- A top - performing, highly motivated professional with a deep understanding of the biopharmaceutical industry.
- Detail-oriented, committed, and with a consistent track record of delivering high quality solutions to clients.
- Experience in software development, business analysis, project management, full-stack development, and databases.
- Developed applications in major programming languages such as Java, C#, Python, and used bioinformatics tools such as E-Workbook and genomic analysis applications.
- Participated in trade studies and strategic analysis projects.
Development Languages and Environments: Java, C#, Python, R, OpenMP, MPI, Matlab, Apache Commons
Automated Build / Test tools: Ant, Maven, Hudson
Operating Systems: Unix, Windows
Databases: SQL, mySQL, Oracle, SQL Server, JPA, MongoDB
Design Methodologies / Tools: UML, Business Analysis, Object Oriented Design, Design Patterns
Design / Architecture Experience: Standalone, Client-Server, N-Tier, Parallelization, Database design
Scripting languages: Bash, perl, VBA
Specialist development packages/tools: E-Workbook (Biobook), ActivityBase, GATK, IGV, clcBio, BWA, Picard, Samtools, Bioperl, Biopython, BLAST, snpEff, vcfTools, Velvet, Agilent OpenLab
Markup Languages: HTML/XHTML, XML, YAML
SELECTION OF PROJECT EXPERIENCE:
Skills: AngularJS, Node.js, Express, MongoDB, C#, COM Interop
- As a member of the Agile team, was responsible for developing key components of the services such as inventory management
- Had ownership of Excel COM tools that aided in the operation of laboratory robots such as those used in liquid handling.
- Developed components of the web workflow application including a sequence validation tool.
Skills: Project Management, Business Analysis, NGS data analysis with Open Source tools, Perl, Python, bash scripting, Sun Grid Engine
- Worked with multiple stakeholders in understanding scientific requirements and evaluating informatics approaches for solving them.
- For example, studied different approaches in maximizing accurate variant identification while reducing false calls.
- The aim was to create pipelines that were fully configurable to allow the in corporation of different algorithms and toolsets.
- Made key contributions in the development of these pipelines, while setting up standard version-control environments, with testing, release and packaging procedures.
- Created user manuals, performed training, undertook troubleshooting, gathered changing requirements, and made updates to the pipeline.
- Performed tool evaluation, such as MuTect, in identifying somatic mutations in tumor-normal matched samples.
Skills: Python, Biopython, Linux, Fast-X, mySQL
- Designed and developed a highly configurable, modular, and efficient pipeline to identify high-quality sequences associated with specific motifs.
Skills: Perl, Bioperl, shell scripting, IGV, GATK, clcBio, BWA, samtools, Picard tools, snpEff, BLAST, vcfTools, Git
- In collaboration with informatician, performed a study of available open-source tools, and their applicability to this project.
- Designed and developed a modular, customizable pipeline that called high-quality, annotated variants.
Skills: GWT (Google Web Toolkit), Java, Spring, JPA, Weblogic, Eclipse, Maven, Oracle
- Users would annotate and maintain information for selected genes.
- Determined how best to provide scientific value to users, and designed and developed application.
Skills: Java, Perl, shell scripting, Batman, mySQL
- Enabled analysis of methylation patterns in colorectal cancer data by updating and automating this tool.
Skills: Biobook, Java, R, Oracle, Business Analysis
- Worked effectively with scientists in various therapeutic areas in developing templates for each specialized need.
- The templates performed calculations to measure e.g. Confidential induction, cell viability, clearance concentrations and more.
- Implemented statistical calculations such an Anova analysis.
- Conducted training sessions.
- Produced a tool which allowed scientists to easily record, store, and search on experimental data.
- This enabled a transformation in the way scientists conducted research.
Skills: Business Analysis
- Worked in a team to map detailed use cases of scientific workflows.
- These would be analyzed to create custom workflows in the eLN.
Skills: Business Analysis
- Was a member of a team that conducted a requirements study.
- Undertook a trade study of available COTS systems, gathered metrics on suitability, and made recommendations to the client.
Skills: C#, Visual Studio, MSAccess
- Worked in a team in porting the tool from a prototype to a polished solution delivered to the client. Participated in design, and undertook significant code restructuring.
Skills: Java, Excel VBA
- Significantly reduced manual work by writing Excel templates which automated the generation of engineering drawings and graphs.
- Wrote a timecard program enabling easy recording of employee work hours.
Skills: Project management, Business analysis, Java, J2EE, Oracle
- Performed project management duties in liaising with clients and monitoring activities of the offshore development team. Gathered business requirements and created software specifications.