Resume/CV for Greg Colello

(Simulation Software Developer Using Java Technology)

CURRENT ADDRESS

4 Monte Alto Way
Santa Fe, NM 87508
ph: 505-466-1827
email: gcolello@comcast.net
web: http://www.scibizsw.com

CurrentSkills: Bioinformatics Management, GUI Development, Web Applications, Simulations, 25 Years of Computer Applications Experience.

CurrentComputerLangs: Java/Swing, Perl, CGI, HTML.

CurrentOS's: Linux, Solaris, W98/NT, Apple.

CurrentDB's: Sybase, Postgres.

AncillaryExperiences: GCG, Batch Blast, Oracle, MS Access, Visual Basic, C/C++, ObjC, F77, APL, Assembly, Matlab, NeXT OS, Pick OS, QA Manager, Documentation Specialist, Systems Administrator, Business owner, Functional genomics research, Gene expression microarrays, RFLP fingerprinting, PCR, Laboratory image scanning/analysis, T-DNA techniques, Satellite databases, Ecophysiology field work, Neurophysiology experiments, Cell-receptor assays.

1975-1980: Ph.D, Pharmacology, University of Rochester, School of Medicine and Dentistry, Rochester, NY.

1970-1975: B.S., Chemistry and B.S., Psychology, Wright State University, Dayton, OH.

2001-present: On Permanent Medical Leave From NCGR Due To Slow Cancer Recovery, Santa FE, NM.
On and off, since 2001, I have been undergoing various therapies for an abdominal cancer condition. I am cancer-free at the moment, but the GI-reconstruction surgeries have left me in a sickly condition, so that I can only work part-time. As part of a job rehabilitation program to start a part-time home software development business, implementing 3D simulation software; in 2004 I started taking Media Arts Software courses including Imaging, Audio, Video, and 3D Animation and Graphics at Santa Fe Community College. In 2005 I officially began my home software development business under the sole proprietorship name "Science Business Software". On January 1, 2006 I incorporated my sole proprietorship into the New Mexico S-Corportion "Science Business Software, Inc". I am currently engaged in Java software development of a simulation-builder application (see 3-D Physical Object Simulator Proposal). If my health remains as it is, I expect to release a prototype near the end of 2007.

1999-2001: Gene Expression Software Program Leader, National Center for Genome Resources (NCGR), Santa FE, NM (http://www.ncgr.org).
I started at NCGR as a Senior Software Developer doing development on a Java/Swing standalone application for comparative genomic mapping (CGMT). I also helped maintain the map server subsystem of The Arabidopsis Information Resource (TAIR) public sequence repository (http://www.arabidopsis.org), using Perl and Java 1.1. After 3 months I was moved to the role of Program Leader of Gene Expression Software Development. I co-managed 7 employees and three consultants in this capacity. I also interacted with upper management on a regular basis. The GeneX system consists of several components in an Open Source model. This includes a Java/Swing 1.3 standalone application for client-side submission of gene expression lab data and associated experimental protocols; a technology-neutral database schema that runs on Sybase or Postgres; a web server interface to the database through a Perl/CGI API; a plug-in Perl/CGI interface for analysis routines, which currently include hierarchical clustering, permutational clustering, and replicate analysis; and a standard XML transmission format for gene expression data. GeneX can be deployed on a small Linux server in a single lab or on a large Sybase server for an institution. It is being examined for possible use as a "gold standard" public repository for gene expression data. The GeneX project was recently awarded a large two-year NSF grant. The GeneX system is described in detail in an invited paper that appeared in the IBM Systems Journal, "Deep Computing in the Life Sciences" Supplement (http://www.research.ibm.com/journal/sj/402/mangalam.html). All user and developer information about GeneX can be reached from its open source web-site (http://genex.sourceforge.net). Lastly, at NCGR I did research using Blast on all then currently available complete genomes (54 microbial, D.melanogaster, C.elegans, A.thaliana, and 90% of H.sapiens genome). The project involved a new way to identify co-regulatory genes.

1999: Bioinformatician, Stanford Medical Center, Department of Infectious Diseases, Dr. Peter Small Tuberculosis Lab, Stanford, CA (75% time Stanford employee) (http://molepi.stanford.edu).
I added a large number of code improvements to the Molecular Fingerprint Analyzer (MFA) standalone Java 1.1 application to bring it up to production quality. This also included creating a Windows install package and writing full documentation. MFA allows a researcher to perform various mathematical analyses on patient specimen DNA fragments, tagged by a hybridizing probe and visualized on a gel as bands, in conjunction with a patient database. Also I am improving the ProbeBrowser Visual Basic application used to find deletions in microarray site-typing data.

