Department of Commerce, Patent and Trademark Office (PTO), Office of Procurement, Box 6, Washington, DC, 20231

70 -- BIOINFORMATICS EXTERNAL SUPPORT SOL SSPAPT010002 DUE 022900 POC Raymond Witmer, Contracting Officer, Phone (703) 308-5064, Fax (703) 305-8294, Email raymond.witmer@uspto.gov WEB: Visit this URL for the latest information about this, http://www.eps.gov/cgi-bin/WebObjects/EPS?ACode=M&ProjID=SSPAPT010002&; LocID=251. E-MAIL: Raymond Witmer, raymond.witmer@uspto.gov. THIS IS NOT A SOLICITATION. For over ten years the PTO has maintained its Automated Biotechnology Sequence Search (ABSS) computer system to support examination of biotechnology patent applications containing genetic sequence information. Within the last year, the increasing size and complexity of sequences in these applications has increased the ABSS workload dramatically. The PTO is seeking information on the use of services and existing computer systems external to the PTO to support examination of biotechnology patent applications containing genetic sequence information and to reduce the escalating costs associated with infrastructure expansion of internal biotechnology computer systems. All system(s) must be currently functioning, fully supportive of their internal and external customers, and not created specifically for PTO use. The systems and services must allow for a sequential approach to implementation at PTO, including providing PTO staff with electronic access to sequence searching systems via subscription or other arrangement equivalent in function, performing sequence searches for PTO based on PTO requirements, and providing a depository for PTO customers to submit sequence information, with provision for long-term data storage, retrieval, and dissemination. The minimum performance requirements are that the system(s) must: 1) be accessible 24 hours per day seven days per week (with scheduled maintenance downtime) and provide timely sequence search/search results, i.e., results returned within 24 hours for up to 20,000 searches (i.e., one sequence searched against one data base) per day; 2) display system responses within an average of 10 seconds and transmit those responses to the PTO's PC-based and Sun Microsystems workstations; 3) provide access to standard sequence search tools used in the public domain, at a minimum the Smith-Waterman, FASTA, and BLAST search algorithms, and optionally others such as FastDB; 4) process search query strings of 30x106 bases. Search queries of multiple sequences per patent application are to be expected; 5) provide a browser based interface to set up the search and display the results; 6) provide hyperlinks in the results to PTO patents, foreign patents from various offices worldwide, and to non-patent literature; 7) access up-to-date versions of public sequence data bases such as, but not limited to, GenBank, EMBL, SWISS-PROT, and PIR, and provide searches of other commercial type sequence data bases; 8) allow PTO users to control sequence search parameters and allow interchange of variables with regard to each sequence search, and accommodate alterations in search output formats to meet PTO's specific needs as necessary; 9) provide standard Windows features and be compatible with PTO automation software (see http://www.uspto.gov/web/offices/cio/trm/index.htm); 10) average 1-2 seconds per flip-rate from one display subset to the next; 11) allow incorporation of the PTO's own databases as part of the infrastructure; 12) integrate new/upgraded software tools capable of searching and evaluating new forms of biosequence information into the existing suite as they become available; and 13) accommodate periodic changes to existing sequence listing formats as identified in 37 CFR 1.821-1.825. Highly desirable performance requirements are that the system should: 14)accept biosequence data in electronic form, and provide storage estimated in the Terabyte range that meets the PTO's statutory requirements to maintain the confidentiality of patent application information. The system(s) must provide secured ready access to PTO search staff and all appropriate PTO personnel. T1, fiber optic or other similar technologies that provide high speed Internet access secured line shall also be required; 15) provide access to stored sequences and permit sequence searching by PTO personnel. A PTO based system administrator may work in concert with the system(s) administrator(s) at remote hardware installation sites with access only as authorized by the PTO. Editing for incorporation of patent application information must be available as required; and 16) support distribution to the PTO's sequence data partners (e.g., National Center for Biotechnology (NCBI), European Bioinformatics Institute (EBI), DNA Database of Japan (DDBJ), World Intellectual Property Organization (WIPO) and the Trilateral Patent Offices (PTO, European Patent Office, Japanese Patent Office). The system(s) must make sequence listings from issued patents available for printing and ready for duplication onto compact discs or other transportable media for final printing by the PTO. The system(s) and its organizational personnel must meet the PTO's statutory requirement for absolute and total confidentiality of patent application information. Meeting this obligation could require establishment of point-to-point secured communications both internal and external to USPTO. External communication to and from remote sites must use PTO approved security software and hardware for data encryption (i.e., Public Key Infrastructure (PKI); see pto-ebc.uspto.gov). All parties wishing to provide information about available systems and services that can function within the mandatory parameters provided herein should do so in writing (mail or email) to Raymond Witmer. Hard copy materials must be sent to U.S. Patent & Trademark Office, 2011 Crystal Drive, Suite 810, Arlington, VA 22202. E-mail must be addressed to raymond.witmer@uspto.gov. Any response must include a brief (no more than 10 page) description of the company's computing capability, experience with sequence searching, suggested approach to fulfilling our needs, and a description of existing and projected pricing plans for access to sequence searching systems, performance of search services, and storage and dissemination of sequence information. Also include company name, address, telephone and fax numbers, e-mail address, and point of contact. Information must be submitted to this office not later 4:00 PM local time, February 29, 2000. A copy of this Request for Information may also be found at Posted 02/17/00 (D-SN426581). (0048)

Loren Data Corp. http://www.ld.com (SYN# 0283 20000222\70-0007.SOL)