SUMMARY OF KEY SKILLS & EXPERIENCE

• Familiar with bioinformatics tools, methodologies, database resources and their provision.
• SRS Administration on Tru64 multi-processor systems.
• Advanced UNIX programming & shell scripting experience (10+ years) on multiple platforms (Solaris, Tru64, IRIX, Linux).
• Experience (3+ years) installing, maintaining & supporting 100+ UNIX applications, packages and perl modules on multiple UNIX platforms for bioinformaticians.
• Extensive programming experience in Perl, C, Fortran.
• Basic working knowledge of C++, Java, Python, CORBA, Web Services (SOAP, XML), SQL, HTML/CSS, Lisp.
• Familiar with Grid technologies including the Globus Toolkit and OGSA/OGSI.
• Systems Administration experience on IRIX and Linux systems.
• Windows NT network management experience.
• Extensive parallel programming experience on various architectures (MIMD, SIMD, shared), languages (C, Fortran, HPF, *Lisp) and communication libraries (PVM, MPI).
• Led team responsible for benchmarking, workload characterisation, procurement, acceptance testing of large high-performance computer systems at NASA.
• Accustomed to supporting biologists, bioinformaticians, and other scientific computer users, in academic & commercial settings.
• Able to solve software and systems integration problems quickly.
• Adept at understanding and modifying code developed by others.
• Experience tuning and optimising complex scientific codes for floating-point, memory and communication performance.
• Excellent written and verbal communication skills.
• Technical documentation experience, recently managed a large open-source FAQ project.
• Considerable experience teaching, preparing & delivering training courses, organising workshops.
• Highly professional approach, attention to detail, focus on quality, dedicated, hard-working, self-sufficient.
• Generous in helping others, friendly and easy to get along with.

EDUCATION

9/85 - 3/90:  University of California, Los Angeles
Department of Mathematics
Degree Conferred:  Master of Arts, Mathematics, September 1988.
Graduate Course Work:  Advanced Numerical Analysis, Mathematical Aspects of Scientific Computation, Computational Fluid Dynamics, Parallel Programming, Domain Decomposition and Multigrid Methods, Asymptotic Analysis, Applied Differential Equations.
Ph.D. Qualifying Exams Passed:  Applied Real and Complex Analysis, Applied Differential Equations, Numerical Analysis, Parallel Computing.
Ph.D. Language Exams Passed:  French, German.
Thesis Topics:  Domain Decomposition, Fast Multipole Methods.
Thesis Advisors:  Tony F. Chan, Christopher Anderson.

3/83 - 6/85:  University of California, Los Angeles
Degree Conferred:  Bachelor of Science, Applied Mathematics, June 1985.
Honors & Awards:  Summa Cum Laude, Dause Prize, Honors Status, Dean's Honors List, member Phi Beta Kappa.
Additional course work in Biology, Computer Science, Physics, English and Psychology.

9/79 - 5/81:  Harvey Mudd College, Claremont, California
Major Field:  Engineering

EMPLOYMENT

10/2003 - present:  Bioinformatics Application Specialist
Syngenta, Jealott's Hill International Research Centre, Bracknell, Berkshire, United Kingdom
Temporary Contractor in the Bioinformatics Team, sourced through Kelly Services, Reading.

• SRS Administration:  Primary responsibility for overall modernisation and migration to new vendor release of LION Sequence Retrieval System (SRS). Established CVS repository of local configuration and customisation, enabling efficient tracking of vendor revisions against heavily customised customer installation. Identified bugs in vendor releases, often solving them and submitting patches to LION Support. Repaired & modified Icarus parsers for custom databases. Wrote Icarus programs to overcome memory resource issues in getz.
  
• Bioinformatics data management & infrastructure development:  Established ftp mirror of numerous public databases behind corporate firewall, comprising ca. 200GB. Established & managed CVS repository for multiple users. SSH tunnel configuration for intranet access to UNIX command line tools, and to external data protocols not supported by the corporate firewall (rsync, cvs-pserver).
  
• UNIX applications support:  Installation & maintenance of numerous bioinformatics tools (BLAST, ClustalW, EMBOSS, HMMER, InterProScan) and general purpose applications (Bash, Emacs, GCC, other GNU) on multiple Tru64 hosts.
  
• C, Perl & shell programming support:  Wrote custom special-purpose grep in C to detect specific text pattern. Wrote perl program to check quality and compliance of FASTA flatfiles from internal data sources. Repair & maintenance of numerous legacy perl scripts. Extensive shell script development (bash), for example to parallelise creation of blastable FASTA libraries from EMBL, GENBANK and other flatfile databases, under Sun GridEngine.
  
Reason for leaving:  Short-term contract, deliverable met (SRS 7.1 roll-out), no funding for new projects.

