15-35768 BIOINFORMATICS ENGINEER II

Description: Pediatric biomedical research and emerging genomics and translational applications are driving an unprecedented increase in the scale and complexity of data management and analysis tasks. To meet this challenge, the Bioinformatics Engineer II in the Department of Biomedical and Health Informatics will help build, support, and maintain computational environments focused on the management, transfer, formatting, and general processing of complex data types associated with work in genetics, genomics and proteomics. The focus of the position is implementation and understanding of best practices in data manipulation and analysis pipelines, applications, general hardware configurations, and bioinformatics-specific hardware configurations. The Bioinformatics Engineer II will operate in a mostly local computing environment but will also represent the needs of large-scale bioinformatics in strategic discussions where those local environments are mapped to enterprise solutions. The position allows for a wide variety of activities within both research and clinical environments. The Bioinformatics Engineer II is primarily focused on supporting bioinformatics analytical groups and individuals as an engineering domain resource and operational data resource.

Requirements:

  • BS/MS in computational discipline required. BS/MS in systems engineering is preferred.
  • 3-10 years experience in a production clinical or research bioinformatics data processing role required.
  • Extensive knowledge with high performance and parallel computing environments and data processing workflows essential.
  • Extensive experience with data storage frameworks essential.
  • Extensive knowledge of CPU- and IO-intensive bioinformatics data analysis applications.
  • Demonstrated track record of optimizing systems to meet changing performance and load requirements.
  • Extensive knowledge of HPC systems, job management applications, including methods for profiling performance, benchmarking, and optimizing multiple job types and scenarios in bioinformatics data processing.
  • Ability to independently plan and execute pipelines and workflows of high complexity required.
  • Ability to independently engineer systems relative to larger enterprise framework required.
  • Strong UNIX/LINUX expertise required.
  • Expertise with build tools such as Make required.
  • Experience with configuration management tools such as Puppet is required.
  • Experience with system monitoring tools such as Nagios is required.
  • Experience in version control management in tools such as Git required.
  • Expertise in support mechanisms for applications written in common bioinformatics languages such as R, Python, Perl or similar required.
  • Expertise in support mechanisms for common bioinformatics applications, data sources, and data formats required.
  • Knowledge of common microarray, NGS, mass spectrometry, or other high-throughput data formats is required.
  • Expertise with resources of genomic data sets and analysis tools, such as UCSC Genome Browser, Bioconductor, ENCODE, and NCBI databases is required.
  • Demonstrated ability to develop and implement best practices for bioinformatics systems integration, testing, and automated deployment is required.
  • Expert knowledge with cloud computing concepts and applications is required.
  • Ability to lead discussions with various information systems and technology owners to achieve desired bioinformatics outcomes is required.

Click here to apply for this position.

Return to Top

15-36175 BIOINFORMATICS SCIENTIST III

Description: The Bioinformatics Scientist III will apply his or her knowledge of bioinformatics algorithms and analysis platforms to consult with investigators on their projects, analyze data and align with biological systems, and to serve as a collaborative, and sometimes lead, investigator in academic output including assistance in experimental design and grant writing. We are seeking a scientist who has experience in analysis and interpretation of data types including next-generation DNA sequencing, RNA-Seq, CHiP-Seq, DNA and expression arrays, or any other high-dimensional biological data type. This individual will work in a highly skilled, team-oriented environment applying knowledge of cellular, molecular, and computational biology to create novel methods and testable scientific hypotheses. Candidates will have an excellent understanding of the strengths and limitations of commonly used data generating platforms as they apply to experimental endpoints and will readily be able to set expectations and defend results through direct communication with principal investigators and their staff. This position will be able to apply a broad range of statistical methodologies such as generalized linear models, multivariate methods, and machine learning. An expert understanding of systems biology as represented by integrated pathway analysis is expected. This individual must be a functional coder in R, Perl, Python, Java, or other scripting/statistical language. Please note that those individuals who do not possess a strong knowledge of molecular biology and systems should not apply.

