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Resume
Independent consultant
2018 - Present
Design instrumentation, automation, and software to address novel experimental requirements.
Design and implementation of intra and inter-company data processing, registration and reporting workflows
Strategic IT and informatics systems and staff planning for new or changing scientific organizations.
Isolate issues then propose and implement workable solutions whether the issues are technical, procedural, human, or a mixture.
Extend and integrate hard-to-extend software systems.
Hands-on full-stack developer in a variety of technology platforms.
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John McNeil & Co., Inc., La Jolla, CA, President
2005 - 2018
With the JM&Co team, created the Assay Capture and Analysis System and Compound Registration which are used by small and medium sized research laboratories as their primary data platform. Designed and developed custom registration and data analysis modules to support a wide variety of novel science.
Developed information systems strategies for several start-up drug development companies and helped these clients implement them. Worked with some clients through due-diligence and acquisition.
Worked with a new mid-sized biotech to develop their IT and informatics architecture and organization. Helped hire and train staff. Oversaw the development and installation of primary systems. They are now fully self-sufficient.
Selected and coordinated implementation of hosted document management and SAS systems for clients.
Worked with a client to design and implement a cognitive test apparatus. Designed the software and control electronics architecture. Supervised and performed mechanical design. Helped supervise construction, and deployment.
Designed, developed, and launched LabSynch for experiment recording, analysis, and discussion. LabSynch was used by protein therapeutic research laboratories. One client's internal study shows LabSynch has provided time savings sufficient to offset the entire cost of deployment.
Served as interim CIO of a biotech company. Was retained to rebuild research informatics group; integrate IT and informatics; improve internal customer support; and improve data analysis, mining, and presentation systems. These objectives were all met.
Took over IT management of a biotech during close-out operations. Virtualized a full server room of equipment onto two small servers that preserved fully operational research database and tools. These systems enabled the sale of the data and IP. Roles included technical and project management, as well as hands-on windows systems administration.
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XARDAs, President
2005 - 2014
Founded and operated one of the industry’s first 3D Printing services.
Helped diverse clients learn the benefits and limitations of the new technology leading to successful products ranging from electric guitar pickups to novel drone configurations.
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IBIS (Division of Isis Pharmaceuticals), Carlsbad, CA, Vice President, Ibis Product Development
2004 - 2005
Helped design and create TIGER, the Universal Pathogen Sensor, a revolutionary system that can identify any infectious agent whether known or new to science.
Established collaboration leading to initial DARPA funding for TIGER.
Created or identified business opportunities, and organized proposal efforts, leading to over $40M in revenue from government agencies including DARPA, CDC, NIAID, FBI, and DHS.
Developed TIGER business plan, in collaboration with senior TIGER team, leading to board approval and Isis investment.
Developed phase I engineering and design concept for third-generation TIGER instrument that provides a product roadmap to commercialize TIGER in 15 months.
Designed the Microbial Rosetta Stone Database for the FBI and DHS to support their microbial forensics mission. The database is unique in that it gracefully stores conflicting scientific data (for example, taxonomic information) in a manner that minimizes confusion and maximizes delivery of relevant knowledge.
Participated in, and influenced, the development of Isis corporate strategy as a member of the executive team.
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Isis Pharmaceuticals, Inc., Carlsbad, CA, Vice President, Informatics
2000 - 2004
Hired managers and rebuilt informatics team to support all computer systems for a 500-person company, enabling corporate objectives across the company and enhancing productivity of Isis employees.
Built service team and trained them in attitude, problem solving, and flexibility, so they could support diverse computing platforms and support rapid change. This gave research, development, manufacturing, accounting, and finance the flexibility to change their processes to improve efficiency, adapt to new business needs, and pursue new research.
Learned process and regulations for clinical data management, then rapidly applied this knowledge to develop and implement a new data management system after the failure of a previous development effort.
Mentored two PhD Directors, each responsible for supporting independent biological research groups. Their teams provided excellent tools, gracefully supported change, and contributed to the basic science.
Participated in, and influenced, the development of Isis corporate strategy as a member of the executive team.
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Isis Pharmaceuticals, Inc., Carlsbad, CA, Director, BioInformatics
1997 - 2000
Founded Isis bioinformatics department. Developed core databases and bioinformatics tools to enable Isis’ antisense discovery pipeline to increase throughput 100x.
Created universal object-relational model for DNA-like antisense molecules enabling storage and retrieval of over 300,000 molecules incorporating thousands of chemical modifications.
Developed computational biology infrastructure and algorithms to predict RNA structures for small-molecule antibiotic and antiviral drug discovery.
Selected and managed deployment of cheminformatics and LIMS software enabling small-molecule screening to launch a novel mass spectrometer-based high-throughput screening process.
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Science Applications International Corporation (SAIC), San Diego, CA, Laboratory Sensors and Automation Division Manager
1994 - 1997
Developed combinatorial chemistry synthesis robot with three independent tool-changing platen-motor heads and a variety of custom-designed pipetting and plate manipulation tools. System allowed client to rapidly set up and wash hundreds of concurrent solid-phase reactions from a pool of over 100 building-block reagents. This put them at the forefront of the emerging chemical diversity market.