4/1997 - 4/2003:  Staff Member
European Bioinformatics Institute, Hinxton, Cambridge, United Kingdom
Initially, responsible for the following technology transfer activities at the EBI:
• BIOTITAN Technology Transfer Node (TTN).
  Part of the HPCN TTN Network, Esprit Project 24722: "Transfer of Bioinformatics into European Industry". Project goal was to stimulate uptake of High Performance Computing and Networking (HPCN) technology by the biotechnology, biomedical, agricultural and pharmaceutical industries in Europe. Sub-projects included "Bioinformatics Visualisation" (BIOVIS) and "Replication of Bioinformatics Databases Using CORBA" (REBDUC).
• Industry Affiliates Initiative.
  Part of the EBI Industry Support Programme, an effort to expand the EBI's industry partnership with SMEs (small-to-medium enterprises).
Subsequently:
• Technical Contact for Esprit Project 23486: "Distributed Pharmaceutical Applications Server" (PHASE).
• Windows Network Administrator. Responsible for procurement, installation & maintenance of a network of 25 Windows NT PCs.
• Established a "grid testbed" based on the Globus Toolkit, supporting Grid activities at the EBI (EU DataGrid, MyGrid).
Most recently:
• Lead maintainer of UNIX applications on Tru64, Solaris, IRIX & Linux. Including EMBOSS, Perl, GNU and more.
• Developing, deploying & maintaining prototype Web Services, in support of the MyGrid project.
• Local representative of the EMBL Staff Association Committee.
Reason for leaving:  End of fixed-term contract, no further funding.

6/95 - 4/97:  Visiting Scientist
European Molecular Biology Laboratory, Heidelberg, Germany
Supercomputing Resource for Molecular Biology
Parallel programming and high performance computing consultant to computational molecular biologists. Organised, prepared and delivered parallel programming courses. Ported and optimised scientific codes for parallel supercomputer architectures. Provided technical support for systems integration, procurement, workload management and software installation & maintenance. Led introductory courses in computing & programming.
Reason for leaving:  New post at the EBI.

6/94 - 6/95:  Member Technical Staff
Computing Centre, Delft University of Technology, The Netherlands
Planning, analysis and implementation of project "High Performance Computing and Scientific Visualisation in a Distributed Heterogeneous Environment." Developed tools to instrument modules within the Application Visualization System (AVS). Used these tools to characterise computation and communication requirements of AVS modules, particularly for remote modules in distributed visualisation applications. Addressed systems integration issues in a distributed AVS environment consisting of HP & SGI workstations and Convex & Cray vector supercomputers. Identified performance bottlenecks and data format conflicts and re-wrote modules to address them.
Reason for leaving:  End of fixed-term contract, no further funding.

7/90 - 9/93:  Senior Member Technical Staff -- Analyst
Computer Sciences Corporation, Moffett Field, California
Numerical Aerodynamic Simulation Facility, NASA Ames Research Center
Awarded the H. Julian Allen Award 1994 as co-author of the outstanding technical paper The NAS Parallel Benchmarks.
Technical Lead, Applications Analysis Group
• High Speed Processor (HSP) Procurement:  Constructed benchmark programs and workloads from scientific application codes. Conducted performance analysis and characterisation of benchmark programs. Estimated throughput performance on future HSPs via workload analysis and machine characterisation. Specified requirements for future HSPs, prepared Requests For Proposals, conducted Acceptance Tests of new HSPs.
  
• Parallel Benchmark Development:  Co-authored The NAS Parallel Benchmarks, wrote PVM versions, tested vendor performance claims.
  
• Math Library Development:  Selection, procurement, installation and testing of mathematical software for the HSPs.
Reason for leaving:  Left the United States.

6/86 - 6/89:  Teaching and Research Assistant
UCLA Mathematics Department
Assisted students with examinations and homework exercises, assisted professors with preparation and grading, prepared and conducted lectures. Courses included intermediate programming (using Pascal), precalculus, calculus, numerical analysis, mathematics of computer graphics and other applied mathematics courses.
Reason for leaving:  Left PhD program.

6/88 - 9/88:  Member Technical Staff
Thinking Machines Corporation, Cambridge, Massachusetts
Implemented ADI-like solver for underwater acoustics problem on Connection Machine 2, using *Lisp (parallel LISP). Algorithm featured substructured Gaussian elimination and folding odd-even cyclic reduction, under direction of S. Lennart Johnsson.
Reason for leaving:  Summer-student position.

OTHER TECHNICAL ACTIVITIES

Past FAQ maintainer for the Cygwin Project. Contributed to development of mail hosting services at gradwell dot com ltd. A 4-PC LAN at home, behind a i486 Linux firewall/router, is all home-built. I build economy Windows PCs and host web pages for charities.

PUBLICATIONS

• The NAS Parallel Benchmarks, edited by David Bailey, et al, NASA Ames Technical Report RNR-91-002, January 1991.
• The NAS Parallel Benchmarks, with David Bailey, et al, International Journal of Supercomputer Applications, Vol. 5, No. 3, Fall 1991, pp. 63-73.
• NAS Kernels Survey Report, NASA Ames Technical Report RND-92-003, February 1992.
• Embarrassingly Parallel Benchmark Under PVM, NASA Ames Technical Report RND-92-017, November 1992.
• The NAS Parallel Benchmarks (94), edited by David Bailey, et al, NASA Ames Technical Report RNR-94-007, March 1994.

AVAILABILITY

Available from October, 2004, for full-time or contract employment. An earlier start date can be negotiated.

NATIONALITY & PERMITS

American. Permission to reside and work in the UK granted by the IND on 24 January, 2003, through the Highly Skilled Migrant Programme. This is a category leading to settlement in the UK. No further permit application is required of the employer.