1998-1999: Owner/Consultant, Science Business Software, Mountain View, CA (www.scibizsw.com).
On a part-time basis I developed scientific and business software systems using Perl, CGI, HTML, Java, Front Page, Visual Basic, and C. I specialized in web applications for bioinformatics, (LAB-ORDER (on-line ordering and lab data tracking)), and communications. I also programed simulations. My customer list:

1. Gryphon Sciences (Synthetic Proteins, S.SanFranciso) - Used a Perl/CGI/Linux-Apache-WebServer operating environment to implement an on-line protein ordering system. It established customer credit; took protein orders; scheduled the necessary lab protein synthesis steps; and tracked the subsequent synthesis, shipping, billing, and payment events. The system was equipped with a special read-only public protein database (275,000 non-redundant sequences) used to make protein synthesis business decisions. As a side project, I implemented a simulation of the entire company as part of an operations retooling analysis.
2. LearnKey (An On-line Training Company, St. George, UT) - I constructed a "from-scratch" Java Chat applet and chat server combination as an upgrade to an existing on-line training system. The Java Chat system was designed to allow students and coaches to chat with each other in both public and private sessions through an easy-to-use graphical interface while in the midst of training over the Internet.
3. Micheal Levitt Lab (Protein Structure, Stanford Univ) - Determination of the mapping of PDB protein database sequences with the Swiss Prot (SP) database. The mapping was 50% identical and 40% similar sequences. The remaining 10% of the PDB sequences had no correspondants in SP regardless of what similarity heuristics were used. (Paper in progress)
4. Peter Small Lab (Stanford Med Ctr) - I started as a consultant and became a part-time employee (see Bioinformatician above).

1997-1998: Bioinformatician, Mendel Biotechnology, Hayward, CA (www.mendelbio.com).
I produced plant functional genomics software written in Perl, CGI, HTML, Java, C, and Visual Basic. My duties included reviewing current major bioinformatics 3rd party software (Pangea, Incyte, Oxford Molecular, MAG); batch downloading of public genomic sequences and subsequent data processing; use of a local Blast server; interaction with a GCG database; automated generation and viewing of DNA sequence features; creation of laboratory data bases in MS Access 97; design of algorithms for expression array analysis and viewing; setup of a Sun/W95/NT/Mac 100BaseT intranet with a T1 connection and system security; and setup of a telephone system. Attended the November 1997 TIGR Computational Genomics Conference.

1990-1997: Ecosystem Simulation Scientist, Postdoctoral Research Associate, Carnegie Institution of Washington (CIW), Department of Plant Biology (http://carnegiedpb.stanford.edu), Dr. Joseph A. Berry Lab, Stanford, CA (http://biosphere.stanford.edu).
I produced plant photosynthesis, stomatal conductance, and ecosystem simulation software written in C, Fortran, and Matlab; accessing large satellite, lab, and field-site databases:

• 1992-97: I helped add photosynthetic and stomatal conductance components to ecosystem and global climate models; as part of the NASA EOS/IDS Biosphere-Atmosphere Interactions working group (http://sequoia.espm.berkeley.edu/ids/ids.html) with a focus on the utilization of global satellite and field data from NASA (ie. FIFE and BOREAS, see http://daacl.esd.ornl.gov). As part of this work I thoroughly tested and improved the SiB2 ecosystem module using the FIFE and BOREAS datasets (see reference below Colello, et al., 1997). (NASA/FIFE/EOS Grants).
• 1996-97: Implement a Biosphere 2 Simulation Project (Biosphere2 Grant) (www.bio2.edu). Simulate 1.5 continuous years of the Biosphere 2 Wilderness area operation at a 5 minute timestep, using SiB2 and other standalone algorithms.
• 1995-96: Put the CASA Soil Respiration Submodel in the SiB2 ecosystem module (W/GEC NSF Grant).
• 1990-92: Test the Plant Physiology Submodel in SiB2 for the CSU-GCM Project (CIW Fellow).

1990-1991: Technical Writing Consultant, Technical documentation of the KAR microfiche system for the State of Michigan (a book), Eastman Kodak, Technical Publications, Rochester, NY.

1989-1990: Manager of Systems Test Engineering, QA of Unix/OS for multi-CPU computers, managed 12 employees, ARIX Corporation, San Jose, CA (now out of business).

1988-1989: Software Quality Assurance Engineer, QA of Pick/OS computers, Fujitsu Microsys of America, San Jose, CA (www.fcpa.com).

1986-1988: Software Systems Engineer, Credit union software written in Pick/OS Data/BASIC, Ultradata Corporation, Pleasanton, CA (www.ultradata.com).

1985-1986: Software Systems Consultant, KAR microfiche software written in Pick/OS Data/BASIC, Eastman Kodak, BIS, Rochester, NY (http://www.kodak.com/US/en/business/index.shtml).

