMBOSS (or similar tool).

1.13 Capability to create and search a 'mini-database' of specified sequences retrieved from nucleic and protein databases.

1.14 Capability to display a local alignment in context by displaying a specified number of residues adjacent to the region of best local similarity.

1.15 The output file for the search results must be printable and in a defined format:

• Search input information

• Table of scores (output statistics) for database sequences

• Alignments, output statistics, and annotations associated with database sequences.

1.15.1 Output results saved in customer defined format (relational tables, XML, etc.).

1.16 Capability of filtering out specified database sequence records from results set, primarily applicable for instances when many sequence records from a large family of related patents contain the same sequence. Need to see the results for only one representative patent and mask the rest. Filter by assigned sequence identifier for the records

1.17 Capability to set default naming of search output files. Must be configurable at an administration level.

1.17.1 Users have the option to include part of file name structure in the filename.

1.18 Capability to provide search output results to end-users.

1.18.1 Provide end-user with estimate of time of completion for a search that has been entered.

Form # USPTO-OP-020 (08/2020) Page 6 of 22

1.18.2 Provide end-user with access to search output results files, i.e., view and download.

1.18.2.1 Must be viewable/downloadable with USPTO systems.

1.18.2.2 Capability to select multiple search result files to copy to a user-designated location.

1.18.3 Access to search output results files to be available within 20 min of completion of search.

1.19 Capability to store more results (hits) for a search than is to be provided in an initial result set.

1.20 Capability to sort and filter search results.

1.21 Capability to select patent numbers or Pre-Grant Publication, (PGPub) numbers from sequence search result sets and generate a query from these identifiers to initiate a search in USPTO designated databases.

2 Sequence Analysis Tools Requirements for Use by Biosequence Examiners and

Biosequence Searchers:

2.1 Capability to perform global or local pairwise sequence alignments between specified database sequences.

2.1.1 Algorithms/heuristics for pairwise sequence alignments to include but not limited to Needleman-Wunsch, Smith-Waterman, BLAST, and Hidden Markov Model.

2.1.2 Capability to add and run alignments using any other pairwise alignment algorithm/heuristic.

2.2 Capability to perform multiple sequence alignments between specified database sequences, and when required by the user, create a “consensus sequence” from multiple sequences.

2.2.1 Algorithms/heuristics for multiple sequence alignments to include but not limited to ClustalW or equivalent, EMBOSS “emma” or equivalent.

2.2.2 Capability to add and run alignments using any other multiple sequence alignment algorithm/heuristic.

2.3 Capability to map restriction enzyme cleavage sites in a nucleotide sequence.

• Output to show sites in context of nucleotide sequence, and also translate amino acid sequence. (e.g., EMBOSS “remap”).

Form # USPTO-OP-020 (08/2020) Page 7 of 22

2.4 Capability to translate a nucleotide sequence and backtranslate a protein sequence, and also allow the use of such translations as queries in a search. (e.g., EMBOSS “transeq” and “backtranseq”)

2.5 Capability to predict antigenic sites within an amino acid sequence. (e.g., EMBOSS

“antigenic”)

2.6 Capability to calculate a hydropathy plot for an amino acid sequence. (e.g., EMBOSS “pepwindow”)

2.7 Capability to determine protein statistics, including molecular weight, number and mole fraction for each amino acid. (e..g., EMBOSS “pepstats”)

2.8 Capability to compare different search results sets to identify hits common to all sets (i.e., intersection).

2.9 All alignments must be run in the distributed environment (no single point of failure or execution).

3 User-friendly Interface requirements for Biosequence Searchers to Enter Search Requests into the Automated Information System:

3.1 Search Entry Interface for search staff.

3.1.1 Input and output parameters for the chosen algorithm/heuristic to be configurable by the user e.g., gap penalties, scoring matrix, word size, scores and alignments to save.

• When entering a new search, the default parameters should be displayed (see Requirements 1.4), and further configurable by the user.

3.1.1.1 Interface must not retain any user-configured input/output parameters from a preceding search session but shall display default algorithm/heuristic and default input/output parameters for a new search.