Requirements:

  • MS or Ph.D. In a biological, computational or related discipline
  • Five to ten (5-10) years experience in applied bioinformatics, genomics and computational work.
  • 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, using major databases and data standards in the field.
  • Ability to write and implement complex computer programs.
  • Knowledge and proficiency in commonly used bioinformatics open source resources and software.
  • Familiarity with repositories of genomic data sets and analysis tools, such as UCSC Genome Browser, Bioconductor, ENCODE, and NCBI databases.
  • Fluency in ORACLE/SQL, Java, Perl, Python, C, and etc.
  • Proficiency in Unix or Linux operating systems.
  • Strong working knowledge or training in advanced biomedical research.
  • Ability to work efficiently on multiple projects.
  • Ability to choose the correct statistical tests for the problem and help researchers in experimental design.
  • Ability to communicate scientific and informatics concepts to a wide range of audiences.
  • Knowledge of technologies commonly used in biological labs, such as PCR, cloning, electrophoresis gels, and cell culture.
  • 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 work in a academic team environment.

Click here to apply for this position.

Return to Top

15-35181 RIA PROGRAMMER I

Responsibilities include:

  1. Design, develop, and test software and applications.
  2. Write automated unit and functional tests of complex application logic while adhering to principles and best practices of containerization and continuous integration and deployment.
  3. Document code and generate appropriate technical and user documentation for software and applications.
  4. Manage all code, documentation, and issues in modern source control repositories.
  5. Manage small projects and subprojects within larger initiatives, identifying, tracking, and reporting on tasks and deliverables against project timelines.

Summary:

  1. Develop, test, and implement translational informatics software and application solutions under direct supervision.
  2. Create re-usable open source and proprietary software and application products.
  3. Evaluate, adopt and use multiple technologies to create innovative solutions that have a high impact on data-intensive clinical and translational research.
  4. Continuously learn about a wide variety of biomedical domains in order to translate domain requirements into high-impact technical solutions.
  5. Work independently and as part of a project team in a highly matrixed research environment, including direct interaction with clinicians and biomedical researchers.

Requirements

Required Licenses/certificates/registrations
Epic certifications preferred

Required Education and Experience
Core:

  • BS/BA required in computer science, biomedical engineering, information science, or related field. Substitute years of relevant experience for specific field.
  • Zero to five years of programming experience with progressively more complex projects.
  • Demonstrated track record of continuous learning and adoption of new languages and frameworks.

Clinical Decision Support:

  • Zero to five years of experience developing, configuring, or customizing software in a clinical environment is preferred.

Quality Assurance and Continuous Integration and Deployment:

  • Zero to five years of experience in quality assurance, continuous integration and deployment, configuration management, or other aspect of software and application validation is preferred.

Additional Technical Requirements
Core:

  1. Working knowledge of one or more of the following preferred: Python/Django, JavaScript/HTML (as used in Single Page Applications), Java, Objective C, Cache/Mumps, Scala.
  2. Working knowledge of relational and/or non-relational database application development preferred.
  3. Previous experience in data modeling is preferred.
  4. Experience in healthcare and/or biomedical, genomic data management issues is preferred.
  5. Experience with mobile application (native or web) on Android and/or iOS is preferred
  6. Must exhibit excellent oral, presentation, and written communication skills.
  7. Experience with source management, continuous integration, containerization, and automated testing tools and processes is preferred.

Clinical Decision Support:

  1. Working knowledge of Epic or other electronic health record workflows is preferred.
  2. Experience with Cache/Mumps is preferred.
  3. Experience with health data application programming interfaces such as FHIR or interchange specifications such as HL7 is preferred.

Click here to apply for this position.

Return to Top

15-35361 RIA PROGRAMMER II

The Analyst/Programmer II in the Translational Informatics Unit at the Department of Biomedical and Health Informatics (DBHi) develops and implements innovative software and applications that solve challenging problems in the collection, management, analysis and interpretation of biomedical, genomic and clinical data. The successful candidate will create and contribute to DBHi open source projects (http://github.com/chop-dbhi) as well as proprietary products such as mobile health applications and implementations of data science algorithms. We are looking for highly creative people who share our mission to advance child health and who will thrive in a continuous learning environment, acquiring and applying both new technical skills and biomedical domain knowledge. Specifically, the Analyst/Programmer II will:

  • Independently develop, test and rollout translational informatics software and application solutions.
  • Create re-usable open source and proprietary software and application products.
  • Evaluate, adopt and use multiple technologies to create innovative solutions that have a high impact on data-intensive clinical and translational research.
  • Continuously learn about a wide variety of biomedical domains in order to translate domain requirements into high-impact technical solutions.
  • Work independently and as part of a project team in a highly matrixed research environment, including direct interaction with clinicians and biomedical researchers.
  • Contribute to the development, evolution, and implementation of software development methodologies that are optimized to a biomedical research setting.
  • Design, develop, and test software and applications.
  • Write automated unit and functional tests of complex application logic while adhering to principles and best practices of containerization and continuous integration and deployment.
  • Document code and generate appropriate technical and user documentation for software and applications.
  • Manage all code, documentation, and issues in modern source control repositories.
  • Manage projects and subprojects of increasing complexity within larger initiatives, identifying, tracking, and reporting on tasks and deliverables against project timelines.

