AFS Informatics was born on February 13, 1996; Since that date, we've helped clients to exploit Maspars, TimeLogic Accelerators, DEC, HP and Sun workstations, Convey Computers, multiple types of HPC clusters and supercomputers, always with an eye on helping to create successes in scientific research and development. Recently, I've worked with the FDA Food Safety Center to create an HPC Cluster for scientists, and ensured a friendly and efficient center to host GenomeTrakr (tracking full sequences of food borne pathogens) and various metagenomics research.
At this time, I am actively seeking new engagements.
To contact me, please send E-mail to:
Current telephone contact via: 919-323-7585
Computational Biology Consulting Services
My consultations have been about solving your problems and advancing your science, using creativity, drive, and calling upon my broad experiences.
I have provided a broad range of services to my clients, based on strong understandings of technical concepts and issues.
I have conceived and developed stand-alone programs and pipelines, developed and offered exceptional training programs and
offered strategic advice to start-ups that pointed them in valuable and
successful directions. I
have taken slow codes and optimized them for specialized hardware,
and developed friendly interfaces for ugly command-line programs.
I have offered valuable advice to companies and individuals on technology acquisitions and intellectual property concerns, and spent
considerable time with start-up companies in their initial assessment
and strategy sessions.
Recent work has been in my origins --> Ensuring that genetics and bioinformatics processes run as well as possile on high performance computing environments. In addition to my longtime work with specialized hardware, I've returned to the fundamentals of the generic hardware high performance cluster. It is still all about allowing our scientists to do effective science!
My work is consulting in the truest sense--> I have helped to ensure success at a diverse collection of goals and needs! My actual work varied with my client's needs, but has certainly included design and implementation of custom applications, optimization/speed-up of programs, design and delivery of excellent technical training and education, systems integrations, as well as timely, cogent, and relevant strategic advice and direct support for technical marketing and sales efforts.
My practice spans much of the breadth of the rapidly developing discipline of Computational biology which has been evolving from its origins in bioinformatics, computer science, mathematics, molecular biology and other traditional and non-traditional disciplines.
Some notable community activities
CSB, an annual bioinformatics conference that was held at Stanford University (and once at UCSD), was an activity that I directly supported, as a member of the organizing committee, local arrangements coordinator, and, in 2006-7, as chair of the Tutorial Committee.
From 2001 through 2006, I enjoyed teaching classes in bioinformatics data analysis, and modelling, as a part-time instructor, in the award-winning certificate program offered by the University of California at Santa Cruz extension program in Silicon Valley and also at the University of California Berkeley's Extension program. I currently welcome training and teaching opportunities in computational biology, high performance computing, big data and its analysis, and especially high performance software.
Some Posters and Talks to break out of my more customary non-disclosure mode which regrettably prevents discussion of many of my projects:
At FDA/CFSAN, I've been part of the group producing the CFSAN SNP pipeline. New version formal publication (co-author credit) in PeerJ Computer Science. CFSAN SNP Pipeline: an automated method for constructing SNP matrices from next-generation sequence data, https://peerj.com/articles/cs-20/
50th Maize Genetics Conference: Research poster: "Syngenta's Maize Allelic Diversity Platform", Sonali Gandhi et. al.
Pacific Biocomputing Symposium 1999 Research Poster described work on EST clustering using Smith-Waterman analysis on the TimeLogic DeCypher accelerator.
ISMB 1999 Research Poster (joint with K. Joho, D. Chang, (both were at Roche BioSciences in Palo Alto at the time) described a nucleic-sequence data mining tool for processing/browsing frameshift Smith-Waterman outputs beginning from protein motifs and fragments. The same process was later used in an interesting micro-array probe-design application.
ISMB 2000 TimeLogic's poster titled "Analytical Methods for Genome to Genome Comparisons". (joint author; the principal author Marty Gollery, is a friend and also a highly recommended colleague.
September, 2001 talk at Bay Area Bioinformatics group, "What have they done to my BLAST?"
(We've moved on to Nebraska...so you won't see those old license plates on the road...)
Have Bioinformatics (and more), Will Travel.
Compute Fast and Prosper!
Remember, to contact me for any reason, please send E-mail to:
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