Project History of Bradley K. Sherman

1998-2008:  Director of Bioinformatics, Mendel Biotechnology

1996-1997:   I was in charge of production bioinformatics at Incyte Pharmaceuticals, Inc. with primary responsibility for the PhytoSeq and ZooSeq products, which are specialized EST databases for plants and animals respectively. My responsibilities lay in the transformation of data from lab to database, including screening raw sequences for laboratory artifacts, annotation of the sequences against a variety of databases and preparation of the data for various proprietary presentation tools. In addition to producing programs in Perl and C, I supervised dataflow operators and other programmers.

1991-1996:   The Dendrome project of the Institute of Forest Genetics is a primary electronic resource for the study of the molecular genetics of forest trees. It acts as a gathering and filtering mechanism for data for the Plant Genome Database being constructed at the National Agricultural Library. It includes large datasets derived from genome mapping experiments and provides various interfaces to the data: World-Wide Web servers, free text searchable compendia and TreeGenes-- a hierarchical dataset within the ACeDB genome database software. The Internet services were the first of their kind within the U.S. Forest Service. In conjunction with IUFRO, Dendrome compiled a definitive index of forest geneticists for the planet. I supported the research activities of the molecular biologists at the Institute, writing various automation and data transformation tools for use with analysis software and Internet research services. As the sole computer scientist for the project I served as software architect, database curator, network administrator, teacher, purchasing agent, technical writer and public relations officer. In connection with the project I was co-chair of the Biology Workship at the First World-Wide Web Conference held at CERN in Geneva, Switzerland, 1994.

1987-1991:   The Computer-assisted Survey Methods Program at U.C. Berkeley provides data gathering and statistical software products for use by social scientists in academia, government, industry and the news media. These are multi-user products, maintained and enhanced for UNIX, PC-LAN's, VMS and CMS. This custom database does byte-level locking across platforms and allows roll-back to prior states. Besides maintaining and improving existing software, I wrote and ported several major new components of the system: a consolidated file system with integrated data compression, a program which creates and checks the file system environment for the survey software, and an interview scheduling program.

1986-1987:   I designed and wrote an inventory control system used by the Travel Book division of Banana Republic, Inc. This software runs under Xenix and employs the Informix relational database system. The system became operational in September, 1986. In November, 1986, Banana Republic contracted a number of enhancements to the system including expert determination of store stocking levels and automatic ordering. These became operational in February, 1987 and were installed with almost no perturbation of day-to-day operations of the company. The system handles inventory at more than 50 stores with an average of 2000 distinct types of item in each store.

1986:   I designed and wrote a telecommunications program for use on IBM PC's and compatibles. The program is used by chains of book stores to handle ordering and order confirmation. The program maintains a database for up to 100 stores and manages user scheduled automatic two- way file transfers via modem. The data sent and captured is used to moderate communications with parent company mainframes. The remote stores have point-of-sale and inventory control systems designed by IBID, Inc. (my employer at the time). The proprietary protocol used for the transfers uses cyclic redundancy checks and variable block sizes to ensure data integrity and maximize bandwidth.

1984 - 1985:   I implemented a software system for creating, modifying and archiving mortgage credit reports. This system ran on Plexus super-micro class Unix systems in the offices of Credit Fax, Inc. The system was written in C using C-ISAM database tools. Accounting information was extracted for transfer to an electronic billing system running on Data General equipment.

1982 - 1984:   I worked with a team of programmers at Berkeley Systems Works (later Berkeley Speech Technologies) to develop a speech synthesis system. My responsibilities included cross-compiling C written for a Unix development system to firmware for a proprietary box containing a 6809 microprocessor and a prototype of the General Instruments SP1000 speech chip. Some of the compilation had to be done by hand. I also worked with linguists to create and implement phonological and prosodic algorithms in the product. This software has been licensed to several corporations to add speech capabilities to various devices.

Ironic Systems -->