Joseph Coco

Freelance Database Expert & Website Architect

Location:Savannah, Georgia, United States
2 Skills
613 Walden Ln.
Savannah, GA 31405

-Coco, J. R. (2011) PARSES: A Pipeline for Analysis of RNA-Sequencing Exogenous Sequences. M.S. Thesis. University of New Orleans: U.S. Retrieved from
-Coco, J. R., Flemington, E. K., & Taylor, C. M. (2011). PARSES: A Pipeline for Analysis of RNA-Seq Exogenous Sequences. Bioinformatics and Computational Biology (Vol. 7, pp. 196-200). New Orleans, LA. Retrieved from

-Fall 2009 - Spring 2011. M.S., Computer Science (Bioinformatics), University of New Orleans, New Orleans, LA, GPA 3.444.
-Fall 2005 - Spring 2009. B.S., Computer Science, University of New Orleans, New Orleans, LA, Major GPA 3.445.

-July 2010 - May 2011, 40 Hours per Week, Research Assistant, University of New Orleans, New Orleans, LA. Develop PARSES, a pipeline for analysis of exogenous RNA using Perl and Ruby. Publish and present results regularly. Explore best methods to analyze exogenous RNA.
-August 2009 - June 2010, 20 Hours per Week, Teacher's Assistant, University of New Orleans, New Orleans, LA. Teach Java labs. Assist students with lab reports and software development issues. Grade lab reports.
-June 2008 - June 2010, 25 Hours per Week, Software Developer, SPAWAR Atlantic New Orleans, New Orleans, LA. Develop web applications in Java and PL/SQL. Develop applications in C#. Write documentation following waterfall and CMMI processes. Procure software for various projects. Handle procurements for four software projects.
-January 2008 - April 2008. 20 Hours per Week, Software Developer, Archon Information Systems, New Orleans, LA. Design GUIs in ASP.NET, C#, and CSS for web applications. Write unit test classes for existing code in C#. Write in house applications for data organization in C#

-Etiology of exogenous agents in human cancers using next generation sequencing.
-Classification of human viruses via their integration sites using genome annotation information.
-Next generation sequencing data visualization.
-Metagenomics (human microbiome interrogation against diseases and environmental science community functional potential).
-Biological data storage, sanitation, uniqueness and distribution.
-Hidden Markov Model bioinformatics data classification optimization.
-Computer-human interaction for analysis and research tools for experts.

-Nucleic acid and protein sequence analysis.
-Eukaryotic and prokaryotic genome analysis/annotation.
-Metagenomics (soil, water, and human samples).
-Algorithms for gene prediction, motif recognition, sequence alignment.
-Cheminformatics, nanopore detectors.
-Statistical genetics (linkage analysis, association studies).
-Bioinformatics Algorithm implementations, dynamic programming, HMMs, SVMs, dimensionality reduction, feature selection, classification.
-Object-Oriented Programming, Java (Spring, TomCat, Beans, JSP, jReport, AspectJ, NetBeans, Eclipse), C# (LINQ, Visual Studio, Crystal Reports), Perl, Ruby, and C++.
-Procedural Programming/Scripting, Perl, MATLAB, shell scripting (bash, sed, awk, curl, wget, etc.), Python (SciPy), Galaxy, x86 Assembly, C/C++, Ruby (Rake),Haskell, LISP (Common LISP), and familiarity with R.
-Database development, designed PL/SQL database, familiarity with NoSQL and MySQL.
-Design patterns, Abstract Factory, Factory Method, Lazy Initialization, Prototype, Singleton, Adapter, Bridge, Composite, Decorator (via aspects), Facade, Chain of Responsibility, Command, Iterator, Mediator, Observer, Template Method, Visitor, Balking, Messaging, Lock, Monitor object, and Read-Write Lock.
-Requirements, member and compentency leader of 2 CMMI level 3 teams, specification, use cases, user stories, quality control, configuration management (versioning, tool analysis), risk management, and requirements.
-UNIX system administration, Slackware, Ubuntu, Open-SuSE, Solaris, Debian, Fedora, Knoppix, FreeBSD, MacOS, familiarity with Plan 9.
-Gene expression, regulation, pre-mRNA processing/alternative splicing, gene sets.
-Virus, structure, reverse transcription, integration, progression, tumor treatment, retroviruses, transmission, XMRV, HTLV-1, vaccines, virophage.
-Cancer, etiology, progression.
-Sequence alignment, heuristic, global, local, and multiple alignment.
-Artificial neural networks, LDA, QDA, SVMs,
-Hierarchical clustering, MCMCs, Maximum Likelihood.

-PARSES: A Pipeline for Analysis of RNA-Sequencing Exogenous Sequences is a pipeline constructed from existing sequence analysis tools which allows a researcher to interrogate RNA-Sequencing experiments for possible biological contamination or the presence of exogenous sequences that may shed light on other factors influencing an organism's condition. Built upon Rake (Ruby), with some Perl scripts, PARSES allows simple analysis of RNA-Sequencing data in an automated and repeatable fashion. Usability, logging, and versatility are the keynotes of this pipeline. It has been resigned as a fork of the Galaxy project.
-CSAMS: Calibration Standards Asset Management System, a web application written in JavaEE using a seven tier web architecture backed by PL/SQL 11g with a JSP and Javascript front end using JReport for reporting. Developed using CMMI Level 3 practices. It ensures the readiness of test equipment to perform accurate measurements and provides valid data with reporting. It also schedules the testing for preciseness and accuracy of equipment regularly.
-MEASURE: Metrology Automated Systems for Uniform Recall and Reporting, a desktop application written in C# 2.0 with a PL/SQL 9 back end and WinForms front end. Developed using CMMI Level 3. It provides all Navy METCAL users with access to calibration production, recall and inventory tracking data for calibrateable support equipment. The data and information products generated by MEASURE facilitate Fleet maintainers using safe, reliable, calibrated support equipment on aircraft, ships, and weapons systems.
-FASOR: Family Advocacy System of Records Suite, a web application to collect and store maltreatment data, patient case details, and treatment and prevention plans. Automatic generation of secure administrative support materials, based on case data entered at Family Advocacy Program field offices and stored on the central FASOR server. Generation of customized statistical reports and data queries. Was in the process of being redesigning with C# 3.5 with a PL/SQL back end and ASP.NET front-end using Crystal Reports for reporting.
-TWPAM: Team Work Plan Automation Module, a web application written in Java with hard coded PL/SQL and a JSP front-end for planning personnel, material & logistic requirements, resource allocations, and individual resource assignments across field activities supporting multiple SYSCOMs. It is being redesigned using CMMI level 3 practices in JavaEE with a PL/SQL back end and a JSP and Javascript front end using a five tier web architecture with JReports for reporting.
-Civic Source Auctioneer, a web application written in C# 3.5 and ASP.NET to provide an online forum for banks, cities, counties and parishes to sell tax liens and delinquent, foreclosed and adjudicated properties. It was developed using Agile processes. It harnesses a SQL Server spatial database back end using LINQ to display properties to users with information regarding the property harvested from legal documents via advanced OCR techniques and regenerated using Crystal Reports templates.

-CSCI 1581 Software Design and Development I Laboratory (4 sections)
Applications, exercises, and explorations in methodologies, software design, and development. Object-Orientation basic premises using Java intended for CS majors.
-CSCI 2121 Software Design and Development II Laboratory (2 sections)
Two hours of laboratory each week to accompany CSCI 2120. Applications, exercises, and explorations in methodologies for software design and development. A continuation of CSCI 1581. Object-Orientation premises using Java pre-data structures intended for CS majors.
Skills (2) Rating
Website Architecture