1984-1985: Software Systems Consultant, Telephone billing software written in IBM PL/1, Rotelcom Data Inc., Fairport, NY (no web page).

1983-1984: Software Systems Consultant, Warehousing software written in DEC PL/1, Hartman Material Handling, Victor, NY (now out of business).

1980-1983: Software Systems Consultant, Management software for world headquarters written in Sharp APL, Xerox Corporation, Rochester, NY (www.xerox.com).

1980-1980: Postdoctoral Research Fellow, Endogenous valium polypeptide research, Biomedical Institute, Univ of Texas, Austin, TX (with Dr. Karl Folkers).

1975-1979: Summer Research Employee (while pusuing my doctorate), Opiate peptide research, Pennwalt Pharmaceuticals, Rochester, NY.

2001: Mangalam, H., Stewart, J., Zhou, J., Schlauch, K., Waugh, M., Chen, G., Farmer, A., Colello, G. and Weller, J., GeneX: an open source gene expression database and integrated tool set, IBM Systems Journal, 40(2), 552-569, 2001.

1997: Berry, J.A., Sellers, P.J., Randall, D.A., Collatz, G.J., Colello, G.D., Denning, S. and Grivet, C., SiB2. A model for simulation of biological processes within a climate model, in: Scaling up from cell to landscape, eds P. Van Gardingen et al, 347-369, 1997.

1997: Colello, G.D., Collatz, J.G., Sellers, P.J., and Berry, J.A., Modeling of energy, water, and CO2 flux in a temperate grassland ecosystem with SIB2: May through October, 1987. J. Atmos. Sci., 55, 1141-1169, 1997. (reprints available upon request; colorfigure=http://sequoia.espm.berkeley.edu/ids/SiB2/index.html)

1996: Denning, A.S., Collatz, G.J., Zhang, C., Randall, D.A., Berry, J.A., Sellers, P.J., Colello, G.D. and Dazlich, D.A., Simulations of terrestrial carbon metabolism and atmospheric CO2 in a general circulation model. part 1: surface carbon fluxes, Tellus, 48, 521-542, 1996.

1996: Sellers, P.J., Randall, D.A., Collatz, G.J., Berry, J.A., Field, C.B., Dazlich, D.A., Zhang, C., Colello, G.D., and Bounoua, L., A revised land surface parameterization (SiB2) for atmospheric GCMs. part 1: model formulation, J. Clim, 9(4):676-705, 1996.

1994: Berry, J.A., Sellers, P.J., Randall, D.A., Collatz, G.J., Colello, G.D., Denning, S. and Grivet, C., SiB2C, a model for simulation of biological processes in climate models, J. Exper. Bot., 45(suppl), 5, 1994.

1991: Colello, G.D., Book: Kodak KAR Microfilm System Documentation for the State of Michigan Credit Reporting, pp. 1128, 1991.

1980: Colello, G.D., Chisolm, J., Heusner, J., Kellogg, C., and Bosmann, H.B., The benzodiazepine receptors from birth to old age, Life Sci, 1980.

1980: Colello, G.D., Ph.D. Thesis: Benzodiazepine receptor studies, University of Rochester, School of Medicine and Dentistry, 1980.

1979: Distefano, P., Case, K.R., Colello, G.D., and Bosmann, H.B., Increased specific binding of H3 diazepam in rat brain following chronic diazepam administration, Cell Biol. Inter. Rep., 3: 163-167, 1979.

1978: Colello, G.D., Case, K., and Bosmann, H.B., Competitive inhibition of benzodiazepine binding by fractions from porcine brain, Proc Natl. Acad. Sci., 75: 6319-6323, 1978.

1978: Colello, G.D., Case, K., and Bosmann, H.B., Benzodiazepine binding in rat brain, The Pharmacologist, 20: 273, 1978.

1977: Colello, G.D., The neural aspects of sex. Chapter in: The University of Rochester Medical School Neural Sciences Manual, 1977.

January 2001: Invited Speaker. Plant & Animal Genome IX Conference, Genomic Computing Techniques and Applications Workshop, San Diego, CA.

February 2001: Session Chair and Invited Speaker. Cambridge Healthtech Institute's Molecular Analysis for Research and Diagnostics conference, Molecular Profiling session, San Diego, CA.

Co-author on U.S. Patent application titled "Method and Apparatus for Gene Expression Data Storage, Retrieval and Analysis", filed January 26, 2001 as continuation of provisional applications Ser. No. 60/178,554 and 60/216,172.

Co-author on U.S. Patent application titled "N-dimensional coordinate mapping database method and apparatus", filed April 17, 2001; Ser. No. 60/284,156.

(references will be provided upon request)