Requirements

  • BS/BA required, Masters preferred in computer science, biomedical engineering, information science, or related field. Substitute years of relevant experience for specific field.
  • Three to eight years of programming experience with progressively more complex projects.
  • Demonstrated track record of continuous learning and adoption of new languages and frameworks.
  • Working knowledge of more than one of the following preferred: Python/Django, JavaScript/HTML (as used in Single Page Applications), Java, Objective C, Cache/Mumps, Scala.
  • Working knowledge of relational and/or non-relational database application development preferred.
  • Previous experience in data modeling is preferred.
  • Experience in healthcare and/or biomedical, genomic data management issues is preferred.
  • Experience with mobile application (native or web) on Android and/or iOS is preferred.
  • Must exhibit excellent oral, presentation, and written communication skills.
  • Experience with continuous integration, containerization, and automated testing tools and processes is preferred.

Click here to apply for this position.

Return to Top

14-35021 SUPERVISOR OF SCIENTIFIC COMPUTING

Pediatric biomedical research and emerging clinical applications are driving an unprecedented increase in the scale and complexity of data management and analysis tasks. To meet this challenge, the Supervisor of Scientific Computing (SSC) in the Department of Biomedical and Health Informatics will build and lead a team that will evolve CHOP in the application of advanced computing technologies to pediatric biomedical research. The Scientific Computing team will perform intensive outreach to CHOP researchers to identify computationally- and data-intensive research tasks and workflows. The successful candidate will recruit and manage a team of scientific computing experts spanning multiple disciplines, as well as contribute hands-on to solving complex technical problems directly related to research and clinical diagnostics.

The team’s ‘product’ will be specialized computing environments for both one-off research studies and for generalizable production functions such as data analysis pipelines, large data warehouses and real-time analytic services. The team will partner with the Department of Information Services to build upon and contribute to the acquisition of computing infrastructure spanning CHOP’s ongoing large investments in virtualization, high performance computing and network storage as well as multiple contracted cloud services.

Technologies include but are not limited to:high performance and parallel computing, very large relational and non-relational databases, high-throughput data transfer, and analysis and visualization platforms.

Applications include but are not limited to genomic data analysis, including next-generation sequencing,systems biology algorithms,real-time model-based clinical decision support, imaging analysis and large clinical epidemiological and surveillance studies.

Requirements

  • Bachelor’s degree required, masters or Ph.D. preferred in computer science, computer engineering, information systems, information science, or related field.
  • 10 plus years of experience in increasingly challenging systems engineer or systems administrator roles, in part in a research and development or scientific environment. Ideally, this will be in a biomedical or genomic research organization

Additional Technical Requirements

  • Experience building or leading small focused technical teams in either a matrixed or direct line management role, coupled with a strong interest in mentorship and staff development.
  • Ability to identify a wide variety of computing problem types and optimize code, software, job management, system, and hardware configurations to deliver high performance solutions.
  • Experience writing, optimizing, or troubleshooting parallel computer programs is preferred.
  • Demonstrated track record or a strong interest in education and outreach to the user community.
  • Demonstrated track record of building collaborative relationships with scientific researchers, technical colleagues, and IT/IS.
  • Demonstrated track record of finding the ‘best path’ technical or process solution for complex computationally- and data-intensive problems.
  • Demonstrated track record of using configuration management and continuous deployment tools and processes to support reproducibility of computing tasks.
  • Ability and interest in documenting, testing and controlling the development and release of code and system configurations, especially in generally-available production systems.
  • Experience with genomic or next-generation sequencing computing is desired, though not absolutely required.

Click here to apply for this position.

Return to Top

15-35360 POST DOCTORAL FELLOW

A postdoctoral fellow position is open in the Bioinformatics Group at the Department of Biomedical and Health Informatics (DBHI) at the Children’s Hospital of Philadelphia, reporting to the Director of Bioinformatics. This position offers several opportunities to develop bioinformatics methods and applications to address basic and clinical research problems in the analysis and interpretation of next-generation sequencing data. Academic output in the form of journal articles and professional meeting presentations is a focus of this position and is expected with some degree of supervision and collaboration with our experienced bioinformatics scientists. It is expected that this individual will conduct independent scholarly research, and will contribute directly to the overall research goals of the project and the research group. The individual will be expected to participate in project planning, interpretation/evaluation of data, and communication of results. The successful candidate will also be expected to acquire technical, coding, data stewardship, and manuscript/grant writing skills, and participate in seminars, lectures, poster sessions and presentations at national meetings. Postdoctoral fellows also may be required to supervise junior bioinformatics staff, develop new methods, and assist with the development of other research projects.