3.2 Capability to upload existing sequences from a sequence database record as query

3.3 Capability to upload existing sequences from a local file as query.

3.4 Capability to import query sequence from Sequence Editor. See Section 4.

3.5 Capability for user to display several sequences from a patent application and select them to search. Applies only to sequences from in-house patent application sequence databases.

• All queries must be searched with same algorithm/heuristic and set of parameters.

Form # USPTO-OP-020 (08/2020) Page 8 of 22

3.5.1 Capability to select multiple sequences for batch searching:

• selecting a range of sequences, e.g., 1-8;

• selecting various sequences, e.g., 2, 4, 7;

• combination of a range and various, e.g., 12, 53-55, 75-80, 121;

3.5.2 Capability to select multiple fragments of a single sequence from a patent application to be searched.

3.6 Provide for length-limited searches, including minimum length, maximum length and a range of length options. Length limitations apply to database sequences retrieved.

3.7 Capability to define unique length limitations (including but not limited to: “same length”, “any length”, or selected minimum and/or maximum lengths) for each query sequence in a multi-query search within one iteration of use of the GUI. Length limitations apply to sequences retrieved from the databases searched."

3.8 Capability to set minimum and/or maximum percent query match limitations for all queries within a search."

3.8.1 Capability to set minimum and/or maximum percent query match limitations for individual queries in a multi-query search within one iteration of use of the GUI

3.9 Capability for user to see progress and estimated completion time for searches that have been entered.

3.10 Capability for user to access results output for completed search requests.

3.11 Capability to retrieve historical results (hits) for a previously run search that (n) was provided in a prior result set without having to re-enter the search.

3.12 Capability to sort and filter search results.

3.13 Capability to select patent numbers or PGPub numbers from sequence search result sets and generate a query from these identifiers to initiate a search in USPTO designated databases.

3.14 Capability to choose among sets of databases to further do a combined text search based on the sequence result output.

3.15 ABSS shall provide the ability to define a minimum length for the contiguous region of exact matches in an oligomer search.

3.16 Ability to define the minimum score/length ratio in a score/length search.

Form # USPTO-OP-020 (08/2020) Page 9 of 22

3.17 Ability to retrieve sequences from PCT, Issued Patents, Published Patent Applications, and Pending Patent Applications using the “Fetch sequences” link on the ABSSWeb GUI.

3.18 Ability to conduct searches against sequence databases or user-defined collections of sequences wherein the maximum percent query match is less than 100%.

3.19 Continuous updates to recognize accepted amino acid codes and nucleobase codes (e.g., ST. 26 updates).

3.20 Ability to fetch fragments of sequences from PCT, Issued Patents, Published Patent Applications, and Pending Patent Applications using the “Fetch sequences” link on the ABSSWeb GUI.

3.21 Ability to define regions of query sequences where gaps are allowed and other regions of the same query sequences where gaps are not allowed (e.g., allow gaps between CDRs of antibody sequence queries, but not within CDRs of antibody query sequences).

3.22 Ability to require exact matches (i.e., not ambiguity codes or conservative substitutions) at multiple specific positions within a query sequence.

3.23 Descriptive error messages for all tools/features used (including Emboss/Jemboss, ABSS GUI, ABSS unix-based functions) to allow the user to correct input.

4 Examiners requirements for a Separate User Interface Which Will Enable Them to Use the

Various Search Capabilities of ABSS:

4.1 Capability for user to select sequences from a patent application for search. Applies only to sequences from in-house patent application sequence databases. All queries must be searched using the same algorithm/heuristic and set of parameters.

4.2 Capability for user to select algorithm, including but not limited to Smith-Waterman or

BLAST 3.2.8.

4.2.1 Capability for user to choose a pre-determined set of search parameters, e.g., standard or oligomer.

4.2.2 Capability for user to choose the number of scores and alignments to save. Limit to be set by administrator.

4.2.3 Capability for users to access and use BLAST to search NCBI databases through the cloud.

4.2.4 Provide for length-limited searches, including minimum length, maximum length and a range of length options. Length limitations apply to database sequences retrieved"

4.3 Capability for user to choose among sets of databases to search.

Form # USPTO-OP-020 (08/2020) Page 10 of 22

4.4 Interface must not retain any user-configured input or output parameters from a preceding search session.

4.5 Capability for user to see progress and estimated completion time for searches that have been entered.

4.6 Capability for user to access results output for completed search requests.

4.7 Capability to retrieve more results (hits) for a previously run search than was provided in an initial result set without having to re-enter the search.

