Al's Professional Experience

To contact me about possible work, please send E-mail to: al@afs4dna.com

AFS Informatics

  1. Developed, documented, implemented and maintained Time Logic's Unix API and remote-machine command-line facilities.
  2. Developed TeraClu system for sequence clustering using TimeLogic's TeraBlast
  3. Provided optimization for STACKPACK clustering code to implement a greater than 10-fold increase in performance.
  4. Developed a data mining tool for using Smith-Waterman outputs generated from protein motifs to find related nucleic acid sequences in databases. (See poster about this at ISMB99 ).
  5. Created a free-standing HTML-based application to manage sequence data subject to various formal partnership agreements between my client and other biotech companies.
  6. Provided bioinformatics systems integration for a large pharmaceutical company (has included development of a "nucleotide decision tree" pipeline for high throughput screening, making use of shell scripts, utility programs, web interfaces, database curation strategies, and optimization of applications developed by others).
  7. Parallelized (for MasPar execution) a combinatorial chemistry program used by a well known biotechnology research company up to the end of its Maspar's life.
  8. Provided strategic optimization and algorithmic advice to a semi-commercial supplier of bioinformatics software that increased their delivered speed by an order of magnitude.
  9. Assisted in the specification of bioinformatics hardware and/or software to meet diverse research and production needs for several biotech companies.
  10. Provided strategic technical sales support to vendors of automated biotechnology sequence searching applications. (Have been accused by my friends, and even an occasional recruiter, of "knowing everyone"...).
  11. Provided expert witness and technical advice in legal matters with respect to biotechnology. Example transcripts (involving hearings about Cost Effective Sequence Searching at the patent office) can be examined at FreeBsd Archive (previous online link is dead...).
  12. Provided training for new MasPar customers and assisted their customer support on solution of technical problems.
  13. Have provided integration and specification advice to a government agency in Asia, on the outfitting of their new (2001) bioinformatics facility for agricultural research.
The list is necessarily more vague than I would like, as particular agreements limit what I'm permitted to say about my experiences. In more than six years as an independent business, I've worked with almost two dozen direct clients, several dozen additional indirect clients, and have enjoyed many repeat engagements. New clients have often resulted from personal referrals and recommendations, which can be supplied on (qualified) request. I'm certainly not claiming to be perfect; I can also supply you with a couple of names of folks who weren't as happy with my work as I thought they should be....


Syngenta Stories

Contributed, as a consultant to rice sequencing processing and mining, and in an employee role, to microarray data processing, and to studying diversity in maize.


Experience as an employee at MasPar

Alas, it seems that these machines have now moved on to the domain of hobbyists and computer museums. They were notable as examples of general purpose SIMD computing, and owned several important niches in computer markets for a number of years.

  1. Redeveloped course materials on parallel programming, database software, program optimization, and systems administration for MasPar's SIMD computer systems.
  2. Offered courses and consulting to new customers both domestically and internationally on a wide variety of applications, especially in CFD and bioinformatics.
  3. Management responsibility for planning future directions and implementations of customer training.
  4. Lead consultant on bioinformatics system integration project for major pharmaceutical company.
  5. Member of post-sales Professional Services organization (Consulting, other services).


Experience as a Senior Consultant and founding member of Scientific Visualization Associates in Concord, MA

  1. Provided software development and optimization services, training materials development, and consulting services to Massively Parallel Systems Group at DEC, to MasPar Computer, and to the customers and third-party software developers for both companies.
  2. Provided training and consulting to AVS (3D visualization software) users on a variety of workstations (SGI, IBM, Kubota, Sun, Convex and DEC).


Ardent, Stellar and/or Stardent Computer

I often wonder if this enterprise could have turned into a large computer company that realized the bright future that it was created for. There was no shortage of talented people here, many of whom have gone on create successful enterprises and make great fortunes. Unfortunately, even staying with the enterprise to the very end, my myriad stock options never turned into anything but attractive wallpaper...

  1. Developed and offered Porting/Optimization Training for Fortran/C on Titan
  2. Offered and Updated courses in System Administration, Unix, DORE Graphics, Scientific Visualization using AVS and Programming AVS modules
  3. Provided custom consultations at customer sites on Systems Performance, Graphics, and AVS applications development (3D visualization)
  4. Developed and offered Compiler and System Administration Cross-Training after the Ardent-Stellar merger for analysts and field-support personnel
  5. Assisted customer support organization by handling difficult and unusual service calls, and by training new support-engineers
  6. Led customer training operations, coordinated sales training
  7. Appointed "Corporate Technical Specialist" for the Titan computer family, to recognize activities in a broad range of pre-sales & post-sales technical problem-solving
  8. Defender of Ardent's 30-day satisfaction guaranteed policy; unhappy customers got a quick post-sale technical assist and became happy customers.


College and University positions:

  1. Advanced Courses taught include Theory of Programming Languages, Compiler Construction, Data Structures, Programming Methodology, Automata and Formal Languages, Computer Organization and Artificial Intelligence.
  2. Programming Languages taught include Pascal, Fortran, C, Cobol, Algol, Lisp, Scheme, Prolog, SNOBOL, ICON and Assembly Languages (MIX, IBM370, VAX).
  3. Curriculum Development activity included serving as Chairman of the Curriculum Committee at Math/CS Department of U of Nebraska/Omaha, and designing/updating numerous courses at each institution.
  4. Served as internal consultant in purchase of new university computer systems at Morningside, UNO and U of Akron, and during UNO's initial implementation and management of DEC VAX/VMS systems and VAX/Ultrix systems.
  5. Published an introductory text on VAX/VMS, customized for use at University of Nebraska/Omaha (The UNO VAX Book, Kendall-Hunt, 1985) {Although quite obsolete by now, it is still indexed many places and can be ordered through Amazon, or directly from me}.


To contact me about possible work, please send E-mail to: al@afs4dna.com .