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Clinical and Statistical Software Systems Engineer/Developer - Integrator
Ref No.: 16-00352
Location: Groton, Connecticut
Position Type:Contract
Start Date / End Date: 01/26/2016 to 01/26/2017
This is a long term contract position based in Groton, CT. Please see the job description below.

Department: Global Innovative Pharma Clinical Pharmacology/Pharmacometrics


Research Statistics, Primary Care Clinical Pharmacology and Statistics are commonly utilized in a computing environment which provides needed software and end-user facilities. This software includes R, Webstat, ePharm, Nonmem, PsN, OpenBUGS, and the network publishing systems and libraries these applications require. These departments require services to build, develop and maintain a number of discipline specific software platforms that support these organizations. The individual in this role will continue to maintain these platforms, continuously build and deliver new versions according to the individual department requirements, using requirements, tools and processes that are currently in place. The Scientific Software Engineer in this role would be expected to be an expert in these systems, assist end users with these systems, have extensive knowledge of the computing environments, assist support personnel who work across the HPC computing environment and are responsible for the support of platform scientific computing tools.

  • Installation and maintenance of needed software, and development of tools to automate this process.
  • Preparation of documentation supporting the controlled platform environments and scientific software tools required for Good Clinical Practices (GCP)
  • Configuration of the runtime computing environment, and development of tools that assist in providing and maintaining this configuration
  • Development of integration components for the software mentioned above
  • Expert support for end users utilizing the computing environment
  • Assist users in to enhance their productivity in the compute environment
  • Direct support of Knowledge Transfer to the Business Technology (BT) HPC Support team for support of testing and production releases of statistical software and PKPD tools.
  • R version 3.2.x for release in 2015 built for 64-bit Linux
  • The primary responsibilities include overall management, with guidance and direction from the project manager from Clinical Pharmacology and points of contact from Research and Clinical Statistics of the scientific software portfolio.
  • Maintain Unix account shell configuration files
  • Provide support to ePharm integration scripts with PKPD toolset comprised of R, NONMEM, PsN, etc.
  • Maintain the StatComp wrapper
  • Maintain the YPKG installation system
  • Collaborate on with the OpenBUGS development teams with guidance from the Point of Contact from Clinical Statistics
  • Maintain and further development the WebStat and MiDAS systems
  • Prepare new versions of R and associated packages for testing and production installation
  • Be thoroughly familiar and expert in Software Delivery Lifecycle approaches.
  • Collaborate on the development of an integrated testing framework for GCP PKPD software tools.
  • Collaborate on development of DOCKER based containers to ensure long term reproducibility of GCP PKPD software tools.
  • Contribute to maintenance and diagnostics of Unix infrastructure issues, such as account configuration, access control, storage management, job queuing systems, etc
  • Provide support for MiDAS infrastructure, including CCT protocols, Java Web Start, and integration with HPC computing environment.
  • Maintain the research statistics web presence
  • Administrate the pcsl statistical computing servers
  • Collaborate with Business technology and Support personnel as required.
  • Assume administration of the official OpenBUGS website
  • Bachelor Degree plus a minimum of 10 years experience in software development and demonstrated 10 years experience in scientific software configuration and management.
  • Exposure, experience or education in scientific software and high performance computing
  • Strong understanding of GCP and relationship to management of software installation stacks to ensure reproducibility
  • Extensive experience with administering Linux-like and BSD derived systems such as Red Hat, Slackware, Gentoo, and OS X operating Systems
  • Experience building complex software on Linux/Unix systems, including the ability to diagnose build scripts written in autoconf, Make, automake, cmake, libtool, scons, etc.
  • Experience and building libc, gcc, and ghc in a highly-customized environment, including the ability to write custom compiler specs files, linker scripts, and system header patches
  • Deep knowledge of Linux/Unix static and runtime linkers, including symbol versioning, and differences in symbol scoping and resolution between Windows and Unix
  • Proficiency using gdb, gcov, lsof, strace, valgrind, and wireshark to diagnose software behavior
  • Extensive experience with scientific computing languages and ability to read and write programs written in Bash, C, C++, Component Pascal (required for WinBugs/Openbugs), Fortran, Java, Javascript, TCL, Perl, Python, R, and SQL
  • Extensive experience in SQL based databases to support integration of software tools and data sources
  • Extensive experience in developing and integrating web-based statistical dashboard systems, e.g. Shiny, with scientific systems and data sources.
  • Extensive experience with software build cycles and resolution of build dependencies
  • Extensive experience with version control systems such as SourceForge, Git, etc.
  • Demonstrated experience with continuous build and testing systems and approaches.
  • Demonstrated experience with build and delivery of statistical software languages and associated packages and libraries such as R, openbugs, Stan
  • Demonstrated experience with build and delivery of new versions of Pharmacokinetic/Pharmacodynamic Software Tools such as NONMEM, PsN, openbugs, R, etc.
  • Strong understanding of IT business processes, including system life cycle
  • Demonstrated experience in technical writing and communication
  • Experience in using containerized systems such as Docker to control software dependencies and control reproducibility of software systems.
  • Have scientific computing experience with XML and JASON based data structures.
  • Experience administering Tex distributions
  • Experience developing and administering Documentum systems
  • Experience with OpenBUGS, Nonmen, PsN, D3, Tomcat, Apache HTTPD
  • Experience deploying and administering Oracle database products
  • Understanding of Unicode, including issues surrounding support of Unicode in scripting languages, database systems, and document preparation systems.
  • Experience with Centrify and Centrify tools for Unix.

    **Manager is willing to consider the resource working remote after training complete and based on performance**