Contact: Harry Mangalam <hjm@tacgi.com>
Address: 1 Whistler Ct, Irvine, CA, 92617
Phone: 949 856-2899(h) 949 285-4487(c)
Immigration Status: Canadian Citizen, Permanent Resident of the US

What I do

I am deeply familiar with a wide range of research computing domains and work with researchers to help them accelerate their work in large scale visualization, bioinformatics, evolutionary biology, high-throughput sequencing, large scale data processing, compute cluster planning & implementation, system administration, data center planning, and grant preparation. I am comfortable dealing with research scientists in many fields (having been one and having married one). I have led and assisted in successful grant preparation and application for non-profit and academic institutions.

A frequent task is finding software to support a research need. Being research, quite often there isn’t a packaged or commercial system available, so I have to knit together multiple pieces of software into a pipeline or complex script, usually addressed with Perl, Python, and R/Bioconductor. If it involves computational bottlenecks I can program in C and am familiar with the GNU build toolchain. I also assist in general infrastructure problems such as campus-wide software distribution & licensing, storage & backup issues, network problems, outreach to faculty to identify and resolve bottlenecks, representation to campus groups and UC-wide discussion & planning groups.

Education

PostDoc: Medical Research Council of Canada Post-Doctoral Fellowship, with John B Thomas of the Molecular NeuroBiology Laboratory, Salk Institute, La Jolla, 1991. Genetics and biochemistry of the Drosophila singleminded gene and its gene products.

PhD: with Michael G Rosenfeld, HHMI, UCSD. Physiology and Pharmacology, University of California at San Diego, La Jolla, Dec. 1989. Transcriptional Regulation of the Growth Hormone and Prolactin genes; Cloning and characterization of Pit-1, one of the first POU-homeo genes.

MSc: with David R Jones, Zoology, University of British Columbia, Vancouver, May, 1985. Physiology and pharmacology involved in the diving response in mammals and birds.

BSc: Zoology, University of British Columbia, Vancouver, May. 1980. Honours thesis with David R. Jones.

Employment History

Dates Position Organization

5.2006-present

Research Computing Specialist

Office of Information Technology, UC Irvine

2.2005-5.2006

Research Associate

Earth System Science, UC Irvine

7.2001-2.2005

Principal

tacg Informatics LLC, Irvine, CA

1.2002-7.2002

Sr Bioinformatics Scientist

Acero Inc, Menlo Park, CA

8.2001-12.2001

Principal

tacg Informatics LLC, Irvine, CA

2000-7.2001

Sr Research Scientist & Project Manager (Gene Expression)

National Center for Genome Research, Santa Fe, NM

Previous Relevant Experience

Earth System Science: I worked with Charlie Zender of Earth System Science at UC Irvine on the tuning and analysis of the NetCDF Operators (NCOs), a suite of utilities for subsetting and manipulating climate model data in the form of NetCDF formatted files. These data sets are among the largest in the world and the NCO programs are responsible for a significant amount of the data reduction used in analysing them. See publication.

tacg Informatics: I have done bioinformatics contract work for the Epidemic Outbreak Surveillance taskforce (now part of the Homeland Security Department), GeneCodes, the CDC, Allergan, Accelerys, and startups.

Acero: I worked in the Science group on their Genomics Knowledge Platform (GKP), which provided both syntactic and semantic integration of biological information from a number of sources through their "Biological Object Model".

NCGR: I worked on the GeneX gene expression database project, an Open Source Gene Expression database for storing and analyzing results from large scale gene expression projects. See publication.

tacg: I created the sequence analysis application tacg and it’s CGI Web interface tacgi to make a small, fast (~30X faster than GCG or EMBOSS), free, and capable molecular biology tool available for Linux/Unix. See publication and the Sourceforge site.

Awards

Co-PI (with Drs. Carl Cotman, Ken Longmuir, Tatsuya Suda, David Walker, all of UC Irvine) of a Pacific Bell CalREN grant: Medical Informatics Use of Asynchronous Transfer Mode (ATM) service across the LA basin (June '94-September '97)

Co-PI (with Dr. Thomas Cesario) of Irvine Health Foundation Grant to implement ATM-based telemedicine applications using the infrastructure of the above CalREN grant (July, 1995 - September, 1997).

Medical Research Council of Canada Post-doctoral Fellowship to study Drosophila genetics with Dr. John Thomas at the Salk Institute (1990-1991).

Journal Publications

Coding and Technical Writing Examples

References

Available on Request

Latest Version

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