Bioinformatics Spec I
Children's Hospital Philadelphia - Philadelphia, PA

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  • Bachelor’s degree in Bioinformatics, Computational Biology or closely related fields. Master’s degree preferred.
  • 3-5 years bioinformatics development experience in genomics
  • Advanced skills utilizing and in depth knowledge of bioinformatics algorithms, tools and resources, e.g. sequence retrieval, alignment and clustering techniques, expression profiling and protein related analysis, major databases and standards in the field
  • Expertise on nucleic acid and protein databases both in flat file and relational forms
  • Fluency in ORACLE/SQL, JAVA, PERL, C, HTML, XML and etc.
  • Strong working knowledge or training in advanced biomedical research
  • Proficiency in operating systems, UNIX, LINUX, Mac OS X, and Windows
  • Familiarity with PC/MAC hardware and software, e.g., databases and etc.
  • Knowledge of networking, TCP/IP, DECnet preferred
  • Excellent interpersonal skills to interact with both research and technical staff
  • Ability to work independently with minimal guidance while consistently exercising good judgment
  • Ability to learn new technology quickly
  • Ability to work efficiently on multiple projects
  • Ability to write and implement complex computer programs
  • Ability to independently set up and maintain multiple computer systems including cluster/server/workstation/PC/MAC
Mandatory Requirements:
All CHOP employees who work in a patient building or who provide patient care are required to receive an annual influenza vaccine unless they are granted a medical or religious exemption.
  • Child Abuse Clearances
  • FBI Fingerprint Clearance
  • Drug Screening
Job Description:
Provide strong bioinformatics expertise and support to the Molecular Genetics Laboratory in the areas of data mining (including next generation sequencing, copy number arrays), data integration, data management, data analysis, algorithmic, data visualization, and bioinformatics training. Consult with lab members on high throughput experimental design and optimization and perform project requirement analysis and provide pertinent user support. Apply sequence analysis methods, clustering algorithms, functional and statistical analysis methods to conduct data mining and in depth data analysis of genomic data in patients. Develop pipeline, application and databases as needed. Leverage existing public and commercial bioinformatics resources and tools. Develop algorithms, software tools, and resources as needed. Coordinate bioinformatics projects and activities with other internal and external partners. Enable integration and construction of scientific databases and applications in a growing clinical genomics environment. Utilize standard technologies like ORACLE, XML and large flat file systems. Design, program, test, modify, enhance, maintain, and support applications Assess computer hardware and software for scientific computing. Work in a team environment and interact with experts in molecular biology, bioinformatics and IT to contribute to cutting edge clinical diagnostics at CHOP.

1. Perform data analysis for various projects in the Molecular Genetics Laboratory. Identifies, ports/develops, maintains, and makes accessible all bioinformatics software for Molecular Genetics Laboratory as needed on the Unix/Linux platform. (45%)
  • Primary data analyst for genomics data in the Molecular Genetics Laboratory. Includes monitoring and assessment of the data quality, variant prioritization, data modeling, and statistical analysis.
  • Design, implement, and execute bioinformatics analysis strategies for various bioinformatics analysis tasks as requested by the Molecular Genetics Laboratory.
  • Actively collaborate and communicate with MGL team, core sequencing lab, and Bioinformatics Core throughout project life-cycles and for pipeline development.
  • Present and deliver analysis results to end-users.
  • Installs, maintains and updates existing software and all related programs that require installation on the main server, including software for genomic, proteomic, and microarray analysis. Determines effective porting, implementation, and maintenance plan for optimized use.
  • Continually updates and maintains locally stored datasets required for software, such as GenBank and SWISS-PROT.
  • Works on the Unix/Linux platform. Analyzes, specifies, designs and implements computer applications within the time frame established.
  • Programs in C, C++, java, and/or perl as needed and appropriate
  • Writes documentation of software implementation, maintenance, and customization according to standard programming protocols.
  • Writes protocols and documentation for tests in compliance with CAP regulatory standards.
  • Help with data presentation for manuscripts and grant proposals.
2. Works with the Molecular Genetics Laboratory to help determine needs. Analyzes user requirements, determines user software, hardware, and data management needs. Based on feedback, implements bioinformatics solutions. (45%)

  • Helps to identify and assess demands, requirements, and effective software solutions for the laboratory. Thoroughly researches market and custom options for fulfilling demand, including functionality, ease-of-use, compatibility, and integration with existing systems, interface, and value. Communicates and establishes relationships with software vendors.
  • Install, implement, maintain, and update commercial and open-source bioinformatics software for common bioinformatics and genomics data analysis.
  • Implement, update and maintain locally stored data resources required for various analysis tasks.
  • Make required software and software/data accessible to end-users.
  • Develop and implement policies, procedures, training materials and design specifications, as needed.
  • Familiarizes end-users with access to and usage of data analysis and data maintenance software, including initial training of software, either through direct interactions or by arranging 3rd party expertise.
  • Develops any customized applications or scripts with friendly graphic or form-based user interfaces, full database access functions and other specific features as required by individual studies. Correctly chooses most efficient programming language(s).
  • Assumes responsibility for troubleshooting, error resolution, and user support. Determines causes of problems as well as resolutions.
  • Provides software and hardware documentation and creates multiple forums for end-user self-assistance in simple problems (FAQs, user groups, help website).
  • Periodically determines the need for and facilitates end-user training sessions.
  • Recognizes areas of improvement in software implementation, usage, and performance; implements improvements as appropriate and suitable for the Molecular Genetics laboratory to implement.
3. Establishes direct, efficient, fast, and convenient data flows from data-generating parties to data analysis. (5%)

  • Works closely with the Bioinformatics Core, other data generation core facilities, to create a data pipeline.
  • Establishes methods to allow end-users to seamlessly transfer data from one data realm to another, and to access both data and data analysis tools from their desktop environments if possible. Creates user and group workspaces, websites, ftp repositories, and other solutions to ensure efficiency.
  • Works closely with IS Technical Services to establish and maintain data pipeline.
  • Works with Penn and other shared collaborative groups to establish methods for fast, efficient, and secure cross-institutional data sharing solutions.
4. Helps to manage and maintain computer systems for the Molecular Genetics Lab. (5%)

  • Works closely with IS Technical Services to assure proper installation, including upgrades, of new computer systems hardware and software (operating systems, database management systems, network, compilers and all others) for the computing systems acquired by the Molecular Genetics Lab, resulting in computers being operational >95% of the time.
  • Evaluates system-wide hardware and software requirements. Evaluates vendors; recommends modifications and expansions. Makes recommendations each year for the purchase of new computer system, hardware or software to meet the requirements of the Molecular Genetics Lab.
  • Provides annual evaluation of and recommendations for system-wide computer productivity.
  • Works closely with IS Technical Services to manage and maintain the computing systems acquired by the Molecular Genetics Lab. Manages user accounts, authorization, system security, backup and recovery, batch and print queue set-up, system resources accounting, and establishment of network and other system administration tasks. Monitors and adjusts system performance.
  • Evaluates and provides solution for equipment malfunction within 4 hours of request 90% of time.
  • Sets up or assists in the design and maintenance of systems networking for the computing systems acquired by the Molecular Genetics Laboratory, in conjunction with Information Systems.

About this company
The Children's Hospital of Philadelphia (CHOP) is the nation's first hospital devoted exclusively to the care of children. Since our start...