4.8 Capability to perform a pairwise alignment of one sequence against a different sequence.

4.9 Users must have the options to retrieve these sequences from sequence databases and/or type them into the GUI and/or or copy them from text and paste them into the GUI. Any of these options must be available within the same iteration of use (e.g., retrieve one sequence from a database and paste the other sequence into the GUI).

The results of the alignment must be available in real time, accessible from the GUI, and downloadable from the GUI with the ability to save the downloaded alignment.

The alignment must use an algorithm acceptable in the art, including, but not limited to: Smith-Waterman, BLAST."

4.10 Capability to construct fuzzpro, fuzznuc, preg, and dreg (specific to EMBOSS) and pattern match (STN) query-patterns (i.e., allows syntax characters (special characters and numbers) in addition to letters) as a separate mode from construction of queries containing only letters.

5 Query Sequence Editor with the Following Minimum Capabilities: For Creating Custom

Query Sequences:

5.1 Capability to generate new and/or edit search query sequences.

5.2 Capability to retrieve a specified sequence from nucleic or protein databases into text editor window.

5.3 Provide system-created numbers for system-created residue positions.

5.4 Display residue-position number when the cursor is hovered over a residue.

5.5 Move the cursor to the correct residue when its position number is typed in. When a number is typed in, the system moves the cursor to a residue with that number.

5.6 Copy a sequence or part of a sequence from another source and paste it into the editor window.

Form # USPTO-OP-020 (08/2020) Page 11 of 22

5.6.1 Strip or filter non-sequence characters (numerals) and white space, if present, from a pasted sequence.

5.6.2 Convert case of residue symbols in a pasted sequence.

5.6.3 Convert 3-letter amino acid sequence to 1-letter, and vice versa.

5.7 Delete a residue or a block of residues by typing in a range and not having to delete one by one.

5.8 Capability to insert new residues within an existing sequence without overwriting.

5.9 Capability to replace one or more residues with another one or more residues.

5.10 Capability to name the final product or file as desired, such that it can be used as a query in any of the search tools.

5.11 Capability to construct fuzzpro, fuzznuc, preg, and dreg (specific to EMBOSS) and pattern match (STN) query-patterns (i.e., allows syntax characters (special characters and numbers) in addition to letters) as a separate mode from construction of queries containing only letters.

6 The Requirements Listed Below are for Users

6.1 Ability to retrieve sequences directly from Patent Cooperation Treaty (PCT), pending, published, and issued US patents databases using Unix-based commands within a PuTTY window and define the format for the output (e.g., retrieve a sequence from an IG-formatted database and display the sequence in FASTA format without using a separate conversion tool) with the capability of outputting multiple retrieved sequences to a single file.

6.2 Ability to retrieve fragments of sequences directly from PCT, pending, published, and issued US patents databases using Unix-based commands within a PuTTY window and define the format for the output (e.g., FASTA) without using a separate conversion tool, with the capability of outputting multiple retrieved sequences to a single file.

6.3 Ability to generate complements of nucleotide sequences and write them in 5’ to 3’ direction (as with Jemboss revseq) in order to generate customized query sequences.

6.4 Ability to fuse sequences and/or fragments of sequences from PCT, pending, published, and issued US patents databases into single query sequences using Unix-based commands within a PuTTY window (i.e., without using a separate editor) with the capability of outputting multiple fused sequence queries to a single file.

6.5 Ability to conduct pairwise alignments using Unix-based commands within a PuTTY window for a single sequence against another single sequence or against a “subdatabase” of sequences selected by the user.

