Bioinformatics and Software Engineering: Pharmaceutical Technology (1330)
Expertise
Bioinformatics, particularly pre-clinical data management.
Software-engineering for pharmaceutical, manufacturing, financial and educational environments.
Relational database design, programming, and data warehousing.
Object Oriented Analysis and N-Tier Plug %u2018n Play Architecture.
Expert in Excel VBA, Perl, BioPerl, Oracle 9i SQL & PL/SQL, Toad, Java/JavaScript, Visual Basic 6.0, C, CGI, MySql, SmallTalk, Spotfire, Linux, Apache, Sybase/MS SQL Server, Windows XP, DEC VAX.
Experience
Consultant, Bioinformatics, Principal Software Engineer 1999 - Present
Developed web application to manage bioinformatics workflow and resulting data. Coding in Perl (ClassDBI, FormBuilder, Template_Toolkit) and CGI and uses MySql database.
Created Hub-Item-Shop (HIS) n-tier VB 6 client/server architecture that provides plug'n play ability for developing interface screens with ActiveX controls and data source DLL's and facilitates automated testing in all tiers. Design is object oriented and pattern based and reduces UI programming time and source code by 75% or more.
Created Oracle types for SQL select statements. Types eliminated 90% of query syntax errors.
Developed object oriented Perl program to play Mancala. Discovered first move winning strategy.
Independent Consultant, Bioinformatics Consultant and Web Engineer, 2005-2006
Designed and created database of miRNA information including local copy of miRBase, target predictions, published expression data and assay results. Database integrates several internal islands of information, provides data for web display and querying and allows faster and more sophisticated analyses. Database supports research on miRna's as potential biomarkers and therapeutic targets for cancer and other diseases.
Used database to combine pilot expression data, assay results and cell line properties to identify differential expression of miRna%u2019s. Identified some putative miRna%u2019s whose differential expression correlated with drug sensitivity.
Created derivative database views and Excel macros to analyze relation of size of utrs to presence of predicted miRna binding sites.
Converted web applications to new format. Modified code to be more object oriented providing better reuse and faster development. (ClassDbi, CGI, Oracle, Sybase)
Monell Chemical Senses Center, Systems Biology Computer Consultant 2004 - present
Developed Excel Vba application to process and summarize microarray results in preparation for upload to statistical packages. Developed methods for dynamic creation of record classes without coding overhead of static classes. Methods simplify coding and standardized access of class data.
Aventis Pharmaceuticals, Scientific Database Consultant 2003 - 2004
Created CGI/Perl/Oracle web application to display data in Genome Sequence Data Base.
Created CGI/Perl web shell for testing client side processing and GUI functions including new subclasses of CPAN ClassDBI to generate test data as if they came from a database.
Enhanced Ensembl, an international web application providing annotation on eukaryotic genomes, to display new track of gene related data using Perl and MySql
Enhanced Pfaat, an open-source multi-sequence Java alignment tool, to sort sequences by their similarity at one or more selected positions to a selected sequence, show trans-membrane regions.
Developed Excel spreadsheet to create and edit protein residue annotations ready for upload into Pfaat.
Fox Chase Cancer Center, Scientific Database Consultant 2002
Designed and implemented yeast transcription factor data staging, data warehouse and data mart databases with source data downloade from web or Perl-automated web queries.
Honors & Publications
Presented many papers, for example, "Object Oriented Programming Using Oracle Types," at April, 2002 annual meeting of International Oracle Users Group.
Education
PhD Molecular Biology, Indiana University, Bloomington, IN
BS Biology, cum laude, Brooklyn College, New York