Scientific software developer -consultant with 25 years experience providing informatics solutions for biotech and pharmaceutical research. Jamey has built and integrated many full stack applications for life science research as well as implemented and managed the customization and integration of commerical systems. Willow Data Consulting (Jamey) is looking for contract or full time opportunities to help with your scientific informatics challenges
Developer and Data Science Engineer in the Human Biology and Data Science informatics group:
-Developed tools for processing, querying, exporting and visualizing genetic association and cheminformatic operational big data
-JAVA , Python, Javascript, Pipeline Pilot, RESTful web application development with both relational and noSQL databases on Tomcat, Apache and Flask servers
-Developed mongoDB data repository aligning whole genome and whole exome disease association PLINK statistics and variant consequences for over 12K individuals in multiple association tests
-Developed a human genome Target Gene Explorer that integrated various disease association data, expression, variant consequences and epigenetic databases and file types for the disease of interest
-Automated data gathering and reporting of numerous public genomic datasources
-A development team member for a Target Gene Notebook web application to record genetic findings and manage publications.
-Built a human disease variant data processing pipeline using Python and executables including Plink, vcftools, snpEff
-Developed data visualizations with open source packages in Java, Javascript, Python and R Shiny
-Data engineering for registration, processing, inventory management and analysis of laboratory high throughput data and materials
-Built and supported a LIMS- compound and biological archive including integration of various robotic equipment
-Developed compound, extract, siRNA, physchem, DMPK data registries and associated data loading and viewing web application tools
-Evaluation, integration, configuration and support of various commercial scientific platforms for high throughput screening and lab robotics.
-Configuration and support of Chemcart, Certara D360, Sapphire Biobank installations
-Built data management tools that were components of a novel biomedical information “Knowledge capture” system. This involved coding extensive PERL applications that process complex relational spreadsheet and biomedical database information.
-Developer for “BIGR”, a validated JAVA enterprise application for biomaterials and information for genomic research. Enterprise Struts/EJB architecture with over 3000 class files. Developed and supported all layers of this dynamic application for managing biological specimens and associated clinical annotation.
.
-Developed a microbial gene expression microarray analysis platform for systems biology research. This included relational database design and management with MySQL. Developed front end web application analysis tools using JDBC, SQL, J2EE, JSP, JAVA Servlets. Produced statistical and visual analysis applications using JAVA integrated MATLAB
-Developed LIMS system for high-throughput screening of chemical libraries against antimicrobial targets and pathogenic organisms.
-Designed and maintained company website and internal knowledge web server
.
-Built a protein interaction information system. This involved Oracle database design, JDBC applications, Java servlets, and graphical display JAVA applets
-Designed environmental sample microbial DNA analysis system. Automated the BLAST analysis, annotation and display of genes identified from environmental samples
Software development duties included building and designing the following:
-JAVA and PERL based executables for the human genome project quality control
-Co-supervisory role for the development team
.
Scientist for various genomic analysis projects
.