Form # USPTO-OP-020 (08/2020) Page 12 of 22

7 GenBase Optional User Interface / Sequence Explorer Tier Real-Time Requirements for refining Homology Search Results

7.1 Enhanced presentation of search results, including:

7.1.1 Tabular presentation

7.1.1.1 Hyper-links to viewing and exploring sequence records, lists of duplicates etc.

7.1.1.2 Sorting by various columns, filtering by various criteria

7.2 Querying sequence data by various criteria, such as, but not limited to:

7.2.1 Pending patent application number

7.2.1.1 Publication number

7.2.1.2 Issued patent number

7.2.1.3 Ordinal number of sequence within the sequence listing

7.2.1.4 Publication date range

7.3 Searching text in sequence meta-data.

7.3.1 Ingestion of homology search results into GenBase.

7.3.2 Querying and text searches in homology search results.

7.3.3 Linking search results to relevant sequence listing records, and vice versa.

7.4 The ABSS Contractor shall provide training as need in addition to the ABSS Users instruction manuals for all components of the system including but not limited to:

• Searchers’ Graphical User Interface (GUI) (do not have at this time, needs to be created)

• Examiners’ Graphical User Interface (GUI) (currently have, need to maintain)

• Query Sequence Editor (currently have, need to maintain)

8 System requirement/Data management

8.1 System must run on heterogeneous commodity hardware.

Form # USPTO-OP-020 (08/2020) Page 13 of 22

8.2 System must have no single points of failure.

8.3 System must be portable to commercial/private clouds on demand with no re-work.

8.3.1 System must have ability to recover from compute node failure without reloading all data to all nodes.

8.4 System must be highly scalable with little to no configuration changes.

8.4.1 System must provide user defined reporting statistics on demand.

8.5 Data must be replicated across compute nodes to user configurable level.

8.6 Data management must be distributed to compute nodes.

8.7 System must maintain data integrity.

8.8 System must allow for partial reloads and updates.

9 Job management/queuing

9.1 System must be able to ensure completion/re-execution of all requests without manual intervention.

9.2 System must be able to provide different queue management for customer-defined job populations -- rush, default, etc.

9.3 System must be adaptive to varying loads and allocate compute and storage resources accordingly.

9.4 Relative light loads would change number of resources available to jobs. If only one job queued at historically light load time, all resources allocated to that one job.

10 High Level Requirements

10.1 Update ABSS to enable examiners enhanced processing, sorting and analysis of

Search Result data sets including sorting result sets by, for example, but not limited to, pPatent nNo., PGPub no, date order, sequence length or organism. Enable more examiner flexibility in how searching is performed, how results are displayed and ability to sort and further search results.

10.2 Ability to extract and export data, including Patent No., Pre-Grant Publication

(PGPub) No.

10.3 Export to CMS, Docket Application Viewer, (DAV) and/or Patents End to End- Search; (PE2E-Search), and generate query

Form # USPTO-OP-020 (08/2020) Page 14 of 22

10.4 Capability for user to choose among sets of ABSS search results databases to further do a combined text search based on the sequence result output.

10.5 Ability sort on fields like sequence length, date (of record or within record), organism. This will allow National Center for Biotechnology Information (NCBI), to begin identifying hits that are not prior art.

10.6 Ability to robustly text search ABSS hit sets using operators similar to as in

PE2E-Search.

10.7 Capability to compare different results sets to identify hits common to all sets.

This is useful for when claim requires two or more sequences that have to be searched separately.

10.8 Update ABSS to complete changes needed for Certified Copies in Certified Copy

Center (CCC) or Order Entry Management System (OEMS), which falls under DAV.

10.9 Update all ABSS export work including but not limited to exports for ABSS, Reed Technology Information Services (RTIS), National Center for Biotechnology Information, Publication Site for Issued and Published Sequences, World Intellectual Property Organization (NCBI, PSIPS, On Demand to OEMS for certified copies, PCT Contractor and WIPO).

10.10 Update all ABSS scripts for sequence listing processing and enable access and control via the admin module including makepat, makepub, allow script, sssaddnew, score splitter, ptoform script, etc.

10.11 In ABSS, Enable BLAST searching as well as user modification of search algorithm parameters. Implement a sequence query editor for ABSS sequence searching. Ability on examiner search tool to pull up a Sequence ID Number (SEQ ID NO), and then have automated entry of that sequence into NCBI BLAST or other publicly available search tools, such as EMBOSS. A simple selection button shown in the ABSS interface which allows the capability for users to select Smith-Waterman algorithm or BLAST algorithm.