Requirements

  • PhD in computational science, statistics, or mathematics, engineering, or related fields
  • Ability to, under supervision, conceive of, plan, implement, validate, and disseminate entire projects
  • UNIX/LINUX experience
  • Proficiency in R or similar commonly used statistical languages
  • Basic proficiency with Python, Perl, or other languages
  • Excellent organizational and communication skills with an emphasis on strong presentation skills
  • Ability to independently plan and execute analyses of moderate complexity
  • Ability to provide objective validation of results
  • Ability to work in a team environment
  • Strong research skills
  • Effective problem solving/critical thinking skills
  • Ability to work independently
  • Ability to exercise discretion and judgment
  • Value research integrity and collaborative research
  • High level of motivation
  • Good communication skills
  • Strong interpersonal skills

Click here to apply for this position.

Return to Top

15-35927 POST DOCTORAL FELLOW

A postdoctoral fellow position is open in the Bioinformatics Group at the Department of Biomedical and Health Informatics (DBHI) at the Children’s Hospital of Philadelphia (CHOP), reporting to the Director of Bioinformatics. CHOP postdoctoral fellows receive mentored training in a rich scientific environment that includes both CHOP and University of Pennsylvania research communities.

This position offers the opportunity to work in the research laboratory of Dr. Sharon Diskin at The Children's Hospital of Philadelphia (CHOP) Research Institute, an interdisciplinary institution dedicated to conducting basic, clinical and translational research on conditions and diseases that affect children. Dr. Diskin is an Assistant Professor of Pediatrics in the Division of Oncology and a member of the Genomics and Computational Biology Graduate Group and Abramson Cancer Center at the University of Pennsylvania. Her laboratory is interdisciplinary, encompassing both dry- and wet-bench research aimed at understanding the genetic basis of childhood cancers and response to treatment.

The desired candidate must have a terminal degree (PhD) in computational biology, cancer genetics, computer science, statistics, or related field. The postdoctoral fellow will be responsible for analysis of high-dimensional next-generation genome, transcriptome, and epigenome sequencing and array-based data sets in the childhood cancer neuroblastoma. This will include, but not be limited to, data generated though a neuroblastoma genome-wide association study and the National Cancer Institute (NCI) sponsored TARGET project (https://ocg.cancer.gov/programs/target).

The postdoctoral fellow will assume responsibility for a specific, on-going research project under the direction/guidance of his or her mentor. The postdoc experience will serve to extend, refine and enhance skills necessary for professional and career development, and will enable the individual to broaden his/her scientific background by acquiring new research capabilities. It is expected that this individual will conduct independent scholarly research, and will contribute directly to the overall research goals of the project and the research group. Postdocs will be expected to participate in project planning, recording and interpretation/evaluation of data, and communication of results.

Postdocs will also be expected to acquire technical, lab management, and manuscript/grant writing skills; and participate in seminars, lectures, poster sessions and presentations at national meetings. Postdoctoral fellows also may be required to supervise junior lab members, develop new methods and protocols for research, and assist with the development of other research projects in the lab.

Requirements

  • PhD in computational biology, cancer genetics, computational science, statistics, or mathematics, engineering, genomics/genetics or related fields
  • UNIX/LINUX and high performance computing experience
  • Proficiency in R or similar commonly used statistical languages
  • Basic proficiency with Python, Perl, or other languages
  • Values research integrity and collaborative research
  • Strong research skills
  • Effective problem solving/critical thinking skills
  • Ability to work independently and with a strong work ethic
  • High level of motivation
  • Excellent communication/interpersonal skills
  • Ability to exercise discretion and judgment
    • Click here to apply for this position.

      Return to Top

      MANDATORY REQUIREMENTS

      • Child Abuse Clearances
      • FBI Fingerprint Clearance
      • Drug Screening
      • Tobacco screening

      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.

      The Children's Hospital of Philadelphia is an equal opportunity employer. We do not discriminate on the basis of race, color, gender, gender identity, sexual orientation, age, religion, national or ethnic origin, disability or protected veteran status.