Invented and built imaging fluorimeter which enabled biotechnology client to measure calcium flux in living cells simultaneously in 384 wells of microtiter plate, where they previously measured one well at a time.
Designed, built, and programmed robotic high-throughput screening system that let the imaging fluorimeter operate 24 hours per day. This required creation of LIMS, scheduling, and analysis software, none of which were commercially available at the time. Two systems were deployed, one of which functioned continuously for over seven years and screened over 2 million compounds.
Hired and managed instrument sales team, while directly interacting with most customers, yielding $8 million in robot orders.
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Science Applications International Corporation (SAIC), San Diego, CA, Physicist
1989 - 1994
Developed signal processing algorithms and systems-engineering models to analyze various sensor systems and data, enabling government customers to make program funding decisions based on the physics, not marketing hype.
Built prototype and software for an imaging laser radar.
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Cinematronics, El Cajon, CA, Customer Service Manager
1982 - 1985
Managed customer support department during the launch of the video game industry’s first laser-video disk based game, Dragon’s Lair. Kept systems running by quickly building and training opto-electronic servo repair group and training distributors. Speed was critical because video game popularity only lasts a few months.
Developed optical jigs and techniques to repair first generation laser disk players, which used HeNe tube lasers and five analog servo loops. This allowed our team to rapidly repair and return players experiencing > 50% failure-rates in the field, without returning them to Pioneer, who did not have the support facilities to meet demand, or replacement units.
Publications
Hari K.L. et al. The Microbial Rosetta Stone: a database system for tracking infectious microorganisms. Int J Legal Med. 2009 Jan;123(1):65-9. Epub 2008 Jul 8.
Ecker, D.J. et al. Rapid identification and strain-typing of respiratory pathogens for epidemic surveillance. in press, PNAS 2005 (2005).
Sampath, R. et al. Rapid identification of emerging pathogens: Coronavirus. Emerging Infectious Diseases 11, 373-379 (2005)
Hofstadler, S. A. et al. TIGER: the universal biosensor. International Journal of Mass Spectrometry 242, 23-41 (2005).
Ecker, D.J. et al. The Microbial Rosetta Stone Database: A compilation of global and emerging infectious microorganisms and bioterrorist threat agents. BMC Microbiology 2005, 5:19.
Ecker, D.J. et al. The Microbial Rosetta Stone Database: A common structure for microbial biosecurity threat agents. Journal of Forensic Science 2005, in press
Fogel, G.B. et al. Discovery of RNA structural elements using evolutionary computation. Nucleic Acids Res., 2002. 30(23):5310-7.
Lesnik, E.A. et al. Prediction of rho-independent transcriptional terminators in Escherichia coli. Nucleic Acids Res., 2001. 29(17): p. 3583-94.
PATENTS
6,429,016 System and method for sample positioning in a robotic system
6,221,587 Identification of molecular interaction sites in RNA for novel drug discovery
6,746,864 Automated system for simultaneously performing a plurality of signal-based assays
6,800,452 Automated methods for simultaneously performing a plurality of signal-based assays
6,911,181 Self-dispensing storage device
7,108,974 Method for rapid detection and identification of bioagents
6,969,763 Molecular interaction sites of interleukin-2 RNA and methods of modulating the same
7,217,510 Methods for providing bacterial bioagent characterizing information
7,226,739 Methods for rapid detection and identification of bioagents in epidemiological and forensic investigations
7,255,992 Methods for rapid detection and identification of bioagents for environmental and product testing
7,321,828 System of components for preparing oligonucleotides
7,427,380 Automated system and method for simultaneously performing a plurality of signal-based assays
WO 1999/053101 Identification of genetic targets for modulation by oligonucleotides and generation of oli-gonucleotides for gene modulation
WO 1999/058947 Modulation of molecular interaction sites on rna and other biomolecules
WO 2002/093409 Multi-paradigm knowledge-bases
WO 2003/001976 A secondary structure defining database and methods for determining identity and geo-graphic origin of an unknown bioagent thereby
WO 2003/091268 Molecular interaction sites of vimentin rna and methods of modulating the same
WO 2003/100035 Method for rapid detection and identification of viral bioagents
WO 2004/052175 Methods for rapid identification of pathogens in humans and animals
WO 2004/053141 Methods for rapid forensic analysis of mitochondrial dna and characterization of mito-chondrial dna heteroplasmy
WO 2004/060278 Methods for rapid identification of pathogens in humans and animals
WO 2004/093644 Methods and apparatus for genetic evaluation
WO 2005/009202 Automatic identification of bioagents
WO 2005/036369 Database for microbial investigations
WO 2005/086634 A secondary structure defining database and methods for determining identity and geo-graphic origin of an unknown bioagent thereby
WO 2005/089128 Rapid identification of microbial agents
US20040121311 A1 Methods for rapid detection and identification of bioagents in livestock
Other Fun Stuff
Holder of two world records for remote control electric helicopter distance