10.12 Work with Enterprise Application Integration Hub (EventHub)/ SLIC related functionality. EventHub - new queues for ST.26 XML files or later standards.

10.13 Patent Application Locating Monitoring (PALM) and Docket Application Viewer (DAV) PALM/DAVchanges to alert examiner when there is a CRFD as most recent submission.

10.14 Warning to Science Technology Information Center (STIC) staff when title in 120 field does not match title in PALM.

10.15 Updates to OC / PALM PreExam / MPEP for ST.26 related form paragraphs changes.

Form # USPTO-OP-020 (08/2020) Page 15 of 22

10.16 PALM Pre-Exam interface to be updated to handle ST.26 including new form paragraphs.

10.17 Update data exchange process with RTIS as needed for ST.23, ST.25 and ST.26 sequence listings including any changes that will be needed for RedBook, YellowBook, and GreenBook data files.

10.18 Transfer all documentation and, procedures to Operations and Maintenance

Team and train them accordingly

10.19 Capability to identify and group identical sequences. For example: in the instances where many sequence records from a large family of related patents containing the same sequence., the user only needs to see the results for only one representative patent, and have the ability to mask the rest. Filter by assigned sequence identifier for the records.

10.20 Provide end-user with estimate of time of completion for a search that has been entered.

10.21 Improve efficiency of ABSS such that access to search output results files to be available in real-time.

10.22 Contractor will assist with updating the Operational Support Procedures (OSP), GEARS, Rally Database and system design documents. Contractor may also participate and provide updates to the Change Request Approval Board (CAB) and provide the Government updates to the software via Technical Strategy Meetings.

Cloud Services Requirements

Provide end-to-end cloud solution to migrate ABSS using a “Lift and Shift” cloud migration strategy to move it from on-premises to the Amazon Web Services (AWS) cloud. ABSS needs to be cloud compatible. Ensure compliance with USPTO Cloud Services Usage Policy and the USPTO Target State Architecture.

High Level Cloud Migration Roadmap:

ABSS Cloud Migration to AWS Cloud:

Preparation for USPTO Dojo intake Lift and Shift to lab AWS EC2. Mirror on-prem infrastructure and application environment Integrate ABSS with AWS native services and features Mirror production data onto allocated AWS storage Deploy ABSS in production AWS Cloud

Service Level Agreement:

Form # USPTO-OP-020 (08/2020) Page 16 of 22

ABSS is measured by the Business performance requirements success rate of 99% of results from search requests returned within 24 hours of submission, and 100% of results from search requests return within 48 hours of submission. The ABSS shall be accessed, and search results delivered via the Internet/Web. The system shall allow for all USPTO licenses to access simultaneously. The system shall be available 24 hours a day, 7 days a week except for allowed pre-scheduled maintenance performed between the period beginning Sunday 12:01 AM to 5:00 AM Eastern Standard Time. There shall be no downtime during the “quiet period” of elevated USPTO activities, defined as September 1 through October 1. System must be configurable to meet SLA requirements by either prioritizing individual jobs or ensuring equal allocation of resources across all jobs. The ABSS Vendor shall meet or exceed the following service level agreements:

Requirement Description Specifications Measurement

Vehicle Availability ABSS shall be available 24/7 to TC1600 examiners and STIC-EIC1600 sequence searchers with a PTONet user account.

End user hours:

Monday thru Friday 8AM – 6PM EST

The system shall be operational, consistent with the Hours of Operations as noted above. Other scheduled outages if required will not be measured against server system availability percentage. Target Availability for

ABSS: 99 %

Service Desk Problem Alerts Problem Notifications

Deployments Production deployments shall have a high success rate.

<2 issues identified in installation process (unavailability of end user does not impact metric) Rollbacks: <Two (2) Rollforwards: <Two (2) Deployment success rate >97% Supplemental deployments as needed < Two (2).

USPTO Install error log,USPTO Change RequestUSPTO CM Build Report

Post Deployment Reliability

The system shall remain fully operational and available to all ABSS users after Production deployments.

Event/Problem/Issue Discovered in 24 hours:

Severity Level 1: < Two (2) per Task Order Severity Level 2: < Three (3) per Task Order Severity Level 3: < Five (5) per Task Order Severity Level 4: < Five (5) per Task Order

Event/Problem/Issue Discovered within One(1) week:

Service Desk Problem AlertsProblem NotificationsUSPTO email

Form # USPTO-OP-020 (08/2020) Page 17 of 22

Requirement Description Specifications Measurement Vehicle

Severity Level 1: < Two (2) per Task Order Severity Level 2: < Five (5) per Task Order Severity Level 3: < Seven (7) per Task Order Severity Level 4: < Seven (7) per Task Order

Event/Problem/Issue Discovered within One(1) month:

Severity Level 1: < Two (2) per Task Order Severity Level 2: < Five (5) per Task Order Severity Level 3: < Ten (10) per Task Order Severity Level 4: < Ten (10) per Task Order

Operations Support

5 days/week 8:00

AM -6:00 PM EST

10 hours x 5days x 365 days Service Now CHG Email requests

Impacts

Customer Impact

ABSS is critical to examination of Biotech applications, carried out primarily by TC1600. Outage of ABSS would prevent STIC-EIC1600 sequence searchers and TC1600 examiners from entering searches of biosequences, which would in turn delay examination of Biotech applications that require searching of biosequences. In some TC1600 art units, ABSS is the primary search system used for search and examination. Examiners in these art units and STIC-EIC1600 sequence searchers may effectively be unable to work until such outage is resolved.

Business Impact

An outage of ABSS could delay examination of some Biotech applications, and possibly lead to Patent Term Adjustment. Some TC1600 examiners may have to be granted non-production time due an ABSS outage.

Deliverables

ITEM Supplies/Services QTY Unit of Measure

CLIN 1001 ABSS Software System to include all aspects of ABSS software system including Software 1 EA

Form # USPTO-OP-020 (08/2020) Page 18 of 22

License(s), maintenance services, installations, training, transition plan, Premiere Operational Support: 24-7 with 3-hour response time from initial call

CLIN 1002 GenWeb (ABSSWeb) software site license and maintenance services 1 EA

CLIN 1003 GenCore-6 software site license and maintenance services 1 EA

CLIN 1004 GenQueue software site license and maintenance services 1 EA

CLIN 1005 GenCore Grid Server software site license and maintenance services 1 EA

CLIN 1006 GenBase software Base Tier site license and maintenance services 1 EA

CLIN 1007 GenBase software, User Interface site license and maintenance services 1 EA

CLIN 1008 EMBOSS support and maintenance services 1 EA

CLIN 1009

Premier Operational support of all software provided in this estimate to include but not limited to data formatting, data analysis, error correction, system metrics evaluation. Support shall be available 24/7 with a three-hour response from initial call. 1 EA

CLIN 2000 Cloud Migration Support 1 EA

Period of Performance

The period of performance will be listed below:

Base period: 05/01/2025-04/30/2026 Option period 1: 05/01/2026-04/30/2027 Option period 2: 05/01/2027-04/30/2028 Option period 3: 05/01/2028-04/30/2029 Option period 4: 05/01/2029-04/30/2030

Place of Performance

The Vendor is expected to perform work offsite, keeping information private and secure, until otherwise notified by the Government. The Vendor must conform to any telework approvals and requirements in order to perform the offsite work. The delivery of work will be provided remotely from the Vendor's remote location to the following location unless otherwise specified by the government:

USPTO Headquarters

Form # USPTO-OP-020 (08/2020) Page 19 of 22

600 Dulany Street Alexandria, Virginia 22314

All necessary USPTO IT security approvals must be met prior to any change, and work shall be conducted in accordance with the latest, applicable USPTO remote work policies. In the event of a national emergency or other type of disaster and/or event, the contractor support services in this contract are deemed non-mission essential. For remote work, the Contractor is expected to obtain the Virtual Private Network credentials and accesses.

Business hours are considered from 8:00am – 6:00pm EST. For hours worked outside of normal business hours, USPTO COR approval is required.

Special Requirements

The Vendor shall be available to meet with the Product Owner and Contract Officer Representative and Technical Lead upon request to present deliverables, discuss progress, exchange information and resolve technical problems and issues. The Vendor will use their company issued computer. The Vendor will receive a SecurID token from the Government in order to login to the USPTO network and will connect to the USPTO network via Cisco Any Connect VPN. Any and all tokens that provide access to the USPTO networks should be returned upon removal or departure from the contract.

The Contracting Officer (CO) and Contracting Officer’s Representative (COR) shall hold a remote kick off meeting / post award conference within 5 business days. The purpose of this meeting is to review and clarify the contract’s objectives, expectations from the government and address any questions the contractor may have. In case there is a change needed after the meeting, the vendor has 5 business days to provide the COR and CO in writing additional clarification or modification if needed.

Travel

Travel reimbursement is not applicable to this contract. If the contractor has to travel to the USPTO campus for administrative purposes, the contractor shall assume responsibility for the travel expense.

Key Personnel

Before replacing any individual designated as key personnel, the contractor shall notify the CO no less than 10 business days in advance, submitting written justification for the replacement, and providing the name and qualifications of any proposed substitute(s). The federal government reserves the right to reject any proposed replacement that does not demonstrate the necessary experience and proficiency required.

All ABSS contractor personnel attending virtual meetings, answering government telephones and working in situations where their contractor status is not obvious to third parties are required to identify themselves as such to avoid creating an impression that they are government officials. They must also ensure that all documents or reports produced are suitably marked as contactor products or that contractor participation is appropriately disclosed.

Form # USPTO-OP-020 (08/2020) Page 20 of 22

Key Personnel for ABSS are identified as: Lead Developer (primary). When Lead Developer is out for an extended period of time such as vacation or illness, a backup (secondary) Developer is required. The backup Developer should be able to perform all duties and have all accesses as the (primary) Lead Developer.

Key Personnel should possess the following qualifications:

• Past development experience which produced useful results for the government.

• Expert knowledge of working with legacy and Next Generation PE2E (Patent-End-To- End) systems and the ability to design and develop similar systems effectively.

• Understanding of Sequence Alignment Algorithms such as BLAST, Smith-Waterman and Needleman-Wunsch.

• Knowledge of Genome and Protein databases like GenBank, UniProt, and Ensembl.

• Knowledge of biological sequences data representation such as ST.23, ST.25 and

ST.26.

• Proficient in programming languages: Perl, Java, JavaScript, Python.

• Full stack Development with expertise in both front-end and back-end development.

• Java Platform Enterprise Edition (J2EE/JEE) frameworks, design patterns and architecture patterns and JavaScript.

• Knowledge of High Availability environment (distributed system, load balancing, AWS cloud platforms).

• 10 years of experience with High-Performance Computing to handle large-scale computations.

• Experience with storage solutions (NAS, File System, Object Storage, Restful API, Amazon S3, EFS).

• Experience with Rocky Linux and Shell Scripts.

• Application and Web server technologies (Apache Tomcat, Apacher Server).

• HTML, XML, XSLT and XML Parsers.

• Web-based application development.

• User-centered conceptual and logical designs (wireframes, mockups, prototypes).

• Experience with User Interface Framework (Angular JS, jQuery).

• Proficient in designing, deploying, and maintaining cloud-based solutions.

Training

The government will provide the contractor with appropriate training as directed by the government and for government-unique systems., such as Information Technology Security Training and other mandatory training that USPTO requires to gain access to the Agency’s computer systems. The contractor is responsible for and shall ensure staff are properly trained and hold the appropriate credentials as required for the services being performed. Training will be provided virtually.

The contractor shall provide the personnel, resources, and facilities, as appropriate, to provide efficient and cost-effective procurement support services for the requirements outlined in this Statement of Work.

Cybersecurity Requirements

Form # USPTO-OP-020 (08/2020) Page 21 of 22

1. Contractors (including sub-contractors) entering into an agreement for services to the U.S. Patent and Trademark Office (PTO) and/or its Federal customers shall be contractually subject to all USPTO and Federal IT Security standards, policies, and reporting requirements. The contractor shall meet and comply with all applicable Federal, Department of Commerce (DOC), and USPTO laws, regulations, standards, policies, and guidelines, other Government-wide laws and regulations for protection and security of Information Technology.

2. The contractor shall comply with all applicable Federal Information Processing

Standards (FIPS). NIST Special Publications (800 Series) are guidance, unless required by a FIPS publication, in which case usage is mandatory.

3. The Contractor is hereby made to be aware that, all Information systems supporting

USPTO must meet the minimum security and privacy requirements using security controls in accordance with NIST Special Publication 800-53, (Current Revision), “Security and Privacy Controls for Federal Information Systems and Organizations.”

4. The Contractor shall use USPTO technical guidelines, NIST guidelines, or industry best practice guidelines in hardening their systems.

5. All USPTO systems and Contractor systems used in the execution of this contract/task order must receive a full Authorization to Operate (ATO) from the USPTO Co- Authorizing Officials. The system must be re-authorized on an annual basis based on the completion of annual assessments and continuous monitoring activities. Any changes to the system after it have been authorized, must be assessed and documented in accordance with OMB Memo 10-15 and 12-20.

6. The Contractor shall appropriately address NIST SP 800-53 (Current Revision) controls, assisting USPTO Cybersecurity Division, as necessary, to ensure security and privacy controls are in place and operating as intended.

7. The Contractor shall comply with security assessment and authorization (A&A) of all systems developed for support of the contract/task order in conformance with the standards set forth by the FISMA and NIST SP 800-37 (Current Revision), Risk Management Framework for Information Systems and Organizations.

8. Vendors for external contractor systems will coordinate with an independent third-party assessment organization to perform initial and annual assessments to obtain and maintain their system authorization consistent with NIST SP 800-53/53A, NIST SP 800- 30, and DOC and USPTO policies. An independent assessor is any individual or a team capable of conducting an impartial assessment of security and privacy controls employed within or inherited by an information system. Impartiality implies that security control assessors and privacy control assessors are free from any perceived or actual conflicts of interest with respect to the development, operation, and/or management of the information system or the determination of security or privacy control effectiveness.

9. Identified gaps between required NIST 800-53 controls and the contractor’s implementation as documented in the Security Assessment/Risk Assessment report shall be tracked for mitigation in a Plan of Action and Milestones (POA&M) document.

Form # USPTO-OP-020 (08/2020) Page 22 of 22

10. USPTO systems shall maintain a System Security and Privacy Plan (SSPP). SSPP updates will be made as material changes occur to the system operated and or maintained by the Contractor with updates occurring no more than 7 calendar days from the time when changes are made to the system. The system must also have a contingency plan and must regularly perform contingency tests to ensure the proper actions are taken in the event that the system fails.

11. The Contractor shall work with Cybersecurity Division after award to gain further details, ensure each stage maintains the proper level of security, and track any future enhancements.

12. A Security Impact Analysis (SIA) and/or risk assessment shall be performed whenever there is a change (major or minor) to a system.

13. The contractor shall notify the responsible ISSO, CISO and USPTO Computer Incident Response Team (CIRT) of any suspected incidents in a timely manner according to DOC/USPTO established guidelines and assist in the investigation of incidents as necessary.

14. As prescribed in the Federal Acquisition Regulation (FAR) Part 24.104, if the system involves the design, development, or operation of a system of records on individuals, the contractor shall implement requirements in FAR clause 52.224-1, “Privacy Act Notification” and FAR clause 52.224-2, “Privacy Act.”

15. The contractor shall follow secure coding best practice requirements, as directed by the

United States Computer Emergency Readiness Team (US-CERT) specified standards and the Open Web Application Security Project (OWASP) that will limit system software vulnerability exploits.

16. Plan and perform the security aspects of configuration management. The contractor shall ensure that computer software developed on behalf of USPTO or tailored from an open-source product, is fully functional and operates correctly on systems configured in accordance with government policy and federal configuration standards. The contractor shall test applicable products and versions with all relevant and current updates and patches updated prior to installing in the USPTO environment. No sensitive data shall be used during software testing.

17. The contractor shall protect information that is deemed sensitive from unauthorized disclosure to persons, organizations or subcontractors who do not have a need to know the information. Information which, either alone or when compared with other reasonably available information, is deemed sensitive or proprietary by USPTO shall be protected as instructed in accordance with the magnitude of the loss or harm that could result from inadvertent or deliberate disclosure, alteration, or destruction of the data. This language also applies to all subcontractors that are